Parallel polygenic urban adaptation despite high gene flow in a coastal marine invertebrate

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..

Methods
Collections & Sample Processing: 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 S. purpuratus 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).

Sequencing & Bioinformatics Methods: 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 <70% of individuals genotyped, and genotype quality <10. Samples with low coverage were filtered out, leaving 183 samples total that were spread across the three regions and urban/nonurban sampling sites.