Browsing by Subject "population structure"
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Item Genetic analysis of the endangered silver rice rat (Oryzomys palustris natator) and Lower Keys marsh rabbit (Sylvilagus palustris hefneri)(Texas A&M University, 2007-04-25) Crouse, Amanda LouiseGenetic analyses of two endangered species of mammals in the Lower Keys of Florida (Lower Keys marsh rabbit, LKMR, Sylvilagus palustris hefneri; silver rice rat, SRR, Oryzomys palustris natator) were performed to evaluate the genetic structure of their populations. Mitochondrial sequence data (control region; 763 base pairs (bp), LKMR; 788 bp, SRR) were used to explore patterns of genetic variation within and among island populations in both species. Analysis of the SRR also included 8 polymorphic nuclear microsatellite loci (9 to 16 alleles). Phylogenetic analyses of mitochondrial sequence data for both species revealed two main lineages corresponding to eastern and western localities, with high levels of genetic structuring (LKMR FST = 0.982, SRR ????ST = 0.916). The two species differed in the level of sequence divergence between eastern and western populations (LKMR, 19 bp; SRR 4 bp). In addition to an overall similar pattern of genetic subdivision, populations of both species possessed low levels of mtDNA variation (haplotypic diversity in the LKMR = 66.1%, SRR = 58.6%). Microsatellite analyses of the SRR revealed subdivision between eastern and western regions. Although less pronounced than the structure observed in mtDNA, the overall pattern was still apparent. Additional examination of divergence between mainland and Lower Keys rice rats revealed a genetic division that indicated a lack of recent gene exchange between the regions (i.e. no shared haplotypes, the presence of private alleles, and distinctive separation in numerous analyses). Although this degree of division does not warrant species designation, the levels and patterns of divergence, both morphological and genetic, do suggest genetic isolation of mainland and island forms. This fact, along with restricted gene flow between the Lower Keys and the Everglades, suggests that the SRR is on an evolutionary trajectory separate from its mainland counterparts and validates its identification as a separate subspecies, Oryzomys palustris natator. Finally, the genetic division between eastern and western populations of the SRR and LKMR suggests that populations of both species in these two regions of the Lower Keys should be treated as separate management units, especially when considering the enhancement of populations via translocations.Item Genetic variation in Atlantic yellowfin tuna (Thunnus albacares) to assess stock structure and reproductive variance(Texas A&M University, 2005-02-17) Farnham, Tiffany TalleyThe population genetic structure of Atlantic yellowfin tuna (Thunnus albacares) has received little attention despite the substantial fishing mortality of juveniles caused by purse seining around fish aggregating devices in the Gulf of Guinea targeting multi-species schools that also include similarly sized skipjack tuna (Katsuwonus pelamis) and bigeye tuna (T. obesus). We used sequence data from 355 bp of the mitochondrial control region I as well as six microsatellite loci to examine: (1) population structure, and (2) to look for evidence of reproductive variance. We analyzed two samples of adults from the Gulf of Mexico (GOM) and one sample of early juveniles (20-50 mm) from the Gulf of Guinea (GOG). We found no evidence of geographic or temporal differentiation among the samples. Accordingly, the null hypothesis of panmixia for yellowfin tuna in the Atlantic Ocean could not be rejected. A sudden expansion analysis based on mtDNA control region I sequence data of yellowfin tuna was highly significant. Time estimates for expansion were between 40,000 and 80,000 years before present. The associated high levels of homoplasy could be masking any existing population structure. Additional sampling from additional locations and across several years will be needed to test the hypothesis of panmixia. We also provide preliminary evidence of the Allendorf-Phelps effect, which may contribute to reproductive variance. This is the first evidence of this effect in any other tuna or pelagic species. Data indicates that early juveniles sharing the same mtDNA control region I haplotype were caught in the same tow and had a significant probability of halfsibship status as calculated from their haplotype and genotype at one microsatellite locus through kinship analysis. Sampling throughout the spawning season and across several years, as well as analysis with additional microsatellite loci that have a more even distribution of alleles, will be needed to more fully identify the sibling status of larvae and early juveniles caught in the same tow as well as the extent of this reproductive variance.Item Historical Demography and Genetic Population Structure of the Blackfin Tuna (Thunnus atlanticus) from the Northwest Atlantic Ocean and the Gulf of Mexico(2010-01-16) Saxton, Brandon L.Little is known about the population structure and genetic variability of blackfin tuna despite catch increases over the past 25 years. In this thesis, levels of genetic variation contained in 323bp of the mitochondrial DNA (mtDNA) control region-I (CR-I) and in six microsatellite loci were characterized for two regions: the Gulf of Mexico (GoM) and the Northwest Atlantic. Large amounts of mtDNA diversity (h>0.99; =0.047) were observed in both regions. Mismatch distribution analysis of the CR-I sequence data, using a mutation rate of 1.6% Ma-1for scombroid fishes, indicate blackfin tuna underwent population expansion about 1.4 Ma, a timeline concordant with the expansion of other tunas and billfishes. Estimates of female effective population size were very large at 7.8 million and 12.8 million individuals for the NW Atlantic and the GoM, respectively. Both mtDNA and six microsatellite loci were used to determine blackfin tuna population structure. Microsatellite and mtDNA AMOVAs revealed significant differentiation (msat st=0.01, p=0.006 and mtDNA st=0.01, p=0.049) between the GoM and the NW Atlantic samples. Migration estimates using mtDNA data indicate that twice as many females enter the NW Atlantic from the GoM (346 individuals/generation) than the opposite direction (150 individuals/generation). Migration estimates using microsatellite data were substantially smaller, with the Gulf receiving 7 individuals/generation and the NW Atlantic 4 individuals/generation. Finally, low levels of genetic differentiation using microsatellite data have been reported in other highly abundant marine fishes, which have been attributed to homoplasy in allele size. To test this hypothesis, the allele frequency distributions of blackfin and yellowfin tuna at six microsatellite loci were compared. The distances between species were surprisingly small (Da=4.0%, (delta mu)squared=1.08), with a large degree of similarity in frequency distributions at four loci. The comparison of bigeye tuna at two microsatellite loci revealed additional inter-specific similarities. A mutation rate for these loci was estimated by modifying an equation used to estimate time since divergence. Microsatellites in tunas appear to evolve at a rate (4.3x10-7 Ma-1) that is two orders of magnitude slower than other fishes (1x10-5 Ma-1). Accordingly, microsatellite allele size similarities are plesiomorphic and not due to homoplasy.Item Mate Choice, Genetic Variation, and Population Structure in Hybrid Zones(2012-02-14) Culumber, Zachary WyattNatural hybrid zones provide opportunities to study a range of evolutionary phenomena from speciation to the genetic basis of fitness-related traits. Additionally, investing the structure of hybrid zones can provide valuable insight in the ecology and evolution of species. The present dissertation approaches the investigation of natural hybrid zones between Xiphophorus birchmanni and X. malinche from a population genetics perspective. The goal of the chapters herein are to investigate the genetic structure of these natural hybrid zones overall and the genetic structure of the populations within them in an effort to better understand the factors producing and maintaining spatial genetic patterns among this species pair and their hybrids. Using informative single nucleotide polymorphisms (SNPs) in one mitochondrial and three nuclear intron loci, I show that hybrid zones occur in replicated fashion in multiple stream reaches along a gradient from high to low elevation. Tests of FIS and linkage disequilibrium (LD) revealed significant genetic structure within a small subset of populations. Specifically, parentals and hybrids all three occur in some locations while other locations appear to be hybrid swarms. I then investigated a behavioral mechanism of reproductive isolation - social association, which might affect population structure. In clean water, individuals shoaled significantly more closely with conspecifics. Additionally, genotyping of females and their embryos revealed signatures of non-random mating in structured populations. Taken together, assortative social grouping, which may translate to assortative female mate choice, likely plays a role in maintaining population structure. Finally, I show that fluctuating asymmetry is significantly higher in unstructured than structure populations. This is a further indication that some form of non-random mating occurs in structured populations and has effects on male phenotypes.Item Molecular and Pheromone Studies of Pecan Nut Casebearer, Acrobasis nuxvorella Neunzig (Lepidoptera: Pyralidae)(2011-02-22) Hartfield, Emilie AnneThe pecan nut casebearer, Acrobasis nuxvorella Neunzig (Lepidoptera: Pyralidae) is the most damaging insect pest of pecan, Carya illinoinensis (Wang) K. Koch (Fagales: Juglandaceae). Two sex pheromones have been identified for this species and are currently being used to assist pecan growers in the timing of insecticide applications. The discovery that there are two pheromone types produced by A. nuxvorella has led to complications in the implementation of pheromone monitoring programs. One pheromone (referred to as standard) is attractive to moths in the southern US, but not in Mexico. The other pheromone (referred to as Mexican) is attractive to moths in the southern US and in Mexico. Because most male lepidopterans respond only to a specific pheromone, it was suspected that there were two pheromone strains of A. nuxvorella, one exclusively present in the northern distribution of A. nuxvorella (US strain) and the other widely distributed from Sonora, Chihuahua, and Durango in Northern Mexico to Texas, Georgia, and Oklahoma in the US (Mexican strain). In order to confirm the existence of the two alleged pheromone strains, AFLP markers were obtained and analyzed, male response to pheromones was observed and phenological differences were assessed. Additionally, the relative abundance of each of the two pherotypes was evaluated and the population structure of this pest across its geographic distribution was determined. Results of genetic analysis show that the genetic differentiation between these insects is not explained by pheromone type. This information is further supported by a pheromone assay in which a large proportion of US collected A. nuxvorella males and Mexican collected A. nuxvorella males chose both pheromones when tested multiple times. Furthermore, no phenological differences were detected between the two pherotypes in the US, although significantly more male A. nuxvorella in the US are attracted to field-deployed pheromone traps baited with the standard pheromone than the Mexican pheromone. Finally, population genetic analyses indicate a high degree of genetic structure in A. nuxvorella across its geographic distribution, with the genetically distinct populations occurring in areas where A. nuxvorella is not native, but has been introduced.Item Molecular systematics and phylogeography of the dusky dolphin (Lagenorhynchus obscurus) derived from nuclear and mitochondrial loci(Texas A&M University, 2006-04-12) Harlin, April DawnThis study presents evidence from mitochondrial and nuclear loci that there is genetic divergence among and within geographic populations of Lagenorhynchus obscurus. The effect of seasonal variation on the genetic structure within New Zealand was examined with mitochondrial DNA control region sequences from 4 localities. Analysis of nested haplotype clades indicated genetic fragmentation and at least 1 historical population expansion within New Zealand. AMOVA and Fst values from nuclear and mitochondrial DNA sequences suggested significant divergence between New Zealand, South Africa, Argentina, and Peru. Dispersal via the west-wind drift was not supported by patterns of population structure among regions. Alternatively, these data support reciprocal exchange among all four regions with 100% posterior probability for a root of origin in the Indian/Atlantic Oceans. The degree of divergence between Peru and other regions indicates the isolation of Peruvian stock is temporally correlated with the constriction of Drake??s passage in the Plio-Pleistocene. There is evidence that the Plio-Pliestocene paleoceanography of the Indian and Southern Atlantic Oceans influenced phylogeography with shifts of temperate sea surface temperatures northward ~5?? of latitude, disrupting the dispersal corridor between New Zealand and Atlantic populations. A preference for temperate waters along continental shelves is proposed as an explanation for lack of contemporary genetic exchange among regions. This study supports the polyphyly of the genus Lagenorhynchus. North Atlantic species form a monophyletic Lagenorhynchus. In the Southern Hemisphere, L. australis/L. cruciger and L. obliquidens/L. obscurus do not form a monophyletic group. I discuss the taxonomic implications and propose taxonomic revision of the genus based on these results. Measures of character interaction indicate that combined evidence from nuclear and mitochondrial genes provide better phylogenetic resolution among delphinid lineages than any data partition independently, despite some indications of conflict among mitochondrial and nuclear data.Item Population structure of Acrotrichis xanthocera (Matthews) (Coleoptera: Ptiliidae) in the Klamath Ecoregion of northwestern California, inferred from mitochondrial DNA sequence variation(Texas A&M University, 2004-09-30) Caesar, Ryan MatthewThe Klamath-Siskiyou Ecoregion of northern California and southern Oregon has extremely high biodiversity, but conservation centers on the protection of habitat for the northern spotted owl. A network of late successional reserves has been established without consideration of potential for protecting overall biodiversity, including genetic diversity. Mitochondrial DNA sequences are used to examine the population structure of Acrotrichis xanthocera (Coleoptera: Ptiliidae) sampled from five late successional reserves within the Klamath-Siskiyou Ecoregion and five comparison sites from northern California. Measures of gene flow, phylogenetic analysis, and nested clade analysis are employed to infer historical demographic and phylogeographic processes. Results show that A. xanthocera populations have undergone past range expansion, but gene flow is currently limited. Individual late successional reserves do not adequately protect the genetic variation in this species. Although further research is needed, these results are likely to be congruent for other edaphic arthropod species. Improvement of the late successional reserve system is warranted for maximum protection of the genetic diversity of soil arthropod populations.Item Population Structure, Association Mapping of Economic Traits and Landscape Genomics of East Texas Loblolly Pine ( Pinus taeda L.)(2013-05-07) Chhatre, Vikram E.Loblolly pine (Pinus taeda L.) is an ecologically and economically important southern pine, distributed across the southeastern United States. Its genetic improvement for breeding and deployment is a major goal of the Western Gulf Forest Tree Improvement Program (WGFTIP) hosted by the Texas A&M Forest Service. Rapid advances in genomics and molecular marker technology have created potential for application of Marker Assisted Selection (MAS) and Genomic Selection (GS) for accelerated breeding in forest trees. First-generation selection (FGS) and second- generation selection (SGS) breeding populations of loblolly pine from east Texas were studied to estimate the genetic diversity, population structure, linkage disequilibrium (LD), signatures of selection and association of breeding traits with genetic markers using a genome-wide panel of 4264 single nucleotide polymorphisms (SNPs). Under- standing the genetic basis of local adaptation is crucial to disentangle the dynamics of gene flow, drift and selection and to address climate change. Bayesian mixed linear models and logistic regression were used to associate SNP variation with geography, climate, aridity and growth season length and markers with strong correlations were investigated for biological functions. Relatively high levels of observed (Ho = 0.178?0.198) and expected (He = 0.180-0.198) heterozygosities were found in all populations. The amount of inbreeding was very low, and many populations exhibited a slight excess of heterozygotes. The population substructure was weak, but FST indicated more pronounced differentiation in the SGS populations. As expected for outcrossing natural populations, the genome-wide LD was low, but marker density was insufficient to deduce the decay rate. Numerous associations were found between various phenotypes and SNPs, but few remained significant after false positive correction. Signatures of diversifying and balancing selection were found in markers representing important biological functions. Strong correlations supported by Bayes factors were found between various environmental variables and several SNPs. Logistic regression found hundreds of significant marker-environment associations, but none remained significant after false-positive correction, which was likely too stringent and will require further investigation. Annotations of significant markers implicated them in crucial biological functions. These results present the first step in the application of MAS to the WGFTIP for loblolly pine genetic improvement and will contribute to the knowledgebase necessary for genomic selection technology. Results from environmental association study provide important information for designing breeding strategies to address climate change and for genetic conservation purposes.Item The Effect of Environmental Contaminants on Mating Dynamics and Population Viability in a Sex-Role-Reversed Pipefish(2010-07-14) Partridge, Charlyn G.Understanding how anthropogenic activity impacts the health and viability of wildlife populations is one of the most important tasks of environmental biology. A key concern related to bi-products of human activity is the accumulation of environmental pollutants within aquatic environments. Pollutants such as endocrine disruptors and heavy metals have the potential to impact both human and wildlife populations in contaminated areas. While much research has focused on how these compounds impact natural selection processes, such as viability and reproduction, their effect on sexual selection processes is not as clear. The goal of this dissertation was to address how environmental contaminants impact sexual selection processes in a sex-role reversed pipefish and evaluate how these effects may impact long-term population viability. Here we show that short periods of exposure to environmentally relevant concentrations of a synthetic estrogen result in male pipefish with female-like secondary sexual traits. While these males are capable of reproduction, exposed males are discriminated against by females in mate choice tests. In natural populations, this type of discrimination could reduce male mating opportunities, potentially reducing their reproductive success. In an additional component of this dissertation, it was discovered that pipefish populations around Mobile Bay, specifically Weeks Bay, are currently being exposed to significantly elevated levels of mercury. These populations are genetically distinct from coastal populations but moderate levels of gene flow occur among sites, and gene flow between contaminated and non-contaminated population may be influencing how environmental contaminants are impacting genetic diversity and population viability. In the case of endocrine disruptors, migration between contaminated and non-contaminated sites may negatively impact population viability. Morphological traits induced with exposure to contaminants may be maintained for extended periods of time, therefore, the effect the exposed phenotype has on mating dynamics and sexual selection could be carried to non-contaminated sites if exposed individuals move to new populations. On the other hand, immigration of individuals from non-contaminated sites into contaminated areas may help maintain genetic diversity within exposed populations. In conclusion, the work presented in this dissertation shows that the presence of environmental toxins can significantly impact sexual selection processes, which in turn can have profound effects on the viability and future evolutionary trajectory of populations. Future work in this area should not only address how these toxins impact individual fitness, but should also address how population structure may be influencing the severity of these compounds on natural populations.