Tesi sul tema "Population and ecological genetics"

A major goal in evolutionary biology is to understand how ecological factors shape the phenotypic and genetic variation that we observe in natural populations and in this thesis I examine how rapid changes in temperature have influenced phenotypic and genetic variation in morphological and life history traits in long-term studies of great tits. In Chapter 1 I review what is known about the effects of environmental change on natural populations, and outline the quantitative genetic framework that is available to study genetic variation in natural populations. Much focus on the effects of climate change has concerned species’ phenology, far less attention has been given to other traits. In Chapter 2 I examine the effects changing environmental conditions have had on the proportion of females that produce second broods. Temperature operates mainly through indirect effects (such as food abundance) but may also have more direct effects. In Chapter 3 I show that over a 36 year period body size have declined in line with predictions from Bergmann’s rule and I explore the genetic basis of this decline and the environmental factors involved. Although we can learn much from population level responses, there is a great deal of additional information to be gained by studying between-individual responses. In Chapter 4 I therefore compare the multivariate pattern of between-individual variation in phenotypic plasticity and its genetic basis for laying date and clutch size, in two great tit populations. Environmental changes may also directly affect the expression of genetic variance as well as the strength of selection acting on a trait, and in Chapter 5 I show that, for laying date, the environment induces a positive covariance between strength of selection and the expression of additive genetic variance, something that may enhance the rate of adaptation. Finally, in Chapter 6 I discuss and summarise the wider implications of the findings from this thesis.

[Truncated abstract] The species-rich Southwest Australian Floristic Region (SAFR) is a global biodiversity hotspot. Characterised by a Mediterranean-type climate and nutrient deficient landscape, this region is endowed with 7380 native vascular plant species/sub species, of which 49% are endemic and 2500 are of conservation concern. Despite the global significance of this region, there is still only a poor understanding of the factors influencing high diversity and endemism, and especially the population genetic consequences of narrow endemism and naturally fragmented species distribution. Holly leaved banksia (Banksia ilicifolia R. Br.), although widespread through Southwest Western Australia (SWWA), has a naturally fragmented distribution, with generally small populations restricted to swales and wetland fringes with depth to groundwater less than 10 m. As such, it provides an excellent model to better understand the ecological genetic consequences of local endemism, population size and natural population fragmentation . . . Products of wide outcrossing (over 30 km) showed a heterosis effect over local outcrossing, indicating increased ecological amplitude of offspring following interpopulation mating. These results suggest that the breeding and mating biology of B. ilicifolia counters the negative genetic erosion effects of narrow ecological amplitude and small population size. Recent habitat fragmentation, and reductions in population size and increased isolation, is impacting on these processes, but further research is required to assess the ultimate consequences of these genetic effects for population viability.

Dispersal is a fundamental ecological and evolutionary process that can create demographic and genetic linkage between neighbouring and distant locations, influencing the dynamics, structure and ultimately the persistence of populations. To understand observed population dynamics and structure and to predict future change, accurate and comprehensive data are required describing the pattern and magnitude of dispersal and gene flow across all relevant spatial scales. However, this is a major empirical challenge. In this thesis, I aimed to obtain comprehensive empirical data quantifying natal dispersal patterns and population genetic structure across multiple spatial scales using the European shag (Phalacrocorax aristotelis) as a model species. I used a combination of field observations of shags individually ringed on the Isle of May, Scotland and molecular genetic techniques to accomplish these aims. By locating adult shags that had been ringed as chicks on the Isle of May at their breeding locations across eastern Scotland, I demonstrated divergent dispersal distributions at small versus large spatial scales. Using both mitochondrial DNA markers and a newly developed set of microsatellite markers, I quantified population genetic structure across a pan-European scale. This was weak across both molecular markers suggesting a role for occasional effective long-distance dispersal. However, a suite of evolutionary forces besides gene flow can create observed population genetic structure. Therefore, I quantified population genetic structure across populations in eastern Scotland, and quantitatively linked this indirect estimate of gene flow with my direct field observations of dispersal. Dispersal parameters derived explicitly from field observations and the spatial organisation of populations were shown to strongly influence observed population genetic structure. Overall, these data demonstrate the need to utilise both field observations and genetic methods to comprehensively estimate the extent and effectiveness of dispersal and highlight the importance of accurately quantifying long-distance dispersal in particular for predicting future change.

Thesis (Ph. D.) -- University of Maryland, College Park, 2009.<br>Thesis research directed by: Behavior, Ecology Evolution and Systematics Program. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

Doctor of Philosophy<br>Department of Entomology<br>James F. Campbell<br>Thomas W. Phillips<br>Movement is a fundamental feature of animals that impacts processes across multiple scales in space and time. Due to the heterogeneous and fragmented nature of habitats that make up landscapes, movement is not expected to be random in all instances, and an increase in fitness is an expected consequence for those that can optimize movement to find valuable and scarce recourses. I studied the movement of Rhyzopertha dominica (Coleoptera: Bostrichidae), one of the most important pests of stored grain worldwide, within and between resource patches. At a fine spatial scale, I identified factors that contribute to overall and upward movement in the grain mass. Three-week-old insects tented to stay closer to the surface than one or two-week-old insects. Females tended to be more active and to explore more than males. I also found that males tended to stay closer to the surface than females and that might be related to the ability to attract females from outside the patch since there was no significant difference regarding female’s attraction within the grain patch. Interaction with feeding sites or other individuals of the same sex creates positive feedback and a more clumped spatial pattern of feeding and foraging behavior. On the other hand, interaction with individuals of different sex creates negative feedback and a more random or overdispersed pattern. At a broad spatial scale, I studied the long-term consequence of R. dominica movement on the development of population structure within the U.S. To evaluate population structure, I used reduced representation of the genome followed by direct sequencing of beetles collected from different locations across the U.S where wheat or rice is produced and stored. Ecoregions were more important in explaining structure of R. dominica populations than crop type. I also found significant isolation by distance; however, model selection primarily elected grain production and movement variables to explain population differentiation and diversity. Understanding animal movement is essential to establishing relationships between distribution and surrounding landscape, and this knowledge can improve conservation and management strategies.

Laboratory studies on speciation have revealed that selection must be disruptively applied on traits related to the mating system in order to produce deviations from random mating in experimental populations. One problem with these experiments, however, has been the complexity of the model organism used, most frequently Drosophila species. Due to the multi genic nature of the mating systems of such organisms, it has been difficult to obtain the necessary gene combinations that result in complete sexual isolation. In the present study, I have used a simple sexual organism, the unicellular green algae Chlamydomonas reinhardtii, as a model for ecological and sexual differentiation. Disruptive selection was applied on the flagella, by selecting simultaneously for photo taxis and mating, behaviours for which these organelles are of fundamental importance. An asymmetric response to selection for photo taxis and zygote production was obtained in populations selected for conditions at opposite ends of the environmental spectrum used, differentiating these two populations in both movement capacity and mating efficiency. These results are discussed in relation to previous experiments on speciation and to the implications of future experimental studies on the same subject.

The Arabidopsis HapMap project, and follow-on work carried out by the Bergelson and Nordborg groups, established in broad outline the demographic history and population structure of wild Arabidopsis thaliana. Genome‐wide association studies are likewise making considerable advances in identifying genes associated with ecologically significant traits, and thus in identifying candidate genes likely to be under the action of natural selection. The aim of this project has been to further expand and combine these lines of investigation, by using genomic data to test ecological hypotheses and to grant more complete insight into the rangeof selection pressures acting upon wildpopulations. A method to measure and elucidate the genetic similarity of genomic regions between sampled accessions was therefore developed to facilitate this. 250K SNP data from RegMap accessions was then examined for evidence of patterns of migration and gene flow across Europe. Those observations formed the basis of a simple model of the history of the UK population relative to that of Europe. Comparisons of observed genotypes against expectations derived from the modelallowed the identification of genomic regions under the influence of selection. Loci corresponding to signatures of selection indicated positive selection acting upon phenotypes of disease resistance, flowering time, and seed size.

Kyoto University (京都大学)<br>0048<br>新制・課程博士<br>博士(農学)<br>甲第21149号<br>農博第2275号<br>新制||農||1059(附属図書館)<br>学位論文||H30||N5123(農学部図書室)<br>京都大学大学院農学研究科地域環境科学専攻<br>(主査)教授 田中 千尋, 教授 本田 与一, 准教授 刑部 正博<br>学位規則第4条第1項該当

Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2008.<br>Title from electronic title page (viewed Dec. 11, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biology." Discipline: Biology; Department/School: Biology.

L'isolement géographique est une menace élevée pour le maintien des populations sur le long terme. Il est donc primordial de comprendre selon quel degré la viabilité des populations est affectée par leur isolement, notamment en vue de définir des priorités en terme de conservation. Eryngium viviparum J.Gay (Apiaceae) est une des espèces végétales les plus menacées d'Europe avec une distribution ibéro-armoricaine très fragmentée. En France, son statut de conservation est devenu particulièrement critique avec la disparition de la presque totalité de ses populations au cours des années 1980, à l'exception d'une seule, suite à la destruction de son habitat par les activités humaines. Cette unique population fait depuis plusieurs années l'objet d'une conservation et d'une gestion attentives au sein d'une réserve protégée. Malgré ces actions, l'isolement de cette population soulève des interrogations quant à sa viabilité sur le long terme. Dans ce cadre, et à travers une approche multidisciplinaire, la thèse propose un renforcement des connaissances sur les caractéristiques écologiques et biologiques d'E. viviparum, et plus particulièrement concernant sa dernière population française. Elle s'articule selon trois axes principaux : (1) L'étude de l'amplitude écologique de l'espèce, puis la caractérisation de ses préférences écologiques à fine échelle au sein de la dernière population française (2) L'évaluation de la viabilité de la population isolée d'après ses paramètres démographiques, son niveau de diversité génétique et son degré de différenciation avec d'autres populations. (3) L'expérimentation des modalités de réintroduction en France. Les résultats apportés par ce travail contribueront à définir les prochaines priorités en matière de gestion et de conservation pour assurer le maintien d'E. viviparum sur le long terme en France. Le cas d' E. viviparum fournit un bon modèle d'étude pour évaluer l'effet de l'isolement sur la dynamique d'une population isolée et pour appliquer une conservation adaptée à cette problématique<br>The geographical isolation is an important threat for the long term preservation of populations. It is crucial to understand how the viability of populations is affected in such context, in particular to define conservation priorities. Eryngium viviparum J.Gay (Apiaceae) is one of the most endangered plant in Europe, with a fragmented distribution between the NW of the Iberian peninsula and Brittany. ln France, the species is maintained only on a single locality, after the destruction of its habitat by human activities during 1980s. Despite a conservation program and an attentive management within a protected area, the strong isolation experimented by this population bring up questions about its long-term viability. In this context, through a multidisciplinary approach, this thesis aims to improve the biological and ecological knowledge of E. viviparum, and more particularly within its last French population. This thesis is organized according three main axes : (1) The study of large-scale E. viviparum ecological amplitude, and the characterization of its fine scale ecological preferences within the last french population. (2) The viability evaluation of the isolated population according to its demographic modalities, and to its genetic structure in comparison with Iberian populations. (3) The experiment of its reintroduction modalities in France.The results of this study will contribute to define the long-term conservation priorities of E. viviparum in France. Finally, the case of E. viviparum is a good model to study the effect of the isolation on an isolated population dynamic, and to apply adapted conservation for species in a similar context

This thesis includes two studies: The first examined patterns of neutral genetic diversity within Bromus tectorum L. across the IMW region, and uses patterns of microsatellite (SSR) genotype distribution to make inferences about the respective roles of adaptively significant genetic variation, adaptive phenotypic plasticity, and facultative outcrossing in the ongoing invasion and recent range expansion of B. tectorum. It has been previously demonstrated that, due to extremely low outcrossing rates, it is possible to characterize individual genotypes of this species using four SSR loci. We sampled 20 individuals from each of 96 B. tectorum populations (classified by region and habitat) from throughout the IMW and used these SSR markers to characterize each individual. We found 131 four-locus SSR genotypes; however, the 14 most common genotypes collectively accounted for 79.2% of the individuals sampled. Individuals with certain SSR genotypes sorted strongly into warm or salt desert habitats (stringent habitats) and flowered earlier than individuals with genotypes from more mesic habitats, providing evidence of adaptively significant genetic variation associated with these genotypes. Other SSR genotypes were found across a wide range of habitats though they tended to be less prevalent in stringent habitats, providing evidence that adaptive phenotypic plasticity may be important for the distribution of some common genotypes. We observed very few heterozygous individuals, consistent with the highly inbreeding reproductive strategy of B. tectorum. Because specialist genotypes dominating recently invaded areas within the IMW region contained unique alleles, they are not likely to have resulted from recombination, leading us to doubt the role of facultative outcrossing as a significant mechanism facilitating the current range expansion of B. tectorum in the IMW.Previous research investigating the population and ecological genetics of Bromus tectorum L. in the North American invaded range has relied on either allozyme or microsatellite (SSR) genetic analyses, both of which have proven to have shortcomings. In order to overcome the issues associated with these other marker types, in the second study of this thesis we developed single nucleotide polymorphism (SNP) markers for B. tectorum by 1) obtaining normalized cDNA, 2) sequencing normalized cDNA using 454 sequencing, 3) aligning resultant contigs and looking for SNPs, 4) designing assays for SNP validation and genotyping using KASPar, 5) converting working KASPar assays for use with the Fluidigm EP1 platform using the 96.96 Dynamic ArrayTM IFC. Sequencing resulted in 1258041 reads, which assembled into 65486 contigs (20782 large contigs exceeding 500 base pairs). Using selection criteria of at least 10x coverage and 30% of the minor allele, 3333 putative SNPs were identified. We developed KASP assays for 255 putative SNPs, which resulted in 101 working polymorphic assays. Ninety-six assays were then successfully converted for use with KASP on the Fluidigm EP1 genotyping platform using 96.96 dynamic arrays.

When do novel adaptations arise as rearrangements of ancestral components and when do they arise de novo? Answering this question requires direct study of the proximate mechanisms behind novel phenotypes that arise from diverse starting points along different historical contingencies. Here we capitalize on uniquely replicated historical sequences of population establishment in the house finch (Haemorphous mexicanus) to study the evolution of color-producing enzymatic pathways that underlie population divergence in color phenotypes. We first evaluated genetic diversity and differentiation in a neutral marker (the mitochondrial NADH II dehydrogenase gene) across 12 study populations, both in the ancestral range in Arizona and across the Continental Divide in Montana at the range edge. We uncovered 29 haplotypes in our samples, describing 17 new haplotypes for this species. We then examined the influence of inter-population differences (such as habitat, age, and genetic relationships) on variation in the network of enzymatic reactions that produce carotenoid-based coloration in this species. Placing these comparisons in the framework of historical sequence of population establishment allows us to elucidate likely evolutionary trajectories of novel feather color phenotypes in this species.

Évaluer les stratégies d’histoire de vie d’espèces est indispensable à leur conservation. Un total de 3651 colonies de corail de feu, Millepora platyphylla, ont été mesurées, géoréférencées et collectées dans 5 habitats différents à Moorea afin d’évaluer le contexte biologique et écologique du maintien et du renouvellement des populations. Ce travail de thèse a démontré que la structure des populations diverge entre le lagon et la pente externe. À l’aide de marqueurs microsatellites nouvellement développés, nous avons démontré que cette espèce se reproduit principalement par fragmentation (80%) et que les fragments sont distribués en parfait alignement avec la dispersion des vagues. Les clones d’une même lignée clonale partagés entre habitats expriment différents phénotypes selon leur exposition aux vagues. Surprenamment, M. platyphylla affiche une morphologie vulnérable à la fragmentation dans les habitats exposés à la houle. L’analyse de parenté a révélé une forte contribution de l'autorecrutement (58%), une faible dispersion des propagules sexuées et une tendance à l’agrégation d’individus issus de mêmes parents. Enfin, nous avons démontré de la variabilité génétique intracoloniale, principalement due aux mutations somatiques (mosaïcisme), qui contribue ainsi à augmenter la diversité génétique dans la population. L’interaction de ces processus engendre une diversité génétique et phénotypique élevée dans la population et permet également le renouvellement local et la persistance de cette espèce à Moorea; habitat marginal. Ces stratégies d’histoire de vie augmentent ainsi le potentiel d’adaptation et la résilience de M. platyphylla face aux changements environnementaux<br>Evaluating life history of species carries important implications for conservation biology. A total of 3651 colonies of the fire coral Millepora platyphylla was measured, georeferenced and collected in 5 different habitats in Moorea to evaluate the biological and ecological context of the population maintenance and renewal. This thesis has demonstrated that the population structure of this species varies greatly between lagoonal and fore reef habitats. Using newly developed microsatellite markers, we have shown that M. platyphylla relies heavily on clonal reproduction via fragmentation (80%) and that the fragments are distributed in perfect alignment with wave energy dispersal. Clonal lineages with clones shared among habitats revealed the ability of a single genotype to express different phenotypes depending on its exposure to swell wave energy. Surprisingly, M. platyphylla invests in a vulnerable morphology to wave-induced breakage in high energy reef habitats. Furthermore, parentage analysis revealed a high contribution from self-seeding (58%), limited dispersal of sexual propagules and sibling aggregations. At last, we have demonstrated intracolonial genotypic variability, mostly from somatic mutations (mosaicism), which creates novel genetic diversity within the population. The interaction of these processes generates a high level of genetic and phenotypic variation within the population and allows for local replenishment and the persistence of this fire coral species in Moorea, a marginal habitat. These life history strategies thus increase the adaptive potential and resilience of M. platyphylla in response to rapid and unpredictable environmental changes

Following its introduction to North America in the late nineteenth century, Bromus tectorum L., an inbreeding invasive winter annual grass, has become dominant on millions of hectares of sagebrush steppe habitat throughout Intermountain Western North America. It appears that within the last 30-40 years, B. tectorum has expanded its range southward into the Mojave Desert and also into more climatically extreme salt desert environments. Previous research using microsatellite markers and experimental studies has suggested that lineages found in desert habitats are genetically distinct from those found in the sagebrush-steppe habitat and possess suites of traits that pre-adapt them to these environments. To provide additional support for our hypothesis that desert habitat-specific haplotypes dominate and are widely distributed across warm and salt desert habitats, we genotyped approximately 20 individuals from each of 39 B. tectorum populations from these habitats and adjacent sagebrush steppe habitats using 71 single nucleotide polymorphic (SNP) markers. Our data clearly demonstrate that populations throughout the Mojave Desert region, as well as in salt desert habitats further north, are dominated by a small number of closely related SNP haplotypes that belong to the desert clade. In contrast, populations from adjacent environments are largely dominated by haplotypes of the common clade, which is widely distributed throughout the North American sagebrush steppe. Populations across all habitats were usually dominated by 1-2 SNP haplotypes. This suggests that inbreeding B. tectorum lineages can often maintain their genetic integrity. It also explains the strong association between marker fingerprints and suites of adaptive traits in this species.

Les patrons de structuration des espèces animales à fine et à large échelles peuvent être façonnés par des facteurs environnementaux et des traits comportementaux individuels. Les objectifs de cette thèse combinant des approches sociales, génétiques, isotopiques et morphométriques sont de décrire et comprendre i) les structures sociale, écologique et génétique de la population de grands dauphins du golfe Normand-Breton (NB) et ii) la structure de population de l'espèce à l'échelle de l'Atlantique Nord-Est (ANE). Les grands dauphins du golfe NB forment une unique population génétique qui est composée de trois ensembles sociaux et écologiques distincts. Les associations entre individus semblent être influencées par l'écologie et non par les liens de parenté. La structure génétique du grand dauphin à l'échelle de l'ANE est hiérarchique, avec deux écotypes, l'un côtier et l'autre pélagique, qui sont chacun divisé en deux populations. Les populations côtières sont issues d'une population pélagique et auraient colonisé les habitats côtiers libérés lors de la dernière déglaciation, ce qui a permis la diversification de l'espèce. Cette structure semble maintenue par les spécialisations écologiques et le comportement social des individus. Par ailleurs, l'origine pélagique des grands dauphins du golfe NB pourrait expliquer certains de leurs traits sociaux. Pour conclure, les patrons de structuration à fine et à large échelles de ce prédateur supérieur semblent influencés par les comportements sociaux et écologiques, les conditions environnementales présentes et passées ainsi que par son histoire évolutive. L'absence de différences morphologiques marquées entre les deux écotypes pourrait s'expliquer par leur divergence relativement récente ou par un faible contraste entre les habitats pélagiques et côtiers dans l'ANE. Ce travail souligne l'intérêt de combiner de multiples approches à différentes échelles temporelles et spatiales pour comprendre la structure sociale et la structure de population d'espèces mobiles et cryptiques. Ces résultats ont également des implications majeures pour la conservation, en particulier pour la définition d'unités de gestion<br>Complex interactions between environmental factors and behavioral traits may shape the fine and large scale structuring patterns of animal species. The objectives of this dissertation were to describe and understand i) the fine-scale social, ecological and genetic structures of bottlenose dolphins in the Normano-Breton (NB) gulf and ii) the population structure of the species at the scale of the North-East Atlantic (NEA) by combining social, genetic, stable isotope and morphometric approaches. Coastal bottlenose dolphins in the NB gulf form a single genetic population subdivided in three social and ecological clusters. Ecology but not kinship may influence association patterns. In the NEA, bottlenose dolphin genetic structure is hierarchical. They form two ecotypes, i.e. coastal and pelagic, each of them being further divided in two populations. This genetic structure was likely triggered by past changes in the environment (i.e. deglaciation) that created ecological opportunities for diversification. Ecological specializations and social behavior may maintain genetic divergence. In turn, the pelagic origin of bottlenose dolphins in the NB gulf may explain some of their social structure traits. Thus, an interaction between social and ecological behaviors, current and past environmental conditions, and evolutionary history may drive the fine and large scale structuring patterns of this top predator. The absence of strong differences in morphology between the two ecotypes may be explained by their relatively recent divergence or by low contrasts between the pelagic and coastal habitats in the NEA. This work highlights the power of combining approaches at different temporal and spatial scales for assessing the social and population structures of highly mobile and difficult to access species. The results have also major conservation implications especially for the designation of management units

Invasive species represent a major challenge through their consequences on<p>biodiversity, human health and economy. Their effects are especially important on fragile and<p>unique insular biotas such as the Galápagos Islands. Ants in particular are keystone species<p>implicated in ecosystem functioning and biodiversity and they can be dramatic invaders. In<p>the Galápagos Islands, the tropical fire ant Solenopsis geminata is considered a high-impact<p>invasive species, though it remains surprisingly poorly studied. The objectives of this work<p>are to document the invasion of S. geminata in the Galápagos Islands by 1) updating its<p>distribution; 2) determining its reproduction and dispersal strategies and reconstruct its<p>invasion history throughout the archipelago and 3) evaluating its impact on the native fauna<p>(focusing on ants and arthropods communities and endemic land tortoises).<p>First, we added 66 new records of S. geminata in the Galápagos since 2008. It has<p>now been recorded on seven islands and 11 islets in a wide range of habitats, including<p>nesting sites of 24 endemic and/or endangered vertebrate species, for which it constitutes a<p>potential threat.<p>Secondly, by combining Bayesian clustering methods, coalescent-based scenario<p>testing using microsatellite data and historical records, we determined that genetic diversity<p>of populations of S. geminata collected in Galápagos Islands is significantly lower than the<p>genetic diversity of populations from native areas (Costa Rica). The Galápagos populations<p>form three clusters corresponding to an island or groups of islands. They appear to be the<p>result of a single introduction in the first half of the 19th century, probably from mainland<p>Ecuador, which acted as a bridgehead population to two subsequent introductions within the<p>archipelago, corresponding human colonization fluxes in the archipelago.<p>We sampled ants in all main habitats of Santa Cruz Island. Introduced ant species<p>were largely prevalent, and S. geminata was the dominant species and was associated with<p>low evenness of ant communties and lower abundance of native ants. We found that<p>Galápagos’ ant communities are determined by the vegetation type and altitude, but found<p>only little evidence for competitively structured assemblages, except in disturbed areas.<p>The arthropod diversity was investigated in two agricultural sites of Santa Cruz Island<p>by combining three complementary sampling techniques. More than half of the species were<p>either endemic or native, but introduced species constituted the majority of the catches.<p>Solenopsis geminata was by far the most abundant and common species.<p>Finally, we investigated the mortality of Cheloidis land tortoise’s eggs and hatchlings<p>in an area infested by S. geminata on Santa Cruz Island with regard to the abundance of fire<p>ants and the duration of incubation. Egg survival was negatively associated with longer incubation times but we found no direct relation between ant density and tortoise mortality<p>despite a high abundances of fire ants in the vicinity of the majority of the tortoise burrows.<p>Our work allows addressing ecological and genetical aspects of the invasion of S.<p>geminata in the Galápagos Islands. We analyzed our results in the light of an ecoevolutionary<p>framework presenting different invasion scenarios and discussed S. geminata<p>as an invasive ant. This provided us with information useful for the study and management of<p>this invasive species in the Galápagos Islands.<p>/<p>Les espèces invasives constituent un défi majeur à cause de leur impact sur la<p>biodiversité, la santé humaine et l’économie. Leurs effets sont particulièrement importants<p>sur les environnements insulaires fragiles et uniques comme les île Galápagos. Les fourmis<p>en particulièr sont des espèces clé de voûte du fonctionnement des écosystèmes et de la<p>biodiversité. Elles peuvent de ce fait devenir des envahisseurs spectaculaires. Dans les îles<p>Galápagos, la fourmi de feu tropicale Solenopsis geminata fait partie des espèces invasives<p>à haut impact et cependant elle a été étonnamment peu étudiée. Les objectifs de ce travail<p>consistent à documenter l’invasion de S. geminata dans l’archipel des Galápagos: 1) en<p>mettant à jour sa distribution; 2) en déterminant ses stratégies de reproduction et de<p>dispersion et en reconstruisant l’histoire de son invasion dans l’archipel et 3) en évaluant son<p>impact sur la faune native (particulièrement sur les communautés de fourmis et<p>d’arthropodes et sur les tortues terrestres endémiques).<p>Tout d’abord, nous avons ajouté 66 nouveaux relevés de S.geminata aux Galápagos<p>depuis 2008. À ce jour, la fourmi a été observée sur 7 îles et 11 îlots, et ce dans une grande<p>variété d’habitats. On la trouve également sur les sites de ponte de 24 espèces de vertébrés<p>endémiques ou en voie de disparition, qu’elle menace ainsi potentiellement.<p>Ensuite, en combinant des méthodes bayésiennes de regroupement et des<p>comparaisons de scénarios en se basant sur des séquences microsatellites et des données<p>historiques, nous avons montré que la diversité génétique des populations de S. geminata<p>des Galápagos est significativement inférieure à celle des populations des zones d’indigénat<p>(Costa Rica). Les populations des Galápagos - réparties en 3 groupes correspondant à une<p>île ou un groupe d’îles – sont le résultat d’une introduction unique ayant eu lieu dans la<p>première moitié du 19ème siècle. Elles proviennent vraisemblablement de l’Equateur<p>continental et constituent une population “tête de pont” pour deux introductions ultérieures au<p>sein de l’archipel. Ces mouvements correspondent aux flux de populations humaines.<p>Nous avons échantillonné les fourmis dans tous les principaux habitats de l’île de<p>Santa Cruz. Les fourmis introduites sont largement prévalentes. Solenopsis geminata<p>constitue l’espèce dominante et se trouve associée avec une faible équitabilité des<p>communautés de fourmis ainsi qu’avec une diminution de l’abondance des fourmis natives.<p>Nos résultats indiquent que les communautés de fourmis des Galápagos sont structurées<p>par le type de végétation et l’altitude, alors que les assemblages de fourmis ne sont pas<p>structurés compétitivement, à l’exception des zones perturbées.<p>Nous avons investigué la diversité arthropodienne de deux sites agricoles de l’île de<p>Santa Cruz en combinant trois méthodes d’échantillonnage complémentaires. Plus de la moitié des espèces collectées étaient soit endémiques, soit natives. Les espèces introduites<p>ont toutefois constitué la majorité des individus collectés. Solenopsis geminata était de loin la<p>plus abondante et la plus commune des espèces récoltées.<p>Enfin, dans une zones infestées par S. geminata sur l’île de Santa Cruz, nous avons<p>mis en relation la mortalité des oeufs et juvéniles de tortues terrestres Chelonoidis avec<p>l’abondance des fourmis de feu et la durée d’incubation des oeufs. Le taux de survie des<p>oeufs est négativement corrélé à leur durée d’incubation. Cependant, malgré de très hautes<p>abondances de fourmis de feu à proximité des nids de tortues, nous n’avons pas trouvé de<p>relation directe avec leur mortalité.<p>Pour conclure, ce travail aborde les aspects génétiques et écologiques de l’invasion<p>de la fourmi de feu tropicale dans les îles Galápagos. Nos résultats sont analysés au sein<p>d’un cadre éco-évolutif présentant différents scénarios d’invasion. Nous discutons également<p>de S. geminata en tant qu’espèce invasive. Nous espérons apporter des informations utiles<p>dans le cadre de l’étude et du contrôle de cette espèce invasive aux Galápagos.<br>Doctorat en Sciences<br>info:eu-repo/semantics/nonPublished

The creation of biodiversity involves the evolution of new species. Recent trends in the study of speciation have increased the emphasis on the role of ecology in adaptation and the evolution of reproductive isolation. This includes examining the relative contributions of different types of selection, the role of gene flow and the genomic changes that occur during ecological speciation. The search for speciation genes continues, however our growing knowledge of how the genome translates into phenotypes means we should now consider a broader molecular basis of speciation, which includes genetic, transcriptomic and potentially epigenetic variation that contribute to phenotypic variation. This thesis addresses the molecular basis of speciation by using three different complementary methods to examine the early stages of ecological speciation and the evolution of premating reproductive isolation between two incipient species of the cactophilic fly, Drosophila mojavensis. First, the genetic basis was examined through the sequencing of two candidate genes underlying reproductive isolation (Chapter 2). Second, the historical biogeography of population divergence was uncovered using multiple sequenced loci (Chapter 3). Lastly, gene expression across the whole transcriptome associated with phenotypic plasticity and mating success was assessed (Chapter 4). Further, the role of epigenetic imprinting in the population divergence of a freshwater fish, Girardinichthys multiradiatus, was examined through sequencing of a well known gene involved in sexual conflict (Chapter 5). These studies find that uncovering the genetic variation underlying speciation is difficult, especially when there is extensive phenotypic plasticity. Further, gene expression plasticity may play an important role in the evolution of premating isolation, and this includes a role for epigenetic mechanisms of gene expression. Additionally, it is important to assess the demographic scenario of population divergence to put into context the ecological and functional data on divergent groups. Through these studies this thesis examines the genetic, expression and epigenetic variation associated with on-going population divergence, and emphasises the need to consider the potential role of the full range of gene expression changes during ecological speciation.

S .J. Helyar; Estimating ecological and population genetic parameters in Myodes glareolus, a mammal with cryptic reproduction and dispersal A central theme in ecology is the determination of the factors that regulate population dynamics. For many years research has focused on systems regulated by predation, competition or resource Iimitatiofl, while the host parasite relationship wa~ considered to be neutral or benign, due to host-parasite co-evolution. However, in recent years there has been increasing recognition that parasites can have a key role in population dynamics, by influencing the key population parameters of reproduction and survival, and therefore having the potential to influence the population's intrinsic rate ofincrease. This study applies population genetics to host parasite ecology in order to determine how the endemic Cowpox virus interacts with and affects the host population processes of reproduction and dispersal in the bank vole (Myodes (= ClelhrionomY$) glareolus, Shreber 1780). This is a particUlarly challenging situation for determining parental relationships, as bank voles exhibit cryptic mating and maternal care, meaning that no information is available from behavioural observations to support the pedigree construction. Therefore a simulated population is first used to determine which software was most appropriate to use. A combination of parentage and sibship analyses is then used to maximise the information obtained on relationship structure. The fine scale population structure is also determined. Two events have been shown to cause variation in the levels of relatedness within a population, philopatry and founder events, and both of these are shown to be occurring in this population. This study demonstrates the occurrence of sex-biased dispersal using genetic techniques, so confirming a behavioural mechanism that is hard to identify via CMR studies due to the postnatal dispersal of this species. I also describe the fine scale population structure, and the seasonal fluctuations in this structure, with higher levels of structure evident during the summer than winter, which are determined by a combination of male biased dispersal and changes in population density. These analyses are then extended to consider how the population .genetics of the bank vole can contribute to our understanding of the bank vole-cowpox system. Two hypothesis are investigated; firstly to determine if there are patterns of infection that can be identified from the host genetics, and secondly to build on previous studies, by determining if the delay in the onset of breeding due to cowpox infection has an effect on the Lifetime Reproductive Success (LRS) of. the host. While no conclusive evidence was found for the transmission pathway, we do show that the delay in the onset of reproduction caused by cowpox infection has a major negative effect on LRS, reducing the number of an infected females' offspring by 30-100% compared to an uninfected female. Importantly, as cowpox prevalence increases with density in this species and populations with a high prevalence of cowpox are predicted to have reduced fecundity, cowpox virus infection therefore may be considerably influencing population dynamics.

The last Quaternary ice age strongly influenced the distribution of most plants and animals. Here I used genetics, ecological niche modeling and bioacoustics to understand the possible historical patterns behind the current distribution of the Downy Woodpecker (Picoides pubescens) in North America. Analyses of mtDNA sequences and seven microsatellites loci suggest low genetic differentiation among populations (a maximum of two genetic groups), however population structure is subtle. Ecological niche modeling suggests several refugia SE of US, and some restricted areas east and west of the Rocky Mountains with ecological suitable conditions for the species at 18-21 kya. The analysis of the pik call suggested no geographic variation in the frequency and temporal variables studied. It is likely that the Downy Woodpecker expanded and colonized northern North America quickly after the LGM from a southern refugium<br>x, 96 leaves ; 29 cm

Melaleuca quinquenervia (Cav.) Blake (Myrtaceae) was imported into Florida from Australia over a century ago as a landscape plant. A favorable climate and periodic wildfires helped M. quinquenervia thrive; it now occupies about 200,000 hectares in southern Florida. A biological control (i.e., biocontrol) program against M. quinquenervia has been initiated, but not all biocontrol releases are successful. Some scientists have argued that poor biocontrol agent success may relate to genetic differences among populations of invasive weeds. I tested this premise by determining (1) the number and origins of M. quinquenervia introductions into Florida, (2) whether multiple introduction events resulted in the partitioning of Florida's M. quinquenervia populations into discrete biotypes, and (3) whether Oxyops vitiosa, an Australia snout beetle imported to control this weed, might discriminate among putative M. quinquenervia biotypes. Careful scrutiny of early horticultural catalogs and USDA plant introduction records suggested at least six distinct introduction events. Allozyme analyses indicated that the pattern of these introductions, and the subsequent redistribution of progeny, has resulted in geographic structuring of the populations in southern Florida. For example, trees on Florida's Gulf Coast had a greater effective number of alleles and exhibited greater heterozygosity than trees on the Atlantic Coast. Essential oil yields from M. quinquenervia leaves followed a similar trend; Gulf Coast trees yielded nearly twice as much oil as Atlantic Coast trees when both were grown in a common garden. These differences were partially explained by the predominance of a chemical phenotype (chemotype) very rich in the sesquiterpene (E)-nerolidol in M. quinquenervia trees from the Gulf Coast, but rich in a mixture of the monoterpene 1, 8-cineole and the sesquiterpene viridiflorol in trees from the Atlantic Coast. Performance of O. vitiosa differed dramatically in laboratory studies depending on the chemotype of the foliage they were fed. Larval survivorship was four-fold greater on the (E)-nerolidol chemotype. Growth was also greater, with adult O. vitiosa gaining nearly 50% more biomass on the (E)- nerolidol plants than on the second chemotype. The results of this study thus confirmed the premise that plant genotype can affect the population dynamics of insects released as weed biocontrols.

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.

Paropsis atomaria (Coleoptera; Chrysomelidae) is a eucalypt feeding leaf beetle endemic to southern and east coast Australia, and it is an emergent pest of the eucalypt hardwood industry. Paropsis atomaria was suspected to be a cryptic species complex based on apparent differences in life history characteristics between populations, its wide geographical distribution, and extensive host range within Eucalyptus. In this study genetic and ecological characters of P. atomaria were examined to determine the likelihood of a cryptic complex, and to identify the nature and causes of ecological variation within the taxon. Mitochondrial sequence variation of the gene COI was compared between populations from the east coast of Australia (South Australia to central Queensland) to assess genetic divergence between individuals from different localities and host plant of origin. Individuals from four collection localities used for the molecular analysis were then compared in a morphometric study to determine if observed genetic divergence was reflected by morphology, and common-garden trials using individuals from Lowmead (central Qld) and Canberra (ACT) were conducted to determine if morphological (body size) variation had a genetic component. Host plant utilisation (larval survival, development time, and pupal weight) by individuals from Lowmead and Canberra were then compared to determine whether differential host plant use had occurred between populations of P. atomaria; individuals from each population were reared on an allopatric and sympatric host eucalypt species (E. cloeziana and E. pilularis). Finally, developmental data from each population was compared and incorporated into a phenology modelling program (Dymex(tm)) using temperature as the principle factor explaining and predicting population phenology under field conditions. Molecular results demonstrated relatively low genetic divergence between populations of P. atomaria which is concomitant with the single species hypothesis, however, there is reduced gene flow between northern and southern populations, but no host plant related genetic structuring. Morphometric data revealed insufficient evidence to separate populations into different taxa; however a correlation between latitude and size of adults was discovered, with larger beetles found at lower latitudes (i.e., adhering to a converse Bergmann cline). Common garden experiments revealed body size to be driven by both genetic and environmental components. Host plant utilisation trials showed one host plant, E. cloeziana, to be superior for both northern and southern P. atomaria populations (increased larval survival and reduced larval development time). Eucalyptus pilularis had a negative effect on pupal weight for Lowmead (northern) individuals (to which it is allopatric), but not so for Canberra (southern) individuals. DYMEX(tm) modelling showed voltinism to be a highly plastic trait driven largely by temperature. Results from across all trials suggest that P. atomaria represents a single species with populations locally adapted to season length, with no evidence of differential host plant utilisation between populations. Further, voltinism is a seasonally plastic trait driven by temperature, but with secondary influential factors such as host plant quality. These data, taken combined, reveal phenotypic variability within P. atomaria as the product of multiple abiotic and biotic factors and representing a complex interplay between local adaptation, phenotypic plasticity, and seasonal plasticity. Implications for pest management include an understanding of population structure, nature of local adaptation and host use characteristics, and predictive models for development of seasonal control regimens.

Mestrado em Ecologia Aplicada<br>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.<br>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.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior<br>Crassostrea (Sacco, 1897) é o gênero mais importante do mundo de ostras de cultivo e consiste de 34 espécies distribuídas pelas regiões tropicais e temperadas do globo. C. gasar e C. rhizophorae são as duas espécies nativas que estão distribuídas ao longo de toda a costa do Brasil até o Caribe. C. gasar também ocorre na costa da Africa. Ainda que sua distribuição seja extensa e com disponibilidade abundante, o cultivo de ostras nativas no Brasil ainda é incipiente e a delimitação correta dos estoques mantém-se incerta. O sucesso do desenvolvimento da malacocultura, que é recomendada internacionalmente como forma sustentável de aquicultura, depende da resolução desses problemas. Assim, com o objetivo de determinar geneticamente seus estoques no Atlântico como também estimar sua história demográfica, dois diferentes marcadores moleculares foram empregados: sequências de DNA da região controle mitocondrial e loci de microssatélites espécie-especifícos, desenvolvidos no presente estudo. Foram sequenciados fragmentos da região controle de um total de 930 indivíduos de C. gasar e C. rhizophorae coletados em 32 localidades que incluíram o Caribe, a Guiana Francesa, a costa brasileira e a África. Também foram realizadas genotipagens de 1178 indivíduos, e ambas as espécies, com 9 e 11 loci de microssatélites para C. gasar e C. rhizophorae, respectivamente. Os dados genéticos foram analisados através de diferentes abordagens (índices de estruturação (FST) e de (Jost D), análise molecular de variância (AMOVA), análise espacial molecular de variância (SAMOVA), Bayesian Skyline Plots (BSP), análise fatorial de correspondência (AFC) e análise de atribuição Bayesiana (STRUCTURE)). Os resultados indicaram um padrão geral de estruturação, onde dois diferentes estoques foram detectados para ambas as espécies: grupos do norte e do sul, onde o Rio de Janeiro seria a região limitante entre os dois estoques. Os maiores valores dos índices de estruturação foram encontrados para C. gasar, indicando que esta espécie estaria mais estruturada do que C. rhizophorae. As análises demográficas indicaram uma provável expansão das populações durante o ultimo período glacial e uma possível origem americana das populações africanas. Todos os resultados sugeriram a existência de uma barreira geográfica próxima ao Rio de Janeiro, que poderia ser a cadeia de Vitória-Trindade e o fenômeno de ressurgência que ocorre em Cabo Frio (RJ). Esses resultados serão de grande utilidade para estabelecer critérios para seleção de sementes para cultivo ao longo da costa do Brasil que permitirá o manejo adequado dos estoques ostreícolas, prevenindo seu desaparecimento como já ocorrido em outros recifes no mundo.<br>Crassostrea (Sacco, 1897) is the most important genus of cultivated oysters in the world and consisting of 34 species distributed by tropical and temperate regions of the globe. C. gasar and C. rhizophorae are the two native species which have wide distribution along the entire Brazilian coast up to the Caribbean. C. gasar also occurs on coast of Africa. Despite its extensive distribution and abundant availability, cultivation of those oysters in Brazil is incipient, and the correct delimitation of the existing stocks is still uncertain. The successful development of malacoculture which is recommended internationally as an environmentally sustainable form of aquaculture depends on the resolution of these issues. Thus, in order to genetically determinate their stocks in the Atlantic and to estimate their demographic history, two different molecular markers were employed: sequences of the mitochondrial DNA control region and species-specific microsatellite loci, developed in the present study. We have sequenced a fragment of the mitochondrial control region from a total of 930 individuals of C. gasar and C. rhizophorae collected in 32 localities including the Caribbean, French Guyana, Brazilian coast and Africa. We have also genotyped 1178 individuals of both species with 9 and 11 loci of microsatellites for C. gasar and C. rhizophorae, respectively. Genetic data were analyzed with different approaches (fixation (FST) and differentiation (Jost D) indices, analysis of molecular variance (AMOVA), spatial analysis of molecular variance (SAMOVA), Bayesian Skyline Plots (BSP), factorial correspondence analysis (AFC) and Bayesian attribution analysis (STRUCTURE)). The results indicated a general structure pattern, where two different stocks were detected for both species: north and south groups, where Rio de Janeiro would be the limited region between them. Higher values of fixation indices were found for C. gasar, indicating that this species would be more structured than C. rhizophorae. Demographic analyses showed a probable expansion of populations during the last glacial period and a probable American origin of African populations. All results suggested the existence of a barrier next to Rio de Janeiro, which could be Vitoria-Trindade chain and the upwelling in the region of Cabo Frio (RJ). These results will be useful to establish criteria for the selection of seeds for cultivation along the Brazilian coast which will allow proper management of stocks of oysters preventing its disappearance as in other reefs around the world.

In killer whales, fish- versus mammal-eating ecological differences are regarded as key ecological drivers of sociality, but the potential influence of specific target prey characteristics remains unclear. This thesis aimed to study the social patterns and dynamics of Icelandic killer whales feeding upon herring, a schooling prey that undergoes frequent changes in distribution and school size. I used a multi-disciplinary approach combining photo-identification and genetic data to understand the sociality, role of kinship and genetic differentiation within the population. Individuals sighted in summer-spawning and overwintering herring grounds during at least five separate days (N = 198) were considered associated if photographed within 20 seconds of each other. Photo-identified individuals were genotyped (N = 61) for 22 microsatellites and mitochondrial DNA control region (611 bp). The population had weak but non-random associations, fission-fusion dynamics at the individual level and seasonal patterns of preferred associations. The society was significantly structured but not hierarchically. Social clusters were highly diverse and, whilst kinship was correlated with association, it was not a prerequisite for social membership. Indeed, some cluster members had different mitochondrial haplotypes, representing separate maternal lineages. Individuals with different observed movement patterns were genetically distinct, but associated with each other. No sex-biased dispersal or inbreeding was detected. This study revealed that the Icelandic population has a multilevel society without clear hierarchical tiers or nested coherent social units, different from the well-studied salmon- (‘residents') and seal-eating populations in the Northeast Pacific. In the Icelandic population kinship drives social structure less strongly than in residents. These findings suggest effective foraging on schooling herring in seasonal grounds promotes the formation of flexible social groupings which can include non-kin. Killer whale sociality may be strongly influenced by local ecological context, such as the characteristics of the specific target prey (e.g., predictability, biomass, and density) and subsequent foraging strategies of the population.

Made available in DSpace on 2014-06-11T19:32:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-02-26Bitstream added on 2014-06-13T19:02:41Z : No. of bitstreams: 1 arruda_mp_dr_sjrp.pdf: 3154075 bytes, checksum: 425658b7ce3ff42cf3fde44c2f7d4d75 (MD5)<br>Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)<br>A destruição e a modificação do hábitat são aceitas, entre os biólogos conservacionistas, como as causas primárias da perda da biodiversidade, e a situação para os anfíbios não é exceção. Diversos processos antropogênicos contribuem para a deterioração das paisagens, podendo afetar negativamente as populações de anfíbios, por alterar fisicamente os ambientes aquáticos e terrestres, reduzindo a conectividade dos hábitats e estruturando as populações. Contudo, poucos dados existem sobre os efeitos do cultivo agrícola para as populações de anfíbios. Os programas de preservação atuam na recuperação de populações ameaçadas e, em geral, estão baseados na manutenção da máxima quantidade de diversidade genética, de tal forma que, a primeira etapa de um programa conservacionista, consiste na avaliação da variabilidade genética e distribuição desta entre as populações. A estruturação gênica populacional dos organismos, estimada a partir de técnicas de biologia molecular é um aspecto fundamental na caracterização da aptidão das espécies aos ambientes. Particularmente os marcadores moleculares do tipo microssatélite tem acessado com êxito a variabilidade gênica das populações. Assim, foram desenvolvidos loci microssatélites polimórficos para as espécies Hypsiboas raniceps, Leptodactylus chaquensis e Rhinella schneideri e avaliada a variabilidade genética de populações provenientes de hábitats com diferentes tipos de perturbação antrópica (práticas agrícolas, pastagem), com o intuito de relacionar o impacto de diferentes matrizes sobre a diversidade genética. A espécie generalista R. schneideri exibiu um estoque uniforme de variabilidade genética, baixa estruturação e reduzido nível de endogamia em todas as populações, sugerindo um elevado potencial de dispersão, responsável pela homogeneização das populações...<br>The destruction and modification of habitat are accepted between conservation biologists as the primary causes of biodiversity loss, and the situation for amphibians is no exception. Several anthropogenic processes contribute to the deterioration in the landscape, which can adversely affect amphibian populations by physically altering the aquatic and terrestrial environments, reducing the connectivity of habitats and structuring populations. However, few data exist on the effects of the crop for the populations of amphibians. The conservation programs act in the recovery of threatened populations, and generally are based on maintaining the maximum amount of genetic diversity, therefore, the first step in a conservationist program, is to assess the genetic variability and distribution of this among the populations. Population structure of organisms, estimated from molecular biology techniques is fundamental to characterize the fitness of species to environments. Particularly the molecular markers microsatellite has successfully accessed the genetic variability of populations. Therefore, we developed polymorphic microsatellite loci in the Hypsiboas raniceps, Leptodactylus chaquensis and Rhinella schneideri species and evaluated the genetic variability of populations from habitats with different types of anthropogenic disturbance (agricultural practices, pasture), in order to relate the impact of different matrix on genetic diversity. R. schneideri generalist species showed an even amount of genetic variability, low structure and low level of inbreeding in all populations, suggesting a high potential for dispersal, responsible for the homogenization of populations. However, in L. chaquensis and H. raniceps, the populations located in regions with strong agricultural impact (Tietê Batalha) showed genetically depauperate and strong population structure. It can be concluded... (Complete abstract click electronic access below)

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<br>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 (&gt; 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<br>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 (&gt; 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

Individuals of the cnidarian genus Physalia are a common sight at New Zealand beaches and are the primary cause of jellyfish stings to beachgoers each year. The identity of the species and the environmental factors that determine its presence are unknown. Lack of knowledge of many marine species is not unusual, as pelagic invertebrates often lack detailed taxonomic descriptions as well as information about their dispersal mechanisms such that meaningful patterns of distribution and dispersal are almost impossible to determine. Molecular systematics has proven to be a powerful tool for species identification and for determining geographical distributions. However, other techniques are needed to indicate the causal mechanisms that may result in a particular species distribution. The aim of this study was to apply molecular techniques to the cnidarian genus Physalia to establish which species occur in coastal New Zealand, and to apply models to attempt to forecast its occurrence and infer some mechanisms of dispersal. Physalia specimens were collected from New Zealand, Australia and Hawaii and sequenced for Cytochrome c oxidase I (COI) and the Internal transcribed spacer 1 (ITS1). Three clans were found: a Pacific-wide clan, an Australasian clan and New Zealand endemic clan with a distribution confined to the Bay of Plenty and the East Coast of the North Island. Forecasting Physalia occurrence directly from presence data using artificial neural networks (ANN) proved unsuccessful and it was necessary to pre-process the presence data using a variable sliding window to reduce noise and improve accuracy. This modelling approach outperformed the time lagged based networks giving improved forecasts in both regions that were assessed. The ANN models were able to indicated significant trends in the data but would require more data at higher resolution to give more accurate forecasts of Physalia occurrence suitable for decision making on New Zealand beaches. To determine possible causal mechanisms of recorded occurrences and to identify possible origins of Physalia the presence and absence of Physalia on swimming beaches throughout the summer season was modelled using ANN and Naϊve Bayesian Classifier (NBC). Both models were trained on the same data consisting of oceanographic variables. The modelling carried out in this study detected two dynamic systems, which matched the distribution of the molecular clans. One system was centralised in the Bay of Plenty matching the New Zealand endemic clan. The other involved a dynamic system that encompassed four other regions on both coasts of the country that matched the distribution of the other clans. By combining the results it was possible to propose a framework for Physalia distribution including a mechanism that has driven clan divergence. Moreover, potential blooming areas that are notoriously hard to establish for jellyfish were hypothesised for further study and/or validation.

The larger grain borer (LGB) Prostephanus truncatus (Horn) is the most important pest of farm stored maize and cassava in Africa. This alien invasive species was introduced into the continent from Mesoamerica in the late 1970s and by 2008 had spread to at least 18 countries. In contrast to indigenous primary storage pests, LGB exists as on-farm and as wild populations, hence, sustainable control must target both environments. Biological control is especially attractive for wild populations to reduce early season grain store infestation, while cultural and chemical methods are useful to protect stored produce directly. Two populations of the predator Teretrius nigrescens Lewis were introduced into several African countries' as a biocontrol agent. It has shown long-term success and cost effective control in warm-humid areas. Control has however not been successful in cool and hot-dry zones. The aim of this study was to investigate the possible underlying genetic and ecological explanations for these observations and the possibility of joint use of molecular markers and ecological parameters in the development of sustainable control strategies. A 28-month baseline monitoring and recovery activity was done in from 2004 in five regions in Kenya along an east-westerly transect. Monitoring and live sample collection was also done in the original outbreak area in eastern Kenya. There was greater LGB flight activity in western Kenya (high potential maize production area) than the low potential areas. Very few T. nigrescens were recovered, solely in the eastern regions. LGB flight activity followed a seasonal pattern mostly related to changes in the relative humidity at 12:00, rainfall and dew point temperature but with a 3 - 4 week lag. A linear predictive model based on these factors predicted 27 % of the observed flight activity. The survival and predation of five strains of T. nigrescens were compared at eight temperature levels between 15 °C and 36 °C at low and high humidity. All the strains of T. nigrescens exerted a significant reduction of LGB population build-up between 21 °C and 33 °C with generally better performance under humid conditions. There was no evidence of T. nigrescens development at 15 °C. At 18 °C, T. nigrescens oviposition and development was observed but the effect on LGB did not differ significantly from the control. The KARI population was the least effective in preventing grain damage at lower temperatures, but performed better than other strains above 30 °C at low humidity conditions. There was no control at 18 °C and 36 °C under both high and low humidity conditions. Since the extent of genetic differentiation in T. nigrescens was unclear from prior studies, several molecular marker techniques were progressively used. The RAPD-PCR did not reveal any genetic diversity between geographical populations. A 1000bp region of the mitochondrial mtCOI gene revealed two distinct clades differing consistently at 26 segregating sites. The two clades can be identified by simple PCR-RFLP procedure using single or double sequential restriction with EcoR1, HincII, RsaI and DdeI digestion. However, the two lineages co-exist among the mid-altitude Central American populations. The internal transcribed spacer regions ITS1 and ITS2 with some neighbouring coding sequences of the ribosomal DNA were cloned and sequenced. The spacer regions were so variable in length and sequence between T. nigrescens and related Histeridae species that direct sequence alignment was not meaningful. Within T. nigrescens, there was intragenomic variability of the spacer regions mostly involving insertions and deletions of variable tandem repeat units predominantly within the ITS regions. The short flanking coding (18S, 5.8S and 21S) regions were conserved across populations and six other Histeridae species. There was no significant secondary structure variation of the ITS regions among populations of T. nigrescens. Twenty-four novel variable microsatellite markers were developed and tested on the Honduras populations. Alleles per locus ranged between two and twelve with observed heterozygosity between 0.048 and 0.646. Six loci deviated significantly from Hardy Weinberg Equilibrium and possibly had null alleles. The success of microsatellite amplification in outgroup species and variability of markers declined with an increase in the phylogenetic distance between the test species and T. nigrescens. Genotyping 432 individuals from 13 geographic populations revealed a comparatively higher genetic diversity in field populations. Partial isolation by distance and time was observed. Population bottlenecks were not detected, but recent expansion was evident in laboratory populations. Although five dominant genetic clusters were identified by Bayesian methods, meaningful hierarchical population structure was observed at between two and nine population groups (p < 0.01; 10,000 iterations). Biological control of the larger grain borer using T. nigrescens seems an important aspect of the sustainable integrated control approach of the pest. Ecological adaptations, appropriate release strategies and genetic diversity are all essential considerations in these efforts and could be responsible for the variable success already observed. There is some genetic differentiation between populations of T. nigrescens but, further studies would be necessary to ascertain the contribution of such diversity to its predatory performance. The effect of laboratory culturing in aggravating genetic drift should be accommodated to avoid loss of diversity during sampling, quarantine, rearing and release of the predator.<br>Thesis (Ph.D. (Environmental Science))--North-West University, Potchefstroom Campus, 2009.

Submitted by Erika Demachki (erikademachki@gmail.com) on 2015-01-16T17:09:06Z No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Tese - Monik Oprea - 2013.pdf: 1967380 bytes, checksum: 406bdd6925672cd697798a30f89bc4d5 (MD5)<br>Approved for entry into archive by Erika Demachki (erikademachki@gmail.com) on 2015-01-16T17:32:35Z (GMT) No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Tese - Monik Oprea - 2013.pdf: 1967380 bytes, checksum: 406bdd6925672cd697798a30f89bc4d5 (MD5)<br>Made available in DSpace on 2015-01-16T17:32:35Z (GMT). No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Tese - Monik Oprea - 2013.pdf: 1967380 bytes, checksum: 406bdd6925672cd697798a30f89bc4d5 (MD5) Previous issue date: 2013-06-19<br>Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES<br>Microsatellite markers are important tools for molecular ecology studies, particularly for bats, whose information is difficult to obtain through direct observations. In the first chapter, we conducted searches for scientific articles about the use of microsatellite markers in bats in order to evaluate the current knowledge about the genetic patterns and also to unravel sociological aspects of this knowledge. We found that the use of microsatellite markers to study bats is quite new and little spread. Many questions in molecular ecology can be addressed with a limited number of polymorphic markers, such as microsatellites. This will not only contribute to the knowledge of the species biology, but also to design effective strategies for conservation of bat species. In the second chapter, we report the development and characterization of ten microsatellite loci for the bat Glossophaga soricina isolated from a shotgun genomic library. Among 67 individuals, the number of alleles per locus ranged from 2 to 20, and the observed and expected heterozygosity ranged from 0.015 to 0.606 and from 0.016 to 0.915, respectively. The high combined probability of genetic identity (4.369x10-8) and probability of paternity exclusion (0.996) showed that the microsatellite loci are useful for population genetic structure and detailed parentage studies in natural populations of G. soricina. In the third chapter, we used the nine developed microsatellite loci and spatially explicit analysis to unravel population genetic structure and how landscape features affected genetic diversity of G. soricina at 17 localities in the Brazilian Cerrado. Our results showed that G. soricina populations already have higher inbreeding in fragmented landscapes in small geographic scales. Also, some pairs of populations showed genetic discontinuity as the outcome of landscape modification.<br>Marcadores microssatélites são ferramentas importantes para estudos de ecologia molecular, principalmente para estudos sobre morcegos, cujas informações são difíceis de acessar através de observações diretas. No primeiro capítulo, buscamos artigos científicos sobre o uso de microssatélites em morcegos para avaliar o conhecimento atual dos padrões genéticos e revelar os aspectos sociológicos desse conhecimento. Nós observamos que o uso de marcadores microssatélites é relativamente recente e ainda pouco difundido. Muitas questões em ecologia molecular poderiam ser respondidas com um número limitado de marcadores moleculares, como os microssatélites. Isso não só contribuiria para o conhecimento da biologia, mas também para desenhar estratégias efetivas para conservação das espécies de morcegos. No segundo capítulo, apresentamos o desenvolvimento e caracterização de dez locos de microssatélites para o morcego Glossophaga soricina, isolados a partir de uma biblioteca shotgun. Foram analisados os genótipos de 67 indivíduos, sendo que o número de alelos por locos variou de 2 a 20, e a heterozigozidade observada e esperada variaram entre 0.015 a 0.606 e entre 0.016 a 0.915, respectivamente. A alta probabilidade de identidade genética (4.369x10-8) e a probabilidade de exclusão de paternidade (0.996) mostraram que os locos de microssatélites desenvolvidos são úteis para estudos de estrutura genética e paternidade em populações naturais de G. soricina. No terceiro capítulo, foram usados nove locos de microssatélites desenvolvidos, juntamente com análises espacialmente explícitas para acessar a estrutura genética, e verificar como as características da paisagem afetam a diversidade genética de G. soricina em 17 localidades do Cerrado brasileiro. Nossos resultados mostraram que populações de G. soricina já apresentam altos índices de endogamia em paisagens fragmentadas em pequenas escalas geográficas. Além disso, alguns pares de populações apresentaram descontinuidade genética como resultado da modificação da paisagem.

Studying genetic diversity in natural and domestic populations is of major importance in evolutionary biology. The recent advent of next generation sequencing (NGS) technologies has dramatically changed the scope of these studies, enabling researchers to study genetic diversity in a whole-genome context. This thesis details examples of studies using NGS data to: (i) characterize evolutionary forces shaping the genome of the Atlantic herring, (ii) detect the genetic basis of speciation and domestication in the rabbit, and, (iii) identify mutations associated with skeletal atavism in Shetland ponies. The Atlantic herring (Clupea harengus) is the most abundant teleost species inhabiting the North Atlantic. Herring has seasonal reproduction and is adapted to a wide range of salinity (3-35‰) throughout the Baltic Sea and Atlantic Ocean. By using NGS data and whole-genome screening of 20 populations, we revealed the underlying genetic architecture for both adaptive features. Our results demonstrated that differentiated genomic regions have evolved by natural selection and genetic drift has played a subordinate role. The European rabbit (Oryctolagus cuniculus) is native to the Iberian Peninsula, where two rabbit subspecies with partial reproductive isolation have evolved. We performed whole genome sequencing to characterize regions of reduced introgression. Our results suggest key role of gene regulation in triggering genetic incompatibilities in the early stages of reproductive isolation. Moreover, we studied gene expression in testis and found misregulation of many genes in backcross progenies that often show impaired male fertility. We also scanned whole genome of wild and domestic populations and identified differentiated regions that were enriched for non-coding conserved elements. Our results indicated that selection has acted on standing genetic variation, particularly targeting genes expressed in the central nervous system. This finding is consistent with the tame behavior present in domestic rabbits, which allows them to survive and reproduce under the stressful non-natural rearing conditions provided by humans. In Shetland ponies, abnormally developed ulnae and fibulae characterize a skeletal deformity known as skeletal atavism. To explore the genetic basis of this disease, we scanned the genome using whole genome resequencing data. We identified two partially overlapping large deletions in the pseudoautosomal region (PAR) of the sex chromosomes that remove the entire coding sequence of the SHOX gene and part of CRLF2 gene. Based on this finding, we developed a diagnostic test that can be used as a tool to eradicate this inherited disease in horses.

Orientador: Eliana Morielle Versute<br>Banca: Fabrício Rodrigues dos Santos<br>Banca: Luciana Bolsoni Lourenço<br>Banca: Cláudia Marcia Aparecida Carareto<br>Banca: Lilian Ricco Medeiros<br>Resumo: A destruição e a modificação do hábitat são aceitas, entre os biólogos conservacionistas, como as causas primárias da perda da biodiversidade, e a situação para os anfíbios não é exceção. Diversos processos antropogênicos contribuem para a deterioração das paisagens, podendo afetar negativamente as populações de anfíbios, por alterar fisicamente os ambientes aquáticos e terrestres, reduzindo a conectividade dos hábitats e estruturando as populações. Contudo, poucos dados existem sobre os efeitos do cultivo agrícola para as populações de anfíbios. Os programas de preservação atuam na recuperação de populações ameaçadas e, em geral, estão baseados na manutenção da máxima quantidade de diversidade genética, de tal forma que, a primeira etapa de um programa conservacionista, consiste na avaliação da variabilidade genética e distribuição desta entre as populações. A estruturação gênica populacional dos organismos, estimada a partir de técnicas de biologia molecular é um aspecto fundamental na caracterização da aptidão das espécies aos ambientes. Particularmente os marcadores moleculares do tipo microssatélite tem acessado com êxito a variabilidade gênica das populações. Assim, foram desenvolvidos loci microssatélites polimórficos para as espécies Hypsiboas raniceps, Leptodactylus chaquensis e Rhinella schneideri e avaliada a variabilidade genética de populações provenientes de hábitats com diferentes tipos de perturbação antrópica (práticas agrícolas, pastagem), com o intuito de relacionar o impacto de diferentes matrizes sobre a diversidade genética. A espécie generalista R. schneideri exibiu um estoque uniforme de variabilidade genética, baixa estruturação e reduzido nível de endogamia em todas as populações, sugerindo um elevado potencial de dispersão, responsável pela homogeneização das populações... (Resumo completo, clicar acesso eletrônico abaixo)<br>Abstract: The destruction and modification of habitat are accepted between conservation biologists as the primary causes of biodiversity loss, and the situation for amphibians is no exception. Several anthropogenic processes contribute to the deterioration in the landscape, which can adversely affect amphibian populations by physically altering the aquatic and terrestrial environments, reducing the connectivity of habitats and structuring populations. However, few data exist on the effects of the crop for the populations of amphibians. The conservation programs act in the recovery of threatened populations, and generally are based on maintaining the maximum amount of genetic diversity, therefore, the first step in a conservationist program, is to assess the genetic variability and distribution of this among the populations. Population structure of organisms, estimated from molecular biology techniques is fundamental to characterize the fitness of species to environments. Particularly the molecular markers microsatellite has successfully accessed the genetic variability of populations. Therefore, we developed polymorphic microsatellite loci in the Hypsiboas raniceps, Leptodactylus chaquensis and Rhinella schneideri species and evaluated the genetic variability of populations from habitats with different types of anthropogenic disturbance (agricultural practices, pasture), in order to relate the impact of different matrix on genetic diversity. R. schneideri generalist species showed an even amount of genetic variability, low structure and low level of inbreeding in all populations, suggesting a high potential for dispersal, responsible for the homogenization of populations. However, in L. chaquensis and H. raniceps, the populations located in regions with strong agricultural impact (Tietê Batalha) showed genetically depauperate and strong population structure. It can be concluded... (Complete abstract click electronic access below)<br>Doutor

Many previous studies in evolutionary genetics have been based on few model organisms that can be reared at ease in the laboratory. In contrast, genetic studies of non-model, natural populations are desirable as they provide a wider range of adaptive phenotypes throughout evolutionary timescales and allow a more realistic understanding of how natural selection drives adaptive evolution. This thesis represents an example of how modern genomic tools can be effectively used to study adaptation in natural populations. Atlantic herring is one of the world’s most numerous fish having multiple populations with phenotypic differences adapted to strikingly different environments. Our study demonstrated insignificant level of genetic drift in herring that resulted in minute genetic differences in the majority of the genome among these populations. In contrast, a small percentage of the loci showed striking genetic differentiation that were potentially under natural selection. We identified loci associated with adaptation to the Baltic Sea and with seasonal reproduction (spring- and autumn-spawning) and demonstrated that ecological adaptation in Atlantic herring is highly polygenic but controlled by a finite number of loci. The study of Darwin’s finches constitutes a breakthrough in characterizing their evolution. We identified two loci, ALX1 and HMGA2, which most likely are the two most prominent loci that contributed to beak diversification and thereby to expanded food utilization. These loci have played a key role in adaptive evolution of Darwin’s finches. Our study also demonstrated that interspecies gene flow played a significant role in the radiation of Darwin’s finches and some species have a mixed ancestry. This thesis also explored the genetic basis for the remarkable phenotypic differences between three male morphs in the ruff. Identification of two different versions of a 4.5 MB inversion in Satellites and Faeders that occurred about 4 million years ago revealed clues about the genetic foundation of male mating strategies in ruff. We highlighted two genes in the inverted region; HSD17B2 that affects metabolism of testosterone and MC1R that has a key role in regulating pigmentation, as the major loci associated with this adaptation.

Orientadores: Vera Nisaka Solferini, Ronaldo Bastos Francini<br>Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia<br>Made available in DSpace on 2018-08-15T11:47:43Z (GMT). No. of bitstreams: 1 Ramos_RenatoRogner_D.pdf: 2883716 bytes, checksum: eac9d7277bf9ba106da8bdf2bc840994 (MD5) Previous issue date: 2010<br>Resumo: Espécies com distribuições continentais podem ocupar várias zonas climáticas e diferentes vegetações, e forças seletivas locais podem gerar diferenças entre populações. A borboleta Heliconius erato phyllis possui esse tipo de distribuição e o teste G revelou diferenças significativas nos padrões de coloração das asas anteriores entre machos de diferentes regiões, mas não entre fêmeas. Melanismo, seleção sexual, atividade hormonal e predação podem estar envolvidos. O número de raios vermelhos nas asas posteriores apresentou correlação positiva com o comprimento das asas anteriores (CAA), mas exceções sugerem que tamanho e temperatura atuem como ativadores de hormônios que elevam a concentração de pigmentos para a formação dos raios. ANOVA demonstrou médias do CAA diferentes entre as populações, e o teste de Tukey apontou os maiores indivíduos em 3 sítios costeiros. Uma análise de componentes principais apontou altas temperaturas, pluviosidade e estabilidade climática como fatores ligados ao grande CAA. Esses fatores possivelmente contribuem com o crescimento de hospedeiras e com o desempenho larval. Técnicas moleculares usando marcador microssatélite foram aplicadas nas populações, em três escalas geográficas e uma temporal. Os resultados mostram grande variabilidade genética e populações sem isolamento por distância em escala continental. A reprodução é panmítica e os indivíduos possuem alta capacidade de dispersão mesmo entre fragmentos urbanos. Na escala temporal ocorreram diferenças estruturais moderadas, provavelmente devido a gargalos. Estudos em populações fragmentadas e de ampla distribuição ajudam a entender os efeitos do isolamento sobre a estrutura genética dessas populações e propor planos de manejo e conservação.<br>Abstract: Species with continental distribution can take several climatic zones and different vegetations, and local selective forces can generate differences among populations. The Heliconius erato phyllis butterfly has this kind of distribution, and the ?G? test showed meaningful differences on forewing color-patterns among males from different regions, but not among females. Melanism, sexual selection, hormonal activity and predation may be involved. The number of red raylets on hindwing show positive correlation with forewing's length (CAA), but exceptions suggest that size and temperature as triggers hormones that raise the concentration of pigments in the formation of raylets. The ANOVA showed different average on CAA among populations and the Tukey's test showed greatest individuals on 3 coastline sites. A principal component analysis indicated high temperatures, rainfall and climatic stability as major factors responsible for the large CAA. These factors possibly contribute with the growth of host-plant and the larval performance. Molecular techniques using microsatellite marker were applied on populations under three geographic scales and one temporal scale. The results show has a great genetic variability and populations without isolation by distance on continental scale. The reproduction is panmitic and the individuals have high dispersal ability even among urban fragments. On the temporal scale occurred moderate structural differences; probably due to bottlenecks. Studies on widespread and fragmented populations, help to understand the effects of isolation over the genetic structure of populations, and propose management and conservation plans.<br>Doutorado<br>Ecologia<br>Doutor em Ecologia