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Humboldt State University

1. Gottscho, Andrew. Coalescent analysis of fifteen nuclear loci reveals Pleistocene speciation and low genetic diversity in the Mojave Fringe-toed Lizard, Uma scoparia.

Degree: MA, Biological Sciences, 2010, Humboldt State University

Analyzing DNA sequence data from multiple unlinked nuclear loci in a coalescent Isolation-with-Migration (IM) model is a statistically powerful method for estimating population divergence times, effective population sizes, and gene flow. This approach was used to reconstruct the evolutionary history of the Mojave fringe-toed Lizard, Uma scoparia, which is restricted to windblown sand habitats in the Mojave and Colorado Deserts of southern California and western Arizona, a region that is thought to have undergone dramatic climatic change during and since the Pleistocene epoch. To shed light on the origin of this species, I analyzed 15 nuclear loci (621,694 total bp) representing twenty localities of U. scoparia and four localities from its sister species to the south, U. notata. I found a latitudinal gradient in heterozygous SNPs and indels, low nucleotide diversity in U. scoparia (?? = 0.148%, SD = 0.167%), particularly relative to U. notata (?? = 0.469%, SD = 0.366%), and reciprocal monophyly in 3/15 gene trees. Using the IM model, I estimated with 95% confidence that U. scoparia and U. notata speciated in the Pleistocene epoch (~1 ??? 1.4 mya, 95% CI ~0.7 mya ??? 2.1 mya) without significant gene flow (2Nm < 1), an estimate that is robust to violations of the no-recombination assumption. I also found that U. notata has 2-5 times the effective population size of U. scoparia. These findings suggest that U. scoparia originated in the Pleistocene epoch and was confined to a Colorado Desert refuge during glacial maxima; northern populations represent a recent range expansion. Advisors/Committee Members: Jennings, W. Bryan.

Subjects/Keywords: Lizard; Speciation; Gene flow; Pleistocene; Mojave Desert; Colorado Desert; Uma; Coalescent; Multi-locus; Biogeography; Low genetic diversity

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APA (6th Edition):

Gottscho, A. (2010). Coalescent analysis of fifteen nuclear loci reveals Pleistocene speciation and low genetic diversity in the Mojave Fringe-toed Lizard, Uma scoparia. (Masters Thesis). Humboldt State University. Retrieved from http://hdl.handle.net/2148/581

Chicago Manual of Style (16th Edition):

Gottscho, Andrew. “Coalescent analysis of fifteen nuclear loci reveals Pleistocene speciation and low genetic diversity in the Mojave Fringe-toed Lizard, Uma scoparia.” 2010. Masters Thesis, Humboldt State University. Accessed August 18, 2019. http://hdl.handle.net/2148/581.

MLA Handbook (7th Edition):

Gottscho, Andrew. “Coalescent analysis of fifteen nuclear loci reveals Pleistocene speciation and low genetic diversity in the Mojave Fringe-toed Lizard, Uma scoparia.” 2010. Web. 18 Aug 2019.

Vancouver:

Gottscho A. Coalescent analysis of fifteen nuclear loci reveals Pleistocene speciation and low genetic diversity in the Mojave Fringe-toed Lizard, Uma scoparia. [Internet] [Masters thesis]. Humboldt State University; 2010. [cited 2019 Aug 18]. Available from: http://hdl.handle.net/2148/581.

Council of Science Editors:

Gottscho A. Coalescent analysis of fifteen nuclear loci reveals Pleistocene speciation and low genetic diversity in the Mojave Fringe-toed Lizard, Uma scoparia. [Masters Thesis]. Humboldt State University; 2010. Available from: http://hdl.handle.net/2148/581

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