Abstract Analyses of mitochondrial control region sequences were used to infer phylogeny of Anser species, phylogeography of the lesser white-fronted goose, and genetic background of a captive stock. The genetic distances among the Anser species ranged from 0.9 to 5.5% in the complete control region sequences and supported the view of close relatedness of these species. Among the four most closely related species, the bean, pink-footed, white-fronted and lesser white-fronted goose, the branching order is uncertain. The short internal branches and low support for the branching order suggest that the species have diverged recently within short time-intervals. The mtDNA tree obtained is incongruent with the traditional view of the species relationships, but the reasons for this remain to be clarified. Two diverged mitochondrial lineages were found in the lesser white-fronted goose and a refugial origin was proposed. Basal haplotypes are geographically widespread and indicate a recent common ancestry for populations. The derived haplotypes are confined to singular breeding populations and suggest restrictions to the present female gene flow. A shift in the frequency of the mtDNA lineages approximately coincides with a migratory divide in the Taimyr Peninsula. Low mtDNA diversity and significant difference in the haplotype frequencies observed in Fennoscandian subpopulation suggested that it should be considered as a management unit. The fossil record was examined to gain additional information about the colonisation history of the species, but was found to be of limited use. The captive lesser white-fronted goose stock used for reintroduction/restocking was shown to be incompatible with the Fennoscandian wild population. Some captive individuals carried the mtDNA of the white-fronted goose suggesting a hybrid origin. Hybridisation has probably occurred during captive propagation, but to clarify further the extent of introgression, nuclear markers should be applied. The structure and evolution of the control region were studied by comparing complete avian sequences. Saturation was found to occur at pairwise divergences of 10% as shown for third codon positions of the mitochondrial genes previously. In pairwise comparisons of the control region and cytochrome b sequences, the rate of divergence varied among the lineages. Two conserved sequence blocks showed considerable sequence conservation when compared to mammalian sequences.

No description available.

Understanding whether groups of individuals represent a single panmictic gene pool, or multiple genetically structured populations across a species range should aid in predicting whether specific conservation strategies would be more or less effective for species preservation. Further, contrasting the population structures of multiple coexisting taxa could foster an even deeper understanding of evolutionary divergence among demes and potentially even suggest local adaptation in the form of tight coevolutionary relationships. Finally, the analysis of population dynamics within small and isolated populations could improve our understanding of the relative importance that different evolutionary mechanisms have in predicting population persistence in the wild. Using microsatellite markers I characterized the population genetic structure in the critically endangered Cyclura cychlura cychlura iguanas on Andros Island. I found significant differences between inferred and realized rates of gene flow. This finding demonstrates that evolutionarily independent populations can occur even with high rates of dispersal. In the second and third study I contrasted patterns of genetic variability in Cyclura cychlura cychlura iguanas, ticks in the genus Amblyomma parasitizing these iguanas, and Rickettsia spp., potential pathogens transmitted by these ticks. I determined that genetic differences among Rickettsia samples and Amblyomma samples are highly concordant with genetic divergence among iguana populations. This finding suggests largely vertical dispersal of ticks and their super-parasite, a high specificity of this reptile-tick interaction, and historically low rates of dispersal in iguanas. This finding also indicates that island populations of iguanas may be locally adapted due to tight coevolutionary relationships. Finally, I investigated the mechanisms that eliminate harmful mutations in small isolated and natural populations of the critically endangered Cyclura cychlura cychlura iguanas. Using molecular tools I found indirect evidence suggesting that small natural populations can maintain significant levels of genetic variation in spite of strong selection acting against harmful mutations. Under regimes of random mating, the buildup of harmful mutations in small populations may result in a large number of inviable young. However, harmful mutations may also be eliminated when exposed to natural selection through increased competition, as population density increases. However, quantification of the relative role of competition was not feasible in this study.

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.

Traditionally, conservation genetics has examined neutral-marker (e.g microsatellite) surveys to inform the conservation and management of species. The field expanded together with the expansion of molecular biology, primarily enabled by polymerase chain reaction (PCR) and DNA sequencing technologies. Recently, advances in genomics and bioinformatics, notably next-generation sequencing (NGS), have demonstrated the ability to further enhance conservation genetic assessments. As a result, conservation genetics is rapidly transforming into a field of conservation genomics. Although complete genome sequencing and analysis is still beyond the reach of many conservation genetic projects, researchers can benefit by producing large amounts of genetic data quickly for their species of interest, or by exploiting existing genomic data for a closely related species. The research presented below serves as an example of these two different approaches. First, I review the current state of conservation genomics, utilizing examples when appropriate to illustrate different techniques and approaches. Next, I describe the development of a tool using NGS that is useful for the rapid genetic analysis of pumas (Puma concolor) called PumaPlex. This work details the methods involved and will be useful for anyone interested in working with a species where little genomic data is available. The last three chapters focus on using an existing genomic tool for the domestic dog to analyze admixture, quantify inbreeding, and identify potential adaptive variation in the endangered Mexican wolf (Canis lupus baileyi). The results demonstrated the Mexican wolf has no significant recent ancestry from domestic dogs, and that several loci may potentially be effective in increasing fitness in the reintroduced population.

Rhinoceroses are arguably the most endangered of all large mammal taxa. In order for ongoing conservation of this species to be successful, it is crucial to accurately characterize the remaining genetic diversity for all rhinoceros species. To do this, I optimized a standard suite of 24 taxon-specific rhinoceros microsatellite loci. These loci have the power to provide the most comprehensive estimate of comparative microsatellite genetic diversity within and among the four extant African and Asian rhinoceros genera. These loci were further used to evaluate the comparative influences of rhinoceros species versus microsatellite taxonomic origin as predictors of rhino microsatellite diversity, and finally to examine the evolutionary relationships between extant rhino taxa. The African black michaeli rhino subspecies had the highest level of microsatellite genetic variability of all available rhinos, while southern white and Indian rhinos were the least variable rhinos. These findings also suggested that species and taxonomic origin of microsatellite loci were both significant predictors of microsatellite heterozygosity in rhinoceroses. A weak association between the Sumatran and black rhinos was found with a DLR neighbour-joining tree. The standard loci were able to assign unique genotypes to all available rhinos as well as differentiate between all rhino species by correctly assigning individual rhinos back to their respective populations. / Thesis (Master, Biology) -- Queen's University, 2008-07-02 23:01:32.553

The genus Cochlearia is a taxonomically complex genus with a circumpolar distribution. In common with many other post-glacial colonisers it exhibits complex patterns of morphological and ecological variation. The genus has been the subject of continued taxonomic controversy, especially within the species complex C. officinalis s.l. The focus of this study was to investigate whether the three rare putative endemic Cochlearia officinalis s.l. taxa in Britain: C. micacea, C. officinalis subsp. scotica and C. atlantica were sufficiently distinctive to warrant endemic species or taxon status at any rank. Furthermore, to make conservation recommendations for the species complex based on the outcome of this investigation. The patterns of differentiation in Cochlearia were studied to gain insight into the processes that have driven morphological and ecological diversification in the group. The six putative taxa in Cochlearia officinalis s.l. were considered in this study: C. officinalis s.s., C. officinalis subsp. scotica, C. pyrenaica subsp. pyrenaica, C. pyrenaica subsp. alpina, C. atlantica and C. micacea. Samples of C. danica, a member of the wider genus Cochlearia, were also included for comparison. The samples were screened for variation in AFLP fragments, morphological characters and chloroplast haplotypes. This is the first study focussed on the British Cochlearia to use the amplified fragment length polymorphism (AFLP) technique. Many qualitative morphological characters differences between populations were maintained in cultivation under standard conditions. Variation in some quantitative morphological characters was significantly different between taxon groups. The morphological characters combined did not distinguish between taxonomic groups. Variation was found in samples from the uplands only. Although there were three chloroplast haplotypes all but 6 out of 96 samples had the same haplotype and the chloroplast was not taxonomically informative. The AFLP data did not vary significantly between taxonomic groups, ploidy levels, habitats or geographical regions. There was significant AFLP variation between populations. The morphological and ecological diversity present among populations of Cochlearia officinalis s.l. in Britain is most likely to result from local ecotypic differentiation. The variation in Cochlearia officinalis s.l. could not be divided satisfactorily into taxa of species rank and so specific conservation of taxa within the complex is not recommended. Instead the maintenance of Cochlearia diversity can be achieved by the continued protection of the habitats in which the ecotypes grow.

With the current rate of loss of biological diversity worldwide estimated at 100- 1000x the natural background rate, solutions are urgently needed to avoid a catastrophic and irreversible loss of species. Conservation breeding is a tool now widely used to assist in maintaining populations in a safe environment until such time as they can be released back into their natural habitat. The babirusa (Babyrousa celebensis) is a threatened species for which conservation breeding is an integral part of its conservation management. Native to a few Indonesian islands, the babirusa is under threat from habitat destruction and hunting and is estimated to have a wild population of only a few thousand. Conservation breeding was established in 1972 with the translocation of animals from Sulawesi to the Surabaya Zoo in Java, Indonesia. It is thought that 1.2 animals founded what is now a worldwide ex-situ population of around 200 individuals. With concerns mounting regarding likely levels of inbreeding and reduced reproductive success, particularly within the European population, this thesis aimed to utilise a number of techniques to assist the conservation breeding programme. Extensive studbook analysis was used to assess typical reproductive parameters for the babirusa in a captive setting; genetic analysis using microsatellite and mitochondrial DNA markers was used to clarify some aspects of the studbook and to estimate the level of variation within and between populations in different geographical areas; and faecal steroid analysis has been used to shed light on the physiological processes underpinning female reproduction. The combined output from these studies has added to our knowledge of this species and its performance in an ex-situ setting, and has now been used to inform future management of the conservation breeding programme.

Inbreeding depression has alarming impacts on threatened species with small population sizes. Assessing inbreeding depression has therefore become an important focus of conservation research. In this study, heterozygosityitness correlations (HFCs) were measured in adult and hatchling Lesser Antillean Iguanas, Iguana delicatissima, from a sampling site at Batali Beach in Dominica to assess the role of inbreeding depression on hatchling fitness and recruitment to the adult population in this endangered species. HFCs in hatchlings revealed no significant correlations and no general effects, suggesting that inbreeding depression may not be affecting hatchling fitness. Further, there were no significant differences in heterozygosity between the adult and hatchling groups suggesting that inbreeding depression may not be an important factor in shaping the population dynamics of I. delicatissima in Dominica. HFCs in the adults, however, revealed a significant negative correlation between heterozygosity and snout-vent length, which is more consistent with outbreeding depression in the population.

No description available.