DOI: 10.5061/dryad.ncjsxkssb
title: Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird

description: Elucidating forces capable of driving species diversification in the face
 of gene flow remains a key goal in evolutionary biology. Song sparrows,
 Melospiza melodia, occur as 25 subspecies in diverse habitats across North
 America, are among the continent’s most widespread vertebrate species, and
 are exemplary of many highly variable species for which the conservation
 of locally adapted populations may be critical to their range-wide
 persistence. We focus here on six morphologically distinct subspecies
 resident in the San Francisco Bay region, including three salt-marsh
 endemics and three residents in upland and riparian habitats adjacent to
 the Bay. We used reduced-representation sequencing to generate 2,773 SNPs
 to explore genetic differentiation, spatial population structure, and
 demographic history. Clustering separated individuals from each of the six
 subspecies, indicating subtle differentiation at microgeographic scales.
 Evidence of limited gene flow and low nucleotide diversity across all six
 subspecies further supports a hypothesis of isolation among locally
 adapted populations. We suggest that natural selection for genotypes
 adapted to salt marsh environments and changes in demography over the past
 century have acted in concert to drive the patterns of diversification
 reported here. Our results offer evidence of microgeographic
 specialization in a highly polytypic bird species long discussed as a
 model of sympatric speciation and rapid adaptation, and they support the
 hypothesis that conserving locally adapted populations may be critical to
 the range-wide persistence of similarly highly variable species.
description: Sequence quality was assessed using FastQC version 0.11.8. (www.bioinformatics.babraham.ac.uk/projects/fastqc). Individuals were filtered for quality using the Fast-X Toolkit (http://hannonlab.cshl.edu/fastx_toolkit), removing sequences with Phred quality scores below 10 and sequences with more than 5% of bases with Phred quality scores below 20. We demultiplexed sequences using the command “process_radtags” in Stacks version 1.48 (Catchen et al., 2011) and additionally filtered samples to only retain reads that passed the Illumina chastity filter, contained an intact <i>Sbf</i>I RAD site, contained a unique sample barcode, and did not contain Illumina indexing adapters. To account for differences in length, the remaining filtered and demultiplexed reads were trimmed to 94 base pairs at the 3’ end using Fast-X Trimmer (FAST-X Toolkit).  Sequences were aligned to a song sparrow (<i>Melospiza melodia</i>) reference genome (Feng et al., in review) using Bowtie2 version 2.3. Mapped reads were then analyzed using the ref_map.pl pipeline in Stacks. We allowed five mismatches between sample loci and required a minimum of ten identical raw reads to make a stack. We ran the Populations module in Stacks for one population (-p) and required that a locus be present in a minimum of 80% of individuals to be processed (-r). In addition to obtaining all SNPs per locus (10,270), we created a subset of SNPs that included only the first SNP per stack (2,773). To avoid bias associated with physical linkage (O’Leary et al. 2018), we used the reduced, unlinked dataset with 2,773 SNPs for all analyses, unless otherwise stated.
description: All sample information for individuals included in this VCF can
 be found in Supporting Information Table S1. This is the filtered VCF
 used.