Browsing by Subject "Population structure"
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Item Estimating population histories using single-nucleotide polymorphisms sampled throughout genomes(2013-05) McTavish, Emily Jane Bell; Hillis, David M., 1958-Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We used 47,506 single-nucleotide polymorphisms (SNPs) to investigate cattle population history. Cattle are descendants of two independently domesticated lineages, taurine and indicine, that diverged 200,000 or more years ago. We found that New World cattle breeds, as well as many related breeds of cattle in southern Europe, exhibit ancestry from both the taurine and indicine lineages. Although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. We extended these analyses to compare timing of admixture in several breeds of taurine-indicine hybrid origin. We developed a metric, scaled block size (SBS), that uses the unrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient admixture. By comparing test individuals to standards with known recent hybrid ancestry, we were able to differentiate individuals of recent hybrid origin from other admixed individuals using the SBS metric. We genotyped SNP loci using the bovine 50K SNP panel. The selection of sites to include in SNP analyses can influence inferences from the data, especially when particular populations are used to select the array of polymorphic sites. To test the impact of this bias on the inference of population genetic parameters, we used empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We compared the inference of population histories for simulated data sets across different ascertainment conditions using F[subscript ST] and principal components analysis (PCA). Ascertainment bias that results in an over-representation of within-group polymorphism decreases estimates of F[subscript ST] between groups. Geographically biased selection of polymorphic SNPs changes the weighting of principal component axes and can bias inferences about proportions of admixture and population histories using PCA. By combining empirical and simulated data, we were able to both test methods for inferring population histories from genomic SNP data and apply these methods to practical problems.Item Ontogenic Morphometry and Genetic Diversity of Lygus hesperus (Hemiptera: Miridae)(2011-05) Shrestha, Ram B.; Parajulee, Megha N.; Francisco, Michael J. D. S.; Densmore, Llewellyn D.; Holaday, A. Scott; Strauss, Richard E.; Burow, Mark D.Lygus hesperus Knight (Hemiptera: Miridae) is an economically important pest of many field crops, including cotton, in the United States. Lygus hesperus is commonly found in the western United States, hence, it is commonly known as Western Tarnished Plant Bug. Lygus hesperus populations from different geographic regions respond differently to the identical pest management practices. Population-specific pest management strategy is required for successful management of this pest. Morphological or molecular techniques or biological assays could be used to differentiate these Lygus populations. But scientific information on ontogenic morphometry and genetic diversity of this species is mostly lacking. Therefore, ontogenic morphometry, and genetic diversity studies were conducted in the cotton entomology laboratory at Texas AgriLife Research Center, Lubbock, Texas. Lygus hesperus has allometric ontogenic growth patterns and there was no significant difference between ontogenic shape and size trajectories between male and female. The discriminant function analysis revealed significant differences in pattern of ontogenic shape and size between Lygus hesperus and Lygus lineolaris. Thus, the morphometric technique can be used to differentiate nymphal stages of two species when they are hard to differentiate by visual observation of their morphology. Ten polymorphic microsatellite markers were developed and used in a genetic diversity study of eight Lygus hesperus populations from the Texas High Plains. Lygus hesperus population from this region showed a high degree of genetic diversity. Lygus hesperus from the Texas high Plains showed significant genetic population structure and they were differentiated into three genetically distinct populations. The molecular marker comparison study showed Simple Sequence Repeat (SSR) and Amplified Fragment Length Polymorphism (AFLP) markers are potential markers for genetic diversity study of this species when the capillary electrophoresis facility is available but Inter Simple Sequence Repeat (ISSR) markers can be next alternative when the capillary electrophoresis facility is not available. Morphometric and molecular biology knowledge and techniques developed in these studies will be useful in identification of pest management units and development of population specific precision pest management technology for Lygus hesperus.Item Population structure of the American crocodile (crocodylus acutus) in Coiba Island, Panama, inferred from morphometric measurement and microsatellite markers(2010-12) Garcia, Liza M. M.; Densmore, Llewellyn D.; Bradle, Robert D.; Strauss, Richard E.The purpose of this project was to characterize the genetic and morphological composition of Crocodylus acutus in Coiba Island, Panama, and to infer the population structure derived from the genetic variability between the North and South region of the Island as influenced by geographic barriers and proximity to continental Panama. Multivariate analysis of variance (MANOVA) was performed to analyze the morphometric measurements. The MANOVA for the effect of sample site indicate differences between locations (P = 0.010). Regarding morphometric variables, North and South of Coiba Island overlapped in the discriminant space, but individuals in Mainland were slightly separated from the South of Coiba Island. The analysis of molecular variance (AMOVA) reported a variation among populations of 17.04%, and within populations of 82.96% with an Fst of 0.17 (P < 0.01) implying genetic structure between the populations sampled. The Bayesian analysis based on a clustering method for inferring population structure confirmed the subdivision identifying the maximum likelihood in a K = 3. Geographic barriers influenced the genetic and morphometric variation in the populations of C. acutus in Coiba Island, as confirmed by the presence of three subdivisions, the absence of immigrants and the landscape heterogeneity in the Island. This genetic structure should be considered in conservation programs.Item A simulation approach to studying the relationship between landscape features and social system on the genetic structure of a tamarin primate population(2013-05) Valencia Rodriguez, Lina Maria; Di Fiore, Anthony, Ph. D.Landscape genetics is an emerging field that seeks to understand how specific landscape features and microevolutionary processes such as gene flow, genetic drift, and selection interact to shape the amount and spatial distribution of genetic variation. This study explores, through agent based simulations, how the specific mating and social system of tamarin primates (genus Saguinus) influences population genetic structure and patterns of relatedness within and among groups of this primate species, which might affect the ability of landscape genetic studies to detect the effects of fragmentation on gene flow. I use a spatially-explicit agent-based population genetics simulation model (GENESYS) configured to reflect the particular social system of tamarin monkeys (i.e. small group size, limited numbers of breeders per group, frequent twin births, and short dispersal distances) to assess whether the isolation by distance model of genetic differentiation expected in an unfragmented landscape can be distinguished from the isolation by barrier model expected in a fragmented landscape. GENESYS allows a user to explore the effects of social structure and landscape features on the population genetic structure of social animals, such as primates. I simulated two different landscapes containing an otherwise equivalent population of tamarins. In the first setup I simulated a homogeneous landscape unconstrained by any barriers to gene flow, while for the second setup, a barrier to gene flow restricted dispersal from one half of the landscape to the other. I found that the particular mating system of tamarin results in the rapid genetic differentiation of its social groups and consequently its populations. Social groups in the continuous landscape indeed revealed an isolation by distance pattern, while social groups on the fragmented landscape yielded instead an isolation by barrier model, where the barrier rather than geographic distance per se influenced the spatial genetic structure of the population. The results from this study suggest that features of the tamarin social system influence population genetic structure, which could affect the ability of landscape genetic studies to detect the effects of fragmentation on gene flow. To more fully address that issue, future studies should focus on a range of different primate social systems.