Files and links (1)
Published VersionCC BY-NC-ND V4.0, Open Access
Journal article
The sandfish identity: phylogeographic reconstructions uncover a species complex within the Indo-Pacific distribution of Holothuria (Metriatyla) scabra
BMC Ecology and Evolution, Vol.25, pp.1-23
2025
PMID: 40770302
Abstract
Background
Sea cucumbers are a highly diverse, enigmatic, ecologically and economically important group of echinoderms, however understanding of their taxonomy is complicated by cryptic morphology, hidden diversity and the presence of species complexes. The sandfish Holothuria (Metriatyla) scabra, is a high-value tropical sea cucumber exploited in multispecies fisheries across the Indo-Pacific with historically chaotic taxonomy, that has never been examined using molecular information. To evaluate its taxonomic identity, a phylogeographic approach was used to examine evolutionary relationships at 9 sites (n = 98) across the ~ 16,500 Km Indo-Pacific species distribution. Two genome-wide (1,500 PAV and 2,000 SNP) loci and one mitochondrial marker (cox1: 69 sequences) were employed in phylogenetic reconstructions, estimations of genetic distance, and assessments of species boundaries and evolutionary history.
Results
Both genome-wide and cox1 data indicate sandfish constitute a species complex containing a minimum of 7 operational taxonomic units (OTUs), with inter-ocean divergence patterns supporting non-conspecifity of Indian and Pacific Ocean specimens. Six OTUs were resolved in the Pacific Ocean across 3 broad lineages corresponding to putative subspecies, along with one OTU in the Indian Ocean. Analyses of evolutionary history estimate divergence of H. (Metriatyla) scabra in the early Pliocene ~ 4.36 MYa (95% HPD 3.3–5.42 MYa), from a germinate point likely in Southeast Asia within the Coral Triangle region, with subsequent diversification into the Indian and Pacific Ocean basins.
Conclusions
The presence of a species complex in the sandfish H. (Metriatyla) scabra is reported, providing clarity on its taxonomic identity, which prior to this study had been described exclusively on morphological characters. Given the degree of ambiguity associated with interspecific morphological descriptions of many Holothuroid taxa, data presented here describe intraspecific diversity of this valuable echinoderm.
Details
- Title
- The sandfish identity: phylogeographic reconstructions uncover a species complex within the Indo-Pacific distribution of Holothuria (Metriatyla) scabra
- Authors
- Kelly T. Brown (Corresponding Author) - University of the South PacificPaul C. Southgate - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringNguyen D. Q. Duy - Research Institute for Aquaculture No 3Lindon Havimana - Solomon Islands National UniversityAviti J. Mmochi - University of Dar es SalaamRose K. Basiita - WorldFish (Zambia)Madjid Delghandi - Sultan Qaboos UniversityBrian Stockwell - University of the South PacificMonal M. Lal - University of the Sunshine Coast, Queensland, School of Science, Technology and Engineering
- Publication details
- BMC Ecology and Evolution, Vol.25, pp.1-23
- Publisher
- BioMed Central Ltd.
- Date published
- 2025
- DOI
- 10.1186/s12862-025-02421-8
- ISSN
- 2730-7182
- PMID
- 40770302
- Copyright note
- This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
- Data Availability
- Genotypic data for sandfish sampled and sequenced during this study at genome-wide markers (PAVs and SNPs) are available at https://doi.org/10.17605/OSF.IO/WKA9X. Mitochondrial cox1 sequences are available on NCBI GenBank under the following accession numbers: LC869599–LC869667.
- Grants
- Organisation Unit
- Australian Centre for Pacific Islands Research; School of Science, Technology and Engineering
- Language
- English
- Record Identifier
- 991150940202621
- Output Type
- Journal article
Metrics
201 File views/ downloads
40 Record Views