DOI: 10.5061/dryad.70rxwdc0f
title: Population expansion, divergence, and persistence in western fence lizards (Sceloporus occidentalis) at the northern extreme of their distributional range

description: Population dynamics within species at the edge of their distributional
 range, including the formation of genetic structure during range
 expansion, are difficult to study when they have had limited time to
 evolve. Western Fence Lizards (Sceloporus occidentalis) have a patchy
 distribution at the northern edge of their range around the Puget Sound,
 Washington, where they almost exclusively occur on imperiled coastal
 habitats. The entire region was covered by Pleistocene glaciation as
 recently as 16,000 years ago, suggesting that populations must have
 colonized these habitats relatively recently. We tested for population
 differentiation across this landscape using genome-wide SNPs and
 morphological data. A time-calibrated species tree supports the hypothesis
 of a post-glacial establishment and subsequent population expansion into
 the region. Despite a strong signal for fine-scale population genetic
 structure across the Puget Sound with as many as 8–10 distinct
 subpopulations supported by the SNP data, there is minimal evidence for
 morphological differentiation at this same spatiotemporal scale.
 Historical demographic analyses suggest that populations expanded and
 diverged across the region as the Cordilleran Ice Sheet receded.
 Population isolation, lack of dispersal corridors, and strict habitat
 requirements are the key drivers of population divergence in this system.
 These same factors may prove detrimental to the future persistence of
 populations as they cope with increasing shoreline development associated
 with urbanization.
description: We extracted genomic DNA from liver biopsies using
 salt-extraction and then conducted double digest restriction-site
 associated DNA sequencing (ddRADseq). We double-digested each sample using
 the digestion enzymes SbfI and MspI in CutSmart Buffer (New England
 Biolabs) for 7 hours at 37 C. For fragment purification, we used Sera-Mag
 SpeedBeads. We then prepared a master mix for eight distinct barcodes to
 be ligated to the cut sites of the fragmented DNA. The libraries were
 size-selected (between 415 and 515 bp after accounting for adapter length)
 on a Blue Pippin Prep size fractionator (Sage Science). For the final
 library amplification, we used Phusion Hi-Fidelity DNA Polymerase and
 Illumina’s indexed primers. We determined the concentration and size
 distribution of each indexed pool using an Agilent 2200 TapeStation.
 Lastly, we sent the quantified pools to QB3-Berkeley Genomics, UC Berkeley
 for qPCR to determine sequenceable library concentrations before
 multiplexing equimolar amounts of each pool for sequencing on one Illumina
 HiSeq 4000 lane (51-bp, single-end reads; 11 pools containing up to 8
 samples each). The demultiplexed sequences are deposited at the Sequence
 Read Archive (SRA; BioProject ID: PRJNA757434; Table S1).
 We demultiplexed each sample from their respective pool using
 their unique barcode sequence using iPyRAD v.0.9.50. We conducted a
 reference-based assembly of the RAD loci using a draft of the <em>S.
 occidentalis</em> genome from Yosemite National Park, California. A
 sequence similarity threshold of 90% was used to cluster reads within
 samples and loci between samples. We removed consensus sequences with low
 coverage (&lt; 6 reads), excessive undetermined or heterozygous sites
 (&gt; 5%), too many alleles for a sample (&gt; 2 for diploids),
 and an excess of shared heterozygosity among samples (paralog filter =
 0.5). For the final alignments, we generated output files containing 0%
 missing data (1,037 loci) and 50% missing data (3,491 loci; Table
 S2).