Genomic Divergence of Sympatric Lineages Within Stichopus cf. horrens (Echinodermata: Stichopodidae): Insights on Reproductive Isolation Inferred From SNP Markers
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 additiona...
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Wiley
2025-04-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.71283 |
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| author | Kenneth M. Kim Apollo Marco D. Lizano Robert J. Toonen Rachel Ravago‐Gotanco |
| author_facet | Kenneth M. Kim Apollo Marco D. Lizano Robert J. Toonen Rachel Ravago‐Gotanco |
| author_sort | Kenneth M. Kim |
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| description | 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. |
| format | Article |
| id | doaj-art-edcff1530ba443d7aae7ef7d83bf49ff |
| institution | OA Journals |
| issn | 2045-7758 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Wiley |
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| series | Ecology and Evolution |
| spelling | doaj-art-edcff1530ba443d7aae7ef7d83bf49ff2025-08-20T02:35:33ZengWileyEcology and Evolution2045-77582025-04-01154n/an/a10.1002/ece3.71283Genomic Divergence of Sympatric Lineages Within Stichopus cf. horrens (Echinodermata: Stichopodidae): Insights on Reproductive Isolation Inferred From SNP MarkersKenneth M. Kim0Apollo Marco D. Lizano1Robert J. Toonen2Rachel Ravago‐Gotanco3Department of Ecology and Evolution University of Lausanne Lausanne SwitzerlandMarine Science Institute University of the Philippines Diliman Quezon City PhilippinesHawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology University of Hawaii at Mānoa Kaneohe Hawaii USAMarine Science Institute University of the Philippines Diliman Quezon City PhilippinesABSTRACT 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.https://doi.org/10.1002/ece3.71283ddRAD sequencingechinodermatamicrosatellitesreproductive isolationsea cucumbersSNPs |
| spellingShingle | Kenneth M. Kim Apollo Marco D. Lizano Robert J. Toonen Rachel Ravago‐Gotanco Genomic Divergence of Sympatric Lineages Within Stichopus cf. horrens (Echinodermata: Stichopodidae): Insights on Reproductive Isolation Inferred From SNP Markers Ecology and Evolution ddRAD sequencing echinodermata microsatellites reproductive isolation sea cucumbers SNPs |
| title | Genomic Divergence of Sympatric Lineages Within Stichopus cf. horrens (Echinodermata: Stichopodidae): Insights on Reproductive Isolation Inferred From SNP Markers |
| title_full | Genomic Divergence of Sympatric Lineages Within Stichopus cf. horrens (Echinodermata: Stichopodidae): Insights on Reproductive Isolation Inferred From SNP Markers |
| title_fullStr | Genomic Divergence of Sympatric Lineages Within Stichopus cf. horrens (Echinodermata: Stichopodidae): Insights on Reproductive Isolation Inferred From SNP Markers |
| title_full_unstemmed | Genomic Divergence of Sympatric Lineages Within Stichopus cf. horrens (Echinodermata: Stichopodidae): Insights on Reproductive Isolation Inferred From SNP Markers |
| title_short | Genomic Divergence of Sympatric Lineages Within Stichopus cf. horrens (Echinodermata: Stichopodidae): Insights on Reproductive Isolation Inferred From SNP Markers |
| title_sort | genomic divergence of sympatric lineages within stichopus cf horrens echinodermata stichopodidae insights on reproductive isolation inferred from snp markers |
| topic | ddRAD sequencing echinodermata microsatellites reproductive isolation sea cucumbers SNPs |
| url | https://doi.org/10.1002/ece3.71283 |
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