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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Online Access: | https://doi.org/10.5061/dryad.9qt14 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::e6315c67148816c526d321852235116c 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 Jennings, W. Bryan 2015-05-01 https://doi.org/10.5061/dryad.9qt14 undefined unknown Dryad https://dx.doi.org/10.5061/dryad.9qt14 http://dx.doi.org/10.5061/dryad.9qt14 lic_creative-commons 10.5061/dryad.9qt14 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:85861 oai:easy.dans.knaw.nl:easy-dataset:85861 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 Uma rufopunctata Pliocene coalescent speciation phylogeography Uma notata Uma inornata Phrynosomatidae Miocene Multi-locus Holocene Uma scoparia Pleistocene California Arizona Mojave Desert Colorado Desert United States Life sciences medicine and health care geo envir Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2015 fttriple https://doi.org/10.5061/dryad.9qt14 2023-01-22T17:23:41Z 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 Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Uma rufopunctata Pliocene coalescent speciation phylogeography Uma notata Uma inornata Phrynosomatidae Miocene Multi-locus Holocene Uma scoparia Pleistocene California Arizona Mojave Desert Colorado Desert United States Life sciences medicine and health care geo envir |
spellingShingle |
Uma rufopunctata Pliocene coalescent speciation phylogeography Uma notata Uma inornata Phrynosomatidae Miocene Multi-locus Holocene Uma scoparia Pleistocene California Arizona Mojave Desert Colorado Desert United States Life sciences medicine and health care geo envir Gottscho, Andrew D. Marks, Sharyn B. Jennings, William Bryan Jennings, W. 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 Pliocene coalescent speciation phylogeography Uma notata Uma inornata Phrynosomatidae Miocene Multi-locus Holocene Uma scoparia Pleistocene California Arizona Mojave Desert Colorado Desert United States Life sciences medicine and health care geo envir |
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 Jennings, W. Bryan |
author_facet |
Gottscho, Andrew D. Marks, Sharyn B. Jennings, William Bryan Jennings, W. 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 |
publisher |
Dryad |
publishDate |
2015 |
url |
https://doi.org/10.5061/dryad.9qt14 |
genre |
Elephant Seals Southern Elephant Seals |
genre_facet |
Elephant Seals Southern Elephant Seals |
op_source |
10.5061/dryad.9qt14 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:85861 oai:easy.dans.knaw.nl:easy-dataset:85861 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 |
op_relation |
https://dx.doi.org/10.5061/dryad.9qt14 http://dx.doi.org/10.5061/dryad.9qt14 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.9qt14 |
_version_ |
1766401646947991552 |