Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern
The North America deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographi...
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ftzenodo:oai:zenodo.org:4975049 2023-05-15T16:05:45+02:00 Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern Gottscho, Andrew D. Marks, Sharyn B. Jennings, William Bryan 2015-05-01 https://zenodo.org/record/4975049 https://doi.org/10.5061/dryad.9qt14 unknown doi:10.1002/ece3.1111 https://zenodo.org/communities/dryad https://zenodo.org/record/4975049 https://doi.org/10.5061/dryad.9qt14 oai:zenodo.org:4975049 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode Uma rufopunctata Uma notata Uma inornata Phrynosomatidae Miocene Multi-locus Holocene Uma scoparia info:eu-repo/semantics/other dataset 2015 ftzenodo https://doi.org/10.5061/dryad.9qt1410.1002/ece3.1111 2023-03-10T13:58:34Z The North America deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using Isolation-with-Migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The Likelihood Ratio Test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia, and define this species as a single evolutionarily significant unit for conservation purposes. DNA Sequence DataDiploid nuclear DNA sequence data in fasta format.Sequences.zipPHASEInput and output files for PHASE v2.1.RAxMLInput, output, and gene tree files from RAxML v7.3.0.MrBayesInput, output, and gene tree files from MrBayes v3.2.2.StructuramaInput and output files for Structurama v2.0.GenelandInput files and R script for Geneland v4.0.3.IM and IMaInput and output files for IM and IMa.IM.zipCoalescent SimulationsTree files simulated with Mesquite v2.75 and chi-square test.CoalescentSimulations.zipBEASTInput and output from the Extended Bayesian Skyline Plot implemented in BEAST v1.7.5. Dataset Elephant Seals Southern Elephant Seals Zenodo |
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Open Polar |
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Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
Uma rufopunctata Uma notata Uma inornata Phrynosomatidae Miocene Multi-locus Holocene Uma scoparia |
spellingShingle |
Uma rufopunctata Uma notata Uma inornata Phrynosomatidae Miocene Multi-locus Holocene Uma scoparia Gottscho, Andrew D. Marks, Sharyn B. Jennings, William Bryan Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern |
topic_facet |
Uma rufopunctata Uma notata Uma inornata Phrynosomatidae Miocene Multi-locus Holocene Uma scoparia |
description |
The North America deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using Isolation-with-Migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The Likelihood Ratio Test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia, and define this species as a single evolutionarily significant unit for conservation purposes. DNA Sequence DataDiploid nuclear DNA sequence data in fasta format.Sequences.zipPHASEInput and output files for PHASE v2.1.RAxMLInput, output, and gene tree files from RAxML v7.3.0.MrBayesInput, output, and gene tree files from MrBayes v3.2.2.StructuramaInput and output files for Structurama v2.0.GenelandInput files and R script for Geneland v4.0.3.IM and IMaInput and output files for IM and IMa.IM.zipCoalescent SimulationsTree files simulated with Mesquite v2.75 and chi-square test.CoalescentSimulations.zipBEASTInput and output from the Extended Bayesian Skyline Plot implemented in BEAST v1.7.5. |
format |
Dataset |
author |
Gottscho, Andrew D. Marks, Sharyn B. Jennings, William Bryan |
author_facet |
Gottscho, Andrew D. Marks, Sharyn B. Jennings, William Bryan |
author_sort |
Gottscho, Andrew D. |
title |
Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern |
title_short |
Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern |
title_full |
Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern |
title_fullStr |
Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern |
title_full_unstemmed |
Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern |
title_sort |
data from: speciation, population structure, and demographic history of the mojave fringe-toed lizard (uma scoparia), a species of conservation concern |
publishDate |
2015 |
url |
https://zenodo.org/record/4975049 https://doi.org/10.5061/dryad.9qt14 |
genre |
Elephant Seals Southern Elephant Seals |
genre_facet |
Elephant Seals Southern Elephant Seals |
op_relation |
doi:10.1002/ece3.1111 https://zenodo.org/communities/dryad https://zenodo.org/record/4975049 https://doi.org/10.5061/dryad.9qt14 oai:zenodo.org:4975049 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.9qt1410.1002/ece3.1111 |
_version_ |
1766401647287730176 |