# Genomic Divergence of Sympatric Lineages Within Stichopus cf. horrens (Echinodermata: Stichopodidae): Insights on Reproductive Isolation Inferred From SNP Markers

## TL;DR

This study explores how different groups of sea cucumbers in the same area become reproductively isolated, using genetic markers to identify three distinct clusters and potential genes involved in reproductive barriers.

## Contribution

The study confirms three reproductively isolated genotype clusters in Stichopus cf. horrens and identifies genes potentially involved in reproductive isolation.

## Key findings

- Three reproductively isolated genotype clusters were confirmed in Stichopus cf. horrens.
- Outlier SNP loci related to reproduction, such as rhodopsin and tachykinin receptor signaling, were identified.
- Limited gene flow was inferred among the genotype clusters.

## Abstract

How reproductive barriers arise in early stages of divergence among broadcast spawning organisms that exist in sympatry remains poorly understood. Reproductively isolated lineages (Clade A and B) of Stichopus cf. horrens were previously reported across the western Pacific, with an additional putative cryptic species detected within the Clade B lineage warranting further examination. The present study further examines the hypothesis that the two mitochondrial lineages (Clade A and Clade B) of Stichopus cf. horrens represent putative cryptic species and whether another cryptic species within the Clade B lineage exists using a reduced representation genomic approach. Using double‐digest RAD (ddRAD) sequencing, a total of 9788 single nucleotide polymorphism (SNP) markers were used to examine divergence among Stichopus cf. horrens lineages (n = 82). Individuals grouped into three SNP genotype clusters, broadly concordant with their mitochondrial lineages and microsatellite genotype clusters, with limited gene flow inferred among clusters. Outlier analysis recovered highly divergent SNP loci with significant homology to proteins related to rhodopsin and tachykinin receptor signaling, sperm motility, transmembrane transport, and hormone response. This study confirms the existence of three reproductively isolated genotype clusters within Stichopus cf. horrens and highlights gene regions related to reproduction that may contribute to establishing reproductive barriers between broadcast spawning species at an early stage of divergence.

How reproductive barriers arise in early stages of divergence among broadcast spawning organisms that exist in sympatry remains poorly understood. In this study, we used ddRAD sequencing to confirm the existence of three reproductively isolated genotype clusters within Stichopus cf. horrens, and by using outlier analysis, we identified highly divergent SNP loci related to reproductive processes. This study provides valuable insights into the possible drivers of reproductive isolation in broadcast spawning organisms occurring in sympatry.