Dissertations / Theses on the topic 'Populations and conservation genetics'

Abstract The effects of habitat loss and fragmentation on the genetic structure and vulnerability of populations strongly depend on the behaviour of a particular species. In this thesis, I examined the effects of forest fragmentation on genetic population structure with the aim of identifying and evaluating the different genetic and behavioural factors important for species conservation and management on different geographical scales. The species studied were the mound building red wood ants Formica lugubris and F. aquilonia, and a lekking bird, the capercaillie, Tetrao urogallus. Habitat loss and fragmentation affected the genetic structure in both wood ants and capercaillie. In general, the effects were related to the time since fragmentation and to the level of habitat loss and isolation from the other existing populations. The loss of genetic diversity due to population fragmentation was less observable than the differences in population structure. The response to habitat fragmentation was further dependent on species characteristics such as dispersal and mating behaviour. Sociality affected the genetic vulnerability of wood ant populations by decreasing gene diversity, increasing inbreeding depression and restricting gene flow between subpopulations. The results on the capercaillie in turn suggested that lekking behaviour restricts dispersal of both sexes, thus elevating the occurrence of inbreeding between individuals. The present study provided important information on species conservation and management in terms of better understanding species' biology and behaviour, as well as increased knowledge concerning the genetic issues that should be taken into account when planning conservation actions. By examining the genetic structure of the species it was possible to clarify the conservation status including the effective population size, the question of origin, and the genetic vulnerability (genetic diversity, inbreeding and inbreeding depression) of the populations and/or species. Overall, the results emphasised the importance of preserving the effective population size and the connectivity of habitat patches when planning species specific management strategies. There were great differences in conservation needs among the species, which should be taken into account especially in local management actions.

Population size is a major determinant of extinction risk with small populations experiencing an inherently higher risk of extinction due to genetic threats and stochastic fluctuations in survival, fecundity and environmental conditions. For many species, natural populations are experiencing a dramatic decline in numbers and distribution as a direct result of human activities. The severity of the threats facing some species necessitates the movement of remaining individuals into protected areas or captive breeding programs where resources can be concentrated to promote recovery. Moreover, increasing levels of population fragmentation has led to metapopulation management being regarded as an integral part of many conservation strategies, particularly for large vertebrates. The translocation of individuals between populations across an inhospitable matrix is often needed to offset the detrimental effects of small population size and to maintain natural evolutionary processes. Whilst the benefits of active conservation management involving the mixing of individuals from hitherto isolated populations has been demonstrated in a number of cases, the impact on historic population structure and the potential for outbreeding depression is often poorly understood. Moreover an increasing body of theoretical and empirical work is demonstrating that mate selective choices are mediated not only by additive effects but by non-additive effects, most specifically the amount of genetic similarity between individuals. Recent studies on natural populations have demonstrated that there is a fitness cost associated with choosing maximally dissimilar mates and that even for intrapopulation breeding, individuals exercise a preference for mates of intermediate similarity. Populations subject to active conservation management are typically small admixed populations where individuals are presented with a limited number of potential mates, representing a greater spectrum of genetic divergence than would typically be present in non-managed populations. With many in situ and ex situ conservation programs reporting poor population growth rates linked to low or declining reproduction understanding the genetic influences on mate choice in these populations is potentially of great importance. This thesis examines (1) the effects of active conservation management on levels of genetic diversity and (2) historic population structure in the eastern black rhinoceros (Diceros bicornis michaeli). It also examines the relative influences of additive and non-additive effects on female mate choice in this actively managed conservation priority species. The eastern black rhinoceros (Diceros bicornis michaeli) has been subject to one viii of the severest human induced declines of any mammalian species. The subspecies formally ranged across East Africa from northern Tanzania to Somalia, with its largest populations in Kenya. A significant increase in poaching of rhinoceros for their horn during the 1970s and 1980s eliminated D. b. michaeli from Sudan, Ethiopia, Somalia, Uganda and Rwanda. Extensive populations in Tanzania were reduced to just two small populations and the subspecies was reduced from an estimated Kenyan population of 20,000 in 1970 to just 380 by 1987. In the face of the imminent extinction of the Kenyan population, the Kenya Wildlife Service (KWS) implemented a policy of moving all animals outside protected areas into fenced sanctuaries where resources could be concentrated to counter the poaching threat. The sanctuary system proved successful and as of 2006 Kenya had approximately 540 black rhinoceros protected within 14 separate populations. With the sanctuary system largely successful in countering the continued threat of poaching, emphasis has shifted to metapopulation management to ensure the viability of the small isolated populations within the sanctuary system. To assist in the effective metapopulation management of these isolated populations, data is presented here both on the current levels of genetic diversity and the range of historic genetic diversity captured within five enclosed sanctuary populations. A total of 166 individually identified black rhinoceros were genotyped for 9 microsatellite loci and a 507 bp segment of the mtDNA control region, with the majority of the genotyping conducted on DNA extracted from faeces. To assist in the identification of faecal samples from mixed sex pairings a simple, accurate, single-stage 5′-exonuclease assay for gender determination in the black rhinoceros from low-copy template DNA is presented. Genetic analysis and the examination of translocation records shows that the five sanctuaries are comprised of historic populations from three geographic regions within the country and that significant admixture has occurred between these historically divergent populations. These historically divergent populations are shown by molecular dating to have originated from the south of the country following an expansion which is putatively linked to the contraction of the Pleistocene forests approximately 300 KYA. Examination of mutation bias in the species reveals low levels of mutagenesis in concordance with other studies and evidence of ectopic gene conversion between eutherian sex chromosomes. The current metapopulation retains significant levels of genetic diversity for both nucleic (A = 5.0, HE = 0.689) and organellar (π = 0.007) genomes, with levels of diversity in individual populations related to ix the amount of admixture of former populations. Parentage analysis was undertaken for 107 individuals from three sanctuary populations representing approximately 16 years of successful reproductive activity in these populations. It is demonstrated that in the black rhinoceros male genetic diversity is a significant predictor of reproductive success and that females balance male genetic quality with intermediate levels of genetic similarity in admixed populations. This is the first time these effects have been investigated in a conservation priority species subject to active management and it is anticipated these results will have a profound impact on future management strategies for the species. In particular the overall results of this thesis provide a framework whereby the management of the Kenyan black rhinoceros metapopulation can be guided by the way rhinoceros are shown to manage their own reproductive success.

In the practice of resource management conservation, it is common to introduce new members into small inbred populations in order to increase genetic diversity and reduce the negative effects of inbreeding. Although fitness often increases in the F1 generation immediately following intrapopulation hybridization, few studies have focused on the long-term fitness of such populations. The model organisms Drosophila melanogaster and D. simulans were used to investigate if heterosis, an increase in the fitness in the hybrid population, or outbreeding depression, a decline in the fitness in the hybrid population, occurs over an eight generation period. At each generation, a series of fitness related assays were performed to assess relative fitness. Results of this study were mixed. At best, only some hybridized populations showed slightly higher, but often nonsignificant increases in fitness, never in more than one assay. The lack of consistent strong persistent heterosis suggests that conservation efforts such as habitat preservation maybe be a better use of effort and money for assisting endangered species.

Small and isolated plant populations have a higher probability of extinction – they are more susceptible to a range of environmental, demographic and genetic processes that may reduce population viability. In recent times, the number of populations and species that are susceptible to these processes has increased as a result of world-wide, human-induced habitat fragmentation. Habitat fragmentation typically reduces the formerly more continuous natural distribution of a species to a series of smaller and more isolated populations that occur in smaller and more isolated habitat patches. Such populations are often exposed to a range of additional processes that may threaten their viability, such as changes to disturbance regimes, environmental conditions and interactions with other species. However, our current understanding of the complex effects and interactions of these processes is poor. Species responses vary widely, studies are biased towards trees, herbs and self-incompatible species, and most studies investigate only one or two processes that may affect viability. Consequently, we are unable to make accurate predictions about the likely impacts of habitat fragmentation on population and species viability. I tested several hypotheses about the impact of habitat fragmentation, small population size, and population isolation on populations of two Grevillea species (Proteaceae) that occur in the Sydney region of New South Wales, Australia. These species provided an opportunity to investigate some of the ecological and genetic consequences of small population size and isolation, and to contrast them between a species for which the small size and isolation of its populations is the natural state (G. longifolia) and one for which it arose recently due to severe habitat fragmentation (G. caleyi). This comparative approach is important in identifying the processes involved in reducing population and species viability. The species share many aspects of their biology and ecology. Both are large, perennial shrubs that are self-compatible and naturally bird-pollinated. They are fire-sensitive and regenerate post-fire by mass germination from a long-lived, soil-stored seed bank. Both species consist of populations that vary dramatically in size and degree of isolation. I used microsatellite and AFLP markers to investigate aspects of the population genetics and mating system of these species, with the primary focus on G. caleyi. Both species showed a surprisingly large amount of genetic structuring among populations, although G. caleyi populations showed more structuring (FST = 0.46) than those of G. longifolia (FST = 0.33), despite being distributed over a much smaller area. In addition, for G. caleyi, most (63%) of the structuring was due to differences among recently-fragmented populations. By examining fine scale genetic structure within existing large populations, I determined that this was probably due to historic genetic structuring within formerly larger, more continuous populations. This has probably arisen due to both a lack of gene flow (no seed dispersal and limited pollen dispersal) and a large amount of inbreeding. Indeed, adult fixation indices were very high in G. caleyi (average f = 0.40, f > 0 in 16/18 populations). For both species, genetic diversity was not strongly correlated with population size. Genetic diversity was significantly lower in more isolated populations of G. caleyi, but this was probably due to a historic lack of gene flow to the more isolated parts of the species’ natural range, rather than to recent fragmentation. Levels of inbreeding (fixation indices) among adult plants did not vary with population size or isolation for either species. However, by genotyping fresh seeds from a range of small and large G. caleyi populations, I revealed that current outcrossing rates were much lower in small populations (t = 0.18 cf. 0.37). Observations of pollinator foraging indicated that this might be due to a very low visitation rate by birds and by a less diverse suite of species, resulting in a higher proportion of self-fertilisation. In contrast, even very small G. longifolia populations received many bird visits. In addition, G. caleyi plants in small populations were much smaller, had higher mortality, and produced fewer inflorescences and fruits, while this pattern was not apparent among G. longifolia populations. The contrast among the species in pollinator visits, plant vigour and reproduction may have been due to edge effects combined with the habitat degradation that was apparent at sites containing small G. caleyi populations. Small populations were typically found within very small and disturbed bush remnants, while small G. longifolia populations all occurred in relatively pristine habitat. Therefore, habitat quality rather than population size per se may be the most important factor that determines the mating system, plant vigour and fecundity in G. caleyi. The lack of obvious impacts of habitat fragmentation on the genetic haracteristics of adult G. caleyi plants may have been due to the soil-stored seed bank, which can contain seeds produced by at least two adult generations. Various authors have hypothesised that a persistent seed bank has the potential to reduce the rate of genetic change in a population. The seed banks of both G. caleyi and G. longifolia do appear to have this ability. I found that the seed bank of each species maintains the genetic characteristics of populations and stores genetic diversity and alleles that were not expressed in the extant adult plants. Nevertheless, the seed bank also showed greater spatial structuring than adults, which indicates that genetic changes may be occurring within these small populations despite the buffering power of the seed bank. Finally, I investigated some aspects of the ecology of G. caleyi and G. longifolia seed banks, with the aim of increasing our understanding of this important conservation resource. Soil sieving revealed that the seeds of both pecies occur at very low densities beneath adult plants (1 – 6 m-2), were vastly outnumbered by seed fragments, and were not found away from adult canopies. This supports previous evidence that indicated a lack of seed dispersal and very high rates of post-dispersal seed predation, which will restrict population size and extent. To some degree, the seed bank may buffer demographic changes that affected the previous adult generation – monitoring of post-fire seedling emergence revealed that population size typically increased, often dramatically, after a fire. Germination experiments showed that smoke elicited the greatest germination response from intact seeds of both species, and that dormancy polymorphism in the seed bank may allow both species to survive two fires in rapid succession and long inter-fire intervals. However, germination was low in field fire experiments, which may have been due to low fire intensity, and hence smoke production, resulting from a winter prescription burn. For both species, herefore, population viability may be compromised if the imposed fire regime includes fires that are too cool or too frequent. This study has demonstrated, for these species, that small populations that exist in recently fragmented habitat patches are far more likely to experience adverse ecological and genetic effects than those in continuous, relatively undisturbed, bushland. The process of demographic and genetic decline in small G. caleyi populations is likely to continue with the ongoing pressures of edge effects, habitat degradation and pollinator declines, and the increased isolation of some populations. The seed bank may buffer these declines to some extent, but this ability is limited by a lack of habitat for population expansion, which means that effective population sizes will remain very small or decrease further. The various differences detected between small and large G. caleyi populations emphasises the importance of large populations, and the ecological processes occurring within larger habitat patches, for the long-term conservation of the species.

Paddlefish (Polyodon spathula) is a commercially and recreationally important species, with a native range that extends over 22 US states. This is a large, long-lived, highly mobile riverine species that has been negatively impacted by habitat fragmentation, historic overharvest, and hatchery supplementation. Dams are the primary cause of habitat fragmentation, blocking migration routes, flooding spawning grounds, and isolating populations. A common management action to mitigate the impacts of habitat fragmentation and maintain harvestable populations is hatchery propagation and stocking. Reduction in stock size, isolation of populations, and stocking can all negatively impact the genetic integrity of Paddlefish. I evaluated the impacts of isolation and hatchery supplementation on the effective population size (Ne) of Paddlefish as well as the range-wide genetic structure of Paddlefish.

The saga of the American bison (Bison bison) is a well-known story of death, destruction, and greed circumvented by early conservationists. The foresight of 5 cattlemen and the Canadian and U.S. governments at the apex of the population bottleneck in the 1880s led to the eventual establishment of several federal bison populations, from which virtually all of the 300,000 extant bison are descended. A survey of 54 microsatellite loci spanning each autosomal and both sex chromosomes was used to compare levels of genetic variation among 10 of the 11 federal bison populations in the U.S. Although most populations contain moderate levels of genetic variation, the majority of genetic variation is contained within only 4 of the federal populations surveyed. The distribution and partitioning of genetic variation confirm historical records of founding lineages and transfers among populations. Previously published mitochondrial and nuclear markers were used to survey federal bison populations for evidence of domestic cattle introgression. While only 1 population was found to contain low levels of domestic cattle mitochondrial DNA, 7 of the 10 surveyed populations had detectable introgression of nuclear genes from domestic cattle. From this, 2 federal bison populations were identified that have both high levels of genetic variation and no evidence of introgression of domestic cattle genes. The data obtained from this study were used to examine consequences of past and present management practices in closed bison populations. In the case of the Texas State Bison Herd, observed chronic small population size, low levels of genetic variation, low natality rates, and high juvenile mortality rates combined with the results of population modeling indicate a high risk of extinction within the next 50 years unless new genetic variation is introduced into the herd. Alternatively, analysis of population substructure and nonrandom culling reveal the necessity for further investigation into the long-term effects of current management practices in the Yellowstone National Park bison population. This study illustrates that while bison may be considered a conservation success story, long-term survival of protected federal populations requires the development of effective genetic management strategies.

Plethodon yonahlossee is the largest eastern Plethodontid salamander. It has been classified as a species of greatest conservation need by the Tennessee Wildlife Resources Agency (TWRA). Found only in mountainous areas along the borders of Tennessee, North Carolina, and Virginia, populations of the yonahlossee are considered to be rare and local throughout their range. Genetic differentiation among populations of any species is usually attributable to long-standing, extrinsic barriers to gene flow. Because of their disjunct population structure and some observed morphological variation, genetic differentiation among yonahlossee populations is expected. A genetic structure study of yonahlossee was conducted to identify any genetically differentiated populations as conservation units. One mitochondrial DNA marker as well one nuclear DNA marker were amplified using polymerase chain reaction. After analysis, both markers show genetic differentiation suggesting geographic isolation. This information can be used by management agencies for the protection and conservation of the species.

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
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

Thesis (PhD (Genetics))--University of Stellenbosch, 2009.
ENGLISH ABSTRACT: South African abalone, Haliotis midae, has been the subject of major concern regarding its survival and conservation over the last decade or more. Being the only one of five endemic species with commercial value, there is considerable interest and urgency in genetic management and improvement of this species. Limited genetic information and the increasing conservation concern of this species are considered the key motivations for generating information on the micro- and macro-evolutionary processes of H. midae, the overall objective of this study. This study reported the first microsatellite and Single Nucleotide Polymorphism (SNP) markers developed specifically for Haliotis midae. Both these marker types were applied to elucidate the degree of gene flow in nine natural abalone populations whilst testing for two contrasting hypotheses; panmixia versus restricted gene flow. Data was analysed using a series of methodological approaches ranging from traditional summary statistics to more advanced MCMC based Bayesian clustering methods with and without including spatial information. Using only microsatellite data, the historical demography of the species was also examined in terms of effective population size and population size fluctuations. Finally, the evolutionary positioning and origin of Haliotis midae with regards to other Haliotis species was investigated based on mitochondrial and nuclear sequence data. Both microsatellite and SNP data gave evidence for subtle differentiation between West and East coast populations that correlates with a hydrogeographic barrier in the vicinity of Cape Agulhas. Population substructure was supported by AMOVA, FCA and Bayesian clustering analysis. Clustering utilizing spatial information further indicated clinal variation on both sides of the proposed barrier with a region in the middle coinciding with a secondary contact zone, indicating possible historical isolation during glacial periods. Overall, the similar degree of substructure observed with both microsatellites and SNPs supported the existence of contemporary and/or historical factors with genome-wide effect on gene flow. The population expansion measured with the microsatellites was inconsistent with the known recent decline but taking the species’ life cycle and large effective population size into account, a shrinkage in population size will probably only be apparent in a few generations time. On a macro-evolutionary scale, this study presents the first classification of South African abalone as a monophyletic group within the Haliotidae family. The topology based on the combined mitochondrial and nuclear dataset is highly suggestive of a relatively recent radiation of the SA species from the Indo-Pacific basin. The study concludes by describing the most likely factors that could have affected overall population structure and makes suggestions on how the given genetic information should be incorporated into strategies aimed towards the effective management and conservation of Haliotis midae.
AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse perlemoen, Haliotis midae, is oor die laaste dekade of meer die onderwerp van groot bekommernis betreffende die spesie se oorlewing en bewaring. Aangesien dit die enigste van vyf endemiese SA spesies is met kommersiёle waarde, is daar besonderse belang en erns in die genetiese beheer en verbetering van die spesie. Beperkte genetiese inligting en ‘n toenemende behoefte om die spesie te bewaar is die hoof motivering agter die generering van informasie rakende mikro- en makro-evolusionêre prosesse in Haliotis midae en is die oorhoofse doel van hierdie studie. Hierdie studie beskryf die eerste mikrosatelliete en enkel basispaar polimorfismes wat ontwikkel is spesifiek vir Haliotis midae. Beide tipe merkers is aangewend om die mate van gene vloei in nege wilde perlemoen populasies te ondersoek terwyl twee hipoteses ondersoek is; panmiksie versus beperkte gene vloei. Data is geanaliseer deur gebruik te maak van ‘n reeks metodieke benaderings wat wissel van tradisionele opsommings statistieke tot meer gevorderde MCMC gebasseerde groeperings metodes met of sonder die gebruik van geografiese data. Mikrosatelliet data is ook aangewend om die historiese demografie van die spesie te bepaal in terme van effektiewe populasie grootte asook veranderinge in populasie groottes. Laastens is die evolusionêre posisionering en oorsprong van Haliotis midae teenoor ander Haliotis spesies ondersoek deur gebruik te maak van mitokondriale en nukleêre DNA volgorde data. Beide mikrosatelliet en enkel basispaar polimorfisme data lewer bewys van ‘n subtiele genetiese verskil tussen wes en ooskus populasies wat verband hou met ‘n hidrografiese skeiding in die omgewing van Kaap Agulhas. Populasie struktuur is ondersteun deur die analise van molekulêre variansie (AMOVA), faktoriale komponente analise asook Bayesiese groeperings analise. Groeperings analise wat geografiese informasie insluit dui klinale genetiese variasie aan beide kante van die skeiding aan met ‘n area in die middel wat ooreenstem met ‘n sekondêre kontak gebied. In totaal, ondersteun die soortgelyke mate van struktuur verkry met beide die mikrosatelliete en enkel basispaar polimorfismes die bestaan van hedendaagse en/of historiese faktore met genoom wye invloed op gene vloei. Die toename in populasie grootte vasgestel deur die mikrosatelliet data stem nie ooreen met die onlangse afname waargeneem in die spesie nie, maar met inagneming van Haliotis midae se lewenssiklus en groot effektiewe populasie grootte, sal die afname in populasie grootte moontlik eers oor ‘n paar generasies na vore kom. Op ‘n makro-evolusionêre skaal lewer hierdie studie die eerste klassifikasie van Suid-Afrikaanse perlemoen as ‘n monofiletiese groep binne die Haliotidae familie. Die topologie gebaseer op ‘n gesamentlike mitkondriale en nukleêre datastel is hoogs aanduidend van ‘n relatiewe onlangse verspreiding van die Suid-Afrikaanse spesies uit die Stille-Indiese Oseaan. Die studie sluit af deur die mees algemene faktore te bespreek wat populasie struktuur kon beïnvloed het en maak voorstelle op watter wyse hierdie genetiese inligting aangewend kan word vir die effekiewe beheer en bewaring van Haliotis midae.

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

Les poissons arc-en-ciel (Melanotaeniidae) se distribuent entre la Nouvelle-Guinée et l'Australie. Ils sont très recherchés en aquariophilie en raison de leur coloration remarquable. Il en existe un très grand nombre d’espèces, dont certaines figurent sur la liste rouge des espèces menacées. L’espèce Melanotaenia boesemani, l'une des plus populaires au sein de cette famille, est en voie de disparition. L’aquaculture de cette espèce apparaît donc comme une solution prometteuse pour limiter la capture de spécimens sauvages. Pourtant, le nombre de fermes qui élèvent M. boesmani est très faible. Ceci est probablement dû aux problèmes rencontrés par les aquaculteurs, à savoir une proportion plus élevée de femelles par ponte, une perte de la coloration, un taux de croissance et une fécondité plus faibles, ainsi que l’apparition fréquente de malformations. Dans ce contexte, cette thèse visait à produire de nouvelles données génétiques en vue d’améliorer l'aquaculture et la conservation de cette famille. Plus précisément, les objectifs étaient: 1) de développer de nouveaux marqueurs microsatellites à partir d'ADN de M. boesemani, 2) d'évaluer la diversité génétique des populations sauvages de Melanotaenia et d'affiner leur taxonomie, 3) de définir l’origine géographique des souches de M .boesemani élevées en Indonésie, et d'évaluer la pression de consanguinité résultant de cette domestication. Par séquençage haut débit, 12 marqueurs microsatellites ont été développés et validés sur l’espèce M. boesemani. Les loci correspondant se sont tous révélés polymorphe et des expériences de croisement ont montré qu’ils se conformaient aux lois de Mendel. Ces nouveaux marqueurs ont ensuite été mis en œuvre pour évaluer la variabilité génétique de 44 populations sauvages (correspondant à 1152 spécimens de poissons). Les valeurs de Fis multilocus ont révélé que 5 espèces présentaient des écarts significatifs à l’équilibre de Hardy-Weinberg et suggéré la présence possible de sous-populations génétiquement différenciées. Combinés à une analyse phylogénétique effectuée sur le gène de la cytochrome oxydase I (COI) et à l'observation de plusieurs caractères morphologiques diagnostic, les 12 marqueurs microsatellites ont également permis de caractériser 8 nouvelles espèces non-encore décrites. Enfin, ces marqueurs microsatellites ont été appliqués pour analyser et comparer la variabilité génétique d’échantillons de M. boesemani obtenus à partir de 6 fermes aquacoles autour de Jakarta avec celle des deux populations indigènes de cette espèce, à savoir des lacs Ayamaru et Uter (Papouasie occidentale). Les résultats ont indiqué que toutes les souches élevés provenaient du lac Ayamaru. Aucun déficit en hétérozygotes n’a été mis en évidence, suggérant qu'il n'y avait pas de consanguinité majeure dans ces souches d’élevage. L’analyse des génotypes a également suggéré que l’espèce M. boesemani représentait probablement une métapopulation constituée de populations génétiquement différenciées. En définitive, ces résultats indiquaient que les problèmes rencontrés par les aquaculteurs ne proviennent pas d’une éventuelle consanguinité mais sont plus surement liés à d'autres facteurs tels qu’une gestion inappropriée et / ou une mauvaise qualité des eaux d’élevage. En conclusion, ces nouveaux marqueurs microsatellites se sont avérés utiles pour évaluer la structure génétique et la diversité d'un grand nombre d'espèces de poisson arc-en-ciel, dont beaucoup sont en voie de disparition. Les résultats présentés ici sur l'une des espèces les plus menacées (M. boesemani) montrent qu'il est encore possible d'éviter son extinction. Ceci nécessite cependant d'augmenter sa production aquacole afin de soulager rapidement la pression de surpêche. Ceci passe par une meilleure gestion des pratiques d'élevage
Rainbowfishes (Melanotaeniidae) are widely distributed throughout New Guinea and Australia. They are very famous for ornamental trade because of their vivid coloration. They display amazing species richness and some of them are on the red list of endangered species. The species Melanotaenia boesemani, one of the most popular within this family, is.facing great threats. Rearing of this species in aquaculture setups thus appears as a promising solution to limit capture of wild specimens. Yet, the number of farms that raise M. boesmani is very low. This is probably due to the problems reported by the farmers, i.e. higher proportion of females per spawning, loss of coloration, lower growth rate and fecundity, frequent morphological abnormalities. In this context, this study aimed at gathering new genetic information that would be useful for the aquaculture and conservation of the Melanotaeniidae family. Specifically, the objectives of the research were: 1) to develop new microsatellite DNA markers from the endangered M. boesemani, 2) to evaluate the genetic diversity of wild populations of Melanotaenia and refine their taxonomy, 3) to describe the geographic origins of M. boesemani reared by ornamental fish farmers in Indonesia, and evaluate the inbreeding pressure resulting from this domestication. Using next generation sequencing, 12 microsatellite DNA markers were developed and validated from M. boesemani. All microsatellite loci revealed polymorphic and cross-breeding experiments showed that they followed a Mendelian inheritance pattern. These new markers were subsequently implemented to evaluate the genetic variability of 44 wild populations (corresponding to 1152 fish specimens). Multilocus Fis values revealed that 5 species significantly departed from Hardy-Weinberg expectations and suggested the possible occurrence of genetically differentiated subpopulations. Combined with a phylogenetic analysis performed on the cytochrome oxydase I (COI) gene and with the observation of several diagnostic morphological characters, the 12 microsatellite markers also enabled to characterize 8 new species previously undescribed. Finally, these microsatellite markers were applied to analyze and compare the genetic variability of M. boesemani samples obtained from 6 aquaculture farms around Jakarta with that of the two native populations of this species , i.e. from Ayamaru and Uter Lakes (West Papua). Results indicated that all reared strains originated from Ayamaru Lake. No deficit in heterozygotes was evidenced, suggesting that there was no major inbreeding in these reared populations. Genotype analysis also suggested that M. boesemani species consists of a metapopulation composed of genetically differentiated populations. Altogether, these results indicated that the problems experienced by the farmers are obviously not due to inbreeding depression and are probably caused by other factors such as unsuitable management and/or poor water quality. In conclusion, these new microsatellite markers proved useful to evaluate the genetic structure and diversity of a large number of rainbowfish species, among which many are endangered. The results presented here on one of the most threatened species (M. boesemani) show that it is still possible to prevent its extinction. This, however, implies to increase its aquaculture production in order to quickly alleviate the overfishing pressure. This, in turn, involves a better management of rearing practices

Genetic variation is essential for biological evolution, for maintaining viability of populations, and to ensure ecosystem resilience. Increased human exploitation and environmental change result in rapid loss of biological variation, including genetic diversity. Measures to halt this trend require that biological diversity is assessed and monitored. Assessment of biodiversity includes identifying patterns of distribution of genetic variation within individual species. This thesis focuses on spatial genetic structure and assessment of units for conservation in continuous environments without apparent migration barriers. Empirical data refer to Scandinavia and the model species are northern pike (Esox lucius), brown trout (Salmo trutta), and harbour porpoise (Phocoena phocoena). Questions regarding monitoring genetic diversity and releases of alien populations are also addressed.  The spatial genetic structure of the northern pike in the Baltic Sea is characterized by isolation by distance and continuous genetic change. Positive genetic correlation was found among pike within geographical distances of less than 150 km. This distance may be used to suggest management units in this area. For the brown trout, genetic monitoring identified two sympatric populations within a small mountain lake system. The situation is characterized by a clear genetic but no apparent phenotypic dichotomy. Scientific support for a genetically distinct Baltic harbour porpoise population is limited, and the spatial genetic structure of the harbour porpoise in Swedish waters needs to be clarified. Data for launching conservation genetic monitoring programs is available for only a few Swedish species. Millions of forest trees, fish, and birds are released annually in Sweden and the documentation on these releases is poor. To meet responsibilities of safeguarding biodiversity and surveying biological effects of releases, there is an urgent need for studies aimed at evaluating genetic diversity.
At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.

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

Genetic analyses of increasing power are now regularly incorporated into wildlife management assessments of threatened and endangered species. Genetic data provide valuable information regarding taxonomy, kinship, and population size and structure. Recently transformed by the advent of powerful technologies that expand our view from single genes to the entire genome, the field of conservation may be on the verge of another revolution with the emergence of epigenetics as a promising means of surveying environmental response in natural populations. In this dissertation, I present my doctoral research upon population genetics and epigenetics of pronghorn (Antilocapra americana). Considerable effort has been undertaken to conserve pronghorn, particularly in the periphery of its range in the southwestern United States and northwestern Mexico. Translocation is regularly used to supplement and re-establish populations of the wide-ranging A. a. americana subspecies while captive breeding has been established for two endangered pronghorn subspecies, A. a. sonoriensis found in Arizona and Sonora, Mexico and A. a. peninsularis of the Baja Peninsula. The primary goal of my doctoral work was to provide pronghorn managers with current estimates of genetic diversity, relatedness, and structure within and between pronghorn subspecies in the desert southwest. My work shows that conservation measures for A. a. sonoriensis have successfully maintained genetic diversity within this endangered subspecies. My estimates of population structure within A. a. americana in northern Arizona reveal the influence of translocation and habitat fragmentation and demonstrate the successful reestablishment of gene flow following the removal of highway fences. With the purpose of guiding future release of captive pronghorn, I explored the subspecies status of pronghorn extirpated from a portion of their range in southern California and northern Baja California. My analyses of museum specimens indicate that the historical range of A. a. peninsularis may have extended as far north as the international border while specimens collected just north of the border share more genetic identity with A. a. sonoriensis. To follow my interests in epigenetics, I also conducted the first ever conservation epigenetics study with Arizona pronghorn. I found that pronghorn are more epigenetically than genetically diverse and this is an indicator that further epigenetic study will reveal the signature of response to environmental factors, as it has with other species demonstrating this pattern.

Abstract Rare and elusive species are difficult to study, because they are usually secretive, solitary, occur at low densities and have large home ranges. Wolverines (Gulo gulo) can both hunt and scavenge for food. In Fennoscandia, wolverines co-exist with either wild or semi-domesticated reindeer, which constitute their most important winter food. Approximately half of the 180–220 Finnish wolverines are found in northern Finland within the reindeer management area. However, the other half of the population is distributed in eastern and central Finland, and the ecology of wolverines especially in this area is poorly known. This research examined the habitat selection, diet and population genetics of wolverines in northern and eastern Finland. The results suggest that wolf presence is one of the most important variables influencing the habitat selection of wolverines. This finding supports the speculative idea that wolverines might benefit from being sympatric with wolves through increased scavenging opportunities. Furthermore, both the reproductive status of wolverines and the availability of different prey items were found to affect the wolverine diet. In northern Finland, semi-domesticated reindeer and mountain hare were the most frequently utilized prey species for breeding female wolverines. In eastern Finland, the most important food source for breeding females was moose carrion, whereas males and non-breeding females heavily utilized mountain hares. These results support the predictions of the optimal foraging theory, suggesting that wolverines opportunistically utilize the food source that is most energy-efficiently available. In areas with a low density of medium-sized ungulates, scavenging of wolf- and human-killed carrion plays an essential role in food acquisition by wolverines. According to the results of a population genetics investigation, two wolverine subpopulations exist in Finland: a northern and an eastern one. The overall genetic variability was found to be low, and signs of a recent population bottleneck were detected in both populations. It is likely that the wolverine populations in Finland would benefit from improved connectivity between them, but also with neighbouring populations in Scandinavia and north-eastern Russia
Tiivistelmä Ahma (Gulo gulo) tunnetaan sekä haaskansyöjänä että keskikokoisia hirvieläimiä ja pienriistaa saalistavana petona. Fennoskandian alueella peuran kesy tai villi muoto on ahman merkittävin saalislaji. Noin puolet Suomen 180–220 ahmasta elää Pohjois-Suomessa poronhoitoalueella, ja loput Itä- ja Keski-Suomessa. Poronhoitoalueen ulkopuolella elävien ahmojen ekologiaa on tutkittu erityisen vähän. Väitöstyössäni tarkastelin ahman habitaatinvalintaa, ruokavaliota ja populaatiogenetiikkaa pääasiassa Pohjois- ja Itä-Suomen alueilla. Tutkimukseni tulokset osoittivat, että suden läheisyys oli yksi tärkeimmistä ahman habitaatinvalintaan vaikuttavista tekijöistä. Tämä havainto tukee hypoteesia, jonka mukaan ahma saattaisi hyötyä susien läheisyydestä suuremman haaskatiheyden ansiosta. Todennäköisesti ahmat elävät mielellään samoilla seuduilla susien kanssa, mutta kaihtavat läheistä kanssakäymistä välttääkseen killansisäisen saalistuksen. Tutkimusteni perusteella sekä ahman lisääntymistila että alueen saaliseläinten saatavuus vaikuttivat ahman ruokavalioon. Poro ja metsäjänis olivat lisääntyvien ahmanaaraiden tärkein ravintokohde Pohjois-Suomessa. Itä-Suomessa merkittävin lisääntyvien naaraiden ravintokohde oli hirvi, jota ahmat hyödyntävät lähinnä haaskojen muodossa, mutta urokset ja ei-lisääntyvät naaraat sen sijaan saalistivat eniten metsäjänistä. Ahmat siis näyttävät hyödyntävän opportunistisesti sitä ravintokohdetta, joka kullakin alueella on energiatehokkainta saavuttaa. Susien ja ihmisten jälkeensä jättämät haaskat ovat merkittävä ravintolähde ahmoille alueilla, joilla keskikokoisten hirvieläinten tiheydet ovat alhaisia. Ahman populaatiogeneettinen tutkimus osoitti, että Suomen ahmat ovat geneettisesti jakautuneet kahteen alapopulaatioon, pohjoiseen ja itäiseen. Ahmakannan geneettinen monimuotoisuus oli pientä, ja molemmissa alapopulaatiossa oli nähtävissä merkkejä äskettäisestä pullonkaulailmiöstä. Populaatioiden välisen geenivirran määrän tulisi olla nykyistä korkeampi, jotta ahmakannan elinvoimaisuuden voisi katsoa olevan turvattu tulevaisuudessa

The broad aim of this research, funded by English Nature, was to use genetic techniques to inform conservation strategies and contribute to species action plans for selected Lepidoptera. The three species chosen for the study were the marsh fritillary (Euphydryas aurinia), the high brown fritillary (Argynnis adippe) and the chequered skipper (Carterocephalus palaemon). Allozymes and mitochondrial DNA were used to answer individual questions applicable to each species. All three species seem to have colonised the UK after the last ice-age in one event. Most work took place on E. aurinia forming national and local scale research. Genetic differentiation between populations was fairly high, but it may be that a metapopulation structure ensures local population sizes remain large enough to delay the signs of drift. A. adippe was sampled from two populations; this extremely rare butterfly seems to have lost some genetic diversity, but further samples are required before firm conclusions can be drawn. C. palaemon is being reintroduced into England, and identification of the most genetically appropriate source for a donor population was required, using museum specimens to type the extinct English population. The species seems to have colonised the UK in one post-glacial event, and from a genetic point of view, both northern European and Scotland contain appropriate donor populations. Finally, the ways in which genetics can complement ecological work to aid conservation are discussed.

The okapi (Okapia& johnstoni) is an endangered, evolutionarily distinct giraffid, endemic to the Democratic Republic of Congo (DRC). The okapi is a flagship species for the DRC,a country that contains some of the greatest biodiversity in the world. The okapi is currently under major threat from habitat fragmentation, human encroachment and poaching, yet to date, very little is known about the species in the wild, and no genetic study in the wild or captivity has ever been carried out. This thesis aims to use genetics to aid conservation efforts of okapi,a species that due to its elusive nature, is highly challenging to study using alternative methods.

Abstract The amount and distribution of genetic diversity are likely to affect the evolutionary potential of a species. When feasible and cost-effective policies for management and monitoring of endangered populations or species are planned, knowledge of the spatial genetic structure and the type of population dynamics is of great concern. In this thesis the genetic diversity and population structures of two endangered arctic plant species was examined on different geographical scales in Northern Europe. The species were Siberian primrose (Primula nutans) and pendant grass (Arctophila fulva), which both grow in a seashore habitat and have similar distribution patterns on the shores of the Arctic Ocean and the Bothnian Bay. The goal of the present study was to provide basic population genetic information for the study species using microsatellite and AFLP markers. Both markers were used for the first time in these species, and species-specific microsatellite markers were developed during the study. A further aim was to interlink the population genetic processes of the species into distribution patterns at the regional and population levels and to compile a synthesis of the impact of hierarchical spatiotemporal processes and autocorrelation in genetic variation at different levels. The studies of this thesis provided new information on the diversity and population structure of the endangered study species and new markers that are useful in future genetic studies of primrose species. The diversity of Siberian primrose was low, and there was no dispersal between the study regions. In pendant grass, a relatively high amount of variation was found considering the evident clonal reproduction and gene flow that was detected between populations connected by waterways. The results suggested that both clonal and sexual reproduction are important in this species. On a local scale, pendant grass populations had characteristics of “stepping stone” and classical metapopulation models. The results indicated that on a long time scale, both species will continue to decline without efficient management efforts. Most critical for the persistence of the species is the conservation of suitable habitats. Translocations could be considered in order to enhance the diversity of existing populations and establish new populations. By examining the present day structure of Siberian primrose, it was possible to make inferences regarding the colonisation history of the species in the North European area. The current distribution of Siberian primrose seemed to result from a vicariant process that took place after the last ice-age, when the species colonised the area. It spread first to the White Sea area, probably from the east, and subsequently colonised the Bothnian Bay and the Barents Sea in the west. The isostatic land uplift after the retreat of the Eurasian ice sheet uncovered large areas of land from the Baltic Sea basin that previously were under water. These geological changes resulted in the current disjunct distribution of Siberian primrose.

Reintroduction of Anatolian mouflon population at Bozdag Protection &
Breeding Station to its former habitats(Emremsultan Wildlife Development Area in Ankara-Nallihan, and Karadag in Karaman) started in 2004. The magnitude of genetic change among Bozdag and reintroduced populations was evaluated by 11 microsatellite loci. Study populations revealed close results (±
st.dev.) &ndash
Bozdag population: nk = 2.9091 (±
1.1362), AE = 2.0250 (±
0.9537), Ho = 0.3830 (±
0.2717), He = 0.3956 (±
0.2746)
Nallihan population: nk = 2.9091 (±
1.1362), AE = 2.0592 (±
0.9451), Ho = 0.4086 (±
0.2977), He = 0.4052 (±
0.2767)
and Karadag population: nk = 2.5455 (±
1.1282), AE = 1.8809 (±
0.8758), Ho = 0.3388 (±
0.2775), He = 0.3607 (±
0.2716). Population differences for major genetic parameters were not significant (p >
0.05) by comparisons with paired t-test. Also, temporal change in genetic diversity for Bozdag population was investigated by comparison with temporal data. Temporal changes in genetic parameters were found to be not significant and possible causes for differences were argued. Additionally, genetic diversity and PI computations for different traps were verified and compared to uncover any potential bias due to the catching method. Comparisons did not reveal significant differences illustrating the homogeneity among traps. On the other hand, simulations detected the higher sensitivity of allelic diversity (A) to founder events than P and heterozygosity (Ho &
He) levels which supports heterozygosity excess method for bottleneck analysis. With the same simulation analysis, observed genetic diversity within reintroduced samples were found to be in the ranges of expectation (99% CI) indicating that translocated individuals were chosen randomly. Bottleneck analysis based on heterozygosity excess method (one-tailed test for heterozygosity excess: pSMM = 0.28515, pTPM = 0.06445, pIAM = 0.02441) and allele frequency distributions method (normal L-shaped) could not detect a recent genetic bottleneck for Bozdag population. However, simulations determined that these two methods are prone to type II error. Bottleneck detection failure for the study population is probably due to type II error instead of other sources of error like violations of model assumptions.

The Groot Marico catchment in the North West Province is a National Freshwater Ecosystem Priority Area (NFEPA) because it represents unique landscape features with unique biodiversity that are considered to be of special ecological significance. Three native freshwater species Amphilius uranoscopus, Chiloglanis pretoriae and Barbus motebensis, have high local conservation importance and B. motebensis is endemic to the catchment and is IUCN-listed as vulnerable. The main objective of this study is to contribute towards the effective conservation of these three species in the Groot Marico River system by assessing their genetic structure to determine whether tributary populations of the three species comprise of one genetic population or whether they are divided into genetically distinct subpopulations, in order to prioritise areas for conservation. The central null hypothesis was that there is no genetic differentiation between tributary populations (i.e., panmixia) of B. motebensis, A. uranoscopus and C. pretoriae in the Groot Marico catchment, North West Province. In total, 80 individuals per species were collected, targeting at least 10 individuals per population from a total of eight populations (seven tributaries and the Groot Marico main stem) and across the study area. Samples were collected by electrofishing and specimens were euthanized using an overdose of clove oil. A sample of muscle tissue was removed for genetic evaluation and the remainder of the specimens served as voucher specimens. For the genetic evaluation, mitochondrial (ND2, cyt b) and nuclear (S7) genes were used. Genetic techniques used were DNA extraction, polymerase chain reaction (PCR), purification and sequencing. From the 240 individuals collected, 123 sequences for B. motebensis, 111 sequences for A. uranoscopus and 103 sequences for C. pretoriae were analysed across all three genes. Statistical analysis included looking at cleaned sequences in order to obtain models using MODELTEST (version 3.06). Population structuring and phylogeographic analysis was performed in Arlequin (version 2000), TCS (version 1.2.1) and PAUP*. Results indicated that for B. motebensis the null hypothesis could be rejected as there were two distinct lineages (the Draai and Eastern lineages) that demonstrated significant divergence in both the ND2 and S7 genes, suggesting historical isolation. The low divergence in the mitochondrial cytochrome b gene (0% < D < 0.8%) suggests that this isolation is not very old and is probably not comparable to species level differentiation. The null hypothesis was also rejected for A. uranoscopus as there were also significant levels of differentiation between tributary populations resulting in the identification of two lineages (the Ribbok and Western lineages). However, for C. pretoriae, the null hypothesis could not be rejected as there was no genetic differentiation between tributary populations i.e., one panmictic population. Therefore, due to each species showing different genetic structuring within the tributary populations, more than one priority area for conservation needs to be implemented. These priority areas of conservation where therefore evaluated based on the current conservation status of the species (B. motebensis being vulnerable on the IUCN Red List), the number of Evolutionary Significant Units for each species and the overall genetic diversity of all three species in the Groot Marico catchment. In total, four tributary populations were conservation priorities areas, these were the Draai, Vanstraatens, Ribbok and Kaaloog tributaries. The Draai, Vanstraatens and Kaaloog tributaries were selected as priority areas for B. motebensis (B. motebensis is considered to be the most vulnerable of all three species). The Draai tributary was selected due to the B. motebensis population within the tributary showing isolation from the rest of the tributary populations. In order to conserve B. motebensis from the Southern lineage, the Vanstraatens and Kaaloog tributaries were selected. Reasons for selecting these two specific tributaries within the Southern lineage were that the Vanstraatens tributary had unique alleles (three Evolutionary Significant Units) for B. motebensis and the Kaaloog tributary had high genetic diversity (HD = 0.889, ND2 gene) when compared to the other tributary populations. The Ribbok and Vanstraatens tributaries were selected as priority areas for the conservation of A. uranoscopus. The Ribbok tributary was selected as it showed isolation from the rest of the tributary populations, as seen with the Draai tributary (B. motebensis) and the Vanstraatens tributary was selected to represent the Western lineage as it had the highest diversity for both genes (ND2 and S7). The Ribbok tributary has the highest prioritisation when compared to the Vanstraatens tributary. Chiloglanis pretoriae occurs within the Draai, Vanstraatens, Ribbok and Kaaloog tributaries, therefore by prioritising these tributaries for conservation, C. pretoriae will in turn be conserved.

This research addressed two important issues concerning conservation of orang-utans in Indonesia, the prevalence of diseases in orang-utans at reintroduction centres and the extent of intra-subspecific genetic variation between isolated populations of Bornean orang-utans. The research was conducted at the Wanariset Orang-utan Reintroduction Centre in East Kalirnantan fiom 1994 to 1997, during which time extensive field excursions were made throughout Borneo, and at the Biomedical Primate Research Centre in the Netherlands in 1998. Analysis of clinical records fiom 1991 to 1997 showed that during this period 339 orang-utans were admitted to Wanariset, of which 96 (28.3%) died and 108 (31.8%) were released. Studies were designed to identify and determine the prevalence of diseases, specifically gastro-intestinal parasites, tuberculosis and certain viral diseases. Further studies defined the factors associated with mortalities of orang-utans at the reintroduction centre. Gastro-intestinal parasites, in particular Strongyloides spp. and Balantidium coli, posed health problems for rehabilitant orang-utans. Strongyloides spp. and Strongyle sp. eggs and B. coli were detected in faecal samples from new arrivals, rehabilitant, released and wild individuals. Trichuris trichura was present in new arrivals, released and rehabilitant orang-utans, whereas Ascaris sp., and Cyclospora sp. were present only in rehabilitants. There was a high prevalence of B. coli in new arrivals (41.6%), rehabilitants (100%) and released individuals (100%) and a low prevalence in wild individuals (12.5%). Faecal egg counts of individuals infected with Strongyloides spp. showed that 47.8% of rehabilitants and 14.3% of new arrivals had egg counts over 1000 eggs/gm, 81.8% of released individuals had egg counts less than 500 eggslgm and all wild individuals had egg counts less than 100 eggs/mg. Strongyloidosis was the primary cause of death (21.9%) of rehabilitant orang-utans, prior to the incorporation of oral ivermectin into the parasite control program. There was a low prevalence of tuberculosis, which was detected in one individual (0.8%) and suspected to have caused the death of two others (2.1% of deaths). Diagnosis of tuberculosis in orang-utans was complicated by inaccuracies and difficulties in interpreting the diagnostic tests commonly used in humans and nonhuman primates. Further research is required to develop more reliable and accurate tests for the diagnosis of tuberculosis in orang-utans. A study of the serological prevalence of a number of viral infections in captive orangutans showed evidence of exposure to hepatitis B virus (42.6%), hepatitis A virus (34.9%), herpes simplex viruses (14.7%), simian D-type retroviruses (11.2%) and human T-lymphotrogic viruses (1.4%). There was no evidence of exposure to simian or human immunodeficiency viruses. Molecular studies to determine the origin of the hepatitis B virus, showed the virus was not of human origin as has been generally assumed, but was an indigenous virus which also occurred naturally in wild populations. The virus was subsequently named Orangutan Hepadnavirus. A molecular study using mitochondrial DNA was undertaken to determine whether there was significant genetic diversity between six isolated populations of wild orangutans within Borneo. It was concluded that there are at least four genetically distinct populations located in East Kalimantan, southwest Kalirnantdcentral Kalirnantan, northwest KalimantdSarawak, and Sabah. The findings of this research are discussed in terms of the implications for management policies for reintroduction centres, as well as for the conservation of wild populations. They will also be of relevance to zoos and primate centres.

This research addressed two important issues concerning conservation of orang-utans in Indonesia, the prevalence of diseases in orang-utans at reintroduction centres and the extent of intra-subspecific genetic variation between isolated populations of Bornean orang-utans. The research was conducted at the Wanariset Orang-utan Reintroduction Centre in East Kalirnantan fiom 1994 to 1997, during which time extensive field excursions were made throughout Borneo, and at the Biomedical Primate Research Centre in the Netherlands in 1998. Analysis of clinical records fiom 1991 to 1997 showed that during this period 339 orang-utans were admitted to Wanariset, of which 96 (28.3%) died and 108 (31.8%) were released. Studies were designed to identify and determine the prevalence of diseases, specifically gastro-intestinal parasites, tuberculosis and certain viral diseases. Further studies defined the factors associated with mortalities of orang-utans at the reintroduction centre. Gastro-intestinal parasites, in particular Strongyloides spp. and Balantidium coli, posed health problems for rehabilitant orang-utans. Strongyloides spp. and Strongyle sp. eggs and B. coli were detected in faecal samples from new arrivals, rehabilitant, released and wild individuals. Trichuris trichura was present in new arrivals, released and rehabilitant orang-utans, whereas Ascaris sp., and Cyclospora sp. were present only in rehabilitants. There was a high prevalence of B. coli in new arrivals (41.6%), rehabilitants (100%) and released individuals (100%) and a low prevalence in wild individuals (12.5%). Faecal egg counts of individuals infected with Strongyloides spp. showed that 47.8% of rehabilitants and 14.3% of new arrivals had egg counts over 1000 eggs/gm, 81.8% of released individuals had egg counts less than 500 eggslgm and all wild individuals had egg counts less than 100 eggs/mg. Strongyloidosis was the primary cause of death (21.9%) of rehabilitant orang-utans, prior to the incorporation of oral ivermectin into the parasite control program. There was a low prevalence of tuberculosis, which was detected in one individual (0.8%) and suspected to have caused the death of two others (2.1% of deaths). Diagnosis of tuberculosis in orang-utans was complicated by inaccuracies and difficulties in interpreting the diagnostic tests commonly used in humans and nonhuman primates. Further research is required to develop more reliable and accurate tests for the diagnosis of tuberculosis in orang-utans. A study of the serological prevalence of a number of viral infections in captive orangutans showed evidence of exposure to hepatitis B virus (42.6%), hepatitis A virus (34.9%), herpes simplex viruses (14.7%), simian D-type retroviruses (11.2%) and human T-lymphotrogic viruses (1.4%). There was no evidence of exposure to simian or human immunodeficiency viruses. Molecular studies to determine the origin of the hepatitis B virus, showed the virus was not of human origin as has been generally assumed, but was an indigenous virus which also occurred naturally in wild populations. The virus was subsequently named Orangutan Hepadnavirus. A molecular study using mitochondrial DNA was undertaken to determine whether there was significant genetic diversity between six isolated populations of wild orangutans within Borneo. It was concluded that there are at least four genetically distinct populations located in East Kalimantan, southwest Kalirnantdcentral Kalirnantan, northwest KalimantdSarawak, and Sabah. The findings of this research are discussed in terms of the implications for management policies for reintroduction centres, as well as for the conservation of wild populations. They will also be of relevance to zoos and primate centres.

This research addressed two important issues concerning conservation of orang-utans in Indonesia, the prevalence of diseases in orang-utans at reintroduction centres and the extent of intra-subspecific genetic variation between isolated populations of Bornean orang-utans. The research was conducted at the Wanariset Orang-utan Reintroduction Centre in East Kalirnantan fiom 1994 to 1997, during which time extensive field excursions were made throughout Borneo, and at the Biomedical Primate Research Centre in the Netherlands in 1998. Analysis of clinical records fiom 1991 to 1997 showed that during this period 339 orang-utans were admitted to Wanariset, of which 96 (28.3%) died and 108 (31.8%) were released. Studies were designed to identify and determine the prevalence of diseases, specifically gastro-intestinal parasites, tuberculosis and certain viral diseases. Further studies defined the factors associated with mortalities of orang-utans at the reintroduction centre. Gastro-intestinal parasites, in particular Strongyloides spp. and Balantidium coli, posed health problems for rehabilitant orang-utans. Strongyloides spp. and Strongyle sp. eggs and B. coli were detected in faecal samples from new arrivals, rehabilitant, released and wild individuals. Trichuris trichura was present in new arrivals, released and rehabilitant orang-utans, whereas Ascaris sp., and Cyclospora sp. were present only in rehabilitants. There was a high prevalence of B. coli in new arrivals (41.6%), rehabilitants (100%) and released individuals (100%) and a low prevalence in wild individuals (12.5%). Faecal egg counts of individuals infected with Strongyloides spp. showed that 47.8% of rehabilitants and 14.3% of new arrivals had egg counts over 1000 eggs/gm, 81.8% of released individuals had egg counts less than 500 eggslgm and all wild individuals had egg counts less than 100 eggs/mg. Strongyloidosis was the primary cause of death (21.9%) of rehabilitant orang-utans, prior to the incorporation of oral ivermectin into the parasite control program. There was a low prevalence of tuberculosis, which was detected in one individual (0.8%) and suspected to have caused the death of two others (2.1% of deaths). Diagnosis of tuberculosis in orang-utans was complicated by inaccuracies and difficulties in interpreting the diagnostic tests commonly used in humans and nonhuman primates. Further research is required to develop more reliable and accurate tests for the diagnosis of tuberculosis in orang-utans. A study of the serological prevalence of a number of viral infections in captive orangutans showed evidence of exposure to hepatitis B virus (42.6%), hepatitis A virus (34.9%), herpes simplex viruses (14.7%), simian D-type retroviruses (11.2%) and human T-lymphotrogic viruses (1.4%). There was no evidence of exposure to simian or human immunodeficiency viruses. Molecular studies to determine the origin of the hepatitis B virus, showed the virus was not of human origin as has been generally assumed, but was an indigenous virus which also occurred naturally in wild populations. The virus was subsequently named Orangutan Hepadnavirus. A molecular study using mitochondrial DNA was undertaken to determine whether there was significant genetic diversity between six isolated populations of wild orangutans within Borneo. It was concluded that there are at least four genetically distinct populations located in East Kalimantan, southwest Kalirnantdcentral Kalirnantan, northwest KalimantdSarawak, and Sabah. The findings of this research are discussed in terms of the implications for management policies for reintroduction centres, as well as for the conservation of wild populations. They will also be of relevance to zoos and primate centres.

The Caribbean genus Pseudophoenix (Arecaceae) has its center of taxonomic diversity in Hispaniola (Haiti and the Dominican Republic). Three species (P. ekmanii, P. lediniana, and P. vinifera) are restricted to this island. In this thesis I investigated the population genetic diversity and structure of Pseudophoenix using ten microsatellite loci. Results showed homozygote excess and high inbreeding coefficients in all populations across all polymorphic loci. Overall, there was high differentiation among populations. Results from the Bayesian and Neighbor Joining cluster analyses identified groups that were consistence with currently accepted species delimitation. We included the only known population of an undescribed morph from the Dominican Republic that has been suggested to represent a new species. Results from the cluster analyses suggested that this putative species is closely related to P. sargentii from Turk and Caicos. Our study provided insights pertinent to the conservation genetics and management of this genus in Hispaniola.

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

Conservation biologists require information on the distribution, ecology, behaviour and genetic diversity of endangered species in order to identify threatened populations, determine which mechanisms are driving populations closer to extinction, and design appropriate mitigating solutions. The hazel dormouse, Muscardinus avellanarius, is declining across much of its northern range. Dormice are detrimentally affected by habitat degradation, loss and fragmentation. Despite extensive studies and conservation work on hazel dormice, there remain many gaps in our understanding. This thesis aims to fill some of those gaps. Hazel dormice are elusive, and therefore difficult to monitor in the wild. I demonstrate the utility of novel monitoring techniques for the rapid determination of dormouse presence, and provide algorithms for the objective verification of species identity from small mammal footprints. I design and utilise genetic microsatellite markers to investigate molecular ecology in this species. In one of the first studies of hazel dormouse population genetics, I describe high levels of population differentiation and genetic isolation across the southwest UK range. I find a powerful signal of reduction in genetic diversity, and an increase in differentiation between core and peripheral populations. I consider rival hypotheses for the mechanisms driving this population genetic pattern, and place the results in the context of conservation strategies for UK dormice. Further, I use molecular data to investigate the prevalence of multiple paternity in wild dormouse populations. Results contradict a recent estimate of very high rates of polyandry, but remain high at 50%. I investigate the effect of food availability on the hibernation behaviour of dormice. My findings, which demonstrate dormice are variable and flexible in their response to winter diet, increases our understanding of the trade-offs dormice must make in order to survive winter periods. I hope that the research undertaken for this thesis will add to the understanding and conservation of an iconic British mammal, ultimately contributing to the persistence of this species.

The field of conservation genetics, in combination with non-invasive sampling, provides a powerful set of tools for investigating the conservation status and natural history of rare species that are otherwise difficult to study. A systematic literature review demonstrated that this is certainly the case for many forest associated antelope species, which are poorly studied and yet constitute some of the most heavily hunted wildlife in Africa. The aim of the present study was to use non-invasive sampling to investigate genetic patterns in forest antelope populations in the high-biodiversity Udzungwa Mountains, Tanzania, within the context of the conservation of these species and the wider ecosystem. Genetic information was derived from faecal samples collected across the Udzungwa landscape and assigned to five antelope species (N = 618, collected 2006-09). Faecal pellet length was measured for a subset of samples but statistical assignment to species by this method proved unreliable. Phylogenetic analysis using mitochondrial control region sequences unexpectedly revealed that Harvey’s duiker within the Udzungwas are paraphyletic with respect to sequences from a putative sister species from southern Africa. However, there was no corresponding pattern in the microsatellite dataset suggesting that these mitochondrial lineages do not represent contemporary genetic isolation. Instead, Harvey’s duiker nuclear variation is shaped both by isolation by distance, due to positive spatial autocorrelation at short distances, and clustering of distinct genotypes from western outlying forests. These forests also harbour the endangered Abbott’s duiker and therefore require effective conservation management. Despite being detected throughout the Udzungwas, genetic diversity in Abbott’s duiker was very low in comparison to other species. These results suggest several promising research directions but also have significant conservation implications that will be disseminated to the Tanzanian wildlife authorities and the wider conservation community.

With increasingly warming climate, many bird species have been forced to respond to environmental changes, and the long-tailed duck (Clangula hyemalis) is no exception. The populations of the long-tailed duck have been in decline the past few decades and the species is classified as globally vulnerable and near threatened in both Iceland and Sweden. The long-tailed duck is a circumpolar, migratory sea duck. Its migratory routes and wintering and breeding sites might play an important part in gene flow between populations. The aim of this project was to get a clearer image of the substructure of the long-tailed duck in the northern hemisphere to help identify populations possibly at risk. This was investigated by exploring differences in mitochondrial DNA between the global populations, and by studying the Icelandic wintering and breeding populations in particular applying whole genome sequencing. To do this, samples were obtained for mitochondrial DNA analyses from a previous study by Wilson et al. (2016) from North America and East Russia, samples from other populations around the northern hemisphere as well and new samples from Iceland. Museum samples from Iceland were used for whole genome resequencing. Mitochondrial analyses included haplotype identification, population comparisons, mismatch and neutrality tests. Whole genome analyses included neutrality tests, principal component analysis and genetic admixture analysis.The mitochondrial results revealed two distinct lineages for the long-tailed duck. Two populations showed a difference from the other populations; the Icelandic breeding population and the Yukon-Kuskokwim Delta population from Alaska, which are the southernmost breeding populations. The Yukon population might have been previously isolated with refugial population intermixing. For the Icelandic populations, the mitochondrial results showed little intermixing between the winter and breeding populations. The whole genome results showed more complicated results for the Icelandic populations, with admixture in some individuals. This suggests that there seems to be more variation in the genome than implied by the mitochondrial DNA.

The Bechstein’s bat, Myotis bechsteinii, is known as one of Britain’s most elusive mammals. Critical information on the species is lacking, hindering evidence-based conservation and management in a human-dominated landscape. In this thesis, I used a combination of molecular and landscape approaches to assess the genetic health and population genetic structure of M. bechsteinii and understand how the British landscape affects the species habitat and its connectivity. I also aimed to develop new molecular tools, such as non-invasive genetic sampling and molecular ageing, which could then be used to better monitor the species. Data from nuclear markers (microsatellites) showed high levels of genetic diversity and little inbreeding across the species range, though genetic diversity was slightly lower in Britain than in mainland Europe. Bayesian and spatial Principal Components (sPCA) analysis showed a clear separation between British and European populations. This analysis also revealed that in Europe the Italian population south of the Alps was found to constitute a different group from other sites. In Britain, there was genetic structuring between the northern and southern part of the species range. Despite there being little genetic divergence in mitochondrial DNA (mtDNA) sequences throughout most of Europe, the mtDNA patterns in Britain confirmed this separation of northern and southern populations. Such genetic structuring within Britain — in the absence of any obvious physical barriers — suggested that other features such as landuse may limit gene-flow. To better understand how the species interacts with 4 the British landscape, I used a landscape genetic approach, habitat suitability modelling using presence-only data and a landscape connectivity analysis. The negative association of M. bechsteinii presence with distance from woodland was identified as the main variable determining habitat suitability, while the landscape genetics results highlighted the importance of woodlands for gene flow. M. bechsteinii habitat was highly fragmented and only showed good connectivity if the species was able to disperse over 5,000 m. These results subsequently highlight the importance of woodlands not only for providing suitable habitat, but also in maintaining genetic connectivity between populations. Then, I investigated the use of non-invasive capture-mark-recapture (CMR) and demographic history models to estimate the population size and changes of M. bechsteinii. Bat droppings were collected below roosting sites of a single colony. After species identification, the 123 droppings belonging to M. bechsteinii were genotyped at nine DNA microsatellite loci in order to differentiate all individuals. All microsatellites showed very low amplification rates indicating low quality samples. However, at a larger scale, the use of population demographic models to assess effective population size variation using a dataset of 260 bats of the British population gave an estimate of the effective population size of 6,569 (CI: 5,307-8,006) and suggested that the British population of Myotis bechsteinii is stable and possibly expanding. Finally, I developed an epigenetic assay to estimate the age of individual bats. For this, I measured DNA methylation on bats of known age at seven CpG sites from three genes. All CpG sites from the tested genes showed a significant relationship between DNA methylation and age and provided reliable age estimates. 5 The findings presented in this thesis show that despite exhibiting high levels of genetic diversity throughout its range, the genetic structure, habitat and connectivity of M. bechsteinii populations is highly influenced by woodlands. It also offers a novel method to monitor the species by developing an assay which can provide information on the age structure of an entire colony from a single sampling session. Such approaches are much needed in the field of conservation and could in the future help preserve a wider range of species.

The northern bobwhite (Colinus virginianus) population decline is a severe, rangewide phenomenon beginning >150 years ago and continuing today. In this investigation, I: 1. document the timeline of bobwhite population decline and unintended genetic consequences of attempted remedies, 2) develop a model useful for predicting possible locations of potentially sustainable bobwhite populations in semiarid rangeland in Texas and Oklahoma, and 3) examine the relationship between population monitoring data and meteorological factors. While breeding season call counts of male bobwhite have been used for >70 years to provide estimates of fall populations for hunting, most studies of call counts have focused on mathematics and statistical accuracy of the count, largely overlooking the influence of meteorological factors on call counts. Here, I present the results of >4,400 individual point counts and examine their relationship with meteorological variables recorded at each stop. Humidity was positively correlated with the number of birds recorded (ρ = 0.275, p < 0.001) and temperature was negatively correlated (ρ = -0.252, p < 0.001). The number of birds recorded was significantly higher in wet years than in drought years. There was no significant correlation between wind velocity and number of birds recorded. These results suggest that, while weather does influence call counts and efforts should be made to record meteorological conditions when collecting call count data, the influence of weather may not easily factor into the analysis. These results also provide another line of evidence for decreased breeding behavior during high temperatures. With the increased focus on bobwhite habitat management on a regional scale, there is a need for reliable methods to identify potential bobwhite habitat. To identify bobwhite habitat in semiarid rangeland, I performed classification of LANDSAT scenes of Clay County, Texas from July and December 2015. Stands of mature little bluestem provide excellent bobwhite nesting cover and could be identified using LANDSAT imagery. I scored habitat by type, compared these scores with the results of breeding season call counts from 2014 and 2015 and found significant correlation. When used in combination with other landscape data, this approach can provide a regional context to inform conservation and management decisions.

The Raso lark is a Critically Endangered bird endemic to the islet of Raso, Cape Verde. This thesis investigates two phenomena that particularly put the species at risk: its extreme fluctuations in population size, and its potentially very low genetic diversity arising from small population size and severe past population contraction. More specifically, two chapters estimate year-to-year survival and explore the factors - environmental and individual - that influence it, while two other chapters examine the lark’s genetic characteristics compared to its two continental closest relatives, including phylogenetic relationships and levels of genetic diversity. The conclusion of the thesis then uses these results to make recommendations for the conservation of the Raso lark. Each of the data chapters is summarized below: Chapter 3 estimates adult survival in the Raso lark and tests whether it could be linked to two population phenomena observed in the field: a highly variable population size and a male-biased sex ratio in certain years. Using a dataset spanning 10 years, I estimated survival for both sexes to fluctuate between 0.76 and 0.94 over this period. This is much higher than the survival rate of its closest relative, the skylark. I also found strong evidence for survival fluctuating over time and differing between males and females (with males having higher survival until 2011, at which point the trend inverted), which could play a role in the aforementioned population size fluctuations and male-biased sex ratio, respectively. Chapter 4 aims at understanding which factors shape survival in the Raso lark. Two types of variables were considered: year-dependent (rainfall, population size, population mean clutch size) and individual-dependent (age, body size characters, size ratio with mate, Ase18 genotype). Amongst the year-dependent variables, only sameyear rainfall impacted survival, with a 13% decrease in survival in the wettest year compared to the driest year, making it the most likely explanation for the inter-annual fluctuations in survival found in Chapter 3. Results also hint at some of the individual factors - morphological measurements and Ase18 genotype - influencing survival. The picture that emerges is that of a species whose life history strategy is to invest heavily in maintenance and survival, but less into fecundity, which stands in sharp contrast with the mainland-dwelling skylark. This is consistent with the theory that island birds generally have slower life history strategies than their continental counterparts. Chapter 5 determines the precise relationship between members of the Alauda clade, resolving a node on the phylogenetic tree of all larks that the study by Alström et al. (2013) was unable to resolve. My RADseq results indicate that the Raso lark and the skylark are sister species, and that the Oriental lark is likely to be a subpopulation, or maybe a subspecies, of the skylark. Chapter 6 compares the population genetics of the Raso lark with those of the skylark. In particular, it estimates the genetic diversity of the Raso lark and investigates the drivers behind it. I found unexpectedly high nucleotide diversity in the Raso lark, and explain this by showing that the population contraction that the species underwent was recent enough for most of the diversity to still be present. Moreover, 16% of the Raso lark genome has levels of heterozygosity on average 6.6 times higher than elsewhere on the genome, likely due to suppressed recombination and the existence of a neo-sex chromosome in larks. Despite this, I found high levels of relatedness and of linkage disequilibrium in the Raso lark, two clear genetic signs that it underwent a severe population contraction several centuries ago.

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.

Thesis (PhD)--Stellenbosch University, 2003.
ENGLISH ABSTRACT: The aims of this study were to investigate genetic issues pertaining to the conservation of the Knysna seahorse, Hippocampus capensis, and to determine the phylogenetic placement of this endangered estuarine species among marine seahorses. This was accomplished by focusing on three aspects of the taxonomy: the interspecific level; the inter-population level; and the intra-population level. To determine which species are closely related to H. capensis, and how the evolutionary history of this lineage relates to that of other seahorses, sequence data derived from four gene fragments (the nuclear RPI and Aldolase and the mitochondrial 16S rRNA and cytochrome b genes) were used to determine the phylogenetic relationships among 30 species belonging to the genus Hippocampus. There were marked differences in the rate of evolution among these gene fragments, with Aldolase evolving the slowest and the mtDNA cytochrome b gene the fastest. Among individual partitions, the RPI gene recovered the highest number of nodes supported by >70% bootstrap values from parsimony analysis, and >95% posterior probabilities from Bayesian inference. The combined analysis based on 2317 nucleotides resulted in the most robust phylogeny. A distinct phylogenetic split was identified between the pygmy seahorse, H. bargibanti, and a clade including all other species. Three species from the western Pacific Ocean included in this study, namely H. bargibanti, H. breviceps, and H. abdominalis, occupy basal positions in the phylogeny. This and the high species richness in the region suggest that the genus probably originated in this region. There is also fairly strong molecular support for the remaining species being subdivided into three main evolutionary lineages: two West Pacific clades and a clade of species present in both the Indo-Pacific and the Atlantic Ocean, which includes H. capensis. The phylogeny obtained herein suggests that seahorses belonging to the latter clade colonised the Atlantic Ocean at least twice, once before the closure of the Tethyan Seaway, and once afterwards. Phylogenies reconstructed using mitochondrial DNA gene fragments (l6S rRNA, cytochrome band 382 bp of the rapidly evolving control region) indicate that H. capensis is closely related to an Indian Ocean lineage of H. kuda and a Red Sea lineage of H. fuscus. Other lineages closely associated with these taxa include H. kuda from the West Pacific, the East Atlantic species H. algiricus, the West Atlantic species H reidi, the East Pacific species H ingens, and the Hawaiian species H fisheri. No control region alleles were shared among H capensis and any of the marine seahorses, suggesting that the Knysna seahorse is phylogenetically distinct. The evolutionary history of H capensis, and the extent of gene flow between its three known populations, were investigated using control region sequences from 138 specimens. Most samples were obtained by taking fin clips; this method was studied on captive seahorses and no negative effects were found. Similarly high levels of genetic diversity were found in two of the wild populations (Knysna and Keurbooms Estuaries), whereas diversity in the third population (Swartvlei Estuary) was lower. Although most haplotypes are shared among at least two populations, based on the haplotype frequency distributions the three assemblages constitute distinct management units. The extant population structure of H capensis suggests that the Knysna seahorse originated in the large Knysna Estuary. The presence of seahorses in the two smaller estuaries is either the result of a vicariance event at the beginning of the present interglacial period, or colonisation of the estuaries via the sea, or a combination of the two. Population genetic parameters of the Knysna population and those of two populations of closely related marine seahorses (H kuda from the Philippines and H fuscus from the Red Sea) were similar, suggesting that the Knysna population is not genetically impoverished, despite its comparatively small area of occupancy.
DEUTSCHE ZUSAMMENFASSUNG: Die hier prasentierte wissenschaftliche Studie beschaftigte sich mit genetischen Themen relevant flïr den Artenschutz des Knysna Seepferds, Hippocampus capensis, und den phylogenetischen Beziehungen dieser ausschliesslich in Estuaren (Flussmtindungen) vorkommenden gefahrdeten Art mit den im Meer lebenden Seepferden. Die folgenden taxonomischen Einheiten wurden verglichen: Arten, Populationen und Sub-Populationen. Urn festzustellen, welche Arten nah mit H. capensis verwand sind, und wie die Evolution dieser Gruppe sich von der anderer Seepferdgruppen unterscheidet, wurden genetische Sequenzen von vier Genen (den nuklearen RPI und Aldolase und den mitochondrischen 16S rRNA und Cytochrom b Genen) von 30 Seepferdarten verwendet und phylogenetische Beziehungen rekonstruiert. Betrachtliche Unterschiede wurden festgestellt hinsichtlich der Geschwindigkeit in der Mutationen stattgefunden haben: Aldolase mutierte am langsamsten und Cytochrom b am schnellsten. Eine auf RPI Sequenzen basierende Phylogenie hatte die hëchste Anzahl von Gabelungspunkten, die sowohl von parsimonischen Analysen, als auch von bayesischer Inferenz untersttitzt wurden. Die robusteste Phylogenie wurde jedoch gefunden, wenn Sequenzen von allen vier Genen kombiniert wurden (im ganzen 2317 Nukleotide). Eine betrëchtliche genetische Distanz wurde zwischen dem Pygmaen-Seepferd, H. bargibanti, und einer Gruppe, die aus allen anderen Arten bestand, gefunden. Drei Arten vom westlichen Pazifik, namlich H. bargibanti, H. breviceps und H. abdominalis, hatten basale Positionen in der Phylogenie. Das, und der Artenreichtum dieser Region, sind Anzeichen daflïr, dass Seepferde mëglicherweise ursprtinglich aus dem westlichen Pazifik stammen. Es wurde weiterhin gefunden, dass alle tibrigen Seepferdarten in drei Hauptgruppen unterteilt werden kannen: die Verbreitungsgebiete zweier dieser Gruppen beschranken sich hauptsachlich auf den westlichen Pazifik, aber die dritte Gruppe kommt sowohl im Indo-Pazifik, also auch im Atlantik vor (H. capensis ist mit dieser letzteren Gruppe assoziiert). Es gibt gute Anzeichen dafllr, dass die Seepferde der letztgenannten Gruppe den Atlantik mindestens zweimal kolonisiert haben, einmal vor der Schliessung der tethyschen Seeverbindung, und einmal danach. Phylogenien, die ausschliesslich mit mitochondrischen Genen rekonstruiert wurden (16S rRNA, Cytochrom b und 382 Nukleotide der schnell-mutierenden Kontollregion), zeigen, dass H capensis sehr nah verwandt mit H kuda aus dem Indischen Ozean und H fuscus aus dem Roten Meer ist. Andere nah verwandte Arten sind H kuda from westlichen Pazifik, H algiricus vom ëstlichen Atlantik, H reidi vom westlichen Atlantik, Hingens vom ëstlichen Pazifik, sowie die in Hawaii vorkommende Art H fisheri. Keine der Kontrollregionallele, die in H capensis gefunden wurden, kamen in anderen Arten vor. Dies zeigt, dass das Knysna Seepferd eine eigenstandige Art ist, und Paarungen mit anderen Arten nicht vorkommen. Die Evolutionsgeschichte von H capensis, und das Ausmass von genetischem Austausch zwischen den drei Populationen dieser Art, wurden untersucht, indem Kontrollregionsequenzen von 138 Individuen analysiert wurden. Die meisten Proben stammten von Flossenschnitten; diese Methode wurde zuvor an in Gefangenschaft lebenden Seepferden ausprobiert, und es wurden keine negativen Folgeerscheinungen beobachtet. Genetische Diversitat war ungefahr gleich hoch in zwei der Populationen (Knysna und Keurbooms Estuare), aber eine deutlich niedrigere Diversitat wurde in der dritten Population gefunden (Swartvlei Estuar). Obwohl die meisten Allele in mindestens zwei Populationen gefunden wurden, sind die drei Populationen unterschiedliche genetische Einheiten, eine Schlussfolgerung, die hauptsachlich auf Unterschiede in der relativen Haufigkeit der Allele beruht. Die Populationsstruktur von H capensis deutet darauf hin, dass diese Art ihren Ursprung im Knysna Estuar hat. Die Prasenz von Seepferden in den beiden anderen Estuaren ist entweder das Resuitat von Vikarianz (eine Spaltung der urspri.inglichen Population) zu Beginn der jetzigen Interglazialzeit, oder Kolonisierung der Estuare durchs Meer, oder eine Kombination beider Szenarios. Populationsgenetische Parameter der Knysna Population und die zweier Populationen von nah verwandten Arten (H kuda aus den Philippinen und H fuscus aus dem Roten Meer) zeigten keine grossen Unterschiede. Dies deutet darauf hin, dass das Knysna Seepferd trotz seines vergleichbar kleinen Verbreitungsgebietes nicht unter geringer genetischer Diversitat leidet.
AFRIKAANSE OPSOMMING Die doelwitte van hierdie studie was om die Knysna seeperdjie, Hippocampus capensis, te ondersoek relatief tot die spesie se bewaring asook om die filogenetiese posisie van hierdie bedreigte estuariene spesie binne mariene seeperdjies te bepaal. Drie aspekte van die taksonomie word ondersoek: interspesie verwantskappe, interbevolking verwantskappe en intra-bevolking verwantskappe. Om te bepaal watter spesies na verwant is aan H capensis, asook om die evolusionêre geskiedenis van hierdie groep met die van ander groepe te vergelyk, word nukleotieddata van vier ONS fragmente (die nukleêre RPI intron en Aldolase, en die mitochondriale 16S rRNA en sitokroom b fragmente) van 30 spesies van die genus Hippocampus gebruik. Aansienlike verskille in die tempo van evolusionêre verandering tussen hierdie ONS fragmente word gevind: Aldolase was die stadigste en die mitochondriale sitokroom b die vinnigste. Die RPI intron het die meeste knoesteringe gehad wat ondersteun word deur hoë stewelvasgordnommers (>70%) van parsimoniese analises en hoë agterwaarskynlikheide (>95%) van Bayesiese gevolgtrekkinge. Die kombineerde analise wat 2317 nukleotiede ingesluit het, het die beste filogenie geproduseer. 'n Besliste filogenetise verdeling was gevind tussen die pigmee seeperdjie, H bargibanti, en 'n groep wat al die ander spesies ingesluit het. Drie spesies van die westelike Stille Oseaan wat in hierdie studie ingesluit is, H bargibanti, H breviceps en H abdominalis, neem primitiewe posisies in die filogenie in. Dit, en die hoë spesiesrykdom in daardie gebied dui aan dat dit moontlik is dat die genus in die westelike Stille Oseaan ontstaan het. Daar is ook taamlike goeie molekulêre ondersteuning dat al die ander spesies in drie evolusionêre hoofgroepe verdeel kan word: twee groepe wat hoofsaaklik in die westelike Stille Oseaan voorkom, en 'n groep van spesies wat in die Stille Oseaan, die Indiese Oseaan en in die Atlantiese Oseaan voorkom, wat H capensis insluit. Die filogenie wat hier gevind is dui aan dat seeperdjies van hierdie laas genoemde groep die Atlantiese Oseaan minste twee keer gekoloniseer het, een keer voor die sluiting van die Tetiese Seepad, en een keer daarna. Filogenies wat met mitochondriale ONS fragmente gerekonstrueer is (16S rRNA, sitokroom b en 382 nukleotide van die vinnig evolveerende kontrolestreek) dui aan dat H capensis na verwant is aan 'n groep van H kuda wat in die Indiese Oseaan voorkom en H fuscus van die Rooi See. Ander groepe wat na verwant is aan hierdie takson is H kuda van die westelike Stille Oseaan, H algiricus van die Oos Atlantiese Oseaan, H reidi van die Wes Atlantiese Oseaan, en die Hawaiise spesie H fisheri. Geen kontrolestreek allele was gedeel tussen H capensis en enige mariene seeperdj ie spesies; dit dui aan dat die Knysna seeperdjie filogeneties verskillend is. Die evolusionêre geskiedenis van H capensis, en die omvang van die genetiese interaksies tussen sy drie bekende bevolkings, word ondersoek met kontrolestreek nukleotieddata van 138 monsters. Die meeste van hierdie monsters was verkry deur vinknipsels; hierdie metode was getoets op seeperdjies in gevangenskap en geen negatiewe gevolge was gevind nie. Genetiese diversiteit was omtrent dieselfde in twee van die natuurlike bevolkings (Knysna en Keurbooms Estuariums), maar diversiteit in die derde bevolking (Swartvlei Estuarium) was laër. Alhoewel die meeste allele gedeel was tussen ten minste twee bevolkings, dui die verspreiding van allelfrekwensies aan dat die drie bevolkings aparte bestuurseenhede is. Die ekstante bevolkingsstruktuur van H capensis dui aan dat die Knysna seeperdjie in die groot Knysna Estuarium ontstaan het. Die teenwordigheid van seeperdjies in die twee kleiner estuariums is óf die resultaat van 'n vikariansie voorval aan die begin van hierdie interglasiale tydperk, óf kolonisasie van die estuariums deur die see, óf 'n kombinasie van albei. Bevolkingsgenetiese parameters van die Knysna bevolking en van twee bevolkings van na verwante seeperdjie spesies (H kuda van die Filippyne en H fuscus van die Rooi See) was soortgelyk, wat aandui dat die Knysna bevolking nie geneties verarm is nie, alhoewel dit 'n betreklik kleiner streek bewoon.

Genes are the foundation of evolution and biodiversity. The genetic structure of natural populations needs to be understood to maintain exploited resources rationally. This thesis focuses on genetic variability and methods to determine spatial and temporal genetic heterogeneities. Intense human exploitation generates particular challenges to conserve genetic diversity of fishes since it has genetic effects. My research concerns one of our most valuable fish species: the Atlantic herring (Clupea harengus). I analyzed Atlantic herring samples from the North and Baltic Seas. The objectives were to determine: 1) spatial genetic structure, 2) whether allozymes and microsatellites provide similar descriptions of the differentiation pattern, or 3) if they are influenced by selection, 4) factors affecting statistical power when testing for genetic differentiation, and 5) the temporal stability of the genetic structure. The results show: 1) very low levels of spatial genetic differentiation in Atlantic herring; a major component is a difference between the Baltic and North Seas, 2) a concordant pattern with allozymes and microsatellites, 3) that selection influences a microsatellite locus, which can be a low salinity adaptation, 4) that statistical power is substantial for frequently used sample sizes and markers; the difference in power between organelle and nuclear loci is partly dependent on the populations’ stage of divergence, and 5) no changes in amount of genetic variation or spatial genetic structure over a 24-year period; the selection pattern in one microsatellite locus remained. The notion that the large population sizes make herring unlikely to lose genetic diversity may be disputed. I found small local effective population sizes, and the evidence of selection hints of a distinct evolutionary lineage in the Baltic. When Atlantic herring is managed as very large units, there can be detrimental genetic effects if certain population segments are excessively harvested.

Recently, hybridisation has been increasingly recognised as contributing to the extinction of species; with the risk especially high for rare species hybridising with more common species. Such risks have raised concerns for the Banks Peninsula tree weta, Hemideina ricta, which is restricted to the eastern half of Banks Peninsula and in some areas lives in sympatry with the more widespread Canterbury species, H. femorata. A previous genetics study found evidence of hybridisation between these two species. However, conclusions made by this study were likely limited by its small sample size. To further assess the risk hybridisation poses to the conservation of these species, a larger genetic study was undertaken. With hybridisation between H. ricta and H. femorata previously hypothesized to be a rare event, modelling of likely sympatric zones was undertaken to optimize the sampling effort. The results of genetic analysis on the resulting samples were consistent with the previous study, in that they suggest hybridisation does occur but is fairly rare. To help determine what processes are maintaining the distinction between the two species, the current study has expanded to incorporate observations of mating behaviour and egg hatching experiments. As well as potential risks from hybridisation, H. ricta and H. femorata have also suffered habitat loss. The Canterbury region has been transformed by the introduction of exotic plant species, fire and logging, with only small patches of native bush remaining. The loss and fragmentation of the native forest is likely to impact the forest fauna such as the tree weta. A previous study of a closely related species H. maori, in a naturally fragmented habitat, determined that dispersal between suitable habitat patches was fairly limited. Therefore, similar to their habitat, H. ricta populations may be small and isolated. Such populations are prone to the fixation of deleterious alleles as well as a loss of genetic diversity. Deleterious traits not only have a short term negative impact but a lack of genetic variation can prevent adaptation in the long term. In the past, studies of population structure have included the influence of intrinsic factors, such as dispersal capabilities but neglected extrinsic factors, such as the environment. The current study uses microsatellite markers to determine the population structure of both species and where possible, maps of land-cover are analyzed for a correlation with genetic structure.

Une meilleure compréhension de l’origine et de l’évolution de la diversité du vivant nécessite de développer des approches biogéographiques basées sur la phylogéographie. Ce travail de thèse considère ainsi la structure phylogéographique du myrte commun (Myrtus communis L., Myrtaceae), plante caractéristique et commune des matorrals de Méditerranée, et ses liens de parenté avec le myrte de Nivelle (Myrtus nivellei Batt. & Trab.), endémique des montagnes du Sahara central. Un des objectifs consiste à examiner plus particulièrement l’influence de la paléogéographie et des changements climatiques sur la diversité génétique de ces deux taxons. La démarche choisie se veut intégrative, en combinant données génétiques (séquençage et génotypage multiloci), paléobotaniques, modélisation de l'évolution moléculaire, polymorphisme et héritabilité de la croissance en conditions contrôlées, et modélisation de la niche bioclimatique. L’analyse de 173 populations de myrte commun et de 23 populations de myrte de Nivelle a révélé un fort signal phylogéographique, dont le cadre spatio-temporel provient de la datation des divergences et de la reconstruction des aires ancestrales au sein de phylogénies moléculaires établies grâce aux méthodes bayésiennes d’analyse phylogénétique. Trois résultats principaux peuvent être présentés. (i) A partir d’une origine remontant au début du Miocène, l’histoire du myrte commun se résume à deux périodes de diversification associées aux changements environnementaux survenus à la transition Miocène / Pliocène, et au cours du Pléistocène. Si un phénomène de vicariance ancien a conduit à l’isolement d’une lignée est-méditerranéenne, des phénomènes récents de diversification ont été détectés à l’ouest avec migration en retour vers l’est de la Méditerranée, mais aussi vers la Macaronésie et vers le Sahara. (ii) Au cœur des montagnes-refuges du Sahara central, l’alternance des périodes humides et arides serait à l’origine de l’isolement des populations de myrte de Nivelle par massif et d'une forte érosion génétique. Cette forte différenciation régionale s'accompagne de flux de gènes au sein des massifs, et de multiplication végétative. (iii) Enfin, l’absence de divergence des populations insulaires méditerranéennes comme la Corse, contraste avec la persistance sur le long terme de lignées aux Açores et à Madère, et avec la spéciation au Sahara du myrte de Nivelle. La discussion de ces résultats s'ouvre sur de nouvelles perspectives en phylogéographie comparative, en génomique et en biogéographie de la conservation
A better understanding of the origin and evolution of the diversity of life requires the development of biogeographical approaches based on the phylogeography. This PhD thesis study considers the phylogeographical structure of the Common Myrtle (Myrtus communis L., Myrtaceae), a characteristic and common plant of the Mediterranean matorral, and its relationship with the Nivelle Myrtle (Myrtus nivellei Batt. & Trab.), endemic to the central Saharan mountains. An objective is also to examine especially the influence of palaeogeography and climatic changes on the genetic diversity of these two taxa. Our approach aims at being integrative, combining palaeobotanical data, genetic data (sequencing and multilocus genotyping), modeling of molecular evolution, polymorphism and heritability of the growth in controlled conditions, and modeling of bioclimatic niche. The analysis of 173 populations of the Common Myrtle and 23 populations of the Nivelle Myrtle reveals a strong phylogeographical signal, whose spatio-temporal framework was provided by the dating of divergences and the reconstruction of ancestral areas within the molecular phylogenies using Bayesian analytical methods. Three main results can be highlighted. (i) With an origin dated to the early Miocene, the history of M. communis can be summarized by two periods of diversification associated with the environmental changes occurring in the Miocene/Pliocene transition and in the Pleistocene. A vicariance phenomenon has induced the isolation of an eastern Mediterranean lineage. Recent diversification events have also been detected in the western part of the Mediterranean Basin, with in-return migration to the eastern Mediterranean, and also dispersal to the Azores and Madeira islands, and to the Sahara. (ii) Within the refugia-mountains of the Central Sahara, the alternation of wet and dry periods seems to have induced the isolation of the populations of M. nivellei per mountain range, with a strong genetic erosion. In parallel to this high regional differentiation, gene flows within these mountain ranges and vegetative multiplication have been detected. (iii) Finally, the absence of divergence of Mediterranean insular populations of M. communis contrasts with the long-term persistence of Myrtle lineages restricted to the Azores and Madeira islands, and to the speciation of M. nivellei in the Sahara. The discussion of these results provides new perspectives on comparative phylogeography, genomics and conservation biogeography

The effect of human activity on the natural world is increasingly shaping the evolution of species. The capacity of evolution to occur in individuals of a species, via natural selection acting on the genotypes of local populations through successive generations, is known as local adaptation. In southwest England, historical mining activity has resulted in a patchwork of highly metal-contaminated rivers across the region. Where the ecological diversity in many of these rivers has been decimated, metal-tolerant brown trout (Salmo trutta L.) populations seem to thrive. What are the mechanisms underlying this apparent metal-tolerance? And can it be attributed to processes of local adaptation? This thesis takes a multi-faceted approach in assessing this, by exploring the patterns and processes involved in metal-tolerance in brown trout populations in southwest England. A series of investigations were undertaken, including the use of neutral genetic markers (microsatellites), reduced representation genome sequencing (RAD-seq), common-garden exposure experiments, and genome-wide analysis of hepatic gene expression (RNA-seq). The microsatellite analysis illustrated that metal-tolerant trout have a different genetic architecture compared to fish in clean rivers and, using Bayesian analysis, these demographic differences were correlated with key periods of mining history. We then developed an approach to facilitate robust screening of genome-wide polymorphic loci through a method of parameter optimisation for RAD-seq. This approach formed the basis for identifying loci for investigating the genomic processes of local adaptation in metal-tolerant trout. We present genome-wide (RAD-seq) data highly indicative that neighbouring trout populations, differently impacted by unique ‘cocktails’ of metal pollutants have evolved both parallel and convergent mechanisms of metal tolerance. Through a common garden experiment, exposing metal-tolerant and metal-naïve fish to a mixture of metals, we were able to hone in on the physiological mechanisms underlying metal-tolerance. Finally, through RNA-seq, we observed that metal-tolerant fish showed little to no changes in hepatic gene expression when exposed to metals, pointing to innate mechanisms of metal handling. Together, the marriage of these various investigations showcases the remarkable ability of local adaptation in conferring metal-tolerance to brown trout populations in southwest England, and, importantly, the resilience of species’ in the face of human-altered environments.