Browsing by Subject "genetic population structure"
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Item Assessment of the Contemporary Population Structure and Admixture of Atlantic Swordfish (Xiphias gladius L.) via Mixed Stock Analysis and Bayesian Clustering of Multiple Nuclear SNPS Genotyped through High Resolution Melting(2012-11-28) Smith, Brad 1979-North Atlantic and South Atlantic swordfish (Xiphias gladius L.) are currently managed as two stocks separated at 5?N. While previous studies of genetic population structure using both mitochondrial and nuclear DNA confirm two genetically distinct stocks, sampling coverage has not been uniform or representative of all areas and estimates of admixture in areas of contact have not been provided. In this study, we examined: 1) the applicability of high-resolution melting analysis (HRMA) in population genetic studies of non-model organisms, 2) the use of nuclear markers in Atlantic swordfish and the methodology whereby nuclear gene variation can be quickly screened, identified, and genotyped using short-amplicon (SA) HRMA and unlabeled probe (UP) HRMA, and 3) the use of HRMA to characterize nuclear markers to study the genetic population structure of Atlantic swordfish using representative samples of the entire basin to provide an estimation of population admixture by means of Bayesian individual assignment. High resolution melting analysis (HRMA) is shown to be a highly sensitive, rapid, closed-tube genotyping method amenable to high throughput and, though until recently primarily confined to clinical studies, suitable for population studies in non-model species. Ten nuclear markers were genotyped primarily by SA- and UP-HRMA in North Atlantic (n=419), South Atlantic (n=296), and Mediterranean (n=59) swordfish. Comparisons of pairwise FST, AMOVA, PCoA, and Bayesian individual assignments were congruent with previous finding of three discrete populations with comparatively low levels of estimated gene flow for a marine organism (FST = 0.039-0.126). Population admixture was identified and estimated in the Northeast Atlantic and appeared to be asymmetrical, with swordfish from the South Atlantic found among North Atlantic localities but no North Atlantic migrants identified in the South Atlantic. The Mediterranean boundary currently at the Strait of Gibraltar is found to extend west into Atlantic waters to approximately 8?W. Similarly, the boundary between North and South Atlantic swordfish should be revised to a line that extends north from 0?N 45?W to 25?N 45?W and from that position, as a nearly horizontal line, eastwards to the African coast. Finally, I show that Bayesian individual assignment using the developed marker set can be used for mixed stock allocation in the Northeast Atlantic.Item Bayesian Analyses of Genetic Variation and Population Differentiation in Pacific Swordfish (Xiphias gladius L.) and the Development of High Resolution Melting Assays for Species Identification and Potential Sex-Linked Marker Survey in Istiophorid Billfish(2014-08-06) Lu, Ching-PingSwordfish (Xiphias gladius L.) and istiophorid billfish fisheries in all ocean basins are important commercially and recreationally. Proper assessments of these fisheries are hampered by species misidentification, unknown sex ratios, and unclarified population structure. This dissertation focuses on: 1) genetic assays to identify Pacific billfishes, 2) the characterization of molecular markers potentially linked to gender determination in swordfish and billfishes, and 3) the characterization of the genetic population structure of Pacific swordfish. Unambigous identification of black marlin (Istiompax indica), blue marlin (Makaira nigricans), striped marlin (Kajikia audax) and sailfish (Istiophorus platypterus) was accomplished with two variants of high resolution melting (HRM), including HRM of a 491 bp segment, and melting profiles of a 48 bp unlabeled probe. Both HRM assays target variation in the mitochondrial DNA NADH dehydrogenase subunit 2 (ND2) gene and represent fast and robust alternatives to identify Pacific billfish. Surveys to identify gender-linked molecular markers were conducted using gender-validated samples. The characterization of Randomly Amplified Polymorphic DNA (RAPD) primers suggests a XY chromosomal system in blue marlin, and a ZW chromosomal system in sailfish, and possibly swordfish. Nucleotide sequence analyses of 12 loci known linked to gender determination in other teleosts showed no linkage in blue marlin, sailfish and swordfish. The genetic population structure of Pacific swordfish was surveyed using 16 samples (n=891) with an ample geographic coverage and that included early stages (n=150) and adults (n=741). Bayesian analyses of 20 single nucleotide polymorphisms (SNPs) contained in 10 nuclear loci indicate statistically significant genetic heterogeneity of tropical samples relative to temperate samples, but also with respect to other tropical samples, but no differences among temperate samples. The observed patterns are discussed in light of differences among regions in oceanographic conditions, adult and larval distributions, and tagging experiments.Item Interactive Effects of Geography and Host Plant Species on Genetic and Phenotypic Variation of Cotton Fleahopper Populations(2012-02-14) Barman, ApurbaThe cotton fleahopper, Pseudatomoscelis seriatus (Reuter) is a widely distributed insect across the United States. Although, it feeds on several native wild hosts, its agricultural importance lies as an economic pest of cotton in several states in the southern United States. No studies have addressed intraspecific genetic and phenotypic variation of this insect pest at a large geographic scale. I examined genetic variation among cotton fleahopper populations associated with cotton in different geographic locations across the southern United States (Chapter II). Using dominant, neutral, nuclear molecular markers (AFLP, amplified fragment length polymorphism) and mitochondrial DNA sequences, I found that overall genetic differentiation among different geographic populations, collected from cotton in eleven cotton growing states, was low but significant. AFLP revealed the presence of three regional groups representing western (Arizona), central (Texas, Oklahoma, Arkansas, Louisiana, Mississippi and Alabama), and eastern (Florida, Georgia, South Carolina and North Carolina) populations. I examined if there were distinct lineages of cotton fleahoppers associated with three of its host plant species: cotton (Gossypium hirsutum), horsemint (Monarda punctata) and woolly croton (Croton capitatus) in five different locations of Texas by using AFLP markers (Chapter III). I found two distinct host-associated lineages at three locations and local panmixia in the other two locations. I tested if host preference of cotton fleahoppers were affected by geographic variation and prior experience. Conducting choice tests with a Y-tube olfactometer, I found that host preference in cotton fleahoppers for horsemint (one of its native host plants) is conserved and unaffected by individual?s prior experience with cotton (Chapter IV). Finally, I explored the role of host-plant species in morphological differentiation of the cotton fleahopper in two locations that differ in presence of distinct host-associated lineages. Using a geometric-morphometric approach, I detected significant effect of host plant and geography on body morphology and wing shape of cotton fleahopper populations (Chapter V). Length of antenna and rostrum were two important traits associated with morphological divergence of cotton and horsemint associated insect populations. Cotton associated individuals had relatively longer antenna and rostrum compared to individuals associated with horsemint.