Дисертації з теми "Population genetic connectivity"

A panel of 48 single nucleotide polymorphism markers (SNPs) was developed for use in a population genetic analysis of the Eastern Oyster Crassostrea virginica sampled from the lower Chesapeake Bay. The SNPs were developed from published and unpublished sequencing data and developed to be used on a Fluidigm Biomark. A selection of 95 SNPs were chosen initially for development and the best 48 were selected for downstream applications. This project was a collaboration with the non-profit Chesapeake Bay Foundation (CBF) to examine their oyster reef restoration project in the Lafayette River, Virginia. The CBF wanted to test a hydrodynamic connectivity model designed to predict where oyster larvae produced in the Lafayette River would settle within the river. To test the model, oysters from Tangier Island, VA and the Haskin NEH hatchery strain were planted in the Lafayette River at locations corresponding to locations within the model with the expectation that the oysters would spawn the following summer. Baseline geographic oyster samples were taken from the nearby rivers; the Lafayette, Elizabeth and James Rivers before deployment of the planted test oysters. Newly recruited oyster spat were sampled from the Lafayette River in the summer following deployment of the planted test oysters. The baseline samples and spat were genotyped and compared to each other with the panel of 48 SNPs. Assignment tests were performed to identify the source population(s) for the spat. There was no population structure defined by FST values among oysters sampled from the lower Chesapeake Bay. The Haskin NEH oysters were genetically different from the other oysters in the study; however, the Tangier Island oysters were not different from the oysters in the lower Chesapeake Bay. The low FST values among the oysters from the lower Chesapeake Bay suggest that the connectivity of the reefs is high. The hydrodynamics of the region mix drifting larvae produced by oysters across the region as seen in the genotypic profile of the spat recovered in the Lafayette River. Heterozygote deficiencies suggestive of a Wahlund effect were observed; however, high rates of migration likely work to counterbalance stable population substructure. Alternatively, the heterozygote deficiencies could represent hidden variation not accessible by the methods used in this thesis. Some population structure exists with increasing geographic distance consistent with a pattern of isolation by distance among the populations sampled for this project. Assignment tests did not identify any spat as a product of the NEH oysters and assignment of spat to Tangier Island origin is inconclusive. The genetic data obtained were not able to provide unequivocal support for the predictions of oyster spat distributions by the connectivity model, although, the data do support the overall circulation patterns in the region predicted by the model.

Thesis (M.S.)--University of California, San Diego, 2009.
Title from first page of PDF file (viewed February 6, 2009). Available via ProQuest Digital Dissertations. Includes bibliographical references (p. 27-31).

This dissertation examines aspects of the relationship between connectivity and the development of genetic structure in subdivided coral reef populations using both simulation and algebraic methods. The first chapter develops an object-oriented, individual based method of simulating the dynamics of genes in subdivided populations. The model is then used to investigate how changes to different components of population structure (e.g., connectivity, birth rate, population size) influence genetic structure through the use of autocorrelation analysis. The autocorrelograms also demonstrate how relationships between populations change at different spatial and temporal scales. The second chapter uses discrete multivariate distributions to model the relationship between connectivity, selection and resource use in subdivided populations. The equations provide a stochastic basis for multiple-niche polymorphism through differential resource use, and the role of scale in changing selective weightings is also considered. The third chapter uses matrix equations to study the expected development of genetic structure among Caribbean coral reefs. The results show an expected break between eastern and western portions of the Caribbean, as well as additional nested structure within the Bahamas, the central Caribbean (Jamaica and the reefs of the Nicaraguan Rise) and the Mesoamerican Barrier Reef. The matrix equations provide an efficient means of modeling the development of genetic structure in subdivided populations through time. The fourth chapter uses matrix equations to examine the expected development of genetic structure among Southeast Asian coral reefs. Projecting genetic structure reveals an expected unidirectional connection from the South China Sea into the Coral Triangle region via the Sulu Sea. Larvae appear to be restricted from moving back into the South China Sea by a cyclonic gyre in the Sulu Sea. Additional structure is also evident, including distinct clusters within the Philippines, in the vicinity of the Makassar Strait, in the Flores Sea, and near Halmahera and the Banda Sea. The ability to evaluate the expected development of genetic structure over time in subdivided populations offers a number of potential benefits, including the ability to ascertain the expected direction of gene flow, to delineate natural regions of exchange through clustering, or to identify critical areas for conservation or for managing the spread of invasive material via elasticity analysis.

Mestrado em Ecologia Aplicada
Species persist over time, due to exchange of individuals between subpopulations. In the marine environment, most benthic organisms have complex life cycles including pelagic larvae that are transported by ocean currents promoting species dispersal. Larval dispersal connects geographically distant populations and determines population structure. The knowledge about this biologic process provides relevant information for conservation of marine populations. This study investigates the genetic structure and connectivity of deep-sea mussel populations between fragmented habitats in the NE Atlantic and Mediterranean. The mitochondrial Cytochrome Oxidase I (mtCOI) gene was used to analyze site-specific genetic diversity and the population structure of two mussel species, Idas modiolaeformis and “Idas” simpsoni. Populations of each species are not geographically isolated. The presence of one dominant haplotype for each species suggests shared ancestral polymorphisms between Mediterranean and NE Atlantic populations. The overall high genetic differentiation observed in I. modiolaeformis indicates that the metapopulation is structured. Distant populations, located in Atlantic and E Mediterranean, revealed low genetic distances, suggesting gene flow between the two regions. Genetic and geographical distances support an island model of I. modiolaeformis population structure. A major drawback of this study is concerned with the discrepant number of individuals among populations. Further research will be needed, using more specimens and other gene markers, to investigate connectivity patterns at different spatial scales.
As espécies persistem ao longo do tempo devido à troca de indivíduos entre subpopulações. No ambiente marinho, a maioria dos organismos bentónicos têm ciclos de vida complexos, envolvendo larvas pelágicas que são transportadas por correntes oceânicas contribuindo para dispersão das espécies. A dispersão larvar estabelece conectividade entre populações geograficamente separadas e afeta a estrutura da população. O conhecimento deste processo biológico promove informações importantes para a conservação de populações marinhas. Este estudo investiga a estrutura genética e conectividade de populações de mexilhão de profundidade entre habitats fragmentados no NE Atlântico e Mediterrânico. O gene mitocondrial, Citocromo Oxidase I (mtCOI), foi utilizado para analisar diversidade genética por local e a estrutura populacional de duas espécies de mexilhão, Idas modiolaeformis e "Idas" simpsoni. As populações de cada uma das espécies não se encontram geograficamente isoladas. A presença de um haplótipo dominante para cada espécie sugere a partilha de polimorfismos ancestrais entre populações do Mediterrâneo e do NE Atlântico. As populações de I. modiolaeformis demonstraram uma elevada diferenciação genética, indicando estruturação da metapopulação. Populações distantes umas das outras, localizadas no Atlântico e E Mediterrâneo, revelaram baixas distâncias genéticas, sugerindo fluxo genético entre as duas regiões. Distâncias genéticas e geográficas suportam o modelo de ilha como o modelo para a estrutura populacional de I. modiolaeformis. Uma grande desvantagem deste estudo está relacionada com o número discrepante de indivíduos entre populações. Para investigar os padrões de conectividade em diferentes escalas espaciais serão necessários mais estudos, utilizando mais espécimes e outros marcadores genéticos.

Once so abundant as to be called the ‘common’ angelshark, Squatina squatina has been extirpated from nearly the entirety of its historical range, from the eastern North Atlantic, to the Mediterranean Sea [International Union for the Conservation of Nature (IUCN) Red List: Critically Endangered]. The angelshark now only occurs in any abundance in the waters surrounding the Canary Islands. I present the first genetic assessment of the angelshark’s population dynamics and diversity from three locations within the Canary Islands archipelago: Gran Canaria, Tenerife, and Lanzarote. Using a suite of individual mitochondrial genome regions [Control region (CR), NADH dehydrogenase subunit 2 (ND2), NADH dehydrogenase subunit 4 (ND4), and Cytochrome c oxidase subunit 1 (COI)], the complete mitogenome, and nuclear markers [microsatellites and Internal Transcribed Spacer 2 (ITS2)] this work aimed to i) assess the genetic diversity of the angelshark in comparison to other endangered or historically overfished elasmobranchs, ii) examine the relative nucleotide variability across different marker sets, and iii) assess fine-scale multi-locus population structure within the Canary Islands, as well as broad-scale population genetic structure of angelsharks throughout its historic Eastern Atlantic and Mediterranean range. Results revealed exceptionally low genetic diversity across all individual mitochondrial regions sequenced (CR, π % = 0.0046 ± 0.016; ND2, π % = 0; ND4, π % = 0; COI, π % = 0), yielding some of the lowest values reported to date in any elasmobranch. Mitogenome analysis followed this low diversity trend with only 11 single nucleotide polymorphisms seen across all Canary Island individuals in a genome of 16,689 bp (π % = 0.0257 ± 0.0166). Furthermore, screening of 35 microsatellite markers across 34 individuals revealed all but two loci to be monomorphic and nuclear ITS2 showed negligible diversity. Lanzarote showed significant population differentiation from both Gran Canaria (ΦST = 0.073, p = 0.004, FST = 0.113, p = 0.00) and Tenerife (ΦST = 0.029, p = 0.001, FST = 0.065, p = 0.001) at the CR. Haplotype analysis of whole mitogenomes also demonstrated Lanzarote individuals forming a separate lineage from angelsharks at the other two islands. Broad- scale structure across the angelshark’s historical range was detected between the Canary Islands and Mediterranean (ΦST = 0.792, p = 0.000, FST = 0.785, p = 0.000), indicating a regional break between populations. The exceptionally low levels of genetic diversity in angelsharks in the Canary Islands, as well as indications of population isolation from the rest of the angelshark’s historical range, suggest an immediate need for strong conservation measures to ensure the protection and continued persistence of this highly vulnerable and ecologically unique species.

Mestrado em Ecologia Aplicada
Habitat fragmentation and the consequently the loss of connectivity between populations can reduce the individuals interchange and gene flow, increasing the chances of inbreeding, and the increase the risk of local extinction. Landscape genetics is providing more and better tools to identify genetic barriers.. To our knowledge, no comparison of methods in terms of consistency has been made with observed data and species with low dispersal ability. The aim of this study is to examine the consistency of the results of five methods to detect barriers to gene flow in a Mediterranean pine vole population Microtus duodecimcostatus: F-statistics estimations, Non-Bayesian clustering, Bayesian clustering, Boundary detection and Simple/Partial Mantel tests. All methods were consistent in detecting the stream as a non-genetic barrier. However, no consistency in results among the methods were found regarding the role of the highway as a genetic barrier. Fst, Bayesian clustering assignment test and Partial Mantel test identifyed the highway as a filter to individual interchange. The Mantel tests were the most sensitive method. Boundary detection method (Monmonier’s Algorithm) and Non-Bayesian approaches did not detect any genetic differentiation of the pine vole due to the highway. Based on our findings we recommend that the genetic barrier detection in low dispersal ability populations should be analyzed with multiple methods such as Mantel tests, Bayesian clustering approaches because they show more sensibility in those scenarios and with boundary detection methods by having the aim of detect drastic changes in a variable of interest between the closest individuals. Although simulation studies highlight the weaknesses and the strengths of each method and the factors that promote some results, tests with real data are needed to increase the effectiveness of genetic barrier detection.
A fragmentação do habitat e a consequente perda da conectividade entre populações pode reduzir o intercâmbio de indivíduos e consequentemente o fluxo genético, aumentando as hipóteses de ocorrer consanguinidade e consequentemente aumentar o risco de extinção local. A disciplina da genética da paisagem fornece cada vez mais e melhores ferramentas para detectar barreiras genéticas. No entanto, não se conhecem até à data, comparações de métodos em termos de consistência de resultados com dados observados e espécies com reduzida capacidade de dispersão. O objectivo deste estudo é avaliar a consistência dos resultados de cinco métodos de análise do papel da auto-estrada e de um rio como barreira ao fluxo genético numa população de rato-cego-mediterrânico Microtus duodecimcostatus: estimativas do Festatistico, método de aglomeração não-Bayesianos, métodos de aglomeração Bayesianos, método de detecção de fronteiras (algoritmo Monmonier) e o teste Mantel simples e parcial. Todos os métodos testados foram consistentes em considerar o rio como uma não barreira genética ao rato-cego-mediterrânico. No entanto, não houve consistência nos resultados quanto ao papel da autoestrada como barreira genética. As estimativas do F-estatistico, os métodos de aglomeração Bayesianos e o teste de Mantel parcial que mostram que a autoestrada pode estar a funcionar como um filtro ao movimento dos indivíduos entre os dois lados da estrutura. Os métodos de deteção de fronteiras (algoritmo Monmonier) e de aglomeração não-Bayesiano não detectaram diferenciação genética nas populações de rato-cego-mediterrâneo devido à estrada. Com base nos nossos resultados nós recomendamos a aplicação dos testes de Mantel, os métodos de aglomeração Bayesianos e dos métodos de detecção de fronteiras para esclarecer o papel dos atributos da paisagem como barreiras genéticas uma vez que, todos foram capazes de detectar barreiras mas não obtiveram resultados similares. Apesar dos estudos com base em simulações apontarem as vantagens e desvantagens de cada método e os fatores que associados aos resultados, é necessário que se façam testes com base em dados reais para que sejam mais eficazes na detecção de barreiras genéticas.

The distribution and abundance of many coral reef organisms are affected by their predator’s distribution and abundance. Loss of predators may cause a shift in species compositions that will cascade down to other ecological processes on the reef. One example of a shift like this is the growing sea urchin populations inhabiting the coral reefs of East Africa. Areas with high fishing pressure often have large populations of sea urchins. The large populations of sea urchins have a negative impact on the reef ecology both by their grazing and bio-erosion as well as on fish growth and the recovery of fish populations. Previous population genetic studies conducted on Diadema setsosum, using mtDNA and allozymes, found genetic structuring between populations on a large geographical and evolutionary scale. The aim of this study was to examine the genetic population structure of the sea urchin Diadema setosum, at four sites around Zanzibar. We used the amplified fragment length polymorphism (AFLP) technique, a fast and effective method with high resolution. The long term objective is to understand the migration pattern and colonization of D. setosum to facilitate possible management actions. We found a significant genetic structuring of D. setosum hence the populations can not be considered panmictic. The reason behind this structure does not seem to be based on the geography nor size. One possible explanation might be that the structure lies on a larger geographical scale than we have studied, further studies around the Western Indian Ocean may reveal this. Another explanation may be that the structuring is due to differences in spawning time between the different phenotypes and an analysis of gonad maturations may give information about this. To find the reasons behind the observed genetic structure is of great importance for management of the sea urchins and therefore the management of whole reef ecosystems.

Discerning the extent and patterns of genetic connectivity and understanding population demographic processes is essential for framing proper management and conservation measures for species of concern. Although genetic connectivity may be influenced by numerous biotic and abiotic factors, habitat utilization and dispersal potential are often key factors driving connectivity, especially in marine fishes. While dispersal potential is of key importance with respect to shaping connectivity, other extrinsic (e.g., oceanographic processes) and intrinsic (e.g., reproductive behavior) factors may also influence connectivity; however, the relative influence of such factors is immensely variable across species and life-stages. This dissertation explores genetic connectivity and demographic history in marine fishes with diverse dispersal potentials to determine which processes, in addition to the known dispersal potential of the species, may be shaping connectivity. Genetic connectivity and demographic history is assessed for four marine fishes: two shark species with juxtaposing dispersal potentials, the highly migratory tiger shark (Galeocerdo cuvier) and the reef associated Caribbean reef shark (Carcharhinus perezi), which possess high and low dispersal potentials, respectively, and two teleost species, the pelagic roundscale spearfish (Tetrapturus georgii) and the Nassau grouper (Epinephelus striatus), which possess high and low adult dispersal potentials, respectively. This work demonstrates that dispersal potential does, in fact, play a key role in delineating genetic structure for these species; however, other factors, such as contemporary oceanographic currents (e.g., upwelling and temperature), habitat availability (e.g., coral cover), and historical events, such as cyclical glacial cycles, also influence genetic connectivity across variable spatial scales, thereby creating complex patterns of genetic population structure, requiring composite management strategies to ensure the persistence of these species.

Understanding migratory connectivity is essential for assessing the drivers behind population dynamics and for implementing effective management in migratory species. Genetic markers provide a means to describe migratory connectivity, as well as incorporate population genetic analyses, however genetic markers can be uninformative for species with weak genetic structure. In this study, we evaluate range-wide population genetic structure and migratory connectivity in the prothonotary warbler, Protonotaria citrea, a wetland-dependent neotropical migratory songbird, using high-resolution genetic markers. We reveal regional genetic structure between sampling sites in the Mississippi River Valley and the Atlantic Seaboard with overall weak genetic differentiation among populations (FST = 0.0051). By ranking loci by FST and using subsets of the most differentiated genetic markers (200 – 3000), we identify a maximum assignment accuracy (89.7% to site, 94.3% to region) using 600 single nucleotide polymorphisms. We assign samples from unknown origin nonbreeding sites to a breeding region, illustrating weak migratory connectivity between prothonotary warbler breeding and nonbreeding grounds. Our results highlight the importance of using high-resolution markers in studies of migratory connectivity with species exhibiting weak genetic structure. Using similar techniques, studies may begin to describe population genetic structure that was previously undocumented, allowing us to infer the migratory patterns of an increasing number of species.

The oceanic whitetip shark, Carcharhinus longimanus, is a circumtropical pelagic shark of high conservation concern (IUCN Red List: “Critically Endangered” in the Western North and Western Central Atlantic and “Vulnerable” globally). I present the first, population genetic assessment of the oceanic whitetip shark on a global scale, based on analysis of two mitochondrial genome regions (entire 1066-1067 bp control region and 784 bp partial ND4 gene), and nine nuclear microsatellite loci. No population structure was detected within the Western Atlantic. However, highly significant population structure was detected between Western Atlantic and Indo-Pacific Ocean sharks across all markers. Additionally, a nominally significant signal of matrilineal structure between the Indian and Pacific Ocean sharks was detected by AMOVA and pairwise tests of the ND4 gene only (pairwise ΦST = 0.051, P = 0.046; pairwise Jost’s D = 0.311, 95% CI = 0.020, 0.0614). Although significant inter-basin population structure was evident, it was associated with deep phylogeographic mixing of mitochondrial haplotypes and evidence of contemporary migration between the Western Atlantic and Indo-Pacific Oceans. I theorize that semi-permeable thermal barriers are responsible for the differentiation between the Western Atlantic and Indo-Pacific set in a framework of global phylogeographic mixing. Relatively low mtDNA genetic diversity (concatenated mtCR-ND4 nucleotide diversity π = 0.32% ± 0.17%) compared to other circumtropical elasmobranch species raises potential concern for the future genetic health of this species. Overall, significant population structure exists, at a minimum, between the Western Atlantic and Indo-Pacific Ocean, and effective management strategies must take this into consideration.

How genetic variation is distributed across space (genetic structure) and what factors influence the spatial genetic structuring is one of the primary questions in population genetics. The interaction between species biology (e.g. life-history traits) and physical processes operating in the seascape over time, including palaeo-historical events (e.g. sea level fluctuations) and contemporary processes (e.g. ocean currents), have been predicted to influence the extent of gene flow and the spatial genetic structuring in marine organisms. However, the relative contribution of each factor in governing the genetic pattern remains unclear. This study examined the pattern of genetic structure and the factors influencing this using multiple approaches across different temporal and spatial scales in the Indo-Australian Archipelago (IAA), the world’s hotspot of marine biodiversity. By comparing population genetic data of co-distributed marine species (e.g. fishes, molluscs, etc.), this study shows that for marine organisms, the interaction between species biological traits and the physical/environmental processes (habitat variability, water current, etc.) are the greatest drivers of genetic structure in the IAA. Since the physical/environmental processes fluctuate over time, spanning from hours to millennia, the temporal scale (palaeo-historical vs contemporary) at which physical/environmental processes generate genetic structure were examined using seascape genetic analysis. To minimise the effect of different biological traits, the seascape genetic analysis focused only on one species, Thalassia hemprichii, one of the dominant seagrass species in the IAA. The analysis revealed that both palaeo-historical processes (vicariance due to Pleistocene sea level fluctuations) and more contemporary processes (ocean currents) strongly influence the pattern of genetic structure at a regional scale (>300 km). At this spatial scale, the influence of contemporary ocean currents is much smaller than that of historical vicariance. This finding contrasts with previous studies highlighting a strong effect of ocean currents in seagrass connectivity. Only when the effect of historical vicariance was minimised by spatially down-scaling the study from a regional (>300 km) to local (km) scale, contemporary processes, including ocean currents and habitat heterogeneity, were shown to strongly influence the pattern of genetic structure. This study also revealed that significant genetic structure can occur at both regional and local scales. At the regional scale, the genetic clusters span distances of at least 500 km, suggesting that genetic connectivity of T. hemprichii populations occurs over very large geographic scales. At the local scale, significant spatial genetic structure was detected, negating the prediction of a single panmictic population. The strong genetic structuring occurring at both large and small spatial scales suggests that predicting seagrass connectivity solely based on geographic distance is inaccurate, and the relevant distance between populations in the marine system is not purely geographic, but rather determined by other factors operating on the seascape setting such as water currents and habitat heterogeneity. Thus, seascape setting is very important in seagrass gene flow and structure. Based on the pattern of gene flow, genetic structure, and genetic diversity, this research provides recommendations for seagrass conservation management in the IAA, including spatial design of conservation reserves and restoration including transplantation.

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides. These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O. bimaculoides is more susceptible to over exploitation of small, isolated populations and could have longer recovery times than the other two species. This species may benefit from distinct fishery management within each local population. O. bimaculatus and O. hubbsorum may benefit from fishery management that takes into account metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal driven by ocean currents and population connectivity among individuals of each locality. The distribution of each species and variations in their reproductive phenology is also important to consider when establishing marine reserves or seasonal fishing closures.

La conservation des zones humides fortement modifiées par les pratiques anthropiques, nécessite l’acquisition de données scientifiques sur leur diversité et leur fonctionnement. Cette thèse vise à relier l’anthropisation des zones humides à la diversité génétique, niveau de base de la biodiversité lié à la capacité adaptative des populations et au maintien des espèces. L’effet de l’anthropisation sur la diversité génétique de végétaux aquatiques est étudié à plusieurs échelles d’espaces (zone humide et bassin versant) et de temps (études synchroniques et diachroniques). La diversité génétique de populations de deux espèces rudérales (Berula erecta et Apium nodiflorum) et une compétitive (Nuphar lutea) est comparée dans deux plaines alluviales contrastées (trophie, connectivité hydrologique et restauration), à l’aide de marqueurs microsatellites adaptés à l’étude d’espèces clonales. La diminution de la connectivité hydrologique augmente la différenciation génétique et diminue la diversité génétique pour les espèces rudérales étudiées alors qu’elle n’a pas d’effet sur l’espèce compétitive. L’impact de la connectivité est donc dépendant de la stratégie de reproduction. La diversité génétique des espèces rudérales diminue également dans les zones humides plus eutrophes. L’augmentation de la diversité génétique post-restauration chez B. erecta est corrélée à la fréquence des perturbations (assecs) qui créent des niches favorisant le recrutement des graines. Cette étude propose des préconisations de gestion pour les zones humides et apporte des connaissances sur la dynamique de la diversité génétique des plantes aquatiques en lien avec leur environnement
The conservation of wetlands which are strongly modified by human practices, requires the acquisition of knowledge about their diversity and functioning. This thesis aimed to link the human pressures and plant genetic diversity in wetlands, which is the basic level of biodiversity linked to the adaptive capacity of populations and species maintenance. The effect of anthropization on the genetic diversity of aquatic plants is studied at several spatial and temporal scales (wetland and watershed; synchronic vs. diachronic studies). The genetic diversity of populations of two ruderal (Berula erecta and Apium nodiflorum) and one competitive species (Nuphar lutea) in two contrasting floodplains (in terms of trophic status, hydrological connectivity and restoration) is compared using microsatellite markers suitable for the study of clonal species. A reduction in hydrological connectivity increases genetic differentiation and decreases genetic diversity for ruderal species studied, while it did not affect the competitive species. The impact of connectivity is related to plant reproductive strategy. The genetic diversity of ruderal species also decreases in most eutrophic wetlands. The increase of genetic diversity of B. erecta after restoration is correlated with the frequency of disturbances (dewatering) that create niches for seed recruitment. This study provides management recommendations for the impacted wetlands and provides knowledge about the dynamics of the genetic diversity of aquatic plants in relation to their environment

The American marten (Martes americana) is an endangered species in Vermont and a Regional Species of Greatest Conservation Need in the northeastern United States. Though historically widespread in northeastern forests, their range presumably contracted to northern Maine and the High Peaks region of the Adirondacks by the early 1900s. Regionally, populations appear to be in recovery. Natural recolonization is believed to have occurred in New Hampshire, northeastern Vermont and the western Adirondacks. A reintroduction effort in southern Vermont that was originally declared unsuccessful is now believed to be the source of a recently detected population in the area. However, our current knowledge of distribution, population history and population connectivity relies primarily on occurrence data from harvest records, which are limited in scope and resolution. In Vermont, where population size is estimated to be extremely low, more robust estimates of population status may be critical to continued recovery. I genotyped individuals from Maine, New York, New Hampshire, northeastern Vermont and southern Vermont at ten microsatellite loci and amplified a 320 base pair segment of the control region of mtDNA to estimate the source(s) of the two Vermont populations using statistical tests of genetic differentiation. I also used Bayesian and stochastic genetic clustering methods to estimate population genetic structure in the northeastern United States. Genetic structure exists at multiple scales in the region as a result of natural barriers to gene flow, human-mediated gene flow, and lineage sorting in relic populations. My results suggest that New Hampshire is a major source of colonization of northeastern Vermont and the population in southern Vermont is either a remnant of the reintroduction or a pre-reintroduction relic that has experienced introgression from the reintroduction stock. I identified three regions where relic populations perceived to be extirpated in the 1900s may have persisted. I also developed an occupancy model for American marten in the northeastern United States using mixed-effects logistic regression based on expert opinion data. Eighteen experts from Maine, New Hampshire, Vermont and New York with backgrounds in trapping, wildlife management, and wildlife science participated in the survey. Experts were asked to estimate the probability of marten occupancy at 30 sites in the northeastern United States. Three top models described the data. Habitat covariates in those models were 1) percent canopy cover, 2) percent spruce-fir forest cover, 3) winter temperature, 4) elevation, and 5) road density. An AIC-weighted average of these three models had significant predictive ability (area under an ROC curve = 0.88) with respect to occurrence records in the northeastern United States. In addition, the model predicted that high quality habitat existed patchily along the central and northern Green Mountain spine in Vermont – where no occurrence records exist for at least a century. Top-scoring movement corridors between southern Vermont and nearby populations in northeastern Vermont/New Hampshire and New York occurred in the northern and central Green Mountains and across high resistance movement barriers in the Champlain valley. Corridors to New York were considered strong movement barriers and are unlikely to facilitate gene flow.

Les forêts d’algues brunes (Phaeophyceae) sont soumises à des combinaisons de pressions d’origine anthropique. Le devenir de ces écosystèmes dépendra de la capacité des populations de ces espèces à évoluer dans cet environnement changeant. A travers ma thèse, j’ai étudié les facteurs susceptibles de contrôler la diversité génétiques des forêts marines en me focalisant sur deux espèces endémiques du bassin méditerranéen, la Fucales Ericaria zosteroides et le kelp des milieux profonds Laminaria rodriguezii. Dans une première partie, je me suis intéressé à la connectivité des populations par une méthode de séquençage partiel du génome (RAD-seq). L’analyse de la structure génétique indique une connectivité réduite, que ce soit pour les populations de E. zosteroides ou L. rodriguezii. En couplant structure génétique et modélisation des courants marins, j’ai étudié la dispersion des propagules en prenant comme cas d’étude, les populations de E. zosteroides en Provence. Les résultats obtenus montrent que la structure génétique est davantage prédite par les courants marins que par l’isolement spatial. Dans une deuxième partie, je me suis intéressé au mode de reproduction de L. rodriguezii, cette espèce étant l’une des rares du genre Laminaria à se reproduire par reproduction végétative et sexuée. Les résultats obtenus confirment l’impact de la clonalité sur la diversité génomique de L. rodriguezii, avec des niveaux variables selon les populations. Outre les questionnements fondamentaux soulevés par ces résultats, l’existence d’une forte structure génétique à courte distance pour des populations éparses, a des implications importantes pour la conservation de ces espèces
Marine forests of brown algae (Phaeophyceae) are impacted by a combination of anthropic pressures. The fate of these ecosystems will depend on the adaptive abilities of populations facing this changing environment. Through my PhD, I studied the factors likely to control the genetic diversity of marine forests by focusing on two endemic species of the mediterranean basin, the Fucoid Ericaria zosteroides and the deep-sea kelp Laminaria rodriguezii. In the first part, I studied the connectivity of populations by a method of reduced representation sequencing of genomes (RAD-seq). The analysis of the genetic structure indicates a reduced connectivity for both E. zosteroides and L. rodriguezii populations. By coupling genetic structure and modeling of marine currents, I studied the role of propagules dispersal, taking as a study case, the populations of E. zosteroides in Provence. The results indicate that the genetic structure is predicted by ocean currents rather than spatial isolation. In the second part, I studied the mode of reproduction of the kelp L. rodriguezii, this species being one of the few of the genus Laminaria to reproduce by vegetative and sexual reproduction. The results obtained indicate an impact of clonality on the genomic diversity of L. rodriguezii, with contrasting levels depending on the populations. In addition to the fundamental questions raised by these results, the existence of a strong genetic structure at short distances for populations divided into habitat patches has important implications for the conservation of these species

Nearly all deep-sea cephalopod life history studies have been completed by examination of specimens collected in the wild. Much of this work is like piecing together a puzzle; knowledge of the life history of many species remains fragmented and hence, taxonomically and phylogenetically confused. Molecular approaches and sequencing technologies are powerful tools for deciphering wild-type cephalopod life history and population dynamics. Use of molecular markers offers additional certainty for identifying specimens damaged during deep-sea collections and can elucidate often cryptic, intra- and interspecific diversity. The research presented in this study assessed broad genetic patterns of biodiversity in deep-sea cephalopods from the Gulf of Mexico and northwestern Atlantic Ocean. This study has two key objectives: [1] to examine intraspecies variation among regionally disjunct subpopulations, comparing collections separated by the Florida Peninsula, and [2] to examine intraspecies variation within deep-sea cephalopods in the Gulf of Mexico. Through Sanger sequencing marker genes COI, 16S rRNA, and 28S rRNA, this study has generated a genetic baseline characterization of deep-sea cephalopods in the Gulf of Mexico, assessed intraspecies genetic variation, and linked morphological identification with DNA barcodes, testing morphological hypotheses of species identification and naming. Results of investigating intraspecies variation within regionally disjunct subpopulations reveal there is no regional distinction between the Gulf of Mexico subpopulations of Vampyroteuthis infernalis, Pyroteuthis margaritifera, and Cranchia scabra, and the Bear Seamount subpopulations in the northwestern Atlantic Ocean. Results of investigating intraspecies variation within the Gulf of Mexico displayed potential for cryptic species, novel sequence records, and large expansions to sequence records for species known to inhabit the Gulf of Mexico. Analysis of intraspecies variation within the Gulf of Mexico facilitated identification of damaged specimens used for this study, but also revealed GenBank database issues of misidentified records, and outdated nomenclature in accession records. Because cephalopods play a central role in most oceanic ecosystems, characteristics like a short average life span and a rapid growth rate mean that cephalopod populations have the potential to serve as an invaluable reflection of ecosystem change.

Chapter 1 DNA barcoding based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence is emerging as a useful tool for identifying unknown, whole or partial organisms to species level. However, the application of only a single mitochondrial marker for robust species identification has also come under some criticism due to the possibility of erroneous identifications resulting from species hybridizations and/or the potential presence of nuclear-mitochondrial psuedogenes. The addition of a complementary nuclear DNA barcode has therefore been widely recommended to overcome these potential COI gene limitations, especially in wildlife law enforcement applications where greater confidence in the identifications is essential. In this study, we examined the comparative nucleotide sequence divergence and utility of the mitochondrial COI gene (N=182 animals) and nuclear ribosomal internal transcribed spacer 2 (ITS2) locus (N=190 animals) in the 8 known and 1 proposed cryptic species of globally widespread, hammerhead sharks (family Sphyrnidae). Since hammerhead sharks are under intense fishing pressure for their valuable fins with some species potentially set to receive CITES listing, tools for monitoring their fishery landings and tracking trade in their body parts is necessary to achieve effective management and conservation outcomes. Our results demonstrate that both COI and ITS2 loci function robustly as stand-alone barcodes for hammerhead shark species identification. Phylogenetic analyses of both loci independently and together accurately place each hammerhead species together in reciprocally monophyletic groups with strong bootstrap support. The two barcodes differed notably in levels of intraspecific divergence, with average intraspecific K2P distance an order of magnitude lower in the ITS2 (0.297% for COI and 0.0967% for ITS2). The COI barcode also showed phylogeographic separation in Sphyrna zygaena, S. lewini and S. tiburo, potentially providing a useful option for assigning unknown specimens (e.g. market fins) to a broad geographic origin. We suggest that COI supplemented by ITS2 DNA barcoding can be used in an integrated and robust approach for species assignment of unknown hammerhead sharks and their body parts in fisheries and international trade. Chapter 2 The gray reef shark (Carcharhinus amblyrhynchos) is an Indo-Pacific, coral reef associated species that likely plays an important role as apex predator in maintaining the integrity of coral reef ecosystems. Populations of this shark have declined substantially in some parts of its range due to over-fishing, with recent estimates suggesting a 17% decline per year on the Great Barrier Reef (GBR). Currently, there is no information on the population structure or genetic status of gray reef sharks to aid in their management and conservation. We assessed the genetic population structure and genetic diversity of this species by using complete mitochondrial control region sequences and 15 nuclear microsatellite markers. Gray reef shark samples (n=305) were obtained from 10 locations across the species’ known longitudinal Indo-Pacific range: western Indian Ocean (Madagascar), eastern Indian Ocean (Cocos [Keeling] Islands, Andaman Sea, Indonesia, and western Australia), central Pacific (Hawaii, Palmyra Atoll, and Fanning Atoll), and southwestern Pacific (eastern Australia – Great Barrier Reef). The mitochondrial and nuclear marker data were concordant in most cases with population-based analysis showing significant overall structure (FST = 0.27906 (pST = 0.071 ± 0.02), and significant pairwise genetic differentiation between nearly all of the putative populations sampled (i.e., 9 of the 10 for mitochondrial and 8 of the 10 for nuclear markers). Individual-based analysis of microsatellite genotypes identified at least 5 populations. The concordant mitochondrial and nuclear marker results are consistent with a scenario of very low to no appreciable connectivity (gene flow) among most of the sampled locations, suggesting that natural repopulation of overfished regions by sharks from distant reefs is unlikely. The results also indicate that conservation of genetic diversity in gray reef sharks will require management measures on relatively local scales. Our findings of extensive genetic structuring suggests that a high level of genetic isolation is also likely to be the case in unsampled populations of this species.

Species conservation is typically founded upon a range of management strategies, which integrate both biological and socioeconomic data. In this thesis, population genetics, acoustic telemetry, spawning aggregation surveys and stakeholder assessments were used to address key knowledge gaps limiting effective conservation management for critically endangered Nassau grouper (Epinephelus striatus) stocks in The Bahamas. A panel of polymorphic microsatellite markers was optimised to assess the genetic population dynamics of more than 400 Nassau grouper sampled throughout the country. Microsatellite data indicate that contemporary Nassau grouper populations in The Bahamas are predominantly genetically diverse and weakly differentiated, but lack geographic population structure. Assessments of changes in effective population size (Ne) show substantive reductions in Ne within The Bahamas compared to historic values that are likely due to natural disturbances. Evidence for recent bottlenecks occurring in three islands as well as an active spawning site, along with higher inbreeding coefficients in two islands were also found, and can be attributed to more recent anthropogenic activities. Collapse of a historically important Nassau grouper fish spawning aggregation (FSA) was supported by both acoustic telemetry and spawning aggregation survey dives. Restriction-site-associated DNA sequencing (RAD-seq) of 94 Nassau grouper was used to explore intraspecific population dynamics, loci under selection and patterns of gene flow in The Bahamas. Genomic assessments of diversity were in accord with microsatellite data and examinations of gene flow support higher levels of connectivity in The Bahamas than was previously suggested. The increased resolution gained from assessments of genomic data support intraspecific population structuring that may be driven by differences in gene flow and putative loci under divergent selection. Telemetry data were successfully used to identify the origins of spawning adults, and support demographic connectivity through migrations between an active FSA in the central Bahamas and home reef habitats within the Exumas and a no-take marine protected area. Stakeholder assessments highlight the complexities of fisheries management within The Bahamas, with key stakeholders often exhibiting conflicting opinions regarding the status of Nassau grouper and the efficacy of management options. However, these groups mutually agree upon the need to better manage remaining Nassau grouper stocks within The Bahamas through science-grounded policies. Synthesis of these studies along with a review of fisheries governance in The Bahamas was used to develop a comprehensive national management plan for Nassau grouper to facilitate better conservation for remaining populations of this ecologically important marine species.

Les écosystèmes marins sont soumis à des changements environnementaux rapides sous l’impact des pressions anthropiques croissantes qui menacent la persistance des espèces et des populations locales. Comprendre les effets de la variabilité génétique et des capacités de dispersion sur la persistance des espèces marines, est donc un enjeu majeur pour la conservation de la biodiversité. Mes travaux de doctorat répondent ainsi à deux objectifs principaux : (i) évaluer la distribution spatiale et les déterminants de la variation génétique de populations de poissons marins côtiers (ii) estimer les réponses des populations aux changements climatiques afin de mieux comprendre leur capacité de persistance.J’ai d’abord montré, à partir d’une synthèse bibliographique réalisée sur 31 espèces de poissons méditerranéens, que les traits écologiques liés à la mobilité et à la taille des populations influencent fortement le niveau de diversité génétique intra-populationnelle des espèces. Ensuite, j’ai étudié les déterminants de la variation génétique spatiale à partir des données récoltées sur 727 individus de rouget de roche (Mullus surmuletus) issus de 72 sites autour la Mer Méditerranée et regroupés en 47 groupes génotypés pour 1153 marqueurs SNP. Des analyses de génétique du paysage ont montré que la dispersion larvaire structure la variation génétique de l’espèce à moyenne et petite échelle spatiale (<1 000km), alors que l’isolement géographique, possiblement dû à l’histoire démographique des populations ou à l’adaptation, est le principal facteur structurant à plus large échelle. Finalement, l’étude de la variation génétique adaptative de M. surmuletus réalisée à l’aide d’un criblage génomique a mis en évidence une potentielle réponse adaptative de l’espèce au gradient Est-Ouest de salinité en Méditerranée.Dans un second temps, un modèle démo-génétique simulant la dynamique et la résilience des populations de coraux dans l’Indopacifique a montré qu’un mécanisme de « sauvetage évolutif » permet aux génotypes adaptés aux eaux les plus chaudes de diffuser entre les populations grâce à la connectivité larvaire. Ce mécanisme favorise la persistance des populations en permettant leur adaptation à des changements environnementaux qui conduiraient sans cela à des déclins, voir des extinctions locales.Finalement, l’ensemble de ces travaux ont mis en évidence la nécessité de considérer la connectivité et le potentiel évolutif des espèces dans les stratégies de conservation, afin de maximiser leur capacité de résilience et de persistance à long terme en dépit des crises environnementales de plus en plus prononcées
World marine ecosystems are experiencing unprecedented anthropic pressures inducing rapid environmental changes that threaten the persistence of wild species and their local populations. Hence, understanding the effects of genetic variability and dispersal capacities on marine population persistence is a key issue for the conservation of biodiversity. My PhD work had two main objectives: (i) evaluate the spatial distribution and drivers of genetic variation across coastal marine fish populations, and (ii) estimate the response of populations to climate changes in order to better understand their ability to persist.First, by performing a synthesis of published literature on 31 Mediterranean fish species, I showed that ecological traits related to mobility and population size strongly influence the level of within-population genetic diversity across species. Then, I studied the drivers of spatial genetic variation using genetic data from 727 individuals of the stripped red-mullet (Mullus surmuletus) collected in 72 sites around the Mediterranean Sea, and grouped into 47 pools genotyped for 1153 single nucleotide polymorphism (SNP) markers. Seascape genetic analyses showed that larval dispersal predominantly structures M. surmuletus genetic variation at intermediate and local spatial scales (<1000 km), whereas geographic isolation, due to population demographic history or adaptation, is the main driver at larger spatial scale. Lastly, studying the adaptive genetic variation of M. surmuletus using genome scan revealed a potential adaptive response of this species to the East-West gradient in salinity across the Mediterranean Sea.Subsequently, using a demo-genetic model to simulate coral population dynamics and resilience across the Indo-pacific corals, I showed that the process of ‘evolutionary rescue’ can help genotypes adapted to warm ocean waters to move and migrate between populations thanks to larval connectivity. Evolutionary rescue can thus promote the persistence of populations by allowing them to adapt to environmental changes that would otherwise lead to population declines or even local extinctions.Finally, all of these results highlighted the need to better consider connectivity and the evolutionary potential of species in conservation strategies, in order to maximize their resilience capacity and long-term persistence in the face of more severe environmental crises

Sous l'effet de la pêche, de nombreuses espèces de raies des eaux européennes ont décliné au cours du 20ème siècle. La conservation de ces espèces est un objectif majeur quant à la gestion des ressources marines. La raie bouclée (Raja clavata) est l'espèce de raie la plus répandue d'Atlantique Nord-Est. Sa gestion, basée sur un quota non spécifique, repose principalement sur les observations scientifiques et professionnelles et non sur des méthodes d'évaluations d'abondance. Les objectifs de cette thèse consistent ainsi à comparer les méthodes d'évaluations d'abondances disponibles pour cette espèce et à les appliquer aux données disponiblesDeux grands axes sont creusés : l'utilisation de méthodes basées sur la démographie de l'espèce et de méthodes basées sur la génétique
During the 20th century, several skates and rays species in European waters declined because of fishing. Conservation of these species is a major objective of the management of marine resources. The thornback ray (Raja clavata) is the most widespread species of the North-Est Atlantic. Its management is based on a nonspecific quota and lay on observations only as no stock assessment is available.Thus this thesis aims to compare the available stock assessments methods for this species and to apply them to empiric data. Two types of methods are investigated: methods based on population demography and methods based on population genetics

A hierarchical effect was identified whereby the importance of spatial distance (km) was the strongest predictor of patterns of genetic differentiation above the scale of the genetic patch. Below the genetic patch, spatial distance was still an explanatory variable but was only approximately 30% as relevant as mesic flatwoods or upland oak hammocks. Thus, it appears that habitat types largely influence patterns of population genetic connectivity at local scales but the signal of IBD becomes the dominant driver of regional connectivity. My results highlight some habitats as highly relevant to increased genetic connectivity at all spatial scales (e.g., upland oak hammocks) while others show no association (e.g., silviculture) or scale specific associations (e.g., pastures only at global scales). Given these results it appears that treating habitat as a binary metric (suitable/non-suitable) may be overly simplistic for generalist species in which gene flow probably occurs in a spectrum of habitat suitability. The overall pattern of spatial genetic and landscape genetic structure identified here provides insight into the evolutionary history and patterns of population connectivity for H. squirella and improves our understanding of the role of matrix composition for habitat generalists.; Understanding the nature of genetic variation in natural populations is an underlying theme of population genetics. In recent years population genetics has benefited from the incorporation of landscape and environmental data into pre-existing models of isolation by distance (IBD) to elucidate features influencing spatial genetic variation. Many of these landscape genetics studies have focused on populations separated by discrete barriers (e.g., mountain ridges) or species with specific habitat requirements (i.e., habitat specialists). One difficulty in using a landscape genetics approach for taxa with less stringent habitat requirements (i.e., generalists) is the lack of obvious barriers to gene flow and preference for specific habitats. My study attempts to fill this information gap to understand mechanisms underlying population subdivision in generalists, using the squirrel treefrog (Hyla squirella) and a system for classifying 'terrestrial ecological systems' (i.e. habitat types). I evaluate this dataset with microsatellite markers and a recently introduced method based on ensemble learning (Random Forest) to identify whether spatial distance, habitat types, or both have influenced genetic connectivity among 20 H. squirella populations. Next, I hierarchically subset the populations included in the analysis based on (1) genetic assignment tests and (2) Mantel correlograms to determine the relative role of spatial distance in shaping landscape genetic patterns. Assignment tests show evidence of two genetic clusters that separate populations in Florida's panhandle (Western cluster) from those in peninsular Florida and southern Georgia (Eastern cluster). Mantel correlograms suggest a patch size of approximately 150 km. Landscape genetic analyses at all three spatial scales yielded improved model fit relative to isolation by distance when including habitat types.
ID: 029094250; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Thesis (M.S.)--University of Central Florida, 2010.; Includes bibliographical references (p. 58-70).
M.S.
Masters
Department of Biological Sciences
Sciences

Population genetic and phylogeography of two common mediterranean species were studied in 10 localities located on the coasts of Toscana, Puglia and Calabria. The aim of the study was to verify the extent of genetic breaks, in areas recognized as boundaries between Mediterranean biogeographic sectors. From about 100 sequences obtained from the mitochondrial Cytochrome Oxidase subunit I (COI) gene of Halocynthia papillosa and Hexaplex trunculus genetic diversity, genetic structure at small and large distances and demographic history of both specieswere analyzed. No evidences of genetic breaks were found for the two species in Toscana and Puglia. The genetic structure of H. trunculus evidences the extent of a barrier to gene flow localized in Calabria, which could be represented by the Siculo-Tunisian Strait and the Strait of Messina. The observed patterns showed similar level of gene flow at small distances in both species, although the two species have different larval ecology. These results suggest that other factors, such as currents, local dynamics and seasonal temperatures, influence the connectivity along the Italian peninsula. The geographic distribution of the haplotypes shows that H. papillosacould represent a single genetic pool in expansion, whereas H. trunculus has two distinct genetic pools in expansion. The demographic pattern of the two species suggests that Pleistocene sea level oscillations, in particular of the LGM, may have played a key role in shaping genetic structure of the two species. This knowledge provides basic information, useful for the definition of management plans, or for the design of a network of marine protected areas along the Italian peninsula.

A high proportion of amphibian species are threatened with extinction globally, and habitat loss and degradation are the most frequently implicated causes. Rapid deforestation for the establishment of agricultural production is a primary driver of habitat loss in tropical zones where amphibian diversity is highest. Land-cover change affects native assemblages, in part, through the reduction of habitat area and the reduction of movement among remnant populations. Decreased gene flow contributes to loss of genetic diversity, which limits the ability of local populations to respond to further environmental changes. The focus of this dissertation is on the degree to which common land uses in Sarapiquí, Costa Rica impede the movement of two common amphibian species. First, I used field experiments, including displacement trials, and a behavioral landscape ecology framework to investigate the resistance of pastures to movement of Oophaga pumilio. Results from experiments demonstrate that pastures do impede movement of O. pumilio relative to forest. Microclimatic effects on movement performance as well as limited perceptual ranges likely contribute to reduced return rates through pastures. Next, I linked local processes to landscape scale estimates of resistance. I conducted experiments to measure habitat-specific costs to movement for O. pumilio and Craugastor bransfodrii, and then used experimental results to parameterize connectivity models. Model validation indicated highest support for resistance estimates generated from responses to land-use specific microclimates for both species and to predator encounters for O. pumilio. Finally, I used abundance and experiment-derived resistance estimates to analyze the effects of prevalent land uses on population genetic structure of the two focal species. While O. pumilio did not exhibit a strong response to landscape heterogeneity and was primarily structured by distances among sites, C. bransfordii genetic variation was explained by resistance estimates from abundance and experiment data. Collectivity, this work demonstrates that common land uses can offer different levels of resistance to amphibian movements in Sarapiquí and illustrates the value of investigating local scales processes to inform interpretation of landscape-scale patterns.

L'objectif principal de cette thèse était d’améliorer notre compréhension de la connectivité et de l'adaptation locale entre les principaux gisements de coquille Saint-Jacques à l'échelle de la Bretagne et de la Manche. Ce travail s'est structuré autour de trois axes, (i) Une étude basée sur l'association entre données microsatellites et modèle démogénétique a été réalisée afin d’explorer la structure génétique neutre des principaux gisements de coquilles Saint-Jacques sur l’ensemble de la Manche. Il ressort de cette étude une différenciaton génétique entre les gisements localisés à l'Ouest de Start Point de ceux du reste de la Manche, suggérant l'existence d’une entité indépendante reproductivement. (ii) La structure génétique neutre entre la Manche Ouest, la Mer d'Iroise et la Rade de Brest a été analysée, à l'aide d’approches de ‘Genotyping by Sequencing' (GBS) et d’un modèle hydrodynamique, afin d'étudier le degré de connectivité de la population de Rade de Brest vis-à-vis des populations environnantes, dans un contexte d'ensemencement massif du gisement de Brest par du naissain issu d'écloserie. Les résultats suggèrent (1) le rôle prépondérant du Front de Ouessant comme barrière à la dispersion larvaire entre la Manche Ouest et la Mer d'Iroise et la Rade de Brest et (2) des flux larvaires de la Baie de la Baie de Douarnenez alimentant la Rade de Brest associés à une absence de structure génétique entre ces régions. (iii) Enfin, la structure adaptative des gisements distribués entre la Rade de Brest, la Baie de Morlaix et le Golfe Normano-Breton a été explorée à l'aide des GBS. Pour la première fois sont observés à fines échelles des processus adaptatifs entre les gisements de Rade de Brest et du Golfe Normano-Breton. Ce corpus de résultats révèle l'existence d'isolement démographique et génétique entre les gisements die P. maximus de Manche, Mer d'Iroise et Rade de Brest et suggère pour la première fois des signaux de sélections à fines échelles entre gisements fortement ensemencés. Cette thèse ambitionne de contribuer à la prise de décision en matière de gestion des stocks de coquille Saint-Jacques en Manche et Bretagne
The main objective of this study was to improve knowledge about connectivity and local adaptation among great scallop fishing grounds located in the English Channel, the Ushant Sea and the Bay of Brest, in order to provide concrete information to fisheries managers regarding great scallop population biology. This work was divided in three part.(i) Firstly, population genetic structure of P. maximus among the main fishing grounds of the English Channel was analysed through a multidisciplinary seascape genetics approach coupling microsatellite data and demo-genetic modelling. The main results underlined genetic differentiation between western Start Point population and the rest of the fishing grounds of the English Channel, suggesting reproductive independency. (ii) Secondly, the genetic structure between the Western English Channel, the Ushant Sea, the Bay ofDouarnenez and the Bay of Brest was investigated using ‘Genotype by Sequencing' (GBS) coupled to a hydrodynamic modelling approach, in order to understand connectivity between Bay of Brest and neighbouring populations in a context intensive enhancement of this Bay.Results emphasize(1 ) the importance of the Ushant Front as barrier to larval dispersal between the Western English Channel and theUshant Sea/The Bay of Brest and (2) larval flux from the Bay of Douarnenez to the Bay of Brest. (iii) Finally, adaptative genetic structure was explored using GBS, between the Bay of Brest, the Bay of Morlaix and the Normano-Breton Gulf.For the first time, fine scale adaptative processes were observed among main Brittany fishing grounds, for which reproductive differentiation were previously noticed.This body of research showed demographic and genetic isolation between fishing grounds of P. maximus of the Western English Channel, the Ushant Sea and the Bay of Brest and suggested for the first time fine scale signals of selection between enhanced fishing grounds. This thesis aims to contribute to decision processes regarding management strategies of P. maximus stocks in the English Channel and in Brittany

Processes that influence the early life stages of fishes can significantly impact population dynamics, yet they continue to be poorly understood. This dissertation examined relationships between the environment, early life history traits (ELHTs), behavior, and post-settlement survival for a coral reef fish, Stegastes partitus, in the upper Florida Keys, to elucidate how they influence juvenile demography. Otolith analysis of settlers and recruits coupled with environmental data revealed that S. partitus surviving the early juvenile period settled at larger sizes and grew slower post-settlement. Water temperature also influenced the ranges of these and other ELHTs as well as the intensity and direction of selective mortality processes acting on some of these traits (i.e., pelagic larval duration, mean larval growth). Otolith analysis was paired with behavioral observations of newly settled juvenile S. partitus in the field to reveal that the relationship between size-at-settlement, early juvenile growth and survival is behaviorally-mediated. Individuals that were larger at settlement were more active (i.e., spent less time sheltered, swam farther from shelters) and grew more slowly post-settlement. Likewise, slower juvenile growth was associated with greater activity, more conspecific aggression, and faster escape swimming speeds. A six-year time series of recruitment densities revealed substantial temporal (interannual, seasonal, lunar) and spatial (by microhabitat, conspecific density) variability in recruitment which influenced the composition of recruits. For instance, larvae settling during the darkest phases of the moon were larger at settlement, but selective mortality processes during brighter periods removed more of the smallest settlers, resulting in juveniles with similar sizes-at-settlement regardless of when they arrived to the reef. Because recruitment strength and composition varied temporally, genetic markers (6 microsatellite and 1 mitochondrial loci) were used to determine if the genetic composition of monthly cohorts of settling larvae and juveniles also varies interannually, monthly, or across life stages. A lack of genetic structure suggested that S. partitus has a large effective population size and variation in ELHTs is not likely the result of successful spawning of a disproportionately small group of adults. As a whole, these results reveal processes associated with larval supply and post-settlement life that collectively shape juvenile demography.

La mise en place des réseaux de continuités écologiques dans les paysages nécessite l'estimation de la connectivité fonctionnelle, particulièrement lorsque ces paysages sont fragmentés par les Infrastructures Linéaires de Transport (ILT). Dans ce contexte, des suivis génétiques et démographiques ont été réalisé sur quatre espèces terrestres dans un paysage fragmenté par six types d'infrastructures en Dordogne, France. Les résultats ont montré qu'une part importante de la variabilité génétique (38 %) est expliquée par les ILT, qui agissent majoritairement comme des barrières à la dispersion. Cependant, les effets des ILT varient fortement d'une espèce à l'autre et peuvent, dans certains cas, agirent comme des éléments favorisant la dispersion. Par ailleurs, l'utilisation conjointe des outils de génétique du paysage et des suivis démographiques montre que selon l'approche utilisée, les résultats peuvent diverger. Ces deux approches devraient donc être davantage utilisées simultanément dans les études paysagères
Implementing networks of ecological continuities requires estimation of functional connectivity in landscapes. Particularly when those landscapes are fragmented by Large-scale Transportation Infrastructures (LTIs). In this context, four terrestrial species were monitored using genetic and demographic surveys across six LTIs in south-western France. The results showed that a significant amount of genetic variability was explained by LTIs (38%), that are mostly acting as dispersal barriers. However, LTI effects are variable depending on the species under study and, in some cases, they can even act as infrastructures enhancing dispersal. Furthermore, the combined use of genetic tools and demographic surveys showed that depending on the selected approach, results might differ. Therefore, these two approaches should be more used simultaneously in landscape surveys

MARINE CONNECTIVITY, SEASCAPE GENETICS and IMPLICATIONS for PROTECTED AREAS (MPAs) Population connectivity is a keystone in a wide range of processes, including the shaping of population genetic structure, local and meta-population dynamics and the design of protected areas. Understanding the extent at which connectivity occurs is critical for the conservation of marine species and for the improvement of biological and ecological resources management. Genetic approaches are widely used as a powerful tool for the indirect inference of connectivity among populations of marine organisms, especially when the working-conditions makes the direct measure of dispersal pattern hard to quantify, such as the tracking of larval stage of benthic invertebrates. Despite their power, genetic isolation patterns can be difficult to explain, especially when the genetic differentiation is weak. The integration of genetic data with oceanographic feautures, the biology of species and the modelling of larval dispersal in a multidisciplinary approach, the so-called seascape genetics, can provide new insights into drivers shaping the spatial genetic variability of species. Worldwide, the anthropogenic activities have a strong negative impact to the marine ecosystem, causing coastal-habitat loss or fragmentation and the biodiversity depletion. Given the global extent of these phenomena, restoration of marine ecosystem is actually top conservation priority. Marine protected areas (MPAs), especially the no-take zones, have been increasingly identified as one of the most effective tool for conservation and management in reducing the alteration of marine ecosystem and mitigating the negative effect of human activities. The implementation of network of MPAs, where the individual protected areas can operate in synergy, could offer a greater protection at a wider spatial scale, leading more effectively the conservation goals than individual sites alone. The European Commission funded CoCoNET project aimed to the identification of groups of putatively connected MPAs in the Mediterranean and the Black Seas, shifting from local to regional (Networks of MPAs) and basin (network of networks) scales. It adopted an interdisciplinary approach based on population genetics of 13 selected species, the modelling of the dispersal and the beta diversity. In this thesis, 2 CoCoNET species were studied: the edible common sea urchin Paracentrotus lividus (Lamarck, 1816) and the Mediterranean mussel Mytilus galloprovincialis (Lamarck, 1819). The 2b-RAD protocol was successfully used to processing hundreds samples as well as for genotyping of hundreds SNPs, that were used to evaluating the genetic structure of these 2 species in the CoCoNET study areas. • A seascape genomics approach was applied to explore connectivity patterns of the sea urchin Paracentrotus lividus in the Mediterranean pilot area: the potential larval connectivity and retention (Lagrangian simulations) and the realized connectivity (genomic analyses) were assessed and compared with a focus on the Adriatic and Ionian seas. A total of 275 samples from 10 population samples of Western and Central Mediterranean Sea were processed with the 2b-RAD protocol, and 1122 Single Nucleotide Polymorphisms (SNPs) were genotyped and used for population genomics analysis. Lagrangian simulations was performed with a biophysical model of larval dispersal focused on the Adriatic-Ionian basins and it was integrated with features of the P. lividus larval phase (PLD, temperature constrain, reproductive timing). Genetic homogeneity was found among the eight population samples collected in the focal Adriatic-Ionian area, whereas a weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic-Ionian locations through a relatively persistent flux of propagules from each sites to its closest neighbor, mainly in a counterclockwise direction. Overall, these findings supported the hypothesis of connectivity of P. lividus populations in this area. We also compared our findings with previously published mitochondrial genetic data (cytochrome b gene) showing that our genome-scale SNPs dataset had a greater power in resolving the population structure of this species, providing solid and reliable indirect measures of connectivity, broadly in line with the predictions of Lagrangian simulations. • The population genomics structure of the mussel Mytilus galloprovincialis was explored at different geographic scales (local and wide) in the Mediterranean and Black seas. The application of a genome-wide approach based on single nucleotide polymorphism (SNP) markers, a wide sampling design and a good sample size, allowed to overcome the previous limitations providing the first reliable biogeographic data concerning this species throughout its native range. A total of 19 population samples were analysed, 10 from the Mediterranean Sea and 9 from the Black Sea. To obtain the best resolution for the wide and the local scale, we obtained and investigated 3 different datasets: 1) the overall dataset (461 individuals, 512 polymorphic loci); 2) the Adriatic-Ionian dataset (201 individuals, 811 polymorphic loci) and 3) the Black Sea’s dataset (228 individuals, 998 polymorphic loci). A marked structuring between the Mediterranean and Blacks Seas was found, revealing that the Mediterranean and Black seas are genetically distinct, likely due to oceanographic constrains. In the Black Sea, a completely lack of genetic structure was detected, where the currents pattern and the long pelagic larval duration of this species probably ensure a good connection among the sampled locations. On the other hand, in the Mediterranean Sea, no signal of differentiation was found between the Western and Central, whereas the Central Mediterranean (the Adriatic-Ionian population samples) showed a weak genetic heterogeneity, that underlined an East-West differentiation in the Central Adriatic Sea, and a general homogeneity in the Southern Adriatic and Ionian seas among the Italian, Greek and Albanian localities. This pattern of genetic differentiation likely depends on the Adriatic gyral circulation, that prevents or allows the exchange of larvae, acting as barrier among some localities and determing a certain level of self retention in others. Overall, connectivity data obtained so far in the CoCoNET framework revealed a heterogeneous mosaic of species-specific connectivity patterns throughout the targeted areas in Mediterranean and Black seas, ranging from the total absence of genetic differentiation (P. lividus) to the strong genetic structure even at a local scale (in the habitat former P. oceanica). Overall, the heterogeneity of connectivity patterns depends on species-specific peculiarities in relation to environmental features, and connectivity results so far obtained warns against any generalization in defining conservation units based on the results of the single species. The wide heterogeneity of species-specific connectivity outcomes suggests that the implementation of ecological effective networks of MPAs should standing on meta-community information across a range of spatial scales and a representative set of species to obtain a “collection of networks of genetic variation of all species within a community”. LANDSCAPE GENETICS IN PARASITIC DISEASES Neglected Tropical Diseases (NTDs) are a group of parasitic infectious diseases affecting worldwide approximately 2.7 billion people living in poverty, especially in the tropical areas. The NTDs pathogens have often a complex life-cycle, involving at least one host, including humans. A great heterogeneity exists in the dispersal ability, distribution and transmission routes of parasitic species, that are strongly influenced by ecological settings and landscape variation. Understanding how abiotic and biotic variables interact and affect the movements and distribution of parasites, hosts and vector species is key for predicting and controlling the disease spread. Trypanosoma cruzi is the most important parasite in Latin America, the infectious agent of Chagas disease, a NTD that caused around 14000 deaths annually. In Ecuador, where the Chagas disease is endemic, one of main insect vectors is the kissin bug Rhodnius ecuadoriensis. In this thesis we worked on a pilot study regarding the vector Rhodnius ecuadoriensis based on 20 specimens collected from four communities in Ecuador, with the aims of i) testings the 2b-RAD protocol by assessing and comparing the effectiveness of three type IIB Restriction Enzymes: ii) generating several hundred SNPs markers for this species and iii) performing preliminary genomic analysis to test the efficacy of the identified SNP markers. The three type IIB Restriction Enzymes (AlfI, BcgI, and CspCI) resulted to be effective for processing Rhodnius ecuadoriensis genomic DNA samples and, as expected, the enzyme showing the most abundance of cutting sites (estimated via an in silico digestion of the Rhodnius prolixus genome) provided the smaller number fo usable molecular markers (AlfI). CspCI enzyme produced the largest amount of polymorphic markers whatever the read depth, thus evidencing its good experimental performance in R. ecuadoriensis and likely to other Rhodnius sp. Vectors. Preliminary population genomic analyses were performed with BgcI and CspCI datasets, and a signal of structuring among populations was detected. Specifically, Bayesian clustering detected two distinct clusters without previous location information, one of them was the most distant population (Bejuco) from the others 3 from Loja region, that clustered together. Our findings suggest that 2b-RAD genotyping is both a cost-effective and methodologically simple approach for generating high resolution genomic data for Chagas disease vectors with the power to distinguish between different vector populations at epidemiologically relevant scales.
CONNETTIVITA’ MARINA, SEASCAPE GENETICS E IMPLICAZIONI PER LE AREE MARINE PROTETTE La connettività di popolazione è la chiave di volta di un’ampia varietà di processi, tra i quali la determinazione della struttura genetica di popolazione delle specie, le dinamiche di popolazioni locali e meta-popolazioni e la progettazione di aree protette. Capire e definire le modalità con cui le popolazioni sono connesse e a che scala geografica la connessione avviene, è critico per la conservazione delle specie marine e per migliorare la gestione delle risorse marine economiche e biologiche. Gli approcci genetici sono ampiamente utilizzati come mezzo efficace per la stima indiretta della connettività tra popolazioni di organismi marini, specialmente quando le condizioni di lavoro rendono difficile lo studio diretto dei pattern di dispersione, come nel caso del tracking delle larve negli invertebrati bentonici. Nonostante il potere della genetica, i pattern di isolamento rilevati possono risultare di difficile interpretazione, soprattutto quando il differenziamento genetico osservato è debole. Integrare i dati genetici con le caratteristiche oceanografiche dell’area di studio, dati riguardanti la biologia delle specie e il modelling della dispersione larvale in un approccio multidisciplinare chiamato seascape genetics, può chiarire quali siano i fattori che determinano la distribuzione spaziale della variabilità genetica delle specie. In tutto il mondo, le attività antropiche hanno effetti estremamente negativi sull’ecosistema marino, causando la perdita o la frammentazione degli habitat costieri e il depauperamento della biodiversità ad essi associata. Data l’estensione globale di questi fenomeni, il ripristino dell’ecosistema marino è una delle principali priorità target nell’ambito della conservazione. Le aree marine protette (MPAs) sono state riconosciute come uno dei mezzi più efficaci per conservare e gestire l’intero ecosistema marino, in quanto sono in grado di ridurre e mitigare gli effetti negativi causati delle attività umane. L’implementazione di network di MPAs, all’interno dei quali le singole aree marine protette possono agire in sinergia, potrebbe offrire una maggior protezione su ampia scala spaziale, agendo in modo più efficace rispetto a quanto possano fare le singole aree da sole. Il progetto CoCoNET, finanziato dalla Commissione Europea, è un progetto che mirava all’identificazione di gruppi di MPAs putativamente connesse nel Mediterraneo e nel Mar Nero, sia su scala locale sia considerando l’intero bacino. Il progetto CoCoNET si proponeva di adottare un approccio multidisciplinare basato sulla genetica di popolazione di 13 specie, il modelling della dispersione larvale e la beta diversity. In questa tesi sono state studiate 2 specie del progetto CoCoNET, il riccio di mare Paracentrotus lividus (Lamarck, 1816) e il mitilo del Mediterraneo Mytilus galloprovincialis (Lamarck, 1819). Per il processamento di centinaia di campioni e il genotyping di altrettanti polimorfismi a singolo nucleotide (SNPs) utilizzati per studiare la struttura genetica di popolazione delle 2 specie, è stato utilizzato il protocollo 2b-RAD. • Per il riccio di mare P. lividus è stato utilizzato un approccio di seascape genomics nel Mediterraneo centrale: sono stati stimati e confrontati il potenziale di dispersione larvale e di retention (ottenuti con simulazioni di Lagrange) e la connettività realizzata (ottenuta con i dati genetici) con focus a livello dell’Adriatico e dello Ionio. Sono stati processati un totale di 275 individui da 10 campioni di popolazione provenienti dal Mediterraneo occidentale e centrale, e 1122 SNPs sonno stati genotipizzati ed utilizzati per le analisi di genomica di popolazione. Le simulazioni di Lagrange sono state condotte utilizzando un modello biofisico di dispersione larvale focalizzato nel bacino Adriatico-Ionico, che è stato integrato con caratteristiche dello stadio larvale di P. lividus (durata delle larve, influenza della temnperatura, periodo riproduttivo). Gli 8 campioni di popolazione campionati in Adriatico-Ionio sono risultati essere geneticamente omogenei, mentre è stato rilevato un lieve ma significativo differenziamento di queste 8 rispetto ai 2 campioni di popolazione provenienti dal Mediterraneo occidentale (Francia e Tunisia). Questo risultato non è stato influenzato dalla presenza di alcuni loci probabilmente sotto selezione direzionale. Le simulazioni di Lagrange hanno predetto uno scambio larvale potenziale tra gli 8 campioni di popolazione Adritico-Ionici attraverso un flusso di propaguli relativamente persistente da ogni sito, prevalentemente in direzione oraria. Complessivamente, i risultati ottenuti dalla genetica di popolazione e dalle simulazioni supportano ampiamente l’ipotesi di una buona connessione tra le popolazioni di P. lividus in quest’area. • La struttura genomica di popolazione del mitilo M. galloprovincialis è stata esplorata su diverse scale geografiche nel Mediterraneo e Mar Nero. L’utilizzo di un approccio genome-wide basato su SNPs, un ampio campionamento e una buona dimensione dei campioni di popolazione hanno permesso di superare le limitazioni finora incontrate nell’ottenere dati biogeografici affidabili per questa specie all’interno del suo range di distribuziona nativo. Sono state analizzati 19 campioni di popolazione, 10 provenienti dal Mar Mediterraneo e 9 dal Mar Nero. Al fine di ottenere il miglior potere di risoluzione possibile sia su ampia scala sia su scala ridotta, sono stati utilizzati per le analisi 3 diversi dataset: 1) un dataset complessivo (461 individui, 512 loci); 2) un dataset adriatico-ionico (201 individui, 811 loci) e 3) un dataset per il Mar Nero (228 individui, 998 loci). È stato evidenziato un marcato differenziamento genetico tra il Mar Mediterraneo e il Mar Nero, probabilmente a causa di costrain oceoanografici. Nel Mar Nero è evidente una totale mancanza di struttura, probabilmente dovuta al pattern delle correnti e alla durata dello stadio larvale che permettono una buona connessione tra le popolazioni campionate. Dall’altro lato invece, non è stato notato differenziamento tra il Mediterraneo occidentale e quello centrale, mentre un certo grado di eterogeneità genetica è stato rilevata tra le popolazioni adriatico-ioniche, con un differenziamento est-ovest nell’Adriatico centrale e una relativa omogeneità tra le popolazone dell’Adriatico meridionale e dello Ionio. Il pattern di differenziamento osservato dipende probabilmente dalla presenza di gyres minori in aggiunta alla circolazione adriatica principale, che può favorire o impedire lo scambio di propaguli, fungendo da barriera al flusso genico tra alcune località e favorendo la self-retention in altre. Complessivamente, i risultati ottenuti finora nel progetto CoCoNET hanno messo in luce un mosaico eterogeneo di pattern di connettività specifici per le diverse specie, che vanno dalla totale assenza di differenziamento come nel caso del riccio, alla forte struttura come nel caso dell’habitat former Posidonia oceanica. Questa eterogeneità può dipendere da peculiarità specie-specifiche messe in relazione a caratteristiche ambientali, e i dati di connettività finora ottenuti sconsigliano qualsiasi forma di generalizzazione basandosi sui risultati ottentui in una singola specie. Il quadro che sta emergendo suggerisce che la progettazione di network di MPAs ecologicamente efficaci debbano basarsi su informazioni ottenute a livello di comunità considerando un ampio range spaziale, e un set rappresentativo delle specie che vivono nell’area target. LANDSCAPE GENETICS NELLE PARASSITOSI Le malattie tropicali sono un gruppo di malattie infettive causate da parassiti che infettano quasi 3 milioni di persone in tutto il mondo, specialmente nei paesi poveri delle zone tropicali. I patogeni che causano questa malattie hanno solitamente un ciclo vitale complesso, che coinvolge almeno un ospite, compresi gli esseri umani. Esiste una grande variabilità nelle capacità di dispersione, nella distribuzione e nelle vie di trasmisisone delle specie parassite. Questa variabilità è fortemente influenzata dalle caratteristiche ambientali e del paesaggio. Capire come le variabili biotiche e abiotiche interagiscono e influenzano la distribuzione del parassita, dei loro ospiti e delle specie vettore è un fattore chiave per la predizione ed il controllo della diffusione di queste malattie. Il Tripanozoma cruzi è il parassita più importante del Sud America ed è l’agente infettivo del morbo di Chagas, una malattia tropicale endemica in molte regione dell’Ecuador dove uno dei principali vettori è la cimice ematofaga Rhodnius ecuadoriensis. In questa tesi è stato prodotto uno studio pilota sul vettore R. ecuadoriensis utilizzando 20 individui campionati in 4 comunità dell’Ecuador, con lo scopo di i) testare il protocollo 2b-RAD utilizzando e confrontanto l’efficacia di 3 diversi enzimi di restrizione di tipo IIb, ii) ottenere un numero di marcatori SNPs sufficiente per iii) fornire delle analisi preliminari di genetica di popolazione per questa specie. I 3 enzimi testati (AlfI, BcgI, and CspCI) sono risultati efficaci nel processare il DNA genomico di questa specie e, come era atteso, l’enzima con il maggior numero di siti di riconosciemento (stimato tramite una restrizione in silico del genoma di Rhodnius prolixus) ha prodotto il minor numero di loci utilizzabili (AlfI). L’enzima CspCI ha prodotto il maggior numero di loci polimorfici a qualsiasi read depth considerata evidenziando così l’ottima performance di questo protocollo in questa specie e presumibilmente anche in altre specie appartenenti allo stesso genere. Le analisi preliminari di genetica di popolazione sono state condotte utilizzando i dataset ottenuti dagli enzimi BcgI e CspCI che sono stati in grade di evidenziare un certo grado di struttura genetica tra I 4 campioni di popolazione. Un clustering bayesiano, condotto senza l’informazione a priori riguardante le località, ha identificato la presenza di 2 cluster geneticamente distinti: uno rappresentato dalla popolazione geograficamente più distante rispetto alle altre (Bejuco), l’altro invece formato dalle altre 3 popolazioni che provenivano tutte dalla regione di Loja. Questi risultati evidenziano come il protocollo 2b-RAD sia una metodologia semplice ed efficace nel generare marcatori su scala genomica in uno dei principali vettori del morbo di Chagas, e come permetta di ottenere informazioni sulla struttura di popolazione di questa specie ad una scala rilevante a livello epidemiologico.

L'influence de la diversité génétique sur la stabilité démographique des populations constitue un paradigme de l'écologie évolutive. Au sein des populations naturelles, l'étude de cette relation est complexifiée par l'influence réciproque de la stabilité sur la diversité, et leur degré d'interconnexion. Ces interrelations ont été explorées chez la plante marine Zostera marina et les coraux d'eau froide Lophelia pertusa et Madrepora oculata, des espèces partiellement clonales. Ce trait d'histoire de vie, influençant profondément la dynamique démographique et la trajectoire évolutive des espèces, a constitué le fil d'Ariane de ce travail. L'échantillonnage dans l'espace (échelle régionale) et le temps (un pas de trois ans) d'herbiers de Zostère a permis de mieux comprendre la dynamique clonale de ces plantes. L'architecture et la diversité clonale apparaissent comme la résultante de l'équilibre entre dispersion/recrutement de nuages de graines dispersées collectivement, et la compétition pour l'espace entre clones. Les perturbations affectent localement l'équilibre de l'herbier. Cette dynamique originale rend impossible l'identification des contours populationnels. En revanche, nos résultats semblent indiquer que la diversité génétique au sens strict (hétérozygotie et nombre d'allèles) des herbiers de Zostères constitue un facteur de stabilité démographique, via sa potentielle influence sur les capacités de résistance aux perturbations saisonnières. Les coraux d'eau froide, quant à eux, présentent des patrons biogéographiques en accord avec l'hypothèse d'une extinction dans le Golfe de Gascogne, lors des derniers épisodes glaciaires. Les marques visibles des activités de pêche posent la question des capacités de résilience de ces écosystèmes, qui dépendent entre autres du potentiel de dispersion de ces espèces. L'absence de structure génétique observée chez L. pertusa suggère, au moins pour cette espèce, un fort degré d'interconnexion entre les récifs, tandis que M. oculata montre davantage de structure régionale. La sensibilité de ces espèces aux variations climatiques et à la pression des activités anthropiques souligne la nécessité d'études approfondies, pour leur conservation.Les résultats obtenus pendant cette thèse permettent de mieux comprendre la dynamique populationnelle des herbiers et récifs profonds, le taux de clonalité et la connectivité des populations. Ces informations sont essentielles pour avancer vers une meilleure compréhension de la dynamique et la résistance de ces espèces structurantes, et sont donc primordiales pour la conservation de ces écosystèmes clé.

Doutoramento em Ciências do Mar
The red gorgonian Paramuricea clavata is an engineering species, inhabiting rocky shore in the Mediterranean Sea and Portuguese coast of the Atlantic Ocean. The species was severely impacted by climatically induced mass mortality events in the NW Mediterranean. The general aim of the study was to investigate the genetic diversity of P. clavata in the Ligurian Sea (NW Mediterranean), a region highly impacted by past mass mortality events, and the Atlantic Ocean, where mass mortality was never observed due to generally lower water temperature. Microsatellites were used to study the contribution of clonal reproduction, connectivity pattern, genetic structure and diversity. Additionally one mitochondrial marker (Cytochrome Oxidase I) was used to compare the Atlantic and Mediterranean populations. The results revealed, that clonal propagation does not play an important role in P. clavata, since at four out of nine sites clones were not detected and the maximum prevalence of clones reached only 13%. The study failed to detect any genetic diversity loss in the P. clavata populations affected by mass mortality events. The migration pattern among sites affected by mass mortality and unaffected ones was described. The results confirmed that low larval dispersal capability in the red gorgonian may still be ecologically significant for population replenishment and persistence, enabling migration between local populations. This research has identified an important genetic break within the red gorgonian distribution. Both markers used in the present study, mtDNA and microsatellites, revealed the same discontinuity between the Mediterranean and Atlantic. Significant differences were found in the genetic diversity between the Mediterranean and Atlantic populations, with heterozygosity and allelic richness being slightly, but significantly, higher in the Mediterranean Sea, possibly as a result of colonization history or isolation of the Atlantic sites. The differences in genetic diversity were also detected between deep and shallow populations. Allelic richness increase with depth, being lower in the shallow, less stable populations due to past mortality events induced by warming and other interacting factors and higher in deeper, stable populations.The results should prove to be particularly valuable for the conservation of soft corals communities and thus the overall marine biodiversity.
A gorgónia vermelha, Paramuricea clavata, é uma espécie engenheira que habita costas e recifes rochosos do Mediterrâneo e do Atlântico ao longo da costa de Portugal, a profundidades que variam entre 15 e os 80 m. Esta espécie foi severamente afetada, no Mediterrâneo NO, por eventos de mortalidade induzidos por variações climáticas recentes. O objetivo geral deste estudo foi a investigação da diversidade genética de P. clavata no Mar da Ligúria (Mediterrâneio NO), uma região altamente impactada por eventos de mortalidade em massa causados por temperaturas elevadas, e no Atlântico, onde mortalidade em massa nunca foi observada em consequência de temperaturas genericamente mais baixas. Foram utilizados microsatélites para o estudo da contribuição da reprodução clonal, padrões de conectividade, estrutura genética e diversidade genética. Adicionalmente, um marcador mitocondrial (Cytochrome Oxidase I) foi usado para comparar as populações do Atlântico e do Mediterrâneo. Os resultados revelaram que a propagação clonal não desempenha um papel importante em P. clavata, uma vez que em quatro dos nove sítios não foram detetados clones e que a máxima prevalência de clones detetada atingiu apenas 13%. No entanto, a prevalência de clones detectada no presente estudo foi maior do que o previamente relatado. O estudo não conseguiu detetar qualquer perda de diversidade genética nas populações de P. clavata afetadas por eventos de mortalidade em massa. Foi possível descrever o padrão de migração entre os sítios afetados pela mortalidade em massa e os não afetados. Os resultados confirmaram que a baixa capacidade de dispersão larvar na gorgónia vermelha pode ainda ser ecologicamente significante para a recolonização e persistência populacional, permitindo a migração entre populações locais. A troca de larvas foi mais comum entre recifes separados por 200-300m, mas também foi detectada entre locais separados por 20 km. Os dados indicaram ainda migrações comuns entre recifes localizados a menores profundidades, impactados por mortalidade em massa, e recifes mais profundos, não impactados, do mesmo local. A presente investigação identificou uma importante descontinuidade genética na distribuição da gorgónia vermelha, com ambos os marcadores utilizados no estudo, mtDNA e microsatélites, revelando a mesma descontinuidade entre o Mediterrâneo e o Atlântico. Foram também encontradas diferenças significativas na diversidade genética entre o Mediterrâneo e as populações do Oceano Atlântico, com a heterozigosidade e a riqueza alélica ligeiramente, mas significativamente, mais elevadas no Mediterrâneo, possivelmente como resultado da história da colonização ou isolamento dos locais do Atlântico. Finalmente, foram ainda detectadas diferenças na diversidade genética entre as populações superficiais e mais profundas. A riqueza alélica foi menor nas populações menos profundas, menos estáveis devido a eventos de mortalidade induzidos pelo aquecimento e por outros fatores, e maior nas populações mais profundas e estáveis. Estes resultados devem revelar-se particularmente valiosos para a conservação de comunidades de gorgónias e assim a biodiversidade marinha global.
La gorgonia rossa Paramuricea clavata è una ‘engineering species’, vive sui fondali rocciosi del Mediterraneo e della costa portoghese dell’Oceano Atlantico. La specie è stata severamente impattata da eventi di mortalità di massa indotti dal CC nel Mediterraneo nord-occidentale. Lo scopo dello studio è stato di indagare la diversità genetica di P. clavata nel Mar Ligure (Mediterraneo nord-occidentale), una regione fortemente impattata da eventi di mortalità, e nell’Oceano Atlantico, dove eventi di mortalità non sono mai stati registrati grazie a valori di temperatura dell’acqua generalmente più bassi. Per studiare il contributo della riproduzione clonale, i pattern di connettività, la struttura e la diversità genetica sono stati usati i microsatelliti. In aggiunta, un marcatore mitocondriale (Cytochrome Oxidase I) è stato utilizzato per confrontare le popolazioni atlantiche con quelle mediterranee. I risultati hanno mostrato che la propagazione clonale non gioca un ruolo importante in P. clavata, in quanto in quattro siti su nove non sono stati individuati cloni e la predominanza massima di cloni ha totalizzato solo il 13%. Lo studio non ha riscontrato perdita di diversità genetica nelle popolazioni di P. clavata colpite da eventi di mortalità. Sono stati descritti i pattern di migrazione tra siti colpiti da mortalità e quelli non colpiti. I risultati hanno confermato che la bassa dispersione larvale nella gorgonia rossa può essere ancora ecologicamente significativa per il rifornimento e la persistenza di popolazioni, favorendo la migrazione tra popolazioni locali. Questa ricerca ha identificato un importante break genetico nella distribuzione della gorgonia rossa. Entrambi i marker usati in questo studio, mtDNA e microsatelliti, hanno rivelato la stessa discontinuità tra Mediterraneo ed Atlantico. Differenze significative sono state riscontrate nella diversità genetica tra popolazioni mediterranee e atlantiche, con eterozigosità e ricchezza allelica leggermente, ma significativamente più alte nel Mediterraneo, probabilmente come risultato della storia di colonizzazione o isolamento dei siti atlantici. Le differenze nella diversità genetica sono state riscontrate anche tra popolazioni profonde e superficiali. La ricchezza allelica aumenta con la profondità, risultando più bassa nelle popolazioni più superficiali, meno stabili a causa degli eventi di mortalità indotti dal riscaldamento e da altri fattori interagenti, e più alta nelle popolazioni più profonde e relativamente più stabili. I risultati sono di particolare interesse per la conservazione delle comunità di coralli molli e quindi nel complesso per la biodiversità marina.

The Antarctic silverfish (Pleuragramma antarctica) is a keystone species in the continental shelf waters around the Antarctic, performing an essential role of connecting higher and lower trophic levels in the Southern Ocean ecosystem. Its early life history is dependent on the platelet ice layer found below sea ice, thus intimately intertwining its fate with that of sea ice extent. Antarctic silverfish belong to the family Nototheniidae, part of the Notothenioidei suborder whose species radiation in the Southern Ocean 24 million years ago is one of the most expansive among teleost fish. Most notothenioids inhabit a benthic niche as adults, though many experience a pelagic egg and larval phase. Antarctic silverfish are unique among notothenioids in that they are pelagic throughout their life history. Larvae develop in the platelet ice layer near the surface beneath sea ice, descending into deeper waters as they grow in size as juveniles, finally reaching their maximum depth range as adults at 400 – 700 m below the surface. While they lack a swim bladder, Antarctic silverfish manage to remain in the water column as adults by a type of paedomorphy in which they retain lipids from larval and juvenile life stages, allowing them to achieve neutral buoyancy. Despite their presence in the water column as adults, they practice a similar energy-efficient life strategy to their benthic counterparts. Their feeding strategy involves hanging in the water column and passively consuming prey. Remaining in the water column throughout their life history combined with their passive life strategy renders Antarctic silverfish especially susceptible to transport via local and circumpolar current systems. Thus, local and circumpolar current systems form the hydrographic framework in which hypotheses regarding Antarctic silverfish population connectivity must be tested. How populations of fish are defined, and the extent to which separate populations exchange individuals forms the basis of marine fish population biology. The extent to which Antarctic silverfish, which have a circumpolar distribution, represent one fully connected, panmictic population around the Antarctic continent, remains an open question. It is reasonable to presume that, given their pelagic larval phase, many species of notothenioids with a circumpolar distribution represent large, homogeneous populations. This presumption remains the null hypothesis to test when investigating population structure in notothenioids, and it is especially salient when considering the fully pelagic Antarctic silverfish. The first investigation into Antarctic silverfish population structure employed mitochondrial DNA markers on a circumpolar scale and did not find evidence to reject the null hypothesis of panmixia throughout the Southern Ocean. Intriguingly, while comparisons between regions failed to indicate differentiation, comparisons within regions between years hinted at inter-annual variation in patterns of connectivity. Genetic differentiation within the same geographic area that is lost and gained between sampling years due to variations in recruitment, mortality and hydrography is known as chaotic genetic patchiness. The extent to which chaotic genetic patchiness is relevant to understanding Antarctic silverfish population structure was further studied in a more recent investigation, restricting its geographic focus to the Antarctic Peninsula, and employing a set of highly polymorphic EST-linked microsatellite markers to understand population connectivity around the Antarctic Peninsula. Based on both its more focused regional scale and sampling scheme, as well as the use of genetic markers more adept at capturing population differentiation, this study was able to detect genetic structuring on the scale of the Antarctic Peninsula. Building upon these initial studies, this thesis aimed to characterize the circumpolar population structure of Antarctic silverfish, integrating aspects of life history and hydrography in order to describe mechanisms of connectivity between populations. The first aim was to understand the hydrography underlying life history connectivity on the scale of the Ross Sea region in order to better understand what may be occurring on the circumpolar level. Silverfish larvae were collected from areas in the Ross Sea coincident with hydrographic features hypothesized to influence their connectivity. While a microsatellite-based analysis was precluded due to the poor state of preservation of the larvae, it was possible to confirm species identification using mitochondrial sequence analysis. The genetic confirmation of species was especially important given that this study proposed a new spawning ground for silverfish in the Ross Sea based on size at collection and established growth rates from the time of hatching. Importantly, this study provided renewed support for the life history hypothesis in silverfish, emphasizing the impact of trough circulation in transporting early life stage fish from the ice shelf edge to the continental slope, where retention back towards the coast or entrainment in shelf-long currents modulates connectivity between neighboring populations of silverfish. The Ross Sea investigation was then expanded on a circumpolar scale, now carried out using a suite of highly polymorphic EST-linked microsatellite markers developed in a closely related notothenioid species and shown to successfully amplify in silverfish in a previous study. This analysis was carried out on fish collected over 25 years from six different regions: the western Ross Sea, the eastern Weddell Sea, Larsen Bay, the northern Antarctic Peninsula, the South Orkney Islands, and the western Antarctic Peninsula. The data analyzed included samples from the two previous investigations of silverfish population structure described earlier, the first using mitochondrial markers on a circumpolar scale that had not found evidence of population structuring, and the second using the same suite of microsatellite markers employed in this thesis on a regional scale around the Antarctic Peninsula. The integration of these previous datasets into the present analysis allowed for an increase in the resolving power of the previous mitochondrial marker-based study, as well as for the integration of the Antarctic Peninsular work into the greater circumpolar context. The circumpolar investigation of Antarctic silverfish population structure confirmed that the population structure of silverfish on a circumpolar scale is characterized by high levels of gene flow, and suggested that the Antarctic Slope Front and Current System (AFS) plays an integral role in connecting populations in the Southern Ocean. The importance of the AFS was evident in that reductions in gene flow were only observed in the South Orkney Islands and west Antarctic Peninsula, which were the only two areas in the study where the AFS has not been shown to arrive. This result also expanded to a circumpolar scale the earlier Ross Sea study, which had emphasized the importance of the AFS in connecting Ross Sea populations between local trough systems. It remained however, that small scale population differentiation which had been observed in the Ross Sea based on larval distributions, as well as in the eastern Weddell Sea based on the distribution of older and younger cohorts between sampling areas, was unable to be resolved using genetic techniques. Thus, the final aim of the main project of this thesis was carried out in order to resolve population structure on the regional scale, this time in the Weddell Sea, employing otolith chemistry. Analysis of trace element deposition in otolith nuclei, reflective of oceanographic conditions to which fish were exposed in early life, has been shown to delineate population structure in the Southern Ocean, in both silverfish and related notothenioids. Of the stations for which samples were available in the Weddell Sea, five stations were selected based on their locations with respect to hydrographic features hypothesized to influence population structuring in the region, in Atka Bay, Halley Bay, off of Coats Land, and west and east of the Filchner Trough. Previous studies, as well as data on biomass and abundance from the sampling expedition during which the silverfish were collected, emphasized the importance of the Filchner Trough in supporting a local population of silverfish in the eastern Weddell Sea continental shelf area. Furthermore, hydrographic data collected in the Weddell Sea emphasized the importance of warm water mass intrusion onto the continental shelf carried from the east into the Weddell Sea region by the AFS. These warm water intrusions from the AFS not only have the potential to carry fish from other regions into the Weddell Sea area, but regulate circulation patterns and the strength and directionality of coastal currents in the region, modulating local connectivity. The results of the otolith nucleus chemistry analysis revealed significant population structuring along the eastern Weddell Sea, in contrast to the structure revealed using genetics. The population structure revealed by the otolith chemistry analysis supported the importance of warm water intrusions from the AFS in transporting fish between areas, while highlighting the role of the Filchner Trough circulation in supporting a coherent population in the southeast Weddell Sea. These results emphasize the importance of the integration of multidisciplinary techniques in the context of local hydrography in addressing questions of population structure and life history connectivity in Antarctic silverfish in the Southern Ocean, and for that matter, any pelagic species inhabiting a continental shelf ecosystem.
L’antarctic silverfish (Pleuragramma antarctica) è una specie chiave nelle acque della piattaforma continentale antartica, dove svolge un ruolo essenziale nel collegare i diversi livelli trofici. La sua life history dipende, nella prima fase, dal cosiddetto “ghiaccio a placchette” (platelet ice), che si forma all’interfaccia tra l’acqua marina e lo strato di ghiaccio superficiale, legando strettamente il destino di questa specie all’estensione del ghiaccio antartico. L’antarctic silverfish appartiene alla famiglia Nototheniidae, che fa parte del sottordine dei Nototenioidei, la cui radiazione, avvenuta nell’oceano Antartico a partire da 24 milioni di anni fa, rappresenta una delle più spettacolari radiazioni adattative nei pesci teleostei. I nototenioidei comprendono, nella maggior parte dei casi, specie demersali in fase adulta, ma caratterizzate da uova e larve pelagiche; l’antarctic silverfish è unico sotto questo punto di vista perché è pelagico durante tutto il ciclo vitale. Le larve si sviluppano nello strato di platelet ice sotto il ghiaccio marino superficiale e scendono verso acque più profonde durante la maturazione, arrivando come adulti a profondità massime di 400 – 700 m. Nonostante l’assenza di vescica natatoria, l’antarctic silverfish riesce a mantenersi nella colonna d’acqua nello stadio adulto grazie a un tipo di pedomorfia caratterizzato dal mantenimento e dall’aumento dei lipidi presenti nelle fasi larvali e giovanili, che ne aumenta il potere di galleggiamento. Malgrado l’habitus pelagico da adulto, il silverfish è molto efficiente dal punto di vista energetico, possedendo una strategia alimentare simile alle controparti bentoniche, che consiste in questo caso nel galleggiare passivamente nella colonna d’acqua, consumando le prede che capitano nei paraggi, ma senza investire energia in una vera e propria ricerca attiva delle prede. Il fatto di rimanere nella colonna d’acqua durante tutto il ciclo vitale, in combinazione con la strategia di vita passiva, rende l’antarctic silverfish particolarmente suscettibile al trasporto da parte dei sistemi di correnti locali e circumpolari. Questo aspetto lo rende particolarmente interessante nel contesto della biologia di popolazione dei pesci marini, dove risulta importante identificare la presenza di diverse popolazioni e definire l’entità con cui popolazioni separate scambiano individui. In particolare, il fatto che l’antarctic silverfish, che ha una distribuzione circumpolare, presenti o meno una singola popolazione panmittica attorno al continente antartico, rimane una questione aperta. Dato che le fasi larvali sono pelagiche, è ragionevole presupporre che molte specie di nototenioidei siano organizzate in grandi popolazioni omogenee su scala geografica più o meno ampia. Questo presupposto fornisce l’ipotesi nulla da testare quando si investiga la struttura di popolazione di questo gruppo, ed è specialmente rilevante se si considera l’habitus pelagico dell’antarctic silverfish. Il primo studio della struttura genetica di popolazione dell’antarctic silverfish è stato svolto con marcatori del DNA mitocondriale; questa indagine, svolta su una scala circumpolare, non ha fornito evidenze tali da confutare l’ipotesi nulla di panmissia per l’intero oceano antartico. Tuttavia, mentre i confronti svolti tra diverse regioni non sono riusciti a dimostrare la presenza di differenziamento genetico, i confronti svolti entro regioni tra diversi anni di campionamento hanno suggerito l’esistenza di variazione inter-annuale del grado di connettività. Il differenziamento genetico tra anni di campionamento entro la stessa area geografica è riconducibile al fenomeno della chaotic genetic patchiness e può essere dovuto a variazioni nel tasso di reclutamento e mortalità e nell’idrografia. La presenza di differenziamento genetico di popolazione e di chaotic genetic patchiness nell’antarctic silverfish sono stati recentemente confermati mediante genotipizzazione di microsatelliti EST-linked in uno studio focalizzato su campioni provenienti dalla Penisola Antartica. In questo caso, l’utilizzo di marcatori genetici ipervariabili caratterizzati da un elevato potere risolutivo ha permesso di rilevare una significativa struttura genetica sulla scala regionale della Penisola Antartica. Questa tesi di dottorato mira a caratterizzare la struttura di popolazione circumpolare dell’antarctic silverfish, integrando l’informazione fornita dagli studi iniziali con nuovi campioni ed interpretando i risultati alla luce dei diversi aspetti di life history ed idrografia al fine di descrivere i meccanismi di connettività tra popolazioni. Nel primo studio prodotto nell’ambito di questa tesi di dottorato, sono stati analizzati dei campioni di larve dell’antarctic silverfish provenienti dal Mare di Ross, con l’obiettivo di legare l’idrografia locale alla connettività della specie. Lo stato di conservazione dei campioni non ha permesso di utilizzare marcatori molecolari nucleari (microsatelliti) per studiare il differenziamento tra siti geografici entro il Mare di Ross. Nonostante questo, è stato possibile sequenziare un frammento di DNA mitocondriale che ha permesso di identificare univocamente le larve come apparteneneti alla specie P. antarctica. Questo risultato è particolarmente rilevante perché conferma, grazie all’utilizzo di metodi genetici, la presenza di larve della specie P. antarctica in alcune aree del Mare di Ross che erano state precedentemente solo ipotizzate essere zone preferenziali di nursery del silverfish, sulla base di tempi di raccolta dal momento della schiusa delle uova e del tasso di crescita ipotizzato. Sulla base dell’idrografia locale, questo studio ipotizza che la circolazione legata alle depressioni del fondale sia essenziale per il trasporto delle fasi di vita iniziali dalle zone più costiere fino alla scarpata continentale, mentre l’idrografia costiera potrebbe controllare il trasporto lungo i margini della piattaforma continentale modulando la connettività tra popolazioni adiacenti. In un secondo studio prodotto nell’ambito di questa tesi di dottorato sono stati analizzati campioni raccolti nell’arco di 25 anni da sei regioni antartiche diverse: la parte ovest del Mare di Ross, la parte est del Mare di Weddell, la Baia di Larsen, la parte nord della Penisola Antartica, le Isole di South Orkney, e la parte ovest della Penisola Antartica. Questo studio su scala circumpolare è stato condotto utilizzando un pannello di 18 loci microsatellite isolati in precedenza per varie specie di nototenioidei antartici. Questi loci sono risultati polimorfici anche in P. antarctica e informativi per gli obiettivi di questa tesi di dottorato. Alcuni dei campioni inclusi in questo studio sono stati analizzati in due studi precedenti: un primo studio non aveva evidenziato segnali di differenziamento genetico a livello circumpolare (analisi di un marcatore mitocondriale) mentre un secondo studio, più recente e focalizzato sulla Penisola Antartica, aveva segnalato chaotic genetic patchiness e differenziamento genetico utilizzando lo stesso pannello di 18 microsatelliti genotipizzati in questa tesi di dottorato. Questo secondo studio ha confermato che la struttura di popolazione del silverfish sulla scala circumpolare è caratterizzato da alti livelli di flusso genico suggerendo che il sistema di correnti, in particolare l’Antarctic Slope Front and Current System (AFS), abbia un ruolo critico nel collegamento delle popolazioni nell’oceano Antartico. L’importanza del AFS è suggerita dal limitato flusso genico tra le aree ad ovest della Penisola Antartica e le South Orkneys, le due uniche zone non raggiunte dall’AFS. Questa considerazione è ulteriormente supportata dall’ipotesi che l’AFS mantenga la connettività tra depressioni del fondale anche nel Mare di Ross. Per comprendere se l’assenza di differenziamento nell’area ad est del Mare di Weddell fosse effettivamente un fatto biologico o fosse dovuta alla scarsa sensibilità dei marcatori microsatellite a piccole differenze, è stato condotto un ulteriore studio utilizzando l’analisi della chimica degli otoliti di silverfish. La quantificazione delle tracce di elementi deposti nel centro (nucleus) degli otoliti è indicativa delle condizioni chimiche oceanografiche alle quali gli individui sono stati esposti nelle fasi iniziali dello sviluppo. Questa metodologia permette di conseguenza di testare se gli individui siano stati esposti a masse d’acqua diverse nelle prime fasi di vita e di dimostrare l’esistenza di popolazioni con diversa origine. Tra i campioni disponibili per il Mare di Weddell, sono state scelte 5 aree sulla base degli aspetti idrografici che potrebbero influire sulla struttura di popolazione locale (Baia di Atka, Baia di Halley, vicino alla costa di Coats, ad est ed ovest del Filchner Trough). Dati di abbondanza e biomassa raccolti in parallelo durante in campionamento del silverfish nel Mare di Weddell avevano già evidenziato l’importanza del Filchner Trough nel sostenere la popolazione locale dell’antarctic silverfish. Inoltre, l’idrografia locale, attraverso l’intrusione di acqua più calda dall’AFS verso il Mare di Weddell, permetterebbe sia di trasportare il silverfish verso il Mare di Weddell sia di regolare direzionalità e tasso di connettività locale. In contrasto con quanto evidenziato dall’approccio genetico, le analisi di microchimica degli otoliti segnalano differenze statisticamente significative tra gruppi di individui all’interno del mare di Weddell, in particolare tra nordest e sudest del Mare di Weddell. Questi studi suggeriscono un ruolo chiave dell’idrografia sia su scala circumpolare che locale nel modulare la connettività delle popolazioni dell’antarctic silverfish. Inoltre, questa tesi di dottorato evidenzia come un approccio multidisciplinare possa chiarire questioni di connettività di popolazione proponendo una metodologia applicabile a diversi organismi sia antartici che non.

Face à l’effet des changements d’utilisations de sol sur la dispersion des espèces, des actions ont récemment été menées au niveau des régions françaises pour favoriser et maintenir la connectivité. L’objectif de cette étude a donc été de quantifier la connectivité chez une espèce modèle menacée en Europe occidentale : la vipère péliade (V. berus). Ses mœurs discrètes ont nécessité pour mesurer sa dispersion d’utiliser une approche indirecte basée sur l’individu et des outils moléculaire. Ainsi, les flux de gènes de V. berus ont été analysés à fine échelle spatiale (10 × 7 km²) sur un site d’étude (A0) constitué de deux secteurs paysagers contrastés (A1/A2), à la fois par l’utilisation des sols et leur stabilité temporelle (instable/stable). La différenciation génétique sur A0 est faible et surtout associée à un fort patron d’isolement par la distance (IBD). La dispersion est donc limitée spatialement chez V. berus (dispersion natale ≤ 500 m) et liée aux mâles à l’âge adulte. De plus, les flux de gènes sont aussi expliqués par l’hétérogénéité du paysage : (i) par les prairies (A0), l’urbanisation (A1) les pelouses et boisements (A2), (ii) particulièrement à 300 m autour des individus parmi les étendues spatiales testées (100-500 m) et (iii) plus par l’agencement spatial que le type et la quantité des taches d’habitats. Ces résultats innovants contribuent à (i) la réflexion sur la stratégie de conservation pour V. berus et (ii) souligner la diversité des facteurs à considérer dans l’étude et le maintien de la connectivité à une plus vaste échelle spatiale (patrons et processus de dispersion, échelles spatio-temporelles)
Face to the impact of land-use changes on species dispersal, decisions were recently conducted at French regional scale to favour and to maintain connectivity. The aim of this work was to quantified connectivity for a model species threatened in Western Europe : the common European adder (V. berus). Its secretive behaviour required to use an indirect and individual-based approach to measure its dispersal thanks to molecular techniques. Thus, V berus gene flow were analysed at fine spatial scale (10 × 7 km²) on a study site (A0) made up of two sub-areas with contrasting landscapes (A1/A2), both by land use and their temporal stability (instable/stable). Genetic differentiation on A0 is weak and mainly associated with a strong isolation-by-distance (IBD) pattern. Dispersal is therefore spatially limited in V. berus (natal dispersal ≤ 500m) and related to males concerning adults. Moreover, gene flow is also influenced by landscape heterogeneity : (i) by meadow (A0), urbanisation (A1) and dry grassland and forests (A2), (ii) particularly at 300m around individuals among spatial extent tested (10-500m) and (iii) more by the spatial configuration than the type and quantity of habitat patches. These innovative results contribute to (i) reflection about conservation strategies for V. Berus et (ii) underly the diversity of factors to consider in studying and maintaining connectivity at a more large spatial scale (dispersal pattern and process, spatio-temporal scales)

The straw-coloured fruit bat, Eidolon helvum, has been identified as a reservoir for potentially-zoonotic henipaviruses and Lagos bat virus (LBV) in continental Africa. Longitudinal studies at a large urban colony in Accra, Ghana aim to better understand E. helvum and viral ecology, as well as the nature of human-bat interactions. To assess whether the findings from these studies can be extrapolated across the species’ continental range, more information on the movement ecology of the species and connectivity of populations across its range was required. A multifaceted approach, using techniques from the field of genetics, population ecology, and virology, was used to understand the ways in which the structure and dynamics of fruit bat populations across Africa may affect the viral transmission dynamics within them. Given recent difficulties in using electronic positioning systems on E. helvum to track movement, genetic methods were proposed as the most appropriate way to assess connectivity between populations across such a vast range. Henipavirus and LBV serological analyses were undertaken on samples from 12 populations of E. helvum bats across its continental and offshore-island range. A combination of mitochondrial DNA and microsatellite markers were used to describe the genetic metapopulation structure of E. helvum and data were obtained in each location on population sizes, demographic structure, reproductive and migratory seasonality, as well as bat-human interactions. Consistent with expectations for a vagile migratory species, a panmictic continental population structure was detected across its continental range, although the extent of this panmixia was greater than previously detected in any other mammal or bird. Antibodies to henipaviruses and LBV were detected in all continental populations. Isolated island populations in the Gulf of Guinea were genetically distinct from each other and the continental population. Given the isolation of these island fruit bats and the lack of connectivity with other populations, it was expected that populations would be too small to allow persistence of any viruses that cause acute, immunising infections. Contrary to expectations, island individuals displayed evidence for exposure to both viruses. E. helvum is known to roost close in proximity to human populations across continental Africa, and these results could therefore have important public health implications. Further longitudinal studies across multiple locations and information on social structure, daily and seasonal movements are needed to make inferences about virus transmission dynamics and zoonotic risks within the complex population structure.

We developed a set of hypervariable microsatellite markers for the Pacific red snapper (Lutjanus peru), an economically important marine fish for small-scale fisheries in the west coast of Mexico. We performed shotgun genome sequencing with the 454 XL titanium chemistry and used bioinformatic tools to search for perfect microsatellite loci. We selected 66 primer pairs that were synthesized and genotyped in an ABI PRISM 3730XL DNA sequencer in 32 individuals from the Gulf of California. We estimated levels of genetic diversity, deviations from linkage and Hardy-Weinberg equilibrium, estimated the frequency of null alleles and the probability of individual identity for the new markers. We reanalyzed 16 loci in 16 individuals to estimate genotyping error rates. Eighteen loci failed to amplify, 16 loci were discarded due to unspecific amplifications and 32 loci (14 tetranucleotide and 18 dinucleotide) were successfully scored. The average number of alleles per locus was 21 (+/- 6.87, SD) and ranged from 8 to 34. The average observed and expected heterozygosities were 0.787 (+/- 0.144 SD, range 0.250-0.935) and 0.909 (+/- 0.122 SD, range 0.381-0.965), respectively. No significant linkage was detected. Eight loci showed deviations from Hardy-Weinberg equilibrium, and from these, four loci showed moderate null allele frequencies (0.104-0.220). The probability of individual identity for the new loci was 1.46(-62). Genotyping error rates averaged 9.58%. The new markers will be useful to investigate patterns of larval dispersal, metapopulation dynamics, fine-scale genetic structure and diversity aimed to inform the implementation of spatially explicit fisheries management strategies in the Gulf of California.

Identifying the extent to which coral reef species are connected by dispersal is a fundamental challenge for developing marine conservation strategies. Many coral reef species are relatively sedentary as adults, yet have a pelagic larval phase where larvae can potentially be widely dispersed by ocean currents. This thesis focuses on the role of ocean currents in driving spatially explicit patterns of population connectivity among ecologically and commercially important coral reef species by combining research tools from population genetics, oceanography, and biophysical modeling. Despite the substantial differences among the life histories of each coral reef species in this thesis, some similarities in connectivity patterns were found among all species. The results of the kinship and genetic outlier analyses consistently found high levels of connectivity among distant populations separated by hundreds to thousands of kilometers. Despite the high levels of connectivity among distant populations, there was substantial variation in gene flow among the populations of each species. The findings of this thesis highlight the importance of international cooperation for the sustainable management of ecologically and commercially important coral reef species in the Caribbean. In conclusion, the findings of this thesis suggest that marine conservation strategies should conservatively plan for uncertainty, particularly since the many of ecological and physical drivers of connectivity among coral reef species in the Caribbean remain uncertain.

Patterns of connectivity among local populations influence the dynamics of regional systems, but most ecological models have concentrated on explaining the effect of connectivity on local population structure using dynamic processes covering short spatial and temporal scales. In this study, a model was developed in an extended spatial system to examine the hypothesis that long term connectivity levels among local populations are influenced by the spatial distribution of resources and other habitat factors. The habitat heterogeneity model was applied to local wild rabbit populations in the semi-arid Mitchell region of southern central Queensland (the Eastern system). Species' specific population parameters which were appropriate for the rabbit in this region were used. The model predicted a wide range of long term connectivity levels among sites, ranging from the extreme isolation of some sites to relatively high interaction probabilities for others. The validity of model assumptions was assessed by regressing model output against independent population genetic data, and explained over 80% of the variation in the highly structured genetic data set. Furthermore, the model was robust, explaining a significant proportion of the variation in the genetic data over a wide range of parameters. The performance of the habitat heterogeneity model was further assessed by simulating the widely reported recent range expansion of the wild rabbit into the Mitchell region from the adjacent, panmictic Western rabbit population system. The model explained well the independently determined genetic characteristics of the Eastern system at different hierarchic levels, from site specific differences (for example, fixation of a single allele in the population at one site), to differences between population systems (absence of an allele in the Eastern system which is present in all Western system sites). The model therefore explained the past and long term processes which have led to the formation and maintenance of the highly structured Eastern rabbit population system. Most animals exhibit sex biased dispersal which may influence long term connectivity levels among local populations, and thus the dynamics of regional systems. When appropriate sex specific dispersal characteristics were used, the habitat heterogeneity model predicted substantially different interaction patterns between female-only and combined male and female dispersal scenarios. In the latter case, model output was validated using data from a bi-parentally inherited genetic marker. Again, the model explained over 80% of the variation in the genetic data. The fact that such a large proportion of variability is explained in two genetic data sets provides very good evidence that habitat heterogeneity influences long term connectivity levels among local rabbit populations in the Mitchell region for both males and females. The habitat heterogeneity model thus provides a powerful approach for understanding the large scale processes that shape regional population systems in general. Therefore the model has the potential to be useful as a tool to aid in the management of those systems, whether it be for pest management or conservation purposes.

Ce travail de thèse s'insère dans une démarche globale d'acquisition des connaissances sur la tortue verte (Chelonia mydas) dans l'océan Indien occidental et ce afin de disposer d'éléments scientifiques essentiels à la mise en place d'une gestion cohérente et efficace de cette espèce menacée. Dans un premier temps, appliquant différentes modèles statistiques, ce travail a visé à établir des données de référence sur l'abondance des tortues vertes femelles en reproduction et les tendances sur le long terme des principales populations. Dans un second temps, il a consisté à déterminer la structure génétique et les relations qui existent entre les différentes populations de cette espèce. Enfin, la conservation des tortues marines étant étroitement liée aux pressions extérieures, ce travail a tenté dans un troisième temps de caractériser les pressions anthropiques qu'elles subissent, et notamment celles liées à la pêche. L'ensemble de ces résultats a permis de réaliser des avancées majeures dans la connaissance de la biologie et de l'écologie de la tortue verte et de disposer d'une vision régionale fiable de l'état de conservation de cette espèce dans l'océan Indien occidental. Leur compilation a ainsi permis d'identifier des zones régionales prioritaires de protection mais aussi des sites de vigilance plus spécifiques comme celui d'Europa. Enfin cette synthèse met en lumière les priorités de recherche et les approches scientifiques à favoriser à l'avenir pour améliorer les connaissances et affiner les priorités de conservation non seulement des tortues marines, mais aussi de la mégafaune marine en général
This thesis is a comprehensive work aiming to improve scientific knowledge on the green turtle (Chelonia mydas) in order to provide key scientific evidences needed for the implementation of coherent and effective management measures to protect at the Western Indian Ocean scale this threatened species. In a first step, this work aimed to established baseline data on the abundance of green turtles nesting females and long term trends of some key nesting populations of the region by applying different modelling methods. In a second step, this work determined the regional genetic structure of this species and the relationships that exists between the different populations. Finally, the conservation of marine turtles being closely dependant to external pressures, this work tried to characterize theanthropogenic pressures they face, more specifically those related to fishing activities. All these results allowed unraveling some key gaps on the biology and ecology of the green turtle in the region and led to a global vision of the conservation status of this species in the Western Indian Ocean. The compilation of the results enabled the identification of regional priority areas for protection, but also some more specific threatened sites such as Europa. Finally, this synthesis shedslight on research priorities and scientific approaches to be promote in the future to unlock other keyscientific issues and refine conservation priorities, not only of marine turtles, but also of marine megafauna as a whole

Ce travail de thèse porte sur la connectivité des populations de coraux du genre Pocillopora dans le Sud-Ouest de l'océan Indien et l'océan Pacifique tropical. Ces coraux sont répartis sur toute la frange tropicale des océans Indien et Pacifique. Traditionnellement, les espèces étaient identifiées sur la base critères morphologies [17 espèces décrites dans Veron (2000)]. Différentes études utilisant des données génétiques ont révélé que la délimitation des espèces était parfois floue chez ces coraux. Ainsi, au cours de ce travail, l'utilisation de méthodes de délimitation d'espèces à partir d'ADN mitochondrial (ABGD, GMYC, PTP) et nucléaire (haplowebs) 16 hypothèses primaires d'espèces (PSH) ont été identifiées. Ces PSH ont ensuite été confrontées à des tests d'assignement à partir de marqueurs microsatellites, révélant un minimum de 18 hypothèses d'espèces secondaires (SSH). Une fois que les hypothèses d'espèces sont définies, il est possible de réaliser des études de connectivité. Au cours de ce travail, deux hypothèses d'espèces présentant des écologies différentes ont été choisies pour mener ces analyses. La première, Pocillopora damicornis type β (SSH05) a été échantillonnée dans les lagons et la seconde, Pocillopora eydouxi (SSH09) a, quant à elle, été échantillonnée sur la pente externe. L'estimation de la structure génétique des populations a permis d'estimer les modes de reproduction (sexuée ou asexuée) chez ces deux hypothèses d'espèces et les analyses de connectivité ont révélé des patterns de structuration complexes pour chacune des SSHs
This work focuses on the connectivity among populations of the coral genus Pocillopora in the Southwestern Indian Ocean and the Southwestern Pacific Ocean. These corals are widely distributed throughout the tropical fringe of the Indian and Pacific oceans. Traditionally, species were identified on the basis of morphological criteria [17 species described in Veron (2000)]. Different studies using genetic data revealed that the delimitation of species was sometimes blurred in these corals. Thus, in this work, the use of species delineation methods from mitochondrial (ABGD, GMYC, PTP) and nuclear (haplowebs) DNA, 16 primary species hypotheses (PSH) were identified. These PSHs were then confronted to assignment tests from microsatellite loci, revealing a minimum of 18 secondary species hypotheses (SSH). Once the species hypotheses are defined, it is possible to conduct connectivity studies. In this work, two SSHs with different ecologies were chosen to carry out these analyses. The first, Pocillopora damicornis type β (SSH05) was sampled in the lagoons and the second, Pocillopora eydouxi (SSH09) was sampled on the outer slope. The estimation of the genetic structure of the populations made possible to estimate the reproductive modes (sexual or asexual) in these two SSHs and the connectivity analyzes revealed complex structuring patterns for each of the SSHs

Mettre en place des mesures de protection efficaces contre la dégradation et la fragmentation de l'habitat d'une espèce nécessite d'être capable de comprendre l'impact de l'environnement sur sa dynamique de population ainsi que sa sensibilité à la perte de connectivité entre les populations. Obtenir ces informations est déjà un défi en soi, qui se complique encore pour les espèces trop sensibles au dérangement pour être suivies de manière classique. Lors de ce travail, nous avons étudié la dynamique et la génétique des populations d'une chauve-souris forestière qui a subi un très fort déclin dans le nord de l'Europe, le Petit rhinolophe (Rhinolophus hipposideros), à l'aide de méthodes non-invasives (comptages, génétique non-invasive).Nos résultats ont montré que le climat et le paysage autour des colonies de maternités influence la taille et la dynamique des populations du Petit rhinolophe. Nous avons également confirmé un impact direct du paysage sur la survie des juvéniles. Enfin, nous avons observé que la diversité génétique des populations pouvait être fortement diminuée par leurs histoires démographiques et par un manque de connectivité entre les populations. Ces résultats ont des implications directes pour la conservation du Petit rhinolophe mais aussi pour le développement des analyses intégrant des données de génétique non-invasive pour la biologie de la conservation
Efficient conservation management against habitat degradation and fragmentation of a species requires understanding how the environment impacts its population dynamics and the species’ sensitivity to connectivity loss. Acquiring sufficient knowledge about these processes is challenging for any species, and is even more complicated for species too sensitive to be studied with classical methods. During this work, we studied the population dynamics and genetics of a woodland specialized bat who has undergone a serious decline in the north of Europe, the lesser horseshoe bat (Rhinolophus hipposideros), with non-invasive methods (counts, non-invasive genetics).Our results shown that climate and landscape around maternity colonies explain population size variations and dynamics of the lesser horseshoe bat. We also confirmed a direct impact of landscape on juvenile survival. We finally observed that genetic diversity could be strongly decreased by population history and a lack of connectivity between populations. Our results have direct implications for the lesser horseshoe bat conservation but also for the development of analyses integrating non-invasive genetic data in conservation biology

La mise en place Trame Verte et Bleue sur le territoire français a pour vocation de garantir la connectivité fonctionnelle entre habitats. C’est une des réponses politiques qui vise à enrayer le déclin actuel de la biodiversité, lie notamment à la destruction et à la dégradation des habitats. L’objectif de cette thèse est de quantifier l’effet de la connectivité, au regard d’autres facteurs environnementaux, sur la diversité des communautés et la diversité génétique des papillons de jour dans trois régions agricoles. Deux approches sont utilisées pour comprendre les processus qui sous-tendent ces patrons de diversité : i) l’étude de la communauté dans son ensemble et des groupes écologiques qui la compose, ii) l’étude de la résistance des milieux a la dispersion par génétique du paysage sur une espèce : le Myrtil (Maniola jurtina L.). Les résultats montrent que même si les caractéristiques locales jouent un rôle plus fort, la structure du paysage influence la composition des communautés. Ainsi, la quantité de terres arables réduit la richesse spécifique, la diversité génétique, et les flux de gènes chez le Myrtil. Les prairies hébergent des communautés diversifiées, incluant des espèces peu fréquentes. Les éléments linéaires enherbes supportent des communautés appauvries, mais favorisent la dispersion et la diversité génétique du Myrtil. La diversité des papillons est plus forte a proximité de boisements : les papillons pourraient bénéficier de ressources sur les lisières ; par ailleurs, les milieux boises semblent à la fois limiter les flux de gènes du Myrtil tout en accroissant sa diversité génétique. La complémentarité des milieux soulevée ici nous invite à repenser le modèle classique en ≪ sous-trames ≫ indépendantes de la Trame Verte et Bleue. Selon les enjeux de conservation, les espèces et les contextes paysagers, il est nécessaire de distinguer les situations ou, parmi un panel d’actions envisageables, améliorer la connectivité est une solution pertinente
The implementation of the “Green and Blue Infrastructure” in France intends to ensure the functional connectivity of habitats (green veining). It is one of the nature conservation policies which aim to reduce the loss of biodiversity caused by the destruction and degradation of natural habitats. The objective of this work was to quantify the impact of connectivity, in comparison to other environmental factors, on the diversity of butterfly communities and their genetic diversity in three French agricultural regions. Two different approaches were applied to understand the underlying processes driving these diversity patterns: i) the study of the whole community and of the different ecological groups, ii) the study of landscape features resistances to butterfly dispersal using a landscape genetics approach on one species: the Meadow brown (Maniola jurtina L.). Our findings show that although local characteristics play a dominant role, landscape context does have an influence on community composition. Arable land cover decreases species diversity, and the Meadow brown genetic diversity and gene flow. Grasslands support more species rich communities, including non-frequent species. Grassy linear landscape elements host impoverished communities, but improve Meadow brown dispersal and enhance its genetic diversity. Species diversity is higher within grasslands in proximity to woody habitats: butterflies may benefit from resources on forest edges; moreover, woodlands seem to limit Meadow brown dispersal while increasing its genetic diversity. The habitat complementarity we evidenced here led us to question the classic model of ecological continuities as a collection of independent sub-networks, one for each type of habitat. According to conservation issues, species under interest and landscape contexts, we also need to identify situations where, among a broad panel of possible conservation actions, increasing connectivity is the most effective solution

Au cours des dernières décennies, le nombre de mares a connu un déclin de plus de 50 % dans les pays européens, atteignant parfois jusqu'à 90 % dans certaines régions. Cette diminution a entraîné une forte perte de connectivité entre les mares. Pourtant, ces écosystèmes petits et dispersés sont essentiels au cycle de vie d'une grande diversité d'espèces d'eau douce. Les politiques d'aménagement du territoire, comme la création des Trames Vertes et Bleues en France, visent à améliorer les continuités écologiques pour permettre le maintien des populations existantes et les échanges entre elles. Cependant, les études de connectivité entre les mares doivent prendre en compte les capacités de dispersion des espèces et cette information fait souvent défaut pour orienter les mesures de restauration. Dans le présent travail, nous avons étudié les capacités de dispersion des libellules à plusieurs échelles spatiales ainsi que les caractéristiques biologiques et les facteurs environnementaux qui façonnent leurs mouvements. Dans la première partie, nous avons évalué la colonisation par les libellules de 20 mares normandes pendant les trois années suivant leur création ou leur restauration. Les résultats mettent en évidence des taux de colonisation élevés pendant la première année et aucune différence de richesse spécifique n'a été constatée entre les mares nouvellement créées ou restaurées. Cela suggère que la restauration des mares après un assèchement total ne devrait pas toujours être prioritaire par rapport à la création de nouvelles mares dans les stratégies de gestion. Nous avons constaté que les espèces généralistes étaient davantage présentes la première année après la création ou la restauration des mares, alors que la présence d’espèces spécialistes des forêts augmentait avec l'âge du plan d’eau. Les résultats ont également mis en évidence que le contexte paysager autour des mares (i.e. milieu forestier ou ouvert) avait un effet sur la composition des communautés de libellules. Enfin, l'abondance totale des espèces d'odonates était liée à la densité des plans d’eau alentours. Ce résultat souligne que les mares très connectées peuvent abriter des populations plus importantes que les mares isolées et donc être plus résistantes aux perturbations. La deuxième partie fournit des éléments sur le développement larvaire d'Anax imperator et la relation entre les caractéristiques morphologiques des larves et des adultes. Les résultats suggèrent que la survie de cette espèce pendant la période de maturation pourrait dépendre de la longueur des individus. Nous avons également essayé d'étudier la dispersion natale en marquant 87 individus à l'émergence, mais seuls deux mâles ont été retrouvés après la période de maturation. Enfin, l'effet de deux polluants de l'eau (Round-up et DEET) sur le développement larvaire et les adultes d'Aeshna cyanea a également été étudié à différentes concentrations. Les larves ont été élevées dans des conditions de laboratoire et exposées à des concentrations allant jusqu'à 30 mg.L-1 des deux polluants. Aucun effet des polluants sur les conditions morphologiques des larves ou des ténéraux n'a été détecté, ce qui suggère que A. cyanea est une espèce tolérante aux potentielles pollutions de l'eau dans les mares. Le niveau de la protéine de stress HSP70 était également similaire selon les différents traitements, mais les adultes ténéraux présentaient des niveaux de stress plus élevés que les larves, ce qui suggère que l'émergence a provoqué un stress élevé chez les individus
During the last decades, the number of ponds decreased by more than 50 % in European countries, occasionally reaching up to 90 % in some regions. Their decline in number has led to a strong loss of connectivity between waterbodies. Yet, these small and scattered ecosystems are essential for the life cycle of a high diversity of freshwater species. Land use policies like the creation of Greenways and Blueways in France aim to improve ecological continuities to allow maintenance of existent biological populations and exchanges between them. However, the connectivity between ponds must be considered according to the dispersal abilities of freshwater species and this information often lacks to guide restoration measures. In the present work, we studied the dispersal abilities of dragonflies on several spatial scales and investigated the biological traits and environmental factors that shaped their movements. In the first part, we evaluated the colonization of 20 ponds in Normandy by dragonflies during three years after pond restoration or pond creation. The results highlight high colonization rates during the first year and no difference in species richness was found between newly created or restored ponds. This suggests that restoration of ponds after complete drought should not always be prioritized over pond creation in management strategies. We found that generalist species were more present in the first year after pond creation or restoration, whereas the occurrence of forest specialists increased with the age of the pond. The results also highlighted that the landscape context around ponds (i.e. forest vs. open lands) had an effect on the composition of dragonfly communities. Finally, the total abundance of odonate species was related to the density of other ponds in the surroundings. This result emphasizes that highly connected ponds can support larger populations than isolated ones and thus, be more resilient to perturbations. The second part provides insights into the larval development of Anax imperator and the relationship between morphological traits of larvae and adults. The results suggest that the survival of this species might depend on its body length during the maturation period. We also tried to study the natal dispersal by marking 87 individuals at emergence, but only two males were resighted after the maturation period. Finally, the effect of two water pollutants (i.e. Round-up and DEET) at different concentrations was also investigated on the larval development and adults of Aeshna cyanea. Larvae were reared under laboratory conditions and exposed to concentrations up to 30 mg.L-1 of the two pollutants. No effect of the pollutants was detected on the morphological conditions of larvae or tenerals, suggesting that A. cyanea is tolerant to potential water pollution of ponds. The level of HSP70 stress protein was also similar according to the different treatments, but teneral adults presented higher levels of stress than larvae, suggesting that emergence induced a high stress in the individuals. The third part focuses on the dispersal of A. imperator. We first assessed the local movements within a pond network in the Normandy region

Mongolia is currently undergoing a rapid socioeconomic transition with extensive development driven by increased mineral resource extraction and large scale agriculture and pastoral expansion. There has also been unprecedented urbanisation and continued population growth that has placed added pressure on the ageing public infrastructure including power stations and waste water treatment plants. As a result, the country’s pristine landscapes, including its vast freshwater ecosystems, are now facing widespread degradation, contamination and species losses in the most impacted regions. The proposed large-scale dams and imminent climate change effects will further damage these fragile ecosystems. With a number of rivers and lakes deteriorating, resident aquatic communities, including unique fish species, have suffered significant population declines. However, a more substantial threat currently facing these fish populations is the rapid and largely unregulated rise in fishing activities within an emerging recreational fishery. Although historically fish capture and consumption has not been a traditional part of the Mongolian diet or culture, this is changing rapidly. Therefore a comprehensive set of research projects were developed and implemented across Mongolia, to gather essential information on this new fishery, while also addressing existing knowledge gaps regarding the spatial ecology and genetic structure of the main target species. In addition, a potential human health risk was evident due to the increased consumption of locally caught fish species from a heavily impacted river basin, and thus this was also investigated. Overall, the collective aim of this fisheries research was to increase the scientific understanding and knowledge across a range of issues and ultimately advise authorities on improving current management regulations and conservation strategies. It is hoped that the recommendations can assist in safeguarding the future sustainability and resilience of the threatened fish populations and the emerging recreational fishery across Mongolia for the future. A total of five fisheries related research projects were completed between 2011 and 2014, with the results from each used to formulate the conservation and management recommendations presented in this thesis. Due to the lack of knowledge regarding the emerging recreational fishery, roving creel surveys were conducted across three river basins and covered five key topics including angler demographics, fishing practices, current fishing trip data, fishing gear and costs, and angler knowledge and opinions. Fifty-eight fishing groups (n = 154 anglers) were interviewed and two angler types were identified: rural anglers with no or low incomes, who reside in the basin, fish alone or in smaller groups, fish frequently for shorter periods, and consumed fish more regularly; and urban anglers who have medium to high incomes, live in larger cities, spent more money on fishing gear / trips and fished for multiple days at a time. B. lenok was identified as the most targeted and caught species in the fishery. The results of the creel surveys confirmed increased fish consumption in the Kharaa River basin, which was identified as a potential human health risk due to the widespread heavy metal contamination from both past and present mining activities. Thus heavy metal contaminates in river water, sediment and five consumed fish species were examined at 11 sites across the basin. Heavy metals were evident in all five sampled species, with maximum muscle contents of chromium (Cr), arsenic (As), mercury (Hg) and lead (Pb) detected in fish from the middle and lower reaches, while zinc (Zn) was highly elevated in B. lenok from the upper tributaries. Elevated median contents of Cr, copper (Cu), Hg and Pb increased with trophic level, with the bioaccumulation of Hg posing the greatest threat to human health with over 10 % of all fish sampled exceeded the internationally recommended threshold for Hg in consumable fish tissue (> 0.5 µg g-1 ww). This bioaccumulation in resident fish species could lead to chronic toxicity in people who consume them regularly and have additional exposure to other sources of contamination e.g. gold mining. A further two projects were conducted that utilised passive acoustic telemetry to describe the spatial and temporal autecology, habitat use and behaviour of B. lenok in the Eroo River and H. taimen in the Onon/Balj rivers under Mongolia’s extreme seasonal conditions. The maximum longitudinal movements (home ranges) detected were more extensive than previously reported for both species with 45.3 km for B. lenok and 126.1 km for H. taimen. Increased movements were recorded in spring and summer, with individuals entering surrounding tributaries and remaining there for between four and 85 days before returning to the main river channel. The results highlighted the importance of maintaining the integrity and connectivity of tributary habitats for spawning, feeding and overwintering, as well as hydrological and thermal refuges, which will be increasingly important for these species in the region with the pending impacts of climate change. This increased knowledge relating to the spatial ecology of these threatened species can guide the design and implementation of new protective measures such as the introduction of Freshwater Protected Areas (FPAs) across Mongolia. Further research was conducted to gain a broader, multigenerational understanding of the interconnectedness between conspecific populations of H. taimen, B. lenok and T. baicalensis across the major river basins. Both molecular and nuclear markers were used to demarcate the population’s genetic structure and define Evolutionary Significant Units (ESUs) and priority populations for these species across their Mongolian distributions. Across all species, the most prominent pattern was a strong differentiation among major basins with low differentiation and weak patterns of isolation by distance within basins, which indicates high within-basin connectivity between populations, although exact patterns were not completely concordant among species. The extensive results produced from the current scientific research has facilitated the development of a comprehensive set of key recommendations for implementing new, and enhancing existing, management and conservation measures relating to Mongolia’s threatened salmonid species and its emerging recreational fishery. These recommendations include: 1. Establishing a series of Freshwater Protected Areas (FPAs) throughout Mongolia’s major river basins, with their design and location based upon the spatial ecology and genetic population structure determined by the current research results; 2. Shifting the opening date of the fishing season to encompass the entire spawning period of B. lenok (the fishery’s main target species), which appears to currently not be the case; 3. Adding the blunt-snouted lenok (B. sp.) to the prohibited species list, as it has been genetically proven to be an independent species and has a restricted distribution and low abundance in Mongolia; and 4. Introducing minimum (and potentially maximum) size limits for B. lenok and T. baicalensis, to better protect immature and pre-spawning individuals from being removed from the population. In addition, it is highly recommended to commence fisheries dependent and independent assessments in key river basins and conduct biomonitoring programs (using a bioindicator species) to track toxic heavy metal contamination and identify potential human health risks associated with consuming resident fish species from the more heavily impacted regions. The lack of knowledge of the current fishing regulations by anglers as well as the observed and reported widespread illegal fishing activities demands a wide-ranging angler education program to improve understanding and compliance within the fishery. The future survival of these threatened salmonids and the sustainability of the emerging recreational fishery in Mongolia currently hangs in the balance. However, if these scientifically based recommendations are implemented in full, and can be adequately enforced, then the responsible authorities can take a huge step forward towards reversing the current trends and preserving the country’s imperilled freshwater fish populations and their valuable aquatic ecosystems. Mongolia can be a model for freshwater species conservation and management throughout the region and the world.:DECLARATION OF CONFORMITY I TABLE OF CONTENTS II ACKNOWLEDGMENTS V LIST OF ABBREVIATIONS VI LIST OF FIGURES VII LIST OF TABLES VIII SUMMARY IX SUMMARY IN GERMAN / ZUSAMMENFASSUNG AUF DEUTSCH XII SUMMARY IN MONGOLIAN / ХУРААНГУЙ XVI INTRODUCTION 1 1 RESEARCH OBJECTIVES AND HYPOTHESES 1 1.1 OVERALL THESIS OBJECTIVES 6 2 MONGOLIA’S NATURAL ENVIRONMENT 7 2.1 GEOGRAPHIC ECOREGIONS 7 2.2 CLIMATIC CONDITIONS 7 2.3 HYDROLOGICAL NETWORKS 8 2.4 FRESHWATER FISH FAUNA 9 3 ANTHROPOGENIC FORCINGS 11 3.1 CURRENT SOCIOECONOMIC TRANSITIONS 11 3.2 INTENSIFYING FISHING ACTIVITIES 11 3.3 CONTAMINATION OF AQUATIC ECOSYSTEMS 12 3.4 IMMINENT THREATS 15 RESEARCH CHAPTERS 17 4 AN EMERGING RECREATIONAL FISHERY IN MONGOLIA’S URBANISING SOCIETY: A THREAT TO ITS PRISTINE FISH STOCKS? 17 4.1 ABSTRACT 17 4.2 INTRODUCTION 18 4.3 MATERIALS AND METHODS 20 4.4 RESULTS 22 4.5 DISCUSSION 29 5 REGIONAL PATTERNS OF HEAVY METAL EXPOSURE AND CONTAMINATION IN THE FISH FAUNA OF THE KHARAA RIVER BASIN (MONGOLIA) 36 5.1 ABSTRACT 36 5.2 INTRODUCTION 37 5.3 MATERIALS AND METHODS 39 5.4 RESULTS 43 5.5 DISCUSSION 49 6 MOVEMENTS AND BEHAVIOUR OF AN ARCHAIC TROUT, BRACHYMYSTAX LENOK (PALLAS, 1773) UNDER EXTREME ENVIRONMENTAL CONDITIONS IN MONGOLIA 57 6.1 ABSTRACT 57 6.2 INTRODUCTION 57 6.3 MATERIALS AND METHODS 60 6.4 RESULTS 64 6.5 DISCUSSION 71 7 SEASONAL HOME RANGE SHIFTS OF THE SIBERIAN TAIMEN (HUCHO TAIMEN; PALLAS, 1773): EVIDENCE FROM PASSIVE ACOUSTIC TELEMETRY IN THE ONON RIVER AND BALJ TRIBUTARY (AMUR RIVER BASIN, MONGOLIA) 78 7.1 ABSTRACT 78 7.2 INTRODUCTION 79 7.3 MATERIALS AND METHODS 81 7.4 RESULTS 84 7.5 DISCUSSION 88 8 FISH CONSERVATION IN THE LAND OF STEPPE AND SKY: EVOLUTIONARY SIGNIFICANT UNITS OF THREATENED SALMONID SPECIES IN MONGOLIA MIRROR MAJOR RIVER BASINS 95 8.1 ABSTRACT 95 8.2 INTRODUCTION 95 8.3 MATERIALS AND METHODS 98 8.4 RESULTS 101 8.5 DISCUSSION 108 DISCUSSION 115 9 SOLUTIONS FOR SUSTAINABLE FISHERIES IN MONGOLIA 115 9.1 OVERVIEW AND LINKAGES OF KEY RESEARCH FINDINGS 115 9.2 FRESHWATER FISH CONSERVATION IN A TRANSITIONAL SOCIETY 118 9.3 ADDRESSING MANAGEMENT SHORTFALLS TO CURB INTENSIFYING FISHING ACTIVITIES 119 9.4 BIOMONITORING TO MITIGATE HUMAN HEALTH RISKS 122 9.5 IMPROVING ANGLER COMPLIANCE WITH INCREASED EDUCATION 123 9.6 PRESERVING HYDROLOGICAL CONNECTIVITY AND RIVER INTEGRITY IN THE FACE OF IMMINENT THREATS 124 9.7 MANAGEMENT AVOIDANCES 127 9.8 TRANSFERABILITY OF RESEARCH METHODS, RESULTS AND RECOMMENDATIONS 127 9.9 FUTURE RESEARCH AND MANAGEMENT PRIORITIES 129 10 REFERENCES 132 APPENDIX 1 I APPENDIX 2 II APPENDIX 3 VI APPENDIX 4 VIII APPENDIX 5 XXI APPENDIX 6 XXII APPENDIX 7 XXIV 11 REFERENCES TO OWN PUBLISHED / SUBMITTED MANUSCRIPT IN THE PRESENT THESIS XXV 12 INDIVIDUAL CONTRIBUTIONS TO THE CURRENT THESIS XXVI 13 NOTE ON THE COMMENCEMENT OF THE DOCTORAL PROCEDURE XXVIII 14 CURRICULUM VITAE XXIX 15 LIST OF PUBLICATIONS XXXI
Die Mongolei befindet sich derzeit in einem rasanten sozioökonomischen Übergang mit tiefgreifenden Veränderungen, die v.a. durch eine Zunahme bergbaulicher Aktivitäten sowie einen Ausbau ackerbaulicher Nutzungen wie auch der Viehwirtschaft angetrieben werden. Derzeit vollzieht sich eine noch nie dagewesene Urbanisierung und ein weiteres Bevölkerungswachstum, das auf die alternde öffentliche Infrastruktur, einschließlich Kraftwerke und Abwasserbehandlungsanlagen, einen zusätzlichen Druck ausübt. Infolgedessen zeigen sich in den weitgehend unberührten Landschaften des Landes, einschließlich seiner riesigen Süßwasser-Ökosysteme, deutliche Anzeichen von Übernutzung natürlicher Ressourcen, Umweltverschmutzung und Artenverlusten. Zukünftig geplante große Staudämme werden neben den bevorstehenden Auswirkungen des Klimawandels die Hydrologie deutlich verändern. So sind bereits deutliche Beeinträchtigungen der Fluss-und See-Ökosysteme erkennbar, insbesondere in Hinblick auf ihre aquatischen Lebensgemeinschaften. Einige der weltweit einzigartigen Fischarten haben bereits erhebliche Bevölkerungsrückgänge erlitten. Eine weitere existenzielle Bedrohung für diese Fischpopulationen ist der rasche und weitgehend un-regulierte Anstieg der Fischereitätigkeiten aus einer aufstrebenden Freizeitfischerei. Obwohl Fischfang und -konsum keine traditionellen Elemente der mongolischen Ernährung oder Kultur darstellen, vollziehen sich diesbezüglich derzeit tiefgreifende Veränderungen. Daher wurden in der Mongolei umfangreiche Forschungsprojekte geplant und durchgeführt, um wesentliche Informationen über diese neue Art der Fischerei zu sammeln und gleichzeitig bestehende Wissenslücken in Bezug auf die räumliche Ökologie und die Metapopulationsstruktur der wichtigsten Zielarten zu schließen. Darüber hinaus zeigten Untersuchungen, dass sich aufgrund des erhöhten Konsums von lokal gefangenen Fischarten aus einem stark beeinträchtigten Einzugsgebiet ein potenzielles Risiko für die menschliche Gesundheit ergibt. Insgesamt ist das übergeordnete Ziel dieser Fischereiforschung, das wissenschaftliche Verständnis und Wissen zu erweitern und letztlich die derzeitigen Managementinstrumente zu verbessern und neue Erhaltungsmaßnahmen zu ergreifen, um die Nachhaltigkeit und Widerstandsfähigkeit der bedrohten Fischartenpopulationen und die aufkommende Erholung zu sichern. Insgesamt wurden zwischen 2011 und 2014 insgesamt fünf fischereibiologische Forschungsprojekte abgeschlossen, wobei die Ergebnisse dieser Arbeiten in Erhaltungs- und Managementempfehlungen münden. Wegen des Mangels an Wissen über die aufkommende Freizeitfischerei wurden Anglerbefragungen in drei Einzugsgebieten durchgeführt, welche fünf wichtige Themen wie Angler-Demographie, Fischereipraktiken, Reisetätigkeiten, Fanggeräte und Kosten sowie Anglerwissen und Meinungen umfassten. Fünfundsechzig Angelgruppen (n = 154 Angler) wurden interviewt und zwei Anglertypen identifiziert: ländliche Angler ohne oder niedrige Einkommen, die in dem Becken wohnen, alleine oder in kleineren Gruppen fischen, häufig für kürzere Zeiten fischen und regelmäßig Fisch verzehren; und städtische Angler, die mittlere bis hohe Einkommen haben, in größeren Städten leben, mehr Geld für Fanggeräte / Ausflüge ausgegeben und typischerweise für mehrere Tage am Stück fischen. B. lenok wurde als die bevorzugte und am meisten gefangene Zielarten der Fischerei identifiziert. Die Ergebnisse der Anglerbefragungen bestätigten den erhöhten Fischkonsum im Kharaa-Einzugsgebiet, das aufgrund der weit verbreiteten Schwermetallverunreinigung aus der Vergangenheit und den gegenwärtigen Bergbauaktivitäten als potenzielles Risiko für die menschliche Gesundheit identifiziert wurde. So wurden Schwermetallverunreinigungen im Flusswasser, Sediment und fünf konsumierten Fischarten an 11 Standorten im Einzugsgebiet untersucht. Schwermetalle zeigten sich in allen fünf Stichprobenarten, wobei der maximale Muskelgehalt von Cr, As, Hg und Pb in Fischen aus dem Mittel- und Unterlauf festgestellt wurde, während Zn in B. lenok in den Oberlaufregionen stark erhöht war. Der erhöhte mediane Gehalt an Cr, Cu, Hg und Pb nahm mit trophischer Ebene zu, wobei die Bioakkumulation von Hg die größte Bedrohung für die menschliche Gesundheit darstellte, wobei über 10% aller Fischproben den international empfohlenen Schwellenwert für Hg im verzehrbaren Fischgewebe überstiegen (> 0,5 μg g-1 ww). Diese Bioakkumulation in residenten Fischarten könnte zu chronischen Intoxikationen bei Menschen führen, die sie regelmäßig konsumieren und zusätzliche Exposition gegenüber anderen Kontaminationsquellen haben, z.B. im Goldbergbau. Es wurden weitere zwei Projekte durchgeführt, die eine passive akustische Telemetrie zur Beschreibung der räumlichen und zeitlichen Autökologie, des Lebensraumnutzens und des Verhaltens von B. lenok im Eroo River und H. taimen in den Flüssen Onon und Balj unter den extremen Klimabedingungen der Mongolei verwendeten. Die maximalen Längsbewegungen (Heimatbereiche) wurden -umfangreicher als bisher angenommen- für beide Arten wurden auf 45,3 km für B. lenok und 126,1 km für H. taimen ermittelt. Im Frühjahr und Sommer wurden erhöhte Bewegungen aufgezeichnet, wobei die Individuen in die umliegenden Nebenflüsse eintraten und dort zwischen 4 und 85 Tagen verblieben, bevor sie zum Hauptfluss des Flusses zurückkehrten. Die Ergebnisse zeigen die Bedeutung der Aufrechterhaltung der Integrität und der Konnektivität von Nebenflüssen für Laichen, Nahrungssuche und Überwinterung sowie hydrologische und thermische Schutzräume, die für diese Arten in der Region mit den anstehenden Auswirkungen des Klimawandels zunehmend an Bedeutung gewinnen werden. Die verbesserten Kenntnisse der räumlichen Ökologie dieser bedrohten Arten kann die Gestaltung und Umsetzung neuer Schutzmaßnahmen wie Süßwasser-Schutzgebiete in der Mongolei wissenschaftlich fundieren und leiten. Weitere Untersuchungen wurden durchgeführt, um ein breiteres, multigenerationales Verständnis der Zusammenhänge zwischen den konkreten Populationen von H. taimen, B. lenok und T. baicalensis über die großen Flusseinzugsgebiete zu gewinnen. Sowohl molekulare als auch nukleare Marker wurden verwendet, um die genetische Struktur abzugrenzen und definieren, so z.B. evolutionär signifikante Einheiten (ESUs) und eigenständige Populationen für diese Arten einschließlich ihrer räumlichen Verteilung in der Mongolei. Über alle Arten hinweg war das deutlichste Muster eine starke Differenzierung zwischen den großen Becken mit geringer Differenzierung. Dem gegenüber stehen schwache Muster der Isolation durch die Distanz in den Becken, die eine hohe einzugsgebietsinterne Konnektivität anzeigen, obwohl exakte Muster nicht vollständig unter allen Arten übereinstimmten. Die Prioritäten der Erhaltung müssen sich auf die Verbesserung des Schutzes der vorrangigen Bevölkerungsgruppen innerhalb jeder Art und ESU konzentrieren, um die begrenzten verfügbaren Ressourcen für die Arten- und Populations-Erhaltung und fischereiliche Bewirtschaftung in der Mongolei zu maximieren. Die umfangreichen Ergebnisse aus der aktuellen wissenschaftlichen Forschung ermöglichten die Ableitung umfassender Empfehlungen für die Umsetzung neuer und die Verbesserung der bestehenden Management- und Erhaltungsmaßnahmen in Bezug auf die bedrohten Lachsarten der Mongolei und die aufkommende Freizeitfischerei. Diese Empfehlungen beinhalten 1.die Gründung einer Reihe von Süßwasser-Schutzgebieten (FPA) in den großen Flussgebieten der Mongolei auf der Grundlage der räumlichen Ökologie und der genetischen Bevölkerungsstruktur, die durch die aktuellen Forschungsergebnisse untermauert wird; 2. Eine Verschiebung des Eröffnungstermins der Fangsaison, welche im Gegensatz zur aktuellen Praxis die gesamte Laichzeit von B. lenok (die Hauptzielspezies der Fischerei); umfassen sollte; 3. Hinzufügen des Stumpfschnauzen-Lenok (B. sp.) zur Liste der besonders geschützten Arten, da er sich als eine genetisch unabhängige Spezies erwiesen hat, welche eine begrenzte räumliche Verteilung und geringe Populationsdichte in der Mongolei hat; und 4. Einführung von minimalen (und potentiell maximalen) Körpergrößenbeschränkungen für B. lenok und T. baicalensis, um die unreifen und heranwachsenden Individuen besser vor menschlichen Einflüssen zu schützen. Darüber hinaus empfiehlt es sich dringend, in den wichtigsten Flussgebieten fischereilich genutzte und nicht genutzte Fischpopulationen zu erfassen und Biomonitoring-Programme (unter Verwendung von Bioindikator-Spezies) zu implementieren, um toxische Schwermetallverunreinigungen zu verfolgen und potenzielle Risiken für die menschliche Gesundheit zu identifizieren, die mit dem Verzehr Fischen aus beeinträchtigten Regionen einhergehen. Schließlich verlangt das Fehlen von Kenntnissen über die derzeitigen Fischereiverordnungen durch Angler sowie die beobachteten und gemeldeten weitverbreiteten illegalen Fischereitätigkeiten ein weitreichendes Angler-Bildungsprogramm, um das Verständnis und die Einhaltung fischereilicher Regelungen zu verbessern. Das künftige Überleben der bedrohten Salmoniden und die Nachhaltigkeit der aufkommenden Freizeitfischerei in der Mongolei sind eng miteinander verbunden. Sofern die hier dargestellten wissenschaftlich fundierten Empfehlungen in vollem Umfang umgesetzt werden und hinreichend kontrolliert werden können, würden die zuständigen Behörden einen großen Schritt in Richtung der Umkehrung der aktuellen Trends machen und die gefährdeten Süßwasserfischpopulationen des Landes und ihre wertvollen aquatischen Ökosysteme bewahren. Die Mongolei könnte dann ein Modell für die Erhaltung und Bewirtschaftung von Süßwasserarten in der ganzen Region und der Welt werden.:DECLARATION OF CONFORMITY I TABLE OF CONTENTS II ACKNOWLEDGMENTS V LIST OF ABBREVIATIONS VI LIST OF FIGURES VII LIST OF TABLES VIII SUMMARY IX SUMMARY IN GERMAN / ZUSAMMENFASSUNG AUF DEUTSCH XII SUMMARY IN MONGOLIAN / ХУРААНГУЙ XVI INTRODUCTION 1 1 RESEARCH OBJECTIVES AND HYPOTHESES 1 1.1 OVERALL THESIS OBJECTIVES 6 2 MONGOLIA’S NATURAL ENVIRONMENT 7 2.1 GEOGRAPHIC ECOREGIONS 7 2.2 CLIMATIC CONDITIONS 7 2.3 HYDROLOGICAL NETWORKS 8 2.4 FRESHWATER FISH FAUNA 9 3 ANTHROPOGENIC FORCINGS 11 3.1 CURRENT SOCIOECONOMIC TRANSITIONS 11 3.2 INTENSIFYING FISHING ACTIVITIES 11 3.3 CONTAMINATION OF AQUATIC ECOSYSTEMS 12 3.4 IMMINENT THREATS 15 RESEARCH CHAPTERS 17 4 AN EMERGING RECREATIONAL FISHERY IN MONGOLIA’S URBANISING SOCIETY: A THREAT TO ITS PRISTINE FISH STOCKS? 17 4.1 ABSTRACT 17 4.2 INTRODUCTION 18 4.3 MATERIALS AND METHODS 20 4.4 RESULTS 22 4.5 DISCUSSION 29 5 REGIONAL PATTERNS OF HEAVY METAL EXPOSURE AND CONTAMINATION IN THE FISH FAUNA OF THE KHARAA RIVER BASIN (MONGOLIA) 36 5.1 ABSTRACT 36 5.2 INTRODUCTION 37 5.3 MATERIALS AND METHODS 39 5.4 RESULTS 43 5.5 DISCUSSION 49 6 MOVEMENTS AND BEHAVIOUR OF AN ARCHAIC TROUT, BRACHYMYSTAX LENOK (PALLAS, 1773) UNDER EXTREME ENVIRONMENTAL CONDITIONS IN MONGOLIA 57 6.1 ABSTRACT 57 6.2 INTRODUCTION 57 6.3 MATERIALS AND METHODS 60 6.4 RESULTS 64 6.5 DISCUSSION 71 7 SEASONAL HOME RANGE SHIFTS OF THE SIBERIAN TAIMEN (HUCHO TAIMEN; PALLAS, 1773): EVIDENCE FROM PASSIVE ACOUSTIC TELEMETRY IN THE ONON RIVER AND BALJ TRIBUTARY (AMUR RIVER BASIN, MONGOLIA) 78 7.1 ABSTRACT 78 7.2 INTRODUCTION 79 7.3 MATERIALS AND METHODS 81 7.4 RESULTS 84 7.5 DISCUSSION 88 8 FISH CONSERVATION IN THE LAND OF STEPPE AND SKY: EVOLUTIONARY SIGNIFICANT UNITS OF THREATENED SALMONID SPECIES IN MONGOLIA MIRROR MAJOR RIVER BASINS 95 8.1 ABSTRACT 95 8.2 INTRODUCTION 95 8.3 MATERIALS AND METHODS 98 8.4 RESULTS 101 8.5 DISCUSSION 108 DISCUSSION 115 9 SOLUTIONS FOR SUSTAINABLE FISHERIES IN MONGOLIA 115 9.1 OVERVIEW AND LINKAGES OF KEY RESEARCH FINDINGS 115 9.2 FRESHWATER FISH CONSERVATION IN A TRANSITIONAL SOCIETY 118 9.3 ADDRESSING MANAGEMENT SHORTFALLS TO CURB INTENSIFYING FISHING ACTIVITIES 119 9.4 BIOMONITORING TO MITIGATE HUMAN HEALTH RISKS 122 9.5 IMPROVING ANGLER COMPLIANCE WITH INCREASED EDUCATION 123 9.6 PRESERVING HYDROLOGICAL CONNECTIVITY AND RIVER INTEGRITY IN THE FACE OF IMMINENT THREATS 124 9.7 MANAGEMENT AVOIDANCES 127 9.8 TRANSFERABILITY OF RESEARCH METHODS, RESULTS AND RECOMMENDATIONS 127 9.9 FUTURE RESEARCH AND MANAGEMENT PRIORITIES 129 10 REFERENCES 132 APPENDIX 1 I APPENDIX 2 II APPENDIX 3 VI APPENDIX 4 VIII APPENDIX 5 XXI APPENDIX 6 XXII APPENDIX 7 XXIV 11 REFERENCES TO OWN PUBLISHED / SUBMITTED MANUSCRIPT IN THE PRESENT THESIS XXV 12 INDIVIDUAL CONTRIBUTIONS TO THE CURRENT THESIS XXVI 13 NOTE ON THE COMMENCEMENT OF THE DOCTORAL PROCEDURE XXVIII 14 CURRICULUM VITAE XXIX 15 LIST OF PUBLICATIONS XXXI

Mongolia is currently undergoing a rapid socioeconomic transition with extensive development driven by increased mineral resource extraction and large scale agriculture and pastoral expansion. There has also been unprecedented urbanisation and continued population growth that has placed added pressure on the ageing public infrastructure including power stations and waste water treatment plants. As a result, the country’s pristine landscapes, including its vast freshwater ecosystems, are now facing widespread degradation, contamination and species losses in the most impacted regions. The proposed large-scale dams and imminent climate change effects will further damage these fragile ecosystems. With a number of rivers and lakes deteriorating, resident aquatic communities, including unique fish species, have suffered significant population declines. However, a more substantial threat currently facing these fish populations is the rapid and largely unregulated rise in fishing activities within an emerging recreational fishery. Although historically fish capture and consumption has not been a traditional part of the Mongolian diet or culture, this is changing rapidly. Therefore a comprehensive set of research projects were developed and implemented across Mongolia, to gather essential information on this new fishery, while also addressing existing knowledge gaps regarding the spatial ecology and genetic structure of the main target species. In addition, a potential human health risk was evident due to the increased consumption of locally caught fish species from a heavily impacted river basin, and thus this was also investigated. Overall, the collective aim of this fisheries research was to increase the scientific understanding and knowledge across a range of issues and ultimately advise authorities on improving current management regulations and conservation strategies. It is hoped that the recommendations can assist in safeguarding the future sustainability and resilience of the threatened fish populations and the emerging recreational fishery across Mongolia for the future. A total of five fisheries related research projects were completed between 2011 and 2014, with the results from each used to formulate the conservation and management recommendations presented in this thesis. Due to the lack of knowledge regarding the emerging recreational fishery, roving creel surveys were conducted across three river basins and covered five key topics including angler demographics, fishing practices, current fishing trip data, fishing gear and costs, and angler knowledge and opinions. Fifty-eight fishing groups (n = 154 anglers) were interviewed and two angler types were identified: rural anglers with no or low incomes, who reside in the basin, fish alone or in smaller groups, fish frequently for shorter periods, and consumed fish more regularly; and urban anglers who have medium to high incomes, live in larger cities, spent more money on fishing gear / trips and fished for multiple days at a time. B. lenok was identified as the most targeted and caught species in the fishery. The results of the creel surveys confirmed increased fish consumption in the Kharaa River basin, which was identified as a potential human health risk due to the widespread heavy metal contamination from both past and present mining activities. Thus heavy metal contaminates in river water, sediment and five consumed fish species were examined at 11 sites across the basin. Heavy metals were evident in all five sampled species, with maximum muscle contents of chromium (Cr), arsenic (As), mercury (Hg) and lead (Pb) detected in fish from the middle and lower reaches, while zinc (Zn) was highly elevated in B. lenok from the upper tributaries. Elevated median contents of Cr, copper (Cu), Hg and Pb increased with trophic level, with the bioaccumulation of Hg posing the greatest threat to human health with over 10 % of all fish sampled exceeded the internationally recommended threshold for Hg in consumable fish tissue (> 0.5 µg g-1 ww). This bioaccumulation in resident fish species could lead to chronic toxicity in people who consume them regularly and have additional exposure to other sources of contamination e.g. gold mining. A further two projects were conducted that utilised passive acoustic telemetry to describe the spatial and temporal autecology, habitat use and behaviour of B. lenok in the Eroo River and H. taimen in the Onon/Balj rivers under Mongolia’s extreme seasonal conditions. The maximum longitudinal movements (home ranges) detected were more extensive than previously reported for both species with 45.3 km for B. lenok and 126.1 km for H. taimen. Increased movements were recorded in spring and summer, with individuals entering surrounding tributaries and remaining there for between four and 85 days before returning to the main river channel. The results highlighted the importance of maintaining the integrity and connectivity of tributary habitats for spawning, feeding and overwintering, as well as hydrological and thermal refuges, which will be increasingly important for these species in the region with the pending impacts of climate change. This increased knowledge relating to the spatial ecology of these threatened species can guide the design and implementation of new protective measures such as the introduction of Freshwater Protected Areas (FPAs) across Mongolia. Further research was conducted to gain a broader, multigenerational understanding of the interconnectedness between conspecific populations of H. taimen, B. lenok and T. baicalensis across the major river basins. Both molecular and nuclear markers were used to demarcate the population’s genetic structure and define Evolutionary Significant Units (ESUs) and priority populations for these species across their Mongolian distributions. Across all species, the most prominent pattern was a strong differentiation among major basins with low differentiation and weak patterns of isolation by distance within basins, which indicates high within-basin connectivity between populations, although exact patterns were not completely concordant among species. The extensive results produced from the current scientific research has facilitated the development of a comprehensive set of key recommendations for implementing new, and enhancing existing, management and conservation measures relating to Mongolia’s threatened salmonid species and its emerging recreational fishery. These recommendations include: 1. Establishing a series of Freshwater Protected Areas (FPAs) throughout Mongolia’s major river basins, with their design and location based upon the spatial ecology and genetic population structure determined by the current research results; 2. Shifting the opening date of the fishing season to encompass the entire spawning period of B. lenok (the fishery’s main target species), which appears to currently not be the case; 3. Adding the blunt-snouted lenok (B. sp.) to the prohibited species list, as it has been genetically proven to be an independent species and has a restricted distribution and low abundance in Mongolia; and 4. Introducing minimum (and potentially maximum) size limits for B. lenok and T. baicalensis, to better protect immature and pre-spawning individuals from being removed from the population. In addition, it is highly recommended to commence fisheries dependent and independent assessments in key river basins and conduct biomonitoring programs (using a bioindicator species) to track toxic heavy metal contamination and identify potential human health risks associated with consuming resident fish species from the more heavily impacted regions. The lack of knowledge of the current fishing regulations by anglers as well as the observed and reported widespread illegal fishing activities demands a wide-ranging angler education program to improve understanding and compliance within the fishery. The future survival of these threatened salmonids and the sustainability of the emerging recreational fishery in Mongolia currently hangs in the balance. However, if these scientifically based recommendations are implemented in full, and can be adequately enforced, then the responsible authorities can take a huge step forward towards reversing the current trends and preserving the country’s imperilled freshwater fish populations and their valuable aquatic ecosystems. Mongolia can be a model for freshwater species conservation and management throughout the region and the world
Die Mongolei befindet sich derzeit in einem rasanten sozioökonomischen Übergang mit tiefgreifenden Veränderungen, die v.a. durch eine Zunahme bergbaulicher Aktivitäten sowie einen Ausbau ackerbaulicher Nutzungen wie auch der Viehwirtschaft angetrieben werden. Derzeit vollzieht sich eine noch nie dagewesene Urbanisierung und ein weiteres Bevölkerungswachstum, das auf die alternde öffentliche Infrastruktur, einschließlich Kraftwerke und Abwasserbehandlungsanlagen, einen zusätzlichen Druck ausübt. Infolgedessen zeigen sich in den weitgehend unberührten Landschaften des Landes, einschließlich seiner riesigen Süßwasser-Ökosysteme, deutliche Anzeichen von Übernutzung natürlicher Ressourcen, Umweltverschmutzung und Artenverlusten. Zukünftig geplante große Staudämme werden neben den bevorstehenden Auswirkungen des Klimawandels die Hydrologie deutlich verändern. So sind bereits deutliche Beeinträchtigungen der Fluss-und See-Ökosysteme erkennbar, insbesondere in Hinblick auf ihre aquatischen Lebensgemeinschaften. Einige der weltweit einzigartigen Fischarten haben bereits erhebliche Bevölkerungsrückgänge erlitten. Eine weitere existenzielle Bedrohung für diese Fischpopulationen ist der rasche und weitgehend un-regulierte Anstieg der Fischereitätigkeiten aus einer aufstrebenden Freizeitfischerei. Obwohl Fischfang und -konsum keine traditionellen Elemente der mongolischen Ernährung oder Kultur darstellen, vollziehen sich diesbezüglich derzeit tiefgreifende Veränderungen. Daher wurden in der Mongolei umfangreiche Forschungsprojekte geplant und durchgeführt, um wesentliche Informationen über diese neue Art der Fischerei zu sammeln und gleichzeitig bestehende Wissenslücken in Bezug auf die räumliche Ökologie und die Metapopulationsstruktur der wichtigsten Zielarten zu schließen. Darüber hinaus zeigten Untersuchungen, dass sich aufgrund des erhöhten Konsums von lokal gefangenen Fischarten aus einem stark beeinträchtigten Einzugsgebiet ein potenzielles Risiko für die menschliche Gesundheit ergibt. Insgesamt ist das übergeordnete Ziel dieser Fischereiforschung, das wissenschaftliche Verständnis und Wissen zu erweitern und letztlich die derzeitigen Managementinstrumente zu verbessern und neue Erhaltungsmaßnahmen zu ergreifen, um die Nachhaltigkeit und Widerstandsfähigkeit der bedrohten Fischartenpopulationen und die aufkommende Erholung zu sichern. Insgesamt wurden zwischen 2011 und 2014 insgesamt fünf fischereibiologische Forschungsprojekte abgeschlossen, wobei die Ergebnisse dieser Arbeiten in Erhaltungs- und Managementempfehlungen münden. Wegen des Mangels an Wissen über die aufkommende Freizeitfischerei wurden Anglerbefragungen in drei Einzugsgebieten durchgeführt, welche fünf wichtige Themen wie Angler-Demographie, Fischereipraktiken, Reisetätigkeiten, Fanggeräte und Kosten sowie Anglerwissen und Meinungen umfassten. Fünfundsechzig Angelgruppen (n = 154 Angler) wurden interviewt und zwei Anglertypen identifiziert: ländliche Angler ohne oder niedrige Einkommen, die in dem Becken wohnen, alleine oder in kleineren Gruppen fischen, häufig für kürzere Zeiten fischen und regelmäßig Fisch verzehren; und städtische Angler, die mittlere bis hohe Einkommen haben, in größeren Städten leben, mehr Geld für Fanggeräte / Ausflüge ausgegeben und typischerweise für mehrere Tage am Stück fischen. B. lenok wurde als die bevorzugte und am meisten gefangene Zielarten der Fischerei identifiziert. Die Ergebnisse der Anglerbefragungen bestätigten den erhöhten Fischkonsum im Kharaa-Einzugsgebiet, das aufgrund der weit verbreiteten Schwermetallverunreinigung aus der Vergangenheit und den gegenwärtigen Bergbauaktivitäten als potenzielles Risiko für die menschliche Gesundheit identifiziert wurde. So wurden Schwermetallverunreinigungen im Flusswasser, Sediment und fünf konsumierten Fischarten an 11 Standorten im Einzugsgebiet untersucht. Schwermetalle zeigten sich in allen fünf Stichprobenarten, wobei der maximale Muskelgehalt von Cr, As, Hg und Pb in Fischen aus dem Mittel- und Unterlauf festgestellt wurde, während Zn in B. lenok in den Oberlaufregionen stark erhöht war. Der erhöhte mediane Gehalt an Cr, Cu, Hg und Pb nahm mit trophischer Ebene zu, wobei die Bioakkumulation von Hg die größte Bedrohung für die menschliche Gesundheit darstellte, wobei über 10% aller Fischproben den international empfohlenen Schwellenwert für Hg im verzehrbaren Fischgewebe überstiegen (> 0,5 μg g-1 ww). Diese Bioakkumulation in residenten Fischarten könnte zu chronischen Intoxikationen bei Menschen führen, die sie regelmäßig konsumieren und zusätzliche Exposition gegenüber anderen Kontaminationsquellen haben, z.B. im Goldbergbau. Es wurden weitere zwei Projekte durchgeführt, die eine passive akustische Telemetrie zur Beschreibung der räumlichen und zeitlichen Autökologie, des Lebensraumnutzens und des Verhaltens von B. lenok im Eroo River und H. taimen in den Flüssen Onon und Balj unter den extremen Klimabedingungen der Mongolei verwendeten. Die maximalen Längsbewegungen (Heimatbereiche) wurden -umfangreicher als bisher angenommen- für beide Arten wurden auf 45,3 km für B. lenok und 126,1 km für H. taimen ermittelt. Im Frühjahr und Sommer wurden erhöhte Bewegungen aufgezeichnet, wobei die Individuen in die umliegenden Nebenflüsse eintraten und dort zwischen 4 und 85 Tagen verblieben, bevor sie zum Hauptfluss des Flusses zurückkehrten. Die Ergebnisse zeigen die Bedeutung der Aufrechterhaltung der Integrität und der Konnektivität von Nebenflüssen für Laichen, Nahrungssuche und Überwinterung sowie hydrologische und thermische Schutzräume, die für diese Arten in der Region mit den anstehenden Auswirkungen des Klimawandels zunehmend an Bedeutung gewinnen werden. Die verbesserten Kenntnisse der räumlichen Ökologie dieser bedrohten Arten kann die Gestaltung und Umsetzung neuer Schutzmaßnahmen wie Süßwasser-Schutzgebiete in der Mongolei wissenschaftlich fundieren und leiten. Weitere Untersuchungen wurden durchgeführt, um ein breiteres, multigenerationales Verständnis der Zusammenhänge zwischen den konkreten Populationen von H. taimen, B. lenok und T. baicalensis über die großen Flusseinzugsgebiete zu gewinnen. Sowohl molekulare als auch nukleare Marker wurden verwendet, um die genetische Struktur abzugrenzen und definieren, so z.B. evolutionär signifikante Einheiten (ESUs) und eigenständige Populationen für diese Arten einschließlich ihrer räumlichen Verteilung in der Mongolei. Über alle Arten hinweg war das deutlichste Muster eine starke Differenzierung zwischen den großen Becken mit geringer Differenzierung. Dem gegenüber stehen schwache Muster der Isolation durch die Distanz in den Becken, die eine hohe einzugsgebietsinterne Konnektivität anzeigen, obwohl exakte Muster nicht vollständig unter allen Arten übereinstimmten. Die Prioritäten der Erhaltung müssen sich auf die Verbesserung des Schutzes der vorrangigen Bevölkerungsgruppen innerhalb jeder Art und ESU konzentrieren, um die begrenzten verfügbaren Ressourcen für die Arten- und Populations-Erhaltung und fischereiliche Bewirtschaftung in der Mongolei zu maximieren. Die umfangreichen Ergebnisse aus der aktuellen wissenschaftlichen Forschung ermöglichten die Ableitung umfassender Empfehlungen für die Umsetzung neuer und die Verbesserung der bestehenden Management- und Erhaltungsmaßnahmen in Bezug auf die bedrohten Lachsarten der Mongolei und die aufkommende Freizeitfischerei. Diese Empfehlungen beinhalten 1.die Gründung einer Reihe von Süßwasser-Schutzgebieten (FPA) in den großen Flussgebieten der Mongolei auf der Grundlage der räumlichen Ökologie und der genetischen Bevölkerungsstruktur, die durch die aktuellen Forschungsergebnisse untermauert wird; 2. Eine Verschiebung des Eröffnungstermins der Fangsaison, welche im Gegensatz zur aktuellen Praxis die gesamte Laichzeit von B. lenok (die Hauptzielspezies der Fischerei); umfassen sollte; 3. Hinzufügen des Stumpfschnauzen-Lenok (B. sp.) zur Liste der besonders geschützten Arten, da er sich als eine genetisch unabhängige Spezies erwiesen hat, welche eine begrenzte räumliche Verteilung und geringe Populationsdichte in der Mongolei hat; und 4. Einführung von minimalen (und potentiell maximalen) Körpergrößenbeschränkungen für B. lenok und T. baicalensis, um die unreifen und heranwachsenden Individuen besser vor menschlichen Einflüssen zu schützen. Darüber hinaus empfiehlt es sich dringend, in den wichtigsten Flussgebieten fischereilich genutzte und nicht genutzte Fischpopulationen zu erfassen und Biomonitoring-Programme (unter Verwendung von Bioindikator-Spezies) zu implementieren, um toxische Schwermetallverunreinigungen zu verfolgen und potenzielle Risiken für die menschliche Gesundheit zu identifizieren, die mit dem Verzehr Fischen aus beeinträchtigten Regionen einhergehen. Schließlich verlangt das Fehlen von Kenntnissen über die derzeitigen Fischereiverordnungen durch Angler sowie die beobachteten und gemeldeten weitverbreiteten illegalen Fischereitätigkeiten ein weitreichendes Angler-Bildungsprogramm, um das Verständnis und die Einhaltung fischereilicher Regelungen zu verbessern. Das künftige Überleben der bedrohten Salmoniden und die Nachhaltigkeit der aufkommenden Freizeitfischerei in der Mongolei sind eng miteinander verbunden. Sofern die hier dargestellten wissenschaftlich fundierten Empfehlungen in vollem Umfang umgesetzt werden und hinreichend kontrolliert werden können, würden die zuständigen Behörden einen großen Schritt in Richtung der Umkehrung der aktuellen Trends machen und die gefährdeten Süßwasserfischpopulationen des Landes und ihre wertvollen aquatischen Ökosysteme bewahren. Die Mongolei könnte dann ein Modell für die Erhaltung und Bewirtschaftung von Süßwasserarten in der ganzen Region und der Welt werden

Understanding the mechanisms driving larval dispersal and connectivity is of ecological relevance and is beneficial in fisheries management. Defining population structure and stock boundaries helps in management of spawning stock biomass and annual harvests. Moreover, determining if there are patterns in dispersal can help identifying source populations that need management strategies directed towards maintaining appropriate levels of egg production. The Southern rock lobster, Jasus edwardsii, extends around southeast Australia and New Zealand and supports valuable fisheries in both countries. Adults J. edwardsii do not migrate and their phyllosoma larvae, the dispersal stage, are adapted for drifting for approximately 12 to 24 months of pelagic larval duration. Consequently there has been an assumption of genetic homogeneity within the population throughout Australia. The assumption of panmixia has been supported by larval transport simulations and previous studies on genetic connectivity. The general eastward flow of currents in southeast Australia has been identified as the likely main dispersal mechanism. South Australia is a highly productive area, and is predicted by oceanographic models to be a source of larvae to the Tasmanian fishery. A second prediction from larval transport simulations is that regional self-recruitment varies markedly across the species range in Australia. Long-term monitoring of recruitment throughout the fishery shows high year-to-year variability in recruitment, as well as regional fluctuations. This has been linked to changes in environmental conditions. Fluctuations in recruitment magnitude can reduce the accuracy of population modeling of the stock, which is used to determine harvest strategies. In this thesis I assessed variability in genetic identity of Southern rock lobster at different spatio-temporal scales to evaluate drivers of population structure. I reviewed possible biological, environmental (e.g., dispersal history) or adaptive drivers (e.g., natural selection) by analyzing single nucleotide polymorphisms (SNPs) markers generated using double digest restriction site-associated DNA sequencing (ddRADseq). I measured genetic variability in J. edwardsii across three spatial scales, broad (1,000’s km), medium (100’s km) and fine-scale (10’s km), as well as two temporal scales, within a year and between years. In chapter 2, large-scale connectivity and potential for local adaptation between adult J. edwardsii from Australia and New Zealand was investigated using neutral and outlier markers. There was large-scale genetic divergence between Australia and New Zealand, two countries thousands of kilometres apart, at neutral regions of the genome (F\(_{ST}\) = 0.022), supporting previous findings of limited larval dispersal across the Tasman Sea. A much larger genetic differentiation was detected (F\(_{ST}\) = 0.134), using regions of the genome under putative selection suggesting local adaptation and post-settlement mortality of unfit genotypes. In chapter 3 I assessed the extent and patterns of genetic variability in new recruits through time on a medium spatial scale. To determine the role of genetics in the observed interannual variability and how post-settlement selection acts to modify the observed structure in recruits, pueruli and post-pueruli settling during four consecutive years were analyzed. Interannual genetic variability of recruits within and between two sites located 100’s of kilometres apart in South Australia and Tasmania provided support for chaotic genetic patchiness. Lower genetic diversity was observed during years of low puerulus catch rates at the Tasmanian site, suggesting regional genetic differences in recruitment. Additionally, the magnitude and strength of genetic divergence detected in the markers under putative positive selection also exhibited temporal and spatial variability. Both locations exhibited a single marker under putative positive selection in common across years, providing weak evidence for post-settlement selection. In chapter 4 I assessed fine-scale temporal and spatial genetic and phenotypic divergence in recruits across a latitudinal gradient. This was done using new recruits within one recruitment season in Tasmania from sites 10’s of kilometres apart. There was a lack of overall population structure identified between three sites along a latitudinal gradient, but genetic divergence at a small spatial scale suggested chaotic genetic patchiness. Individuals sampled from the southernmost site during three consecutive monthly collections were genetically divergent from each other. There were also phenotypic differences of pueruli between sites and months of settlement; individuals at the northernmost site were consistently smaller at settlement. Collective dispersal is a possible mechanism of larval J. edwardsii, based on significant phenotypic differences between sites that were persistent through time. This implied that larvae released during the same spawning event could maintain cohesiveness until settlement, leading to genetic patchiness among individuals recruiting during the same year. In chapter 5 I tested a number of the dispersal pathways projected by a larval transport simulation model for J. edwardsii. The predicted population of origin of pueruli caught in collectors in South Australia and Tasmania was then tested using genetic assignment to determine if they were the likely point of origin. All three adult lobster sampling sites were assigned as equally likely source for recruits in both South Australia and Tasmania. These results further evidenced the high level of genetic exchange in the Australian J. edwardsii population. In general, the findings of this thesis provide new evidence on the dispersal mechanisms used by larval J. edwardsii driving the observed genetic variation in recruits. The high level of genetic admixture found herein highlights the need of a coordinated fisheries management strategy between states in order to protect subpopulations that constitute important source of recruits.

With increasing anthropogenic threats to the marine environment, it has become a priority to improve our understanding and conservation of marine fauna. In Antarctic waters, a rich and diverse benthic fauna thrives. However, the relative isolation of these organisms and their adaptation to the unique Antarctic environment potentially heightens their vulnerability to environmental change. Thorough research on the genetic and ecological structure of Antarctic benthic invertebrate populations is lacking, particularly for some of the most dominant taxa, such as the Amphipoda. This study investigated genetic structure, diversity and population ecology in some common Antarctic benthic amphipod species, to build a more rigorous understanding of the Antarctic benthos that will aid in future management planning. Genetic structure was explored over a circum-Antarctic scale in the widespread amphipod species Eusirus perdentatus and Eusirus giganteus from the continental shelf, using DNA sequences of two mitochondrial regions (COI and CytB) and one nuclear region (ITS2). Phylogenies and haplotype networks provided strong evidence that E. perdentatus harbours two previously undetected cryptic species, and E. giganteus harbours at least three, highlighting our current misunderstanding of Antarctic benthic diversity. There were clear differences in the distribution, genetic diversity and connectivity of populations within each cryptic species, and it is proposed that this reflects different modes of post-glacial recolonisation of the continental shelf. Within one cryptic species, high genetic population differentiation (FST > 0.47, p < 0.01) suggested a potential allopatric speciation process at play. Genetic connectivity was explored over large (1000km) to very fine (100m) distances in the ubiquitous nearshore amphipod Orchomenella franklini, using seven highly polymorphic microsatellite markers. Genetic diversity differed significantly among populations, potentially reflecting local environmental conditions including anthropogenic pollution. Hierarchical AMOVA revealed marked genetic subdivision (FST = 0.16, p < 0.001) across the largest geographical scale and evolutionary isolation of these populations was inferred. Furthermore, three loci showed signs of selection across this scale, providing evidence of locally adapted populations. Gene flow was also restricted at smaller scales, indicating a stepping-stone mode of dispersal consistent with the brooded development of amphipods. The ecology of O. franklini was investigated through length measurements, sex and reproductive status of > 6000 individuals, spatial and temporal patterns in abundance, and corresponding relationships with environmental data. The life history of O. franklini revealed several traits that exemplify adaptation to the polar environment, including delayed reproduction, longevity (> 2 years), and seasonal breeding linked to the summer phytoplankton bloom. There was preliminary evidence of inter-annual and spatial fluctuations in reproductive timing, potentially reflecting local sea-ice conditions. O. franklini was found to reach astounding densities (> 65,000/m2) and abundance was highly heterogeneous in space and time. The distribution of O. franklini was related to various sediment properties although the relationship differed with geographic region, highlighting a close association to the local environment as well as broader Antarctic conditions. This study has provided significant insight into the dynamics of Antarctic benthic amphipod populations over a range of scales. Together the results emphasise a considerable degree of heterogeneity largely overlooked in Antarctic benthic organisms (from the taxonomy of entire species down to local-scale intraspecific population dynamics), and thereby support predictions of their vulnerability to anthropogenicinduced change. Results also shed light on speciation processes in Antarctic waters, and will ultimately help inform future planning decisions regarding spatial management of the Antarctic benthic ecosystem.

An almost unbroken fringing reef runs along the east coast of Africa, the lagoon inside the reef is the foundation of almost all artisanal fisheries. It is a low-tech fishery conducted by many people. Some areas can have up to 19 fishermen per square kilometer. High fishing pressures, coupled with declining fish stocks has led to changes in mean size and reproductive age of many exploited species. There is a vital and urgent need for scientifically based management systems, including the utilization of genetic information to guide management practices. This thesis aims to investigate the presence of genetic structures in the western Indian Ocean. In order to do that we first investigated the historical patterns of connectivity throughout the region (paper I). In papers II and III we focused on local scale connectivity in Kenya and Tanzania and finally in paper IV we investigate the large-scale contemporary gene flow throughout the Western Indian Ocean. In paper III we also investigate the temporal genetic variation at one site and compare it to the small-scale genetic variation along a stretch of the Kenyan coastline. Some overall conclusions that can be drawn from my body of work are: there are genetic structures present in the western Indian Ocean even though the apparent lack of physical barriers. Major oceanic currents aid evolutionary dispersal patterns. A single geographic site need not be genetically homogenous or temporally stable. Island sites are genetically more homogenous than mainland sites. In conclusion, there are clear and distinct genetic structures present especially in Siganus sutor, the most targeted fish for the artisanal fishery in East Africa.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.

Patterns of genetic connectivity can help answer key questions about the evolutionary ecology of fishes. This knowledge is particularly useful when considering the management and conservation of species that are impacted by fisheries. Population connectivity in ocean habitats is heavily influenced by environmental and oceanographic factors. These factors can lead to strong genetic differences within populations, causing fragmentation into smaller subpopulations. The Red Sea exhibits pronounced oceanographic gradients in temperature, chlorophyll, and salinity, which have been assessed in various species’ populations and which have been found to have potential impacts on gene flow. The Red Sea also features strong cyclonic and anticyclonic eddies that may facilitate, or possibly inhibit, the transport of larvae throughout the Red Sea, potentially influencing gene flow themselves. The ability of oceanographic factors like eddies to structure wild fisheries populations in this region has yet to be fully determined. To address this, the genetic composition of two of the most highly fished species, (Plectropomus areolatus and Plectropomus pessuliferus marisrubri), in the Red Sea were evaluated utilizing genetic markers (polymorphic microsatellite loci). Samples from three geographically separate regions along the Saudi Arabian Red Sea coastline, as well as from Sudan, were analyzed to address latitudinal and cross-sea connectivity. I was able to determine that little genetic differentiation exists within Plectropomus species across all regions of the Red Sea, indicating high gene flow for these species throughout. These findings highlight the ability of currents and eddies to transport larvae along and across the Red Sea. The results from this study also indicate that a single population of P. areolatus and a single population of P. pessuliferus marisrubri occurs in the Red Sea. The high degree of genetic flow suggests that each species should be managed as individual units. This study presents a plausible avenue for buffering the effects of overfishing currently occurring in Saudi Arabia; Saudi Arabian fish subpopulations may be reseeded by the Sudanese subpopulations.