Seascape genomics of red abalone: Limited range-wide population structure and evidence for local adaptation

Characterizing patterns of genetic diversity including evidence of local adaptation is relevant for predicting and managing species recovering from over-exploitation in the face of climate change. Red abalone (Haliotis rufescens) is a species of conservation concern due to recent declines from over-harvesting, disease, and climate change, resulting in the closure of commercial and recreational fisheries. We hypothesized that the environmental mosaic that defines nearshore habitats in the California current ecosystem, including variable pH and temperature, has enriched some regions for locally adapted genotypes that may be important for species persistence in changing environments. Using whole genome re-sequencing data from 23 populations spanning their entire range (southern Oregon, USA, to Baja California, MEX) we investigated patterns of population connectivity and local adaptation. We discovered high genetic diversity that is shared within and among populations, suggesting high histo..., , , # VCF file of seascape genomics of red abalone

[https://doi.org/10.5061/dryad.z612jm6m8](https://doi.org/10.5061/dryad.z612jm6m8)

In this study, we used whole genome re-sequencing data from 23 populations spanning the entire range of red abalone (southern Oregon, USA, to Baja California, MEX) to reveal patterns of population connectivity and signatures of natural selection. We generated a VCF file from all 264 samples sequenced at a depth of ~10x using snpArcher ([https://snparcher.readthedocs.io/en/latest/index.html](https://snparcher.readthedocs.io/en/latest/index.html)). This pipeline employs a Snakemake workflow that performs quality control, read mapping, and variant calling. We mapped reads to the Haliotis rufescens reference genome assembly (GCA_023055435.1; Griffiths et al., 2022) and called SNPs using GATK in the snpArcher Pipeline. The data files included in this dataset are as follows:

* NoSibs.NoLowDP.filtered.vcf.missing75maf5.min10.maxDP40.plink.LDfiltered_0.8.vcf

- N...