DOI: 10.5061/dryad.4b8gththr
title: Physaria thamnophila microsatellite dataset

description: Taxonomy, genetics and biogeography each make key contributions to
 biological conservation. However, integrating these disciplines to obtain
 a coherent account of the status of a taxon of concern is not always
 straightforward. This is the case for the cross-border endemic
 plant Physaria thamnophila (Brassicaceae). This US
 federally-listed endangered species is restricted to a set of unique
 geological sites just north of the Rio Grande (Rio Bravo del Norte) river
 in south Texas, USA. A single highly-disjunct occurrence of this species
 is found on a geologically and ecologically distinct site 260 km to the
 south, in Tamaulipas, Mexico. In this work, we quantify the genetic
 differentiation between the U.S. and Mexican populations using four
 microsatellite markers and sequences from three nuclear genes. In both
 sets of data, we find a high level of genetic divergence consistent with
 geographic isolation on a time scale of 1–2.5 million years. Further, we
 provide a hypothesis for the geological basis of this geographic
 isolation. Integrating our data with ecological, taxonomic and
 conservation considerations, we propose the sub-specific designation of
 Physaria thamnophila subsp. loretensis for the Mexican population. The
 evolutionary and conservation implications of this designation are
 presented. 
description: Plant collections and DNA sampling.—All
 <em>Physaria</em> species were formerly included in the genus
 <em>Lesquerella</em> (Al-Shebaz & O’Kane 2002).
 Tissues were obtained from 1) laboratory-germinated seedlings, 2) herbaria
 specimens as listed in Appendix 1. Additional tissue collections were made
 from<em> P. thamnophila</em> populations under permit and
 consultation with the US Fish and Wildlife Service. We sampled all known
 populations of<em> P. thamnophila</em> in which plants were
 present at the time of sampling. Four populations were in Zapata County,
 Texas, ten in Starr County, Texas, and one in Tamaulipast, Mexico.
 Approximately 0.5 cm<sup>2</sup> of tissue was used for each
 DNA isolation. DNAs were isolated from both fresh and dried tissue by a
 simple micro-scale preparation described previously (Pepper &
 Norwood, 2001).  Microsatellite marker
 analyses.—Genomic DNAs from a single individual from the <em>P.
 thamnophila </em>SMR population (Starr County, Texas, U.S.A.) were
 used for microsatellite discovery. DNA fragments containing microsatellite
 (CT, CT and GG) repeats were captured using a biotinylated-oligonucleotide
 method described previously (Terry et al. 2006). All primers were designed
 to have a 45-60% GC content and a salt-adjusted (50 mM NaCl) melting
 temperature of 63–64°C. Amplifications were performed with Phusion Hi-Fi
 polymerase (New England Biolabs) using ±10 ng genomic DNA as a template.
 An annealing temperature of 58°C was employed for all reactions. PCR
 buffer and cycling conditions followed the manufacturer’s recommendations
 (New England Biolabs). Four microsatellite markers (Appendix 2) were
 amplified using fluorescently labeled primers (6-HEX and 6-FAM).
 Multiplexed (HEX + FAM) fragment analysis was performed using the ABI 3130
 capillary DNA sequencer as described (Tarin et al. 2014). Fragment sizes
 were determined using GeneScan ver. 3.1 software (Applied Biosystems
 Inc.). Microsatellite genotyping was performed using Genotyper ver. 2.5
 software (Applied Biosystems Inc.).  GeneAlEx ver. 6.5 (Peakall &
 Smouse 2012).
description: Microsoft Excel GeneAlEx ver. 6.5 (Peakall
 & Smouse 2012), plug-in for Microsoft Excel.
description: # Physaria thamnophila microsatellite dataset
 [https://doi.org/10.5061/dryad.4b8gththr](https://doi.org/10.5061/dryad.4b8gththr) ## Description of the data and file structure This .csv file is formatted in GENALEX file format. All details on this data format can be found in this publication: Peakall, R. and Smouse P.E. (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288-295. To use this data, import the .csv file into Microsoft Excel and open using the GENLEX Excel plug-in as described in the cited publication. Can then be converted to many other population genetic dataset formats using GENALEX (e.g. GenePop, GenoDive, Arlequin, Structure, SPAGeDI, etc). Numerical data for allele sizes refers to total fragment size. *Physaria thamnophila* is a US federally-listed endangered species. Some samples were collected based on one-time permission from private land-owners. Information on population geographic locations can be obtained by request from the Austin, TX office of the US Fish and Wildlife Service.