Clinch Dace (Chrosomus sp. cf. saylori) is a newly recognized species of minnow with a restricted distribution in southwestern Virginia. Field sampling and genetic analysis support the hypothesis that Clinch Dace populations are small and fragmented. Analysis of neutral genetic markers shows that most Clinch Dace populations have undergone past bottleneck events and are being operated upon by random genetic drift. Bayesian cluster analysis showed that three out of the seven populations found in 2017 are distinct, while the other four show signs of more recent admixture. However, Fst values among streams were high and analysis of molecular variance indicated differentiation among populations in all streams. These findings support the view that these populations are genetically isolated. Effective populations sizes were low at most sites, enhancing the likelihood of loss of alleles to genetic drift. Low M-ratios, non-zero Fis values, and high degrees of relatedness among individuals indicate that some inbreeding is taking place. Habitat analysis did not identify variables affecting distribution or abundance of Clinch Dace populations. As the collection sites were targeted near known Clinch Dace occupied sites, it is likely that habitat variables known to impact Clinch Dace, such as conductivity, were within the species' range of tolerance. Results showed that Clinch Dace seem particularly resilient to sedimentation, corroborating earlier work showing a negative relationship between Clinch Dace abundance to sediment size. That is, small sediment size does not seem to have a negative impact on Clinch Dace abundance. Of all sites where Clinch Dace were found, only one culvert at one site was clearly perched and may present a barrier to upstream migration, a possibility which is supported by the genetic differentiation found among collections above and below that culvert. While this study demonstrates that selectively neutral genetic differentiation has taken place among Clinch Dace populations, it does address any local adaptation that may be taking place which would render translocations a risk for outbreeding depression. The findings of this study can inform conservation management in identifying possible sources of individuals for translocations among populations or for augmentation following captive breeding. / Master of Science / The Clinch Dace is a small, threatened minnow in the Clinch River basin that was unknown until 1999. Since then, research has addressed the biology, life history, and distribution of this fish. This study used data from selectively neutral genetic markers to analyze the population structure and degree of differentiation of Clinch Dace populations. My study sites were targeted at road crossings near known Clinch Dace populations to assess the effect of habitat fragmentation on Clinch Dace populations and to maximize the likelihood that I would collect enough genetic material for analysis. Genetic analyses showed that while there is some admixture among certain populations of Clinch Dace, there is differentiation at neutral genetic markers. This differentiation does not necessarily indicate adaptive variation among populations which could result in outbreeding depression should populations be mixed through translocations, but it is reason to proceed with caution. Road crossings were generally not found to be a cause of further population fragmentation in Clinch Dace, as demonstrated by genetic analysis and statistical analysis. Almost all of the occupied road crossing sites in this study were either embedded, free-flowing culverts that were not perched or small bridges, and these were not deemed to be obvious barriers to fish movement. The only exception was Hart Creek 2, where the culvert is slightly perched and Fst is high between populations in the upstream and downstream reaches. The results of this study will help to inform managers as to what conservation actions can be taken to improve population viability. One potential management action from this study could be the retrofitting of culverts that have become perched and are acting as barriers to Clinch Dace movement. Another potential conservation strategy is to translocate individuals from large population to small populations. The study determined: 1) which translocations might be acceptable based on the degree of genetic differentiation among populations, and 2) identified potential donor and receiving streams for translocations.

"Local genetic adaptation and homing behavior in anadromous fish favors the formation of local populations across their geographic range of distribution. Spawning- and natal-site fidelity repeated over generations restricts gene flow and allows genetic differences to accumulate resulting in reproductive isolation. This leads to progressive genetic differentiation and population structuring among different river populations. Alewife, Alosa pseudoharengus, are anadromous fish which are estimated to have high rates of reproductive fidelity and hence might show population structuring among different breeding streams. Alewife are fish of economic importance since they have both commercial and recreational value. Alewife populations have been declining over the past decades and conservation measures to restore the populations have been implemented. Since maintaining genetic integrity of natural populations is one of the main concerns, identification of population structure can assist in designing appropriate restocking programs. In this study, I used microsatellite markers developed for shad to study population structuring in alewife. Samples were collected from two sites in Connecticut and one in Lake Michigan and genetic differentiation among these populations was estimated using five microsatellite loci. My studies indicate that microsatellite loci developed for shad can be used for alewife. Results from this preliminary study indicated subtle but significant genetic differentiation among populations. This suggests that care should be taken when restocking alewife from different sites in order to maintain genetic diversity among these populations."

Genetic differentiation in phenotypic traits among populations from heterogeneous environments is often observed in common-garden studies on forest trees, but data on adaptive variation in Scots pine (Pinus sylvestris L.) in Scotland are limited. As a result, current seed transfer guidelines are based on earlier molecular marker studies and do not take into account environmental or adaptive genetic variation. An analysis of spatial variation in climate showed substantial differences in temperature and precipitation among the native Scots pine sites in Scotland. To investigate whether differentiation in response to environmental variation has occurred in Scotland, a glasshouse-based common-garden trial of ~3,360 seedlings from 21 populations and 84 open-pollinated families was established in 2007. At the beginning of the 2nd growing season, timing of bud flush showed evidence of genetic differentiation among populations, with those from cooler origins generally flushing earlier. Variation was also found among families within populations, suggesting that the trait is genetically controlled. Populations and families showed different levels of variability in this trait which could be partly due to variable levels of temporal climate fluctuation in different parts of Scotland. Chlorophyll fluorescence was used to examine drought response in three-year old seedlings from five populations on sites that experience contrasting levels of annual rainfall. It was found that the response was not related to rainfall, but possibly to more complex moisture variables that also take into account additional factors such as evaporation. Also, photosynthetic capacity in response to cold winter temperatures varied significantly among eight populations that were kept outdoors, and the largest reduction was seen in seedlings from the mildest, most maritime coastal site. The following spring, height growth and needle flush started earlier in seedlings from cooler locations. Earlier studies on genetic diversity of native pinewoods have shown high levels of selectively neutral variation in this predominantly outcrossing conifer, and a mating system analysis with a limited number of microsatellite markers supported this pattern. Together, these data suggest that despite significant historic population size decrease, environmental gradients have resulted in genetic differentiation among native pinewoods. In order to minimise the risk of planting poorly-adapted stock and to maximise the success of replanting programmes, it is important that the origins of planting stock are carefully considered in management guidelines for the species.

Norway spruce is one of two dominating species in Swedish forestry and the most economically important tree species in Sweden. In order to preserve the ability to adapt to a changing environment and to keep populations healthy, genetic diversity has to be preserved. When choosing a small number of individuals from a natural stand to establish a seed orchard the population size decrease. With only a small number of genetically different individuals the risk of inbreeding increase. Furthermore if many clones of the same tree are used in one seed orchard there is also an increased risk selfing. The aim of this study was therefore to investigate whether genetic diversity in Norway spruce differs between age groups and if this can be attributed to forestry practices. All sampling was done from a single location in Västerbotten, Sweden and the different age groups were chosen to represent stands not affected by the modern forest industry to recently planted forests. The chosen age groups are young (12-18 years), intermediate (30-45 years), and old (above 85 years). From each age group 150 individuals were sampled. With genomic microsatellite markers each individual was genotyped at eight simple sequence repeat (SSR) loci. Results show an overall high genetic diversity with an average expected heterozygosity (He) at 0.842 and low genetic differentiation with an average fixation index among populations (FST) of 0.003. The genetic diversity of each age group was also high (He 0.832 to 0.843) and the inbreeding coefficient ranged from 0.061 in the old group to 0.078 in the intermediate group. The pairwise FST value was highest between the old group and the young group but the differentiation was only 0.005 (P=0.001). An analysis of molecular variance also showed that only 0.34% of the total genetic variance was explained by differences among age groups. This study found little evidence for a decrease in genetic diversity due to forestry practices and revealed high genetic diversity and low differentiation between the age groups, indicating a healthy population.

Asymmetrical dispersal is when dispersal rates differ in opposite directions. This is expected to be common in natural populations. This work aims to study the symmetrical and asymmetrical dispersal through the use of a simulation program, simuPOP. The main questions were (i) "what are the differences between asymmetrical and symmetrical dispersal in relation to genetic differentiation and equilibrium?" and (ii) "Is it possible to identify asymmetrical dispersal structure from observed patterns of genetic differentiation between populations, and variation within populations?". To address these questions, simulations were conducted with two and three subpopulations subject by three different dispersal rate contrasts and several spatial patterns of dispersal. Variables were estimated at drift-dispersal equilibrium included genetic differentiation between subpopulations (θ) and heterozygosity. With pairwise θ for three subpopulations it was possible to determine whether the metapopulations were subject to symmetrical or asymmetrical dispersal and sometimes to identify the structure of dispersal. Equilibrium heterozygosities did not aid diagnosis of asymmetrical dispersal patterns. I also checked the applicability of two predictions originally made for symmetrical dispersal: Wright's expectations for θ at equilibrium, and Whitlock's expectations fro time to half of equilibrium θ. In most cases these expectations were not applicable. Study of asymmetrical dispersal on living organisms is strongly encouraged.

Asymmetrical dispersal is when dispersal rates differ in opposite directions. This is expected to be common in natural populations. This work aims to study the symmetrical and asymmetrical dispersal through the use of a simulation program, simuPOP. The main questions were (i) "what are the differences between asymmetrical and symmetrical dispersal in relation to genetic differentiation and equilibrium?" and (ii) "Is it possible to identify asymmetrical dispersal structure from observed patterns of genetic differentiation between populations, and variation within populations?". To address these questions, simulations were conducted with two and three subpopulations subject by three different dispersal rate contrasts and several spatial patterns of dispersal. Variables were estimated at drift-dispersal equilibrium included genetic differentiation between subpopulations (θ) and heterozygosity. With pairwise θ for three subpopulations it was possible to determine whether the metapopulations were subject to symmetrical or asymmetrical dispersal and sometimes to identify the structure of dispersal. Equilibrium heterozygosities did not aid diagnosis of asymmetrical dispersal patterns. I also checked the applicability of two predictions originally made for symmetrical dispersal: Wright's expectations for θ at equilibrium, and Whitlock's expectations fro time to half of equilibrium θ. In most cases these expectations were not applicable. Study of asymmetrical dispersal on living organisms is strongly encouraged.

Discerning the basis of phenotypic and genotypic differences within and between taxa is crucial for understanding the evolution of species, subspecies or varieties and races. In this dissertation, I have presented three studies, which use morphological characters and genetic Amplified Fragment Length Polymorphisms (AFLPs) to differentiate cytotypes, populations and species of the genus Xanthisma. The first study is aimed at clarifying the species status of Haplopappus ravenii, which has been considered to be a separate species by some taxonomists and a race of Xanthisma gracile by other researchers. Considering the morphological species concept and the genotypic cluster definition of a species, there was insufficient distinction in either dataset to support these taxa as distinct species. It was found that H. ravenii is more appropriately classified as a a cytotype or a race of X. gracile. In the second study, the genetic structure of X. gracile was quantified across populations occupying distinct habitat types (desert, grasslands, and pinyon juniper woodlands) in order to test the hypothesis of local adaptation and to determine the potential for intraspecific divergence. Samples from desert habitats showed higher genetic divergence than samples in the other two habitats. This study is indicative of local adaptation of populations and that changes in climate and habitat play a very important role in the genetic differentiation of plant systems. The third study evaluated the taxonomy of Xanthisma spinulosum and three of its subspecies that co-occur in Arizona. Herbarium specimens representative of the three subspecies were used to test for significant morphological and genetic divergence that would support their recognition. The morphological characters originally utilized by taxonomists who named these taxa were not significantly different among the three taxa. This finding was further supported by the molecular data, suggesting the presence of one contiguous species. This dissertation aims at stressing the importance of taxonomic status and understanding the role that environment can play on shaping differentiation between taxa.

We determined genetic variance and gene flow across multiple scales (reaches, headwater segments, and catchments) to examine the dispersal ability of the flatworm Polycelis coronata along the Wasatch Mountains of Utah. Multiple models predict patterns of genetic differentiation in stream invertebrates based on dispersal traits and the spatial connectivity of the habitat. The stream hierarchy model predicts genetic differentiation to be low and gene flow to be high between reaches nested in segments, moderate among segments within catchments, and differentiation to be highest and gene flow lowest among catchments, whereas the headwater model predicts the greatest differentiation between headwater segments. Our objective was to determine which model best described genetic patterns observed in P. coronata. Using a nested hierarchical sampling design ensured that if limitations to dispersal had an effect on genetic differentiation, we would be able to identify at what scale these processes operate. We hypothesized genetic variation would be small within headwater segments and reach maximum levels between headwater segments with no increase in differentiation with increasing distance between headwater patches or between drainages. We do not expect high dispersal along the stream network or across the terrestrial environment (actively or passively).We generated DNA sequence data (mitochondrial COI) from 50 sites nested within 24 segments, which were nested in four adjacent catchments. We identified 134 haplotypes from 506 individuals using a 763 bp fragment of mtDNA. Genetic patterns did not conform to the SH model. Evidence from one drainage (Provo River) was consistent with the headwater model. However, high differentiation within sites suggested that the genetic patterns we uncovered may be representative of high ancestral polymorphism among pre-fragmented populations that were historically widespread. Large effective population sizes and no evidence of bottleneck events suggest incomplete lineage cannot be discounted as an explanation of high differentiation at the smallest scales.

Thesis (PhD (Animal Sciences))--Stellenbosch University, 2011. / ENGLISH ABSTRACT: Local pigs in Southern Africa are an important component of resource-based subsistence farming systems and contribute substantially to the improvement of livelihoods of farmers. The objective of the study was to characterise indigenous pigs through the following specific objectives: to characterise the production systems, to give a physical description and to evaluate the genetic differentiation of the indigenous pigs. Surveys were carried out in Chirumhanzu and Mutoko Districts of Zimbabwe, Afred Nzo, OR Tambo and Vhembe districts of South Africa. Blood samples were collected in all of the above and additional three districts in Malawi (Mchinji, Dedza and Salima). The first study showed that most of the indigenous pigs were kept by women. The farmers kept small herd sizes (<7 pigs) to match the available resources. Income was the main determinant of farmer production objectives and breed preference. Several constraints that would militate against in situ conservation included poor quality and quantity of feeds, diseases, lack of housing, lack of markets and lack of support services. The pigs were generally small and black resembling the Windsnyer-Mukota type of pigs. The pigs apparently had a high foraging ability and high thermo-tolerance that made them suitable for production in low-intensity management free range production systems. These types of pigs were distributed throughout the study area. A microsatellite analysis showed high diversity but very little population differentiation among the pig populations from Southern Africa, with 93 % of variety occurring within subpopulations. Development of markets can be a feasible way of mainstreaming the indigenous pigs into the general economy. This will achieve the twin objectives of conserving and improving the breed while, at the same time, benefitting the farmers that keep these genetic resources. Farmers faced similar production constraints and the pigs were similar across the study areas. / AFRIKAANSE OPSOMMING: Plaaslike varke speel ‘n belangrike rol in hulpbron-gebaseerde bestaansboederye in Suider- Afrika, en maak ‘n aansienlike bydrae tot verbetering van die lewensbestaan van bestaansboere. Die studie het die volgende doelwitte: om die produksie van inheemse varke te karakteriseer, die varke fisies te beskryf, en om die genetiese differensiasie van die inheemse varke te evalueer. Opnames is uitgevoer in die Chirumhanzu en Mutoko distrikte van Zimbabwe, Afred Nzo, OR Tambo en Vhembe distrikte in Suid-Afrika. Bloedmonsters is in al die bogenoemde en nog drie distrikte in Malawi (Mchinji, Dedza en Salima) versamel. Die eerste studie het getoon dat die meeste inheemse varke deur vroue aangehou word. Die boere het klein trop groottes vir aanpasbaarheid by die beskikbare hulpbronne. Inkomste en varkras voorkeur was die hoof bepalende faktore vir hierdie boere se produksie doelwitte. Verskeie beperkings wat bots teen in situ instandhouding sluit in swak kwaliteit- en kwantiteit voere, siektes, gebrek aan behuising, die gebrek aan markte en die gebrek aan ondersteunende dienste. Die varke is oor die algemeen klein en swart en vertoon soos die Windsnyer-Mukoto tipe varke. Hierdie varke het blykbaar ‘n hoë voer-soekende vermoë en hitte-verdraagsaamheid wat hulle geskik maak vir die produksie in lae-intensiteit bestuur en vry-weidende produksie sisteme. Hierdie tipe varke was versprei oor die studie area. ‘n Mikrosatelliet analise het aangedui dat daar hoë genetiese variasie is binne die vark populasie, maar daar is klein differensiasie tussen die verskillende vark populasies van Suider-Afrika, met 93% variasie wat voorkom binne sub-populasies. Die ontwikkeling van markte kan ‘n haalbare manier wees om die inheemse varke toegang te gee tot die algemene ekonomie. Hiermee kan beide doelwitte, bewaring en verbetering van hierdie varkras, tergelyktydig bereik word, ten goede van die boere wat hierdie genetiese hulpbronne aanhou.

INTRODUCTION: Head and neck cancer is one of the most common malignancy in the world. While it has been associated with several factors like alcohol consumption and smoking, there is approximately 25% of head and neck cancer that can be attributed to Human Papillomavirus (HPV) especially HPV 16. HPV associated cancer has been associated with a better prognosis as compared to HPV negative cancers. It has also been shown in previous studies that HPV-negative African Americans have a higher mortality rate as compared to HPV associated cancers in European Americans and HPV-negative European Americans patients. The three states of HPV associated cancers have been compared, which included HPV active, HPV inactive and HPV negative. AIM: The study aims include: 1) Compare the differences in the gene expression profiles of HPV negative HNSCC in AA from EA patients, and determine the differences in their biological make up. 2) Explore and compare the genetic expression profiles of HPV-active, HPV-inactive and HPV-negative head and neck cancer patients. METHODS: A secondary data analysis was conducted on 36 oropharyngeal cancer tissues samples with different HPV status (HPV-active, HPV-inactive and HPV- negative). ANOVA was conducted in R to compare all the three groups from each other and identify the genes that were differentially expressed. Bayes Moderated paired t-test was used to compare two groups of HPV-negative European Americans with HPV-negative African Americans. RESULTS: Our analysis revealed that the genes that were differentially expressed in HPV- active and HPV-negative analysis were different from HPV-active and HPV-inactive analysis. Our analysis also identified genes that were differentially expressed in African Americans as compared to European Americans. DISCUSSION: This study provides the genetic expression profiles in different groups (European Americans and African Americans) based on different HPV stages. Despite the small sample size of our data, we were able to identify the genes that were differentially expressed amongst different conditions in patients who had oropharyngeal carcinoma. We were also able to identify the genes involved in HPV-negative oral cancer comparing the African Americans to the European Americans.