title: Persistence of historical population structure in an endangered species despite near-complete biome conversion in California's San Joaquin Desert.
abstract: Genomic responses to habitat conversion can be rapid, providing wildlife managers with time-limited opportunities to enact recovery efforts that use population connectivity information that reflects predisturbance landscapes. Despite near-complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, but comprehensive genetic data sets are lacking for nearly all species in the region. To fill this knowledge gap, we studied the rangewide population structure of the endangered blunt-nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, using restriction site-associated DNA (RAD), microsatellite and mtDNA data to test whether admixture patterns and estimates of effective migration surfaces (EEMS) can identify land areas with high population connectivity prior to the conversion of native xeric habitats. Clustering and phylogenetic analyses indicate a recent shared history between numerous isolated populations and EEMS reveals latent signals of corridors and barriers to gene flow over areas now replaced by agriculture and urbanization. Conflicting histories between the mtDNA and nuclear genomes are consistent with hybridization with the sister species G. wislizenii, raising important questions about where legal protection should end at the southern range limit of G. sila. Comparative analysis of different data sets also adds to a growing list of advantages in using RAD loci for genetic studies of rare species. We demonstrate how the results of this work can serve as an evolutionary guidance tool for managing endemic, arid-adapted taxa in one of the world's most compromised landscapes.
authors.affiliation: U.S. Geological Survey, San Diego, CA, USA.
authors.forename: Jonathan Q
authors.identifier: http://orcid.org/0000-0001-9398-4894
authors.initials: JQ
authors.lastname: Richmond
authors.affiliation: U.S. Geological Survey, San Diego, CA, USA.
authors.forename: Dustin A
authors.identifier: http://orcid.org/0000-0002-7668-9911
authors.initials: DA
authors.lastname: Wood
authors.affiliation: U.S. Bureau of Land Management, Marina, CA, USA.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Westphal
authors.affiliation: U.S. Geological Survey, San Diego, CA, USA.
authors.forename: Amy G
authors.identifier: http://orcid.org/0000-0002-7835-6571
authors.initials: AG
authors.lastname: Vandergast
authors.affiliation: Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA.
authors.forename: Adam D
authors.identifier: http://orcid.org/0000-0001-8929-6300
authors.initials: AD
authors.lastname: Leaché
authors.affiliation: U.S. Bureau of Land Management, Bakersfield, CA, USA.
authors.forename: Lawrence R
authors.initials: LR
authors.lastname: Saslaw
authors.affiliation: The Nature Conservancy, San Francisco, CA, USA.
authors.forename: H Scott
authors.initials: HS
authors.lastname: Butterfield
authors.affiliation: U.S. Geological Survey, San Diego, CA, USA.
authors.forename: Robert N
authors.initials: RN
authors.lastname: Fisher
mesh_terms: D000818:Animals; D002140:California; D004272:DNA, Mitochondrial / Q000235:genetics; D003889:Desert Climate; D017753:Ecosystem; D056727:Endangered Species; D051456:Gene Flow; D005828:Genetics, Population; D008116:Lizards / Q000235:genetics*; D018895:Microsatellite Repeats; D010802:Phylogeny
chemical_list: D004272:DNA, Mitochondrial
keywords: RAD loci; San Joaquin Desert; admixture; habitat conversion; population structure