Extensive introgression among strongylocentrotid sea urchins revealed by phylogenomics

Gametic isolation is thought to play an important role in the evolution of reproductive isolation in broadcast-spawning marine invertebrates. However, it’s unclear whether gametic isolation commonly develops early in the speciation process or only accumulates after other reproductive barriers are already in place. It is also unknown whether gametic isolation is an effective barrier to introgression following speciation. Here, we used whole-genome sequencing data and multiple complementary phylogenomic approaches to test whether the well-documented gametic incompatibilities among the strongylocentrotid sea urchins have limited introgression. We quantified phylogenetic discordance, inferred reticulate phylogenetic networks, and applied the Δ statistic using gene tree topologies reconstructed from multiple sequence alignments of protein-coding single-copy orthologs. In addition, we conducted ABBA-BABA tests on genome-wide single nucleotide variants and reconstructed a phylogeny of mitocho..., 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., , This directory contains all of the code and data used in Glasenapp and Pogson (2023). The scripts/ directory contains the bash, python, and R scripts used to generate the results. The data/ directory contains the input and output data associated with the scripts. There are individual README files for each nested folder.

The raw sequencing reads used to produce all results were deposited in the NCBI Sequence Read Archive under BioProject PRJNA391452.

The hard-filtered genotype calls for all nine strongylocentrotid species are included in the file filtered_genotype_calls_pf.g.vcf.gz