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Unravelling the sandfish species complex: strong genetic structure suggests recent divergence in the Indo-Pacific sea cucumber Holothuria (Metriatyla) scabra
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DOI：10.3389/fmars.2026.1861293.png)
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Abstract
En 中文
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.
Keywords:
conservation
SNP
fishery management
mariculture
demographic history
evolutionarily significant units
ocean basin
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