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Articles 1 - 8 of 8
Full-Text Articles in Genetics and Genomics
Scalable Parallelization Of A Markov Coalescent Genealogy Sampler, Philip E. Davis
Scalable Parallelization Of A Markov Coalescent Genealogy Sampler, Philip E. Davis
Masters Theses
Coalescent genealogy samplers are effective tools for the study of population genetics. They are used to estimate the historical parameters of a population based upon the sampling of present-day genetic information. A popular approach employs Markov chain Monte Carlo (MCMC) methods. While effective, these methods are very computationally intensive, often taking weeks to run. Although attempts have been made to leverage parallelism in an effort to reduce runtimes, they have not resulted in scalable solutions. Due to the inherently sequential nature of MCMC methods, their performance has suffered diminishing returns when applied to large-scale computing clusters. In the interests of …
The Population Genetics Of The Endangered Scalloped Hammerhead Shark, Sphyrna Lewini, Across Its Eastern Pacific Range, Holly Nance
All Dissertations
I have characterized the population genetic structure, inferred the evolutionary processes shaping it, and estimated effective population size (Ne) using different contemporary and coalescent methods in the endangered scalloped hammerhead shark, Sphyrna lewini, throughout its Eastern Pacific (EP) range. I found significant genetic differentiation among seven coastal sites between Mexico and Ecuador using 15 microsatellite loci, and significant isolation by distance among samples of mtDNA control region haplotypes. While Bayesian statistical analyses and coalescent-based methods revealed low levels of ecological connectivity between most sampled sites (point estimates of Nm = 0.6 - 7.3), mismatch analyses showed that all populations experienced …
Phylogeography Of The Frog Leptodactylus Validus (Amphibia: Anura): Patterns And Timing Of Colonization Events In The Lesser Antilles, Arley Camargo, W. Ronald Heyer, Rafael O. De Sá
Phylogeography Of The Frog Leptodactylus Validus (Amphibia: Anura): Patterns And Timing Of Colonization Events In The Lesser Antilles, Arley Camargo, W. Ronald Heyer, Rafael O. De Sá
Biology Faculty Publications
The frog Leptodactylus validus occurs in northern South America, Trinidad and Tobago, and the southern Lesser Antilles (Grenada and St. Vincent). Mitochondrial DNA sequences were used to perform a nested clade phylogeographic analysis (NCPA), to date colonization events, and to analyze colonization patterns using on a relaxed molecular clock and coalescent simulations. L. validus originated on the mainland and first colonized Trinidad with subsequent independent colonizations of Tobago and the Lesser Antilles from Trinidad. The NCPA suggests a historical vicariant event between populations in Trinidad and Tobago from those in the Lesser Antilles. The colonization of Trinidad occurred 1 million …
Evidence For Contrasting Modes Of Selection At Interacting Globin Genes In The European Rabbit (Oryctolagus Cuniculus), R. Campos, Jay F. Storz, N. Ferrand
Evidence For Contrasting Modes Of Selection At Interacting Globin Genes In The European Rabbit (Oryctolagus Cuniculus), R. Campos, Jay F. Storz, N. Ferrand
Jay F. Storz Publications
In hybrid zones between genetically differentiated populations, variation in locus-specific rates of introgression may reflect adaptation to different environments or adaptation to different genetic backgrounds. The European rabbit, Oryctolagus cuniculus, is well-suited to studies of such hybrid zone dynamics because it is composed of two genetically divergent subspecies that hybridize in a zone of secondary contact in central Iberia. A species-wide survey of allozyme variation revealed a broad range of locus-specific divergence levels (FST ranged from 0 to 0.54, mean FST = 0.16). Interestingly, the two loci that fell at opposite ends of the distribution of …
Natural Selection Drives Altitudinal Divergence At The Albumin Locus In Deer Mice, Peromyscus Maniculatus, Jay F. Storz, Jean M. Dubach
Natural Selection Drives Altitudinal Divergence At The Albumin Locus In Deer Mice, Peromyscus Maniculatus, Jay F. Storz, Jean M. Dubach
Jay F. Storz Publications
In populations that are distributed across steep environmental gradients, the potential for local adaptation is largely determined by the spatial scale of fitness variation relative to dispersal distance. Since altitudinal gradients are generally characterized by dramatic ecological transitions over relatively short linear distances, adaptive divergence across such gradients will typically require especially strong selection to counterbalance the homogenizing effect of gene flow. Here we report the results of a study that was designed to test for evidence of adaptive divergence across an altitudinal gradient in a natural population of deer mice, Peromyscus maniculatus. We conducted a multilocus survey of …
Natural Selection On Protein Polymorphism In The Rodent Genus Peromyscus: Evidence From Interlocus Contrasts, Jay F. Storz, Michael W. Nachman
Natural Selection On Protein Polymorphism In The Rodent Genus Peromyscus: Evidence From Interlocus Contrasts, Jay F. Storz, Michael W. Nachman
Jay F. Storz Publications
The effects of natural selection are generally locus-specific, whereas migration, drift, and inbreeding are expected to have relatively uniform effects across the entire genome. This suggests that multilocus surveys of multiple populations can be used to distinguish selection from demographic effects. The purpose of this study was to test for evidence of selection on protein polymorphism in natural populations of mice in the genus Peromyscus. We analyzed published data from geographic surveys of allozyme variation and used a coalescent- based simulation model to identify specific loci that deviated from neutral expectations. Observed FST values generally exhibited a remarkably …
Genetic Effective Size Of A Wild Primate Population: Influence Of Current And Historical Demography, Jay F. Storz, Uma Ramakrishnan, Susan C. Alberts
Genetic Effective Size Of A Wild Primate Population: Influence Of Current And Historical Demography, Jay F. Storz, Uma Ramakrishnan, Susan C. Alberts
Jay F. Storz Publications
A comprehensive assessment of the determinants of effective population size (Ne) requires estimates of variance in lifetime reproductive success and past changes in census numbers. For natural populations, such information can be best obtained by combining longitudinal data on individual life histories and genetic marker-based inferences of demographic history. Independent estimates of the variance effective size (NeV, obtained from life-history data) and the inbreeding effective size (NeI, obtained from genetic data) provide a means of disentangling the effects of current and historical demography. The purpose of this study was to assess …
Testing For Genetic Evidence Of Population Expansion And Contraction: An Empirical Analysis Of Microsatellite Dna Variation Using A Hierarchical Bayesian Model, Jay F. Storz, Mark Beaumont
Testing For Genetic Evidence Of Population Expansion And Contraction: An Empirical Analysis Of Microsatellite Dna Variation Using A Hierarchical Bayesian Model, Jay F. Storz, Mark Beaumont
Jay F. Storz Publications
The role of past climatic change in shaping the distributions of tropical rain forest vertebrates is central to long-standing hypotheses about the legacy of the Quaternary ice ages. One approach to testing such hypotheses is to use genetic data to infer the demographic history of codistributed species. Population genetic theory that relates the structure of allelic genealogies to historical changes in effective population size can be used to detect a past history of demographic expansion or contraction. The fruit bats Cynopterus sphinx and C. brachyotis (Chiroptera: Pteropodidae) exhibit markedly different distribution patterns across the Indomalayan region and therefore represent an …