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Sebastes genomic islands of divergence

Citation

Behrens, Kristen et al. (2021), Sebastes genomic islands of divergence, Dryad, Dataset, https://doi.org/10.5061/dryad.c866t1g6z

Abstract

Depth separation is a proposed driver of speciation in marine fishes, with marine rockfish (genus Sebastes) providing a potentially informative study system. Sebastes rockfishes are commercially and ecologically important. This genus encompasses more than one hundred species and the ecological and morphological variance between these species provides opportunity for identifying speciation-driving adaptations, particularly along a depth gradient. A reduced-representation sequencing method (ddRADseq) was used to compare 95 individuals encompassing six Sebastes species. In this study, we sought to identify regions of divergence between species that were indicative of divergent adaptation and reproductive barriers leading to speciation. A pairwise comparison of S. chrysomelas (black-and-yellow rockfish) and S. carnatus (gopher rockfish) FST values revealed three major regions of elevated genomic divergence, two of which were also present in the S. miniatus (vermilion rockfish) and S. crocotulus (sunset rockfish) comparison. Thses corresponded with regions of both elevated DXY values and reduced nucleotide diversity in two cases, suggesting a speciation-with-gene-flow evolutionary model followed by post-speciation selective sweeps within each species. Limited whole genome re-sequencing was also performed to identify mutations with predicted effects between S. chrysomelas and S. carnatus. Within these islands, we identified important SNPs in genes involved in immune function and vision. This supports the concept of depth-driven speciation, as these are adaptive vectors noted in other organisms. Additionally, changes to genes involved in pigment expression and mate recognition shed light on how S. chrysomelas and S. carnatus may have become reproductively isolated. 

Methods

This dataset consists of the STACKS (Catchen et al., 2013) outputs from 95 Sebastes samples sequenced using double-digest restriction site-associated DNA sequencing (ddRAD-seq, Peterson et al. 2012) and then 2x100bp paired-end Illumina sequencing. The distribution across the six species was S. carnatus (n=20), S. chrysomelas (n=20), S. miniatus (n=15), S. crocotulus (n=16), S. mentella (n=8), and S. alutus (n=16). These were aligned against the S. schlegelii genome (He et al., 2019) using Bowtie2 and then processed using the Stacks v2.52 ref_map.pl pipeline. Additional flags used for the populations sub-program of STACKS were -p 2 -r 0.50 --min-maf 0.05 --max-obs-het 0.7 --fstats --smooth-fstats --hwe --bootstrap --bootstrap-reps 1000 --vcf --genepop. Pairwise FST and phistats output files were filtered using a blacklist method for Hardy-Weinberg disequilibrium in R using the results the GENEPOP v4.4.3 probability test (p < 0.001) as well as pool bias, which assessed for genotypic association in sequencing library pools using GENEPOP.

Funding

Howard Hughes Medical Institute

Howard Hughes Medical Institute, Award: Precollege and Undergraduate Science Education Program

National Science Foundation, Award: DBI-1248096