Unravelling the sandfish species complex: strong genetic structure suggests recent divergence in the Indo-Pacific sea cucumber Holothuria (Metriatyla) scabra

Kelly T. Brown; Paul C. Southgate; Brian Stockwell; Lindon Havimana; Aviti J. Mmochi; Rose K. Basiita; Nguyen D. Q. Duy; Monal M. Lal

doi:10.3389/fmars.2026.1861293

Back

Unravelling the sandfish species complex: strong genetic structure suggests recent divergence in the Indo-Pacific sea cucumber Holothuria (Metriatyla) scabra

Journal article

Open access

Peer reviewed

Unravelling the sandfish species complex: strong genetic structure suggests recent divergence in the Indo-Pacific sea cucumber Holothuria (Metriatyla) scabra

Kelly T. Brown, Paul C. Southgate, Brian Stockwell, Lindon Havimana, Aviti J. Mmochi, Rose K. Basiita, Nguyen D. Q. Duy and Monal M. Lal

Frontiers in Marine Science, Vol.13, pp.1-23

2026

DOI: https://doi.org/10.3389/fmars.2026.1861293

Files and links (1)

pdf

fmars-13-186129310.85 MBDownload View

Published Version Open Access CC BY V4.0

Abstract

conservation

demographic history

evolutionarily significant units

fishery management

mariculture

ocean basin

The high-value tropical sea cucumber Holothuria (Metriatyla) scabra or sandfish is central to the ‘400+ year old global’, bêche-de-mer trade. Consequently, it has faced heavy exploitation and has become extirpated in some regions within its broader Indo-Pacific natural distribution. Recent molecular evidence has provided clarity on its taxonomic identity, indicating it comprises a species complex, with four broad lineages described (one and three in the Indian Ocean and Pacific Ocean, respectively). To further characterise populations within the sandfish species complex, a fine-scale genomic audit was undertaken utilising specimens collected at nine sites (n = 317) across its 16,500 km Indo-Pacific distribution. Genomic data (12,259 selectively-neutral and 430 putatively adaptive SNPs) were used to investigate population genetic structure, diversity, connectivity, adaptive variation, and demographic history. Seven discrete evolutionarily significant units (ESUs) were identified with varying degrees of differentiation, translating to respective regional management units (MUs): 1) Tanzania, 2) Madagascar, 3) Vietnam, 4) the Philippines, 5) Northern Territory (Australia) and Queensland (Australia), 6) Papua New Guinea with the Solomon Islands, and 7) Fiji (pairwise FST range = 0.015–0.497). The drivers of population structure identified at the ocean basin level include isolation by distance, realised vs. potential larval dispersal, prevailing ocean current trajectories, source and sink location geography, and habitat heterogeneity. Demographic history reconstructions reveal effective population size variability, which suggest relatively recent population fragmentation ( 30–40 kya). Analyses of adaptive variation identified selective sweeps potentially influencing sex-determining and sexual differentiation regions of the sandfish genome, particularly at chromosome 10. These findings offer valuable insights into the microevolutionary forces shaping this species complex and inform conservation of wild sandfish populations, replenishment of depleted stocks, accurate fishery management, regional translocation initiatives, and sustainable mariculture for the bêche-de-mer trade.

Details

Title: Unravelling the sandfish species complex: strong genetic structure suggests recent divergence in the Indo-Pacific sea cucumber Holothuria (Metriatyla) scabra
Authors: Kelly T. Brown (Corresponding Author) - University of the South Pacific
Paul C. Southgate - University of the Sunshine Coast
Brian Stockwell - University of the South Pacific
Lindon Havimana - Solomon Islands National University
Aviti J. Mmochi - University of Dar es Salaam
Rose K. Basiita - WorldFish (Zambia)
Nguyen D. Q. Duy - Central Institute of Brackishwater Aquaculture
Monal M. Lal - University of the Sunshine Coast
Publication details: Frontiers in Marine Science, Vol.13, pp.1-23
Publisher: Frontiers Research Foundation
Date published: 2026
DOI: 10.3389/fmars.2026.1861293
ISSN: 2296-7745
Copyright note: © 2026 Brown, Southgate, Stockwell, Havimana, Mmochi, Basiita, Duy and Lal. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Data Availability: Genotypic data for sandfish sampled and sequenced during this study are available at https://osf.io/dmzu4. Files used to produce data reported here are included as Supplementary Materials 1-3.
Grants: Increasing technical skills supporting community-based sea cucumber production in Vietnam and the Philippines, FIS/2016/122, Australian Centre for International Agricultural Research (Australia, Canberra) - ACIAR
ACIAR Small Project Award for John Allwright Fellowship Returnees, C000749, Australian Centre for International Agricultural Research (Australia, Canberra) - ACIAR
Grant note: The University of the South Pacific School of Agriculture, Geography, Environment, Oceans & Natural Sciences research student grant (F3307-FST15-71502-001)
Organisation Unit: Australian Centre for Pacific Islands Research; School of Science, Technology and Engineering
Language: English
Record Identifier: 991250588902621
Output Type: Journal article

Metrics

1 Record Views