Selection shapes the genomic landscape of introgressed ancestry in a pair of sympatric sea urchin species

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 d..., 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., , # Selection shapes the genomic landscape of introgressed ancestry in a pair of sympatric sea urchin species

[https://doi.org/10.5061/dryad.fn2z34v1k](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)