title: The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle.
abstract: As the field of phylogeography has matured, it has become clear that analyses of one or a few genes may reveal more about the history of those genes than the populations and species that are the targets of study. To alleviate these concerns, the discipline has moved towards larger analyses of more individuals and more genes, although little attention has been paid to the qualitative or quantitative gains that such increases in scale and scope may yield. Here, we increase the number of individuals and markers by an order of magnitude over previously published work to comprehensively assess the phylogeographical history of a well-studied declining species, the western pond turtle (Emys marmorata). We present a new analysis of 89 independent nuclear SNP markers and one mitochondrial gene sequence scored for rangewide sampling of >900 individuals, and compare these to smaller-scale, rangewide genetic and morphological analyses. Our enlarged SNP data fundamentally revise our understanding of evolutionary history for this lineage. Our results indicate that the gains from greatly increasing both the number of markers and individuals are substantial and worth the effort, particularly for species of high conservation concern such as the pond turtle, where accurate assessments of population history are a prerequisite for effective management.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Dr. South, Los Angeles, CA, 90095-1606, USA; La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, La Kretz Hall, Suite 300, 619 Charles E. Young Dr. South, Los Angeles, CA, 90095-14966, USA.
authors.forename: Phillip Q
authors.initials: PQ
authors.lastname: Spinks
authors.forename: Robert C
authors.initials: RC
authors.lastname: Thomson
authors.forename: H Bradley
authors.initials: HB
authors.lastname: Shaffer
mesh_terms: D000818:Animals; D002140:California; D003247:Conservation of Natural Resources; D004272:DNA, Mitochondrial / Q000235:genetics; D056727:Endangered Species; D019143:Evolution, Molecular; D049810:Genetic Speciation; D005828:Genetics, Population / Q000379:methods*; D008969:Molecular Sequence Data; D009922:Oregon; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D014426:Turtles / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial
keywords: conservation genetics; ecological genetics; phylogeography; population genetics - empirical; reptiles