Selection shapes the genomic landscape of introgressed ancestry in a pair of sympatric sea urchin species
Data files
Mar 21, 2024 version files 165.44 MB
-
glasenapp_2024_manuscript.zip
-
README.md
Abstract
A growing number of recent studies have demonstrated that introgression is common across the tree of life. However, we still have a limited understanding of the fate and fitness consequence of introgressed variation at the whole-genome scale across diverse taxonomic groups. Here, we implemented a phylogenetic hidden Markov model to identify and characterize introgressed genomic regions in a pair of well-diverged, non-sister sea urchin species: Strongylocentrotus pallidus and S. droebachiensis. Despite the old age of introgression, a sizable fraction of the genome (1% - 5%) exhibited introgressed ancestry, including numerous genes showing signals of historical positive selection that may represent cases of adaptive introgression. One striking result was the overrepresentation of hyalin genes in the identified introgressed regions despite observing considerable overall evidence of selection against introgression. There was a negative correlation between introgression and chromosome gene density, and two chromosomes were observed with considerably reduced introgression. Relative to the non-introgressed genome-wide background, introgressed regions had significantly reduced nucleotide divergence (dXY) and overlapped fewer protein-coding genes, coding bases, and genes with a history of positive selection. Additionally, genes residing within introgressed regions showed slower rates of evolution (dN, dS, dN/dS) than random samples of genes without introgressed ancestry. Overall, our findings are consistent with widespread selection against introgressed ancestry across the genome and suggest that slowly evolving, low-divergence genomic regions are more likely to move between species and avoid negative selection following hybridization and introgression.
README: Selection shapes the genomic landscape of introgressed ancestry in a pair of sympatric sea urchin species
https://doi.org/10.5061/dryad.fn2z34v1k
This directory contains the data and code supporting the findings of Glasenapp and Pogson (2024).
Description of the data and file structure
scripts/ contains the scripts used to produce the findings.
data/ contains both the raw input data and final output files used to support the results.
All folders contain additional README files with folder-specific information about the data and scripts.
Sharing/Access information
Links to other publicly accessible locations of the data: GitHub link in the Related Works section.
Data was derived from the following sources: NCBI SRA (BioProject PRJNA391452)
Methods
The genomes of all strongylocentrotid sea urchin species were sequenced at high coverage depth with the Illumina HiSeq 2500. The raw sequencing reads were deposited in the NCBI Sequence Read Archive under BioProject PRJNA391452.