A national inventory of UK plant genetic resources carried out in 2003-4 covered surveys and documentation of landrace types, occurrences and threats. Among the local varieties found, those with longest histories of local cultivation occurred on the most remote Scottish islands: the Outer Hebrides and Tiree had bere (Hordeum vulgare L.), Small oat (Avena strigosa Schreb.) and rye (Secale cereale L.); bere and Small oat on Orkney and Shetland; and Shetland cabbage (B. olearacea L.) on Shetland. These landraces are not only geographically but also agriculturally marginal; they are confined to crofting agriculture and used in low-intensity pastoralism. Two of these, the oat and the cabbage, were chosen for a characterization study which formed the major part of this PhD thesis. The broad aims of the characterization study were first, to describe the existing diversity within Scotland; to document the ex situ collection of Scottish landraces; to better understand genetic structure and dynamics of the landraces; but also to explore the use of a characterization study to raise awareness about landraces. Morphological and microsatellite results showed distinct identities for both landraces in relation to the respective outgroups; in the oat distinct regional identities were found. High diversity was found, most of the genetic variation however, was within populations, for both inbreeder (oat) and outbreeder (cabbage). This can be attributed to frequent and widespread seed exchange and seed swapping within island groups, while the small but significant regional distinctness is maintained through isolation between the three islands groups. The morphological characterization of Small oats was carried out in situ, on a croft in the Southern Outer Hebrides, aiming at education and raising awareness about landraces among secondary school students, maintainers and the local public in general. The extension and education element of the study seemed useful in raising the issue of landraces locally. Carrying out the trial in the area of origin and amidst maintainers had the additional advantage of identifying and communicating with stakeholders groups. Integrated conservation of ex situ collection and maintainers has been achieved through the Scottish Landrace Protection Scheme. By retaining the link between landraces and maintainers during the characterization, a springboard may have been created for feedback of the genetic results into the local seed system and to discuss further support options for landraces and maintainers.

The exponential growth of the human population is limiting the wildlife habitat all around the word. In recent years habitat loss and fragmentation is one of the main reasons that threats the wild life species. The Grévy’s zebra (Equus grevyi) is the most endangered member of Zebras. Their historical range was previously from north Ethiopia to southwest Somalia and to northern Kenya. Currently they are distributed only in fragmented habitats in central and eastern part of Ethiopia and in the north of Kenya. They are listed as endangered in the IUCN red list, as their population has declined 68% in 27 years. There are very few studies on genetic structure of this species, and investigating the genetic connection between different populations is needed. Molecular markers are one of the best tools to understand the level of fragmentation, population bottlenecks or potential inbreeding. In this study, the population structure of Ethiopian zebra population from Alledeghi Wildlife Reserve (WR) and Sarite area was studied using non-invasively obtained fecal samples collected during 2001-2011. This study analyzes genetic variation at 10 microsatellite loci and a 350-bp fragment of the mitochondrial DNA control region. The results showed that the genetic diversity is very low between the populations (π=0.00116 for Alledeghi WR and π=0 for Sarite population). The population of Alledeghi WR is probably isolated from the population of Sarite, as they don’t share any haplotypes. As the population of Alledeghi WR is separated from the ones from Sarite and Kenya, applying more conservational programs in this area is needed to protect the genetic diversity of the Grévy’s zebras in this area.

Seed dispersal in aquatic habitats is often considered to be a complex multistage process, where initial seed shadows are redistributed by water (hydrochory). The roles of hydrochory in seed dispersal and influencing population genetic structure were examined in Helmholtzia glaberrima using both ecological and genetic techniques. Ecological experiments showed that water can redistribute seeds and seedlings over local scales and that hydrochory can provide the potential for very long distance seed and seedling dispersal. Patterns of seedling genetic structure were affected by micro-drainages that direct water flow within populations and influence water-borne seed dispersal on a local scale. Strong non-equilibrium dynamics and persistent founder effects were responsible for the patterns of genetic structure observed among established populations of H. glaberrima. Classical metapopulation models best described dispersal patterns, while water-borne seed dispersal could potentially explain patterns of genetic differentiation within a stream system, it could not explain the distribution of genetic variation among stream systems. The current study found that although hydrochory influenced seed dispersal and seedling genetic structure within a population, it had little effect on the spatial pattern of genetic variation among established populations of H. glaberrima. Moreover, even though prolonged buoyancy and viability in water provide the potential for long-distance hydrochory, results presented here do not support the hypothesis that flowing water is an effective long distance seed dispersal vector for H. glaberrima. Taken together, these results suggest that the relative importance of gene flow via water-born seed dispersal in H. glaberrima may be low compared with that of some other riparian species.

Mulloway are a large native inshore marine fish that are currently being evaluated by NSW Fisheries for their potential in aquaculture. The current study developed and applied molecular genetic markers to assess the geographical scale at which future hatcheries should be developed for the species. In addition, it evaluated the impact that current breeding practices in NSW have had on genetic diversity in culture cohorts. The study showed that wild Australian populations of this species constitute a single management unit (genetic stock), but that current hatchery practices employed in NSW are eroding natural genetic diversity. Thus a single hatchery could provide cultures stock to the whole Australian industry without compromising wild populations but that hatchery management practices will need to be modified in the future, to minimise levels of inbreeding.

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.

Biodiversity in Southeast Asia has been decreasing as a result of human activities. The findings of the Millennium Ecosystem Assessment, reported in 2005, demonstrated that environmental change, such as deforestation, has resulted in recent major loss of biodiversity at the species level and increased rates of extinction; however, it is unknown whether a similar deficit has occurred at the level of genetic diversity within species. This study aims to understand how the past has shaped the current pattern of genetic diversity, the impact of recent forest loss on genetic diversity and how this information can be used to develop effective conservation strategy. To achieve this aim, microsatellites were developed by sequencing genomic libraries and from comparisons of database sequences. The utility of these markers for population genetics studies has been tested and confirmed for the three main study taxa and across a broad range of other squirrel species. These microsatellites and mitochondrial sequence data (cytochrome b gene) were utilized to determine the genetic diversity and population structure of three squirrel taxa with varying degrees of forest dependency on Thailand’s tropical forests. The most forest dependent taxon is Phayre’s flying squirrel (Hylopetes phayrei). The second taxon is the moderately forest-dependent tree squirrel, the Grey-bellied squirrel (Callosciurus caniceps). The third, and least forest dependent taxon, is the Indochinese ground squirrel, Menetes berdmorei. Our data revealed far more biodiversity in these taxa than previously recognized; there were three genetically distinct lineages in H. phayrei and M. berdmorei and two lineages in C. caniceps. This demonstrates that biodiversity in this region has been underestimated. In the two most forest dependent taxa lineage divergence dated to the Pleistocene indicating that this biodiversity was generated by isolation in allopatric forest refugia during the cool, dry periods of the Pleistocene. In H. phayrei, the most forest-dependent taxon, at least two of the lineages were distinct species occurring sympatrically in Thailand on the border with Myanmar. This taxon supported the biogeographical hypothesis developed in forest dependent mosquitoes of allopatric isolation in northwest and northeastern Pleistocene refugia. Callosciurus caniceps had evidence of a southern refugium in peninsular Thailand or Malaysia. The lower levels of structuring in the least forest dependent taxon M. berdmorei suggest a limited impact of Pleistocene environmental change. All three taxa had eastern lineages which may have been due to Pleistocene forest fragmentation in some of the species. These eastern populations typically had lower levels of microsatellite and mtDNA genetic diversity. This is likely due to the recent loss of genetic diversity as in recent decades these forests have been highly fragmented and reduced in size due to human activity. Our finding that the northern Thai-Myanmar border region is a suture zone in highly dependent forest species and has high within lineage/species diversity makes this region a priority for conservation. The distinct genetic lineages in the east and south should also be managed as separate conservation units. Further efforts are required to assess the impact of loss of genetic diversity in Thailand’s fragmented forests and how this may be remedied.

Acer rubrum L. and Liriodendron tulipifera L. are prolific throughout their ranges in the Southeastern U.S. and also have increasingly important roles in forestry and wood products in this region. The relatively low density and intermediate strength of the wood makes them versatile for use in many different wood products. Exploring the genetic structure of these species could provide a foundation for further genetic and breeding exploration with these economically important trees. This study utilizes amplified fragment length polymorphism to determine the level of genetic diversity of these species in contrasting physiographic provinces. AFLP was performed using five primer combinations on samples collected from six unmanaged populations of each species in the Mountains and Coastal Plain of the Southeastern U.S. Wood density was determined using an X-ray densitometer. A. rubrum lacked strong genetic structure while L. tulipifera showed differentiation between physiographic provinces. Genetic diversity of A. rubrum was lower within the Mountain populations (He: 0.327) than the Coastal Plain populations (He: 0.365). The average wood density for A. rubrum is lower in the Mountains (539.00 kg/m^3) than in the Coastal Plain (575.43 kg/m^3). Genetic diversity of L. tulipifera was higher overall (He: 0.289) than within the Mountain populations (He: 0.281) or the Coastal Plain populations (He: 0.271). The average wood density for L. tulipifera is greater in the Mountains (445.45 kg/m^3) than in the Coastal Plain (441.67 kg/m^3). / Master of Science

Freshwater streams in the developed world are becoming increasingly dominated by treated wastewater. Continually discharged into most surface waters, these effluents contain a suite of bioactive man-made chemicals, including steroid and non-steroid oestrogens, which have been found to feminise male fish, skew sex ratios, and cause reproductive failure. However, the consequences of reproductive disruption remain poorly explored at the population level. This thesis was initiated to evaluate how oestrogenic contaminants might influence the population ecology of a common cyprinid, the roach (Rutilus rutilus). An investigation encompassing population structure, multigenerational exposure and the role of additional drivers of fish population dynamics was undertaken to contextualise the effects of oestrogenic effluents on wild fish populations. Population genetic analysis of UK roach found they exhibit moderately high levels of genetic diversity and significant intra-river genetic structure. Genetically differentiated local subpopulations indicate little interbreeding and limited gene flow, consistent with a typical metapopulation that has not been homogenised by restocking. Similarly, my thesis demonstrates no significant relationship between effluent exposure and Ne (effective population size) or genetic diversity of roach populations, albeit a 65% reduction in Ne is possible at highly polluted sites. River stretches contaminated with high levels of effluent can support breeding populations, which recruit successfully with minimal immigration from less contaminated sites. Multigenerational effects of effluent exposure on roach were also evaluated experimentally using reproductive success from breeding adults over three generations. Lifelong exposure to 100% treated effluent resulted in feminised phenotypes (ovarian cavities and intersex condition) in males but no observable effect on females. Additionally, despite gonadal disruption in males and effluent exposure of their mothers, I found no detrimental effect on their ability to compete with control fish. Instead, reproductive success was primarily determined by body size. A novel approach considering additional fish population drivers suggests that genetic diversity and species diversity decline in parallel with an increasing presence of disturbed land, when combined with geographical isolation. In conclusion, group assemblage and genetic structure of fish populations appears multi-causal and cannot be disaggregated, such that a single environmental characteristic can be shown to drive patterns of population success.

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.

Plasmodium malariae é um parasita protozoário que causa malária em humanos e é geneticamente indistinguível de P. brasilianum, um parasita que infecta macacos do Novo Mundo nas Américas do Sul e Central. P. malariae possui uma ampla distribuição mundial em regiões tropicais e subtropicais, porém de forma pontual, sendo encontrado na América do Sul, Ásia e África. Entretanto, pouco se sabe sobre a genética destes parasitas e a similaridade entre eles pode devido ao pequeno número de sequências genômicas disponíveis para essas espécies de Plasmodium. Recentemente, seis marcadores microssatélites e a sequencia completa do gene que codifica a proteína de superfície do merozoíta 1 (MSP1) foram descritos para estes parasitas. Neste estudo, o polimorfismo genético de 24 isolados brasileiros de P. malariae e P. brasilianum obtidos de diferentes hospedeiros foi analisado através da utilização desses marcadores microssatélites e da região correspondente ao oitavo bloco da MSP1. Os dados epidemiológicos moleculares foram explorados em relação à origem geográfica e hospedeiros. Para todos os marcadores estudados, as amostras de símios apresentaram um polimorfismo mais elevado que as amostras humanas. Na análise de microssatélites, as amostras humanas foram polimórficas em apenas dois alelos, enquanto as amostras de símios foram polimórficas em cinco alelos. O alelo Pm42- 331 foi monomórfico em todas as amostras analisadas. Na análise do bloco 8 da MSP1, as amostras símias foram altamente polimórficas e as amostras humanas apresentaram quatro tipos alélicos, sendo que dois tipos alélicos (A5 e A7) foram encontrados em alta frequência (90%). Em ambas as análises, a amostra de mosquito foi mais similar a amostras simianas. Nossos dados também mostram que há uma possível ausência de dimorfismo alélico na MSP1 de P. malariae e P. brasilianum, ao contrário de outras espécies de Plasmodium. Pela primeira vez, amostras de humanos, símios e mosquito foram analisadas em conjunto e utilizadas para o primeiro estudo de polimorfismos genéticos de isolados de P. malariae e P. brasilianum do Brasil. / Plasmodium malariae is a protozoan parasite that causes malaria in humans and is genetically indistinguishable from P. brasilianum, a parasite infecting New World monkeys in Central and South America. P. malariae has a wide and patchy global distribution in tropical and subtropical regions, being found in South America, Asia, and Africa. However, little is known regarding the genetics of these parasites and the similarity between them could be because until now there are only a very few genomic sequences available from these Plasmodium species. Recently, six microsatellite markers and the complete sequence of the merozoite surface protein 1 (MSP1) gene have been described for these parasites. In this study, the genetic polymorphism of 24 P. malariae and P. brasilianum isolates obtained from different hosts was analyzed using these microsatellite markers and the corresponding region on the block 8 of MSP1. The molecular epidemiological data were explored in relation to geographical origin and hosts. For all markers studied, the simian samples showed a higher polymorphism than human samples. In microsatellite analysis, the human samples were polymorphic only in two alleles, while simian samples were polymorphic in five alleles. The allele Pm42-331 was monomorphic in all samples analyzed. In the analysis of Block 8 of MSP1, the simian samples were highly polymorphic and human samples showed four allele types with two allelic types (A5 and A7) frequently found (90%). In both analyzes, the mosquito sample was more similar to simian samples. Our data also show that there is a likely absence of allelic dimorphism of MSP1 from P. malariae and P. brasilianum, as opposed to other Plasmodium species. For the first time, samples of humans, monkeys and mosquito were analyzed together and used for the first study of genetic polymorphisms in P. malariae and P. brasilianum isolates from Brazil.