The identification of processes governing genetic structure at different spatial scales remains a major challenge in evolutionary biology and is of considerable applied interest in conservation biology. In Euphrasia stricta five varieties have been identified (brevipila, gotlandica, stricta, suecica and tenuis) based on differences in habitat, phenology and morphology. In this thesis, I examined genetic variation at AFLP and microsatellite marker loci in relation to variation in habitat and morphology within and among varieties of E. stricta on the island Gotland in the Baltic Sea. The results are discussed in relation to evolutionary processes acting within this species complex. In a study conducted at the regional scale, the two early-flowering varieties suecica and tenuis each formed a genetically distinct group, while the three late-flowering varieties brevipila, gotlandica and stricta formed a third group. The results suggest that suecica and tenuis have ancient origins since they are genetically different both from the brevipila/gotlandica/stricta group and from each other despite their similar habitat preferences. This pattern was obtained using both marker systems. Discrepancies between AFLP and microsatellites were found in patterns of isolation by distance and in estimates of expected heterozygosity, He. Focusing on the mixed genetic group brevipila/gotlandica/stricta and the causes behind their clustering together despite differences in morphology and habitat preferences, I performed a study at a smaller geographic scale. Studying a population of E. stricta I found that, although gene flow within the population was strong, it had not prevented the formation of genetic groups associated with micro-habitat properties. An important result for conservation of the rare variety suecica is its distinct genetic separation from variety tenuis. If the aim of conservation is to preserve the uniqueness of suecica, the two varieties should be treated as separated entities.

The projected growth in human population, rapid urbanization, and expansion of structures like highways and canals pose a major threat to the future survival of wildlife, particularly large terrestrial mammals. In many cases, wild animal populations have been restricted to fragmented habitat islands due to anthropogenic developments, endangering them to local extinction. Current and future wildlife conservation and management strategies are leading to the implementation of mitigation measures such as creation of wildlife habitat corridors. In this light, novel and interdisciplinary research methods such as approaches in the field of landscape genetics are proving to be increasingly useful and necessary for assessing the status of wildlife populations and furthering efficacy of conservation programs and management efforts. In this 5-year research study, I review literature in the field of landscape genetics, highlighting studies and their applications toward wildlife conservation over the past decade (2005-2014). I then use a landscape genetic approach to understand the potential impact of natural and human-made barriers in and around the northern Sonoran Desert on one of the widest-ranging mammals in the world, the mountain lion (Puma concolor). I employ recently developed genetic tools to assess the current population genetic status of mountain lions in this region and Geographic Information Systems (GIS) tools to relate observations to landscape features through interpretive maps. I further investigate the utility of GIS and expert-based models in connectivity conservation and suggest validating them with information on genetic relatedness and functional connectivity among mountain lions. Lastly, in many parts of this document, I emphasize the use of these methods and data sharing in conservation planning as well as wildlife management.

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.

I combined long-term ecological data and population genetic data using microsatellite DNA markers to examine among- and within-population genetic structure and parentage in Tiger Rattlesnake (Crotalus tigris) populations from the Tucson Basin of southern Arizona located in the northern Sonoran Desert. Based on long-term data from radio telemetry, I determined that C. tigris show strong fidelity to both their home range and winter shelter sites, remaining in close proximity to rocky habitats within mountain ranges, which leads to apparent natural isolation of populations. Therefore, I predicted that C. tigris populations would show substantial genetic differentiation among mountain ranges. However, Bayesian clustering analyses revealed a surprising pattern of extensive admixture among mountain ranges, indicating the presence of gene flow among populations. This pattern of genetic admixture can likely be explained by historical changes in climate and physiognomy in the Sonoran Desert. Analyses of pack rat midden remains clearly show that mountain ranges were previously connected by mesic woodland habitats that may have led to panmixia in C. tigris populations as recently as 5,000-8,000 years ago. At present, C. tigris show a strong preference for xeroriparian washes, which allows individuals to occasionally move relatively long distances, likely resulting in contemporary gene flow. To maintain connections among mountain ranges, I recommend effective management, protection, and restoration (if needed) of wash habitats, which also act as corridors for a suite of other species. At the within population scale, genetic clustering analyses revealed the existence of fine-scale genetic structure in C. tigris subpopulations located in the Rincon Mountains. Further analyses based on location data of individuals indicated the existence of a potential barrier to gene flow, which corresponded to a watershed divide. Although the watershed divide would appear not to present a physical barrier to gene flow, it likely acts to segregate populations based on habitat and movement preferences associated with wash habitats. Data on spatial ecology and reproductive behavior, indicate that C. tigris distribute gametes across the landscape in the absence of actual displacement of individuals due to fidelity to home ranges and winter shelter sites. Analyses of parentage were constrained by the difficulty in obtaining offspring from gravid female C. tigris that give birth deep in rock outcrops. However, I did conduct analyses on over 30 offspring from known mothers and nearly 60 free-ranging offspring found while conducting ecological research. Surprisingly, not a single male C. tigris found courting or copulating with a female was identified as the father, indicating that reproductive behavior is a poor predictor of parentage, and therefore, fitness. Interestingly, males identified as fathers were found up to 2 km distance from their offspring, demonstrating that males from surrounding areas may move relatively long distances to mate. The mating system of C. tigris, which is characterized by promiscuity in both sexes, appears to drive dramatic differences in spatial ecology between males and females, and may lead to fine-scale genetic structure among females and not males who spend a great deal of time searching for receptive females.

French Polynesia relies solely on the collection of wild Pinctada margaritifera spat for pearl oyster culture. This was developed to help protect the wild populations from overexploitation, but it is feared that massive spat collection could lead to erosion of genetic diversity both in farmed and wild stocks. Wild and farmed collections of P. margaritifera from four atolls in French Polynesia were genotyped at eight microsatellite loci to determine whether there was a loss of genetic diversity from the wild to adjacent farmed aggregations. The average allelic richness for wild samples was not significantly different from that seen for farmed samples, but there was a significant effect of atoll and locus. Pair-wise genetic differentiation (FST) was not significant between adjacent wild and farmed collections or across atolls. Overall there was no evidence for a loss of genetic variability in farmed oysters. Both farmed and wild individuals analyzed here were adults and could have originated from multiple spawning events in time and space. This could have masked genetic processes linked to recruitment happening at a finer scale. P. margaritifera demonstrates high recruitment variability, but the number of parents contributing to a successful cohort of juveniles recruited on collectors is unknown. Low effective number of breeders and variable recruitment are assumed to be responsible for the genetic patchiness that has been observed at a small spatial scale for this species and this could lead to a loss of genetic diversity in both the farmed and wild stocks. The genetic diversity and family make-up of three groups of 1.5 year old oysters were assessed using 13 microsatellite markers. These individuals were harvested on collectors in three closely located sites of the Takapoto atoll. Higher recruitment density and higher allelic richness was observed in one zone compared to the other two. Significant genetic differentiation was also observed at a small spatial scale. Pair-wise FST estimates between collectors within zone were not significant, but were generally significant across zones. Estimates of effective population size and number of families present for these individuals were larger than expected and suggested that the numbers of parents contributing to the recruits on these collector lines were not limited. Similar results were obtained when assessing monthly cohorts of recruits collected in Takapoto over 5 months with 11 microsatellites. Levels of allelic richness were not significantly different among monthly cohorts, and were comparable to the levels observed in the adult samples above. Small but significant temporal genetic differentiation was observed between the monthly cohorts. Again, there was no evidence for low effective population size or for significant family structuring and it did not appear that a limited number of parents produced these temporal cohorts. Patchy genetic structure was observed, but recruitment on collectors does not seem to be driven by a limited number of successful parents. It does not appear that the current pearl culture practices are negatively impacting the local farmed and wild stocks of P. margaritifera in French Polynesia by reducing their levels of genetic diversity.

Many Australian marsupial species require active population management to ensure their survival in the wild. Such management should be based on a sound understanding of species biology. This thesis explores how knowledge of reproduction and genetics can be applied to the management of three Australian marsupial species faced with contrasting management scenarios. The ??vulnerable?? greater bilby is the sole remaining desert bandicoot in Australia. They are a secretive, solitary species whose mating system is unclear. This research examined temporal changes in genetic diversity within two captive breeding programs utilising different management strategies. Using seven microsatellite loci, this study found the regular translocation of new individuals into the population maintained genetic diversity. Parentage analysis revealed the bilby to have a promiscious mating system. Sires and non-sires could not be distinguished by morphological traits. The tammar wallaby is a polygynous, solitary species that is threatened on mainland Australia, but overabundant on some offshore islands. The population genetics of tammars from the Abrolhos Islands in Western Australia were examined using nine autosomal and four Y-linked microsatellite loci, and mitochondrial DNA. There was a relationship between island size, population size and genetic diversity. The Abrolhos populations have significantly lower genetic diversity and are more inbred than mainland tammars and all sampled populations were significantly differentiated. The Abrolhos and mainland populations should be treated as separate Management Units. The eastern grey kangaroo is a gregarious, polygynous species that is often locally overabundant. To determine traits influencing male reproductive success, behavioural, morphological, physiological and genetic data were examined and showed dominance status, body size and testosterone concentrations were important factors. Sires were also significantly more heterozygous and genetically dissimilar to females, than non-sires. As body condition influences individual fitness, and management decisions; five body condition indices (BCI) calculated from morphological data were validated using serum biochemistry and haematology in two kangaroo populations with contrasting body condition. Blood parameters were found to be more reliable indicators of condition, questioning the credibility of BCIs currently used in management. These studies demonstrate the importance of reproductive and genetic data in assisting wildlife management, regardless of a species conservation status.

Many Australian marsupial species require active population management to ensure their survival in the wild. Such management should be based on a sound understanding of species biology. This thesis explores how knowledge of reproduction and genetics can be applied to the management of three Australian marsupial species faced with contrasting management scenarios. The ??vulnerable?? greater bilby is the sole remaining desert bandicoot in Australia. They are a secretive, solitary species whose mating system is unclear. This research examined temporal changes in genetic diversity within two captive breeding programs utilising different management strategies. Using seven microsatellite loci, this study found the regular translocation of new individuals into the population maintained genetic diversity. Parentage analysis revealed the bilby to have a promiscious mating system. Sires and non-sires could not be distinguished by morphological traits. The tammar wallaby is a polygynous, solitary species that is threatened on mainland Australia, but overabundant on some offshore islands. The population genetics of tammars from the Abrolhos Islands in Western Australia were examined using nine autosomal and four Y-linked microsatellite loci, and mitochondrial DNA. There was a relationship between island size, population size and genetic diversity. The Abrolhos populations have significantly lower genetic diversity and are more inbred than mainland tammars and all sampled populations were significantly differentiated. The Abrolhos and mainland populations should be treated as separate Management Units. The eastern grey kangaroo is a gregarious, polygynous species that is often locally overabundant. To determine traits influencing male reproductive success, behavioural, morphological, physiological and genetic data were examined and showed dominance status, body size and testosterone concentrations were important factors. Sires were also significantly more heterozygous and genetically dissimilar to females, than non-sires. As body condition influences individual fitness, and management decisions; five body condition indices (BCI) calculated from morphological data were validated using serum biochemistry and haematology in two kangaroo populations with contrasting body condition. Blood parameters were found to be more reliable indicators of condition, questioning the credibility of BCIs currently used in management. These studies demonstrate the importance of reproductive and genetic data in assisting wildlife management, regardless of a species conservation status.

Orientador: Fausto Foresti / Resumo: Populações de elasmobrânquios têm sofrido declínios severos nas últimas décadas devido à massiva pressão pesqueira. Com características de vida que tornam a espécie mais suscetível à pesca, o tubarão-raposa Alopias superciliosus está classificado atualmente como vulnerável na lista vermelha de espécies ameaçadas da IUCN. A espécie apresenta maturação sexual tardia e somente dois (raramente quatro) filhotes a cada gestação, que dura aproximadamente 12 meses. Estas características evidenciam a necessidade de sistemas de manejo pesqueiro adequados à estruturação populacional da espécie, que se apresenta como um instrumento fundamental para sua conservação. Com o advento de novas tecnologias atualmente é viável utilizar ferramentas moleculares para elucidar questões evolutivas e genético-populacionais em organismos não modelos, gerando informações que podem auxiliar na elaboração de planos de manejo. Tendo em vista à escassez de informações sobre a dinâmica populacional do tubarão-raposa, o presente estudo teve como objetivo o desenvolvimento e aplicação de marcadores moleculares em amostras de A. superciliosus provenientes de diferentes localidades dos oceanos Atlântico e Índico. Um total de 12 marcadores moleculares do tipo microssatélite, sendo 11 polimórficos e 1 monomórfico, foram identificados e, a partir desta identificação, primers espécie-específicos foram desenvolvidos e padronizados. Para acessar a diversidade genética e populacional de A. superciliosus foram genotipad... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

Orientador: Fernando Fernandes Mendonça / Resumo: Tubarões são organismos amplamente reconhecidos como predadores de topo de cadeia e sua distribuição geográfica associada à capacidade migratória em diversas espécies, principalmente pelágicas, tornam as avaliações e monitorias de suas populações uma tarefa complexa. O tubarão-azul, Prionace glauca, é uma espécie globalmente distribuída e altamente migradora, classificado como “Quase Ameaçado” na Lista Vermelha de Espécies Ameaçadas da IUCN. No entanto, ao longo de sua história, P. glauca vem sendo frequentemente associado a capturas da pesca industrial e, seus registros recentes, apontam declínios relevantes em suas populações em algumas localidades. Dentre o conhecimento necessário para a gestão adequada e conservação de espécies amplamente exploradas, podemos ressaltar que as informações sobre a variabilidade genética e dinâmica populacional são de grande valia, principalmente quando se trata de uma espécie de elevada capacidade de dispersão. Assim, este estudo é o primeiro a caracterizar a biodiversidade molecular e a estrutura populacional desta espécie globalmente, a partir de 534 indivíduos provenientes de diferentes localidades nos oceanos Atlântico, Índico e Pacífico. Utilizando a região controle de DNA mitocondrial (CR), encontramos 43 haplótipos com diversidade Hd=0,778, diversidade de nucleotídeos de π=0,005 e índice de estrutura populacional global de ΦST=0,054 (P=0,0001). Estes resultados indicam que P. glauca está entre as espécies de tubarões com os maiores ín... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Sharks are organisms widely recognised as top-chain predators and their geographic distribution associated with migratory capacity in several species, mainly pelagic, make evaluations and monitoring of their populations a complex task. The blue shark (Prionace glauca) is a globally distributed and highly migratory species, classified as "Near Threatened" on the IUCN Red List of Threatened Species. However, throughout its history, P. glauca has been frequently associated with industrial fisheries catches, and its recent records indicate relative declines in their populations in some localities. Among the knowledge necessary for the proper management and conservation of widely exploited species, we can highlight the information about genetic variability and population dynamics are of great value, especially when it is a species of high dispersion capacity. Thus, this study is the first to characterise the molecular biodiversity and population structure of this species globally, from 534 individuals from different locations in the Atlantic, Indian and Pacific Oceans. Using the mitochondrial DNA control region (CR), we found 43 haplotypes with diversity Hd = 0.778, nucleotide diversity of π = 0.005 and a global population structure index of ΦST = 0.054 (P = 0.0001). These results indicate that P. glauca is among the species of sharks with the highest indexes of genetic variability and high gene flow among the oceans, with low geographic delimitation and moderate population struct... (Complete abstract click electronic access below) / Doutor

Cariniana estrellensis (Raddi) Kuntez (Lecythidaceae), popularmente conhecida como jequitibá branco, é uma espécie arbórea climácica neotropical cuja sobrevivência encontra-se ameaçada devido aos processos de degradação de seus ambientes naturais e exploração indevida. Visando contribuir para a conservação in situ e ex situ deste recurso genético, o objetivo deste trabalho foi investigar a diversidade genética, o sistema de reprodução, a estrutura genética espacial e o fluxo gênico contemporâneo de C. estrellensis em um pequeno remanescente florestal (8 ha) localizado na Região de Ribeirão Preto SP (município de Cravinhos), usando como ferramenta de análise um conjunto de nove marcadores microssatélites (SSR) desenvolvidos para a espécie. Todas as árvores adultas reprodutivas (30) e regenerantes (39) existentes no referido fragmento foram mapeadas e tiveram tecidos foliares amostrados para as análises genéticas. Sementes de polinização natural foram também aleatoriamente coletadas em algumas destas árvores adultas durante dois eventos reprodutivos, obtendo-se um total de 644 progênies. Através das análises SSR constatou-se que todas as gerações de C. estrellensis apresentaram altos níveis de diversidade genética e ausência de endogamia, evidenciando a alogamia da espécie. Em concordância, as taxas de cruzamentos (tm) estimadas para os dois eventos reprodutivos não diferiram estatisticamente da unidade, permitindo afirmar que C. estrellensis é uma espécie perfeitamente alógama, com indícios de mecanismos de auto-incompatibilidade. Estimativas da correlação de paternidade (rp(m) (evento 1) = 0,121 e rp(m) (evento 2) = 0,145) e do coeficiente de coancestralidade médio dentro de progênies (xy (evento 1) = 0,140 e xy (evento 2) = 0,141) indicaram a ocorrência de pequenos desvios de cruzamentos aleatórios na população de C. estrellensis. O número efetivo de doadores de pólen estimado foi mais alto entre frutos de uma mesma árvore (10,20(evento 1); 10,31(evento 2) ) do que dentro de um mesmo fruto (1,33(evento 1); 1,17(evento 2)). Os resultados também revelaram que não existe estruturação genética espacial na população de C. estrellensis. As análises de parentesco em C. estrellensis revelaram distâncias médias curtas do fluxo de pólen dentro do fragmento tanto para as progênies (69,95±60 m(evento 1); 112,02±94 m (evento 2)) quanto para os regenerantes (146,94±98 m). Além disso, os resultados das análises de parentesco nos regenerantes apontaram ausência de imigração de sementes na população e indicaram que a taxa de imigração de pólen realizado (variando entre 53 % e 62 %) foi maior que as taxas de imigração de pólen efetivo (variando entre 23,5 % e 37 %) para os dois eventos reprodutivos estudados. Os altos níveis de imigração de pólen detectados no fragmento em estudo sugeriram que a população de C. estrellensis não está isolada reprodutivamente, o que pode ser essencial para prevenir perdas de diversidade genética da espécie, garantindo sua sobrevivência em longo prazo. Em termos gerais, a população estudada mostrou resiliência aos efeitos adversos da fragmentação e potencial para fins de conservação in situ e ex situ. / Cariniana estrellensis (Raddi) Kuntze (Lecythidaceae), commonly known as jequitibá branco, is a large neotropical tree, characteristic of the climax forest whose survival is threatened due to processes of degradation of natural environments and improper exploitation. In this study, it was investigated the temporal patterns of genetic variability, reproductive systems, spatial genetic structure and contemporary gene flow in the remaining population of the tropical forest species C. estrellensis that occurs naturally in a small fragment (8 ha) located in the Ribeirão Preto region-SP (municipality of Cravinhos), using nine pairs of microsatellite loci. All adult trees (30) and saplings (39) found in the fragment were mapped and sampled. Naturally-pollinated seeds were randomly collected from seed-trees that were reproductive for two consecutive years resulting in a total of 644 offspring. Through the analysis with SSR, all generations of C. estrellensis (adults, saplings and offspring) showed high levels of genetic diversity and no inbreeding. Estimates of multi-locus outcrossing rates (tm) suggested that C. estrellensis is a perfectly allogamus species, with evidence of selfincompatibility. Estimates of the correlation of paternity (rp(m) (event 1) = 0.121 and rp(m) (event 2) = 0.145) and the average of the coefficient of coancestry within progenies (xy (event 1) = 0.140 and xy (event 2) = 0.141) indicated a small deviation from random mating. The effective number of pollen donors was higher among fruits from the same tree (10.20(event 1), 10.31(event 2)) than within the same fruit (1.33(event 1), 1.17(event 2)). The results also revealed a lack of spatial genetic structure in C. estrellensis population. Parentage analyses revealed short average distances of pollen flow within the fragment for both offspring generations (69.95 ± 60 m (event 1); 112.02 ± 94 m (event 2)) as well as for saplings (146.94 ± 98 m). Furthermore, the parentage analyses in the saplings pointed no seed immigration in the population studied and indicated that the realized pollen immigration (ranging between 53 % and 62 %) was higher than the rates of effective pollen immigration (ranging between 23.5 % and 37 %) for both reproductive events studied. High levels of pollen immigration from outside study site suggested that the population of C. estrellensis is not reproductively isolated, which may be essential to prevent losses of genetic diversity in the species, ensuring its long-term survival. Overall, the studied population shows resilience to adverse effects of fragmentation and potential for in situ and ex situ conservation.