DOI: 10.5061/dryad.4xgxd25ph
title: Parallel polygenic urban adaptation despite high gene flow in a coastal marine invertebrate

description: The file stored here is the vcf file containing whole genome sequencing
 data for Pacific purple sea urchin (Strongylocentrotus
 purpuratus)  samples.  We collected tissue samples from
 209 urchins across 19 sites in Los Angeles, San Diego and Victoria, B.C..
description: <strong>Collections & Sample
 Processing</strong>: A paired urban/nonurban site design was
 implemented across three Eastern Pacific coastal cities: Victoria B.C.,
 Los Angeles, CA and San Diego, CA. These three cities are all within the
 range of <em>S. purpuratus</em> and have distinct outflow of
 wastewater output in areas where urchin populations have been identified.
 Urban sites were on average 4.3km (range: 1.04km to 8.48km) from an urban
 outflow site, while nonurban sites were over double this distance, with
 sample sites an average of 29km (range: 17.48km to 78.77km) away from an
 outflow site. The Mussel Watch program has classified 87 intertidal sites
 based on surrounding land use and found drastic differences in pollutant
 concentrations between low, mixed and urban development sites. Victoria,
 B.C. provides a geographically distinct city in order to disentangle other
 environmental variables such as temperature, salinity and pH . We
 collected tissue samples from 209 urchins across 19 sites in Los Angeles,
 San Diego and Victoria, B.C.. Additionally subtidal sites were also
 collected for Los Angeles and San Diego by collaborators ( Ed Parnell,
 Jason Toy, Zoe Scholtz and Adam and Jenesa Wall).  From each site, we
 collected spine tissue samples from 10-15 urchins and stored them in
 ethanol for DNA extractions using a Qiagen blood and tissue DNA extraction
 kit. Permits were obtained through the California Department of Fish and
 Wildlife (CDFW). <strong>Sequencing &
 Bioinformatics Methods</strong>: Whole Genome Sequencing libraries
 were made  similarly to previous research by Nielsen et al. 2024,
 following the Nextera Lite protocol with modifications. Samples were first
 normalized, then tagmentation and PCR were done before pooling samples and
 finally using bead to size select for large enough fragments. Purified
 samples were run on a Bioanalyzer chip and sent to BGI Genomics for
 whole-genome sequencing on a NovaSeq machine with 150bp paired end reads.
 Samples were sequenced at an average of 7.5x coverage. SnpArcher (v. 0.1),
 an automated snakemake pipeline, was used to process the data from fastq
 format to a single vcf. Briefly, fastqc was done to quality check samples,
 bwa was used to align samples to the reference genome, GATK was used to
 call haplotypes and genotype samples in this pipeline and vcftools (v.
 0.1.16) was used to compile all samples. We conducted additional
 downstream filtering using vcftools to discard SNPs with minor allele
 frequency less than 0.05, SNPs with &lt;70% of individuals genotyped,
 and genotype quality &lt;10. Samples with low coverage were filtered
 out, leaving 183 samples total that were spread across the three regions
 and urban/nonurban sampling sites.
description: # Parallel polygenic urban adaptation despite high gene flow in a coastal
 marine invertebrate Dataset DOI:
 [10.5061/dryad.4xgxd25ph](https://doi.org/10.5061/dryad.4xgxd25ph) ##
 Description of the data and file structure ### Files and variables ####
 File: 5.ubanurchinfull_fullyfiltered10.recode.vcf **Description:** VCF
 containing filtered genomic data for urban and nonurban urchin samples.
 Downstream filtering was done using vcftools to discard SNPs with minor
 allele frequency less than 0.05, SNPs with &lt;70% of individuals
 genotyped, and genotype quality &lt;10. Samples with low coverage were
 filtered out, leaving 183 samples total that were spread across the three
 regions and urban/nonurban sampling sites. ## Access information Other
 publicly accessible locations of the data: *
 [https://github.com/mlarmstrong/urbanurchins](https://github.com/mlarmstrong/urbanurchins)