Preliminary population genomic study on the sandfish <i>Holothuria (Metriatyla) scabra</i>

Lal, Monal M.; Macahig, Deo Angelo; Brown, Kelly T.; Juinio‐Meñez, Marie Antonette; Southgate, Paul C.; Ravago-Gotanco, Rachel

doi:10.1111/age.13116

Cited by 5 publications

(13 citation statements)

References 9 publications

(7 reference statements)

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“…Tissues were preserved in 20% dimethyl sulfoxide (DMSO) salt solution [23], and maintained under refrigeration (4˚C) until DNA extraction at the School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific in Suva, Fiji. Total genomic DNA was extracted using a modified CTAB:isoamyl alcohol protocol [21], and submitted for genotyping to Diversity Arrays Technology Ltd (DArT PL), in Canberra, Australia.…”

Section: Plos Onementioning

confidence: 99%

“…Diversity Arrays Technology (DArT PL) proprietary genotyping by sequencing (DArTseq™) reduced-representation libraries were prepared as described by Kilian et al [24] and Sansaloni et al [25], with a number of modifications optimised for the sandfish genome as described by Lal et al [21]. Briefly, genome complexity reduction was achieved with a double restriction digest, using a PstI and SphI methylation-sensitive restriction enzyme combination.…”

Section: Dartseq™ 10 Library Preparation and Sequencingmentioning

confidence: 99%

“…Identification of loci under potential selection was achieved using two software packages, BayeScan v.2.1 [31,32] and HacDivSel [33], independently. Bayescan computations were carried out at 0.01, 0.05, 0.1, 0.2 and 0.5 False Discovery Rate (FDR) thresholds (see [21] for further details). HacDivSel employs a different approach to BayeScan, in that populations are submitted pairwise for detection of divergent selection.…”

Section: Marker Filtering Genotype Calling and Filteringmentioning

confidence: 99%

“…All studies have identified discrete genetic units in northern Australia and the Solomon Islands [61]; New Caledonia, northern Australia and the Solomon Islands [62]; Darwin and Cape York in northern Australia with Papua New Guinea [58]; and the Philippines [59]. Apart from a preliminary study to assess the efficacy of genome-wide genotyping in sandfish [21], the current study is the first to apply genome-wide SNPs to perform a high-resolution genetic audit of wild populations. From data presented here and with insights from the aforementioned studies, it is evident that detectable genetic structure is commonplace in wild sandfish, governed by the extent of gene flow connecting populations and the availability of suitable habitat.…”

Section: Plos Onementioning

confidence: 99%

“…Consequently, a high-resolution genomic audit of wild Fijian sandfish was completed, using a robust genotyping-by-sequencing approach (DArTseq) which had been previously evaluated for use in this species [21]. Insights from genomic data were combined with an independent oceanographic particle dispersal model to elucidate the genetic diversity, structure, connectivity, signatures of selection and relatedness of Fijian sandfish.…”

Section: Introductionmentioning

confidence: 99%

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Saving the sea cucumbers: Using population genomic tools to inform fishery and conservation management of the Fijian sandfish Holothuria (Metriatyla) scabra

et al. 2022

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The sea cucumber Holothuria (Metriatyla) scabra, known as sandfish, is a high-value tropical echinoderm central to the global bêche-de-mer (BDM) trade. This species has been heavily exploited across its natural range, with overharvesting and ineffective fishery management leaving stocks in the Pacific region heavily depleted. In Fiji, sandfish stocks have not recovered since a 1988 harvest ban, with surveys reporting declining populations and recruitment failure. Therefore, to inform fishery management policy for the wild sandfish resource and to guide hatchery-based restocking efforts, a high-resolution genomic audit of Fijian populations was carried out. A total of 6,896 selectively-neutral and 186 putatively-adaptive genome-wide SNPs (DArTseq) together with an independent oceanographic particle dispersal model were used to investigate genetic structure, diversity, signatures of selection, relatedness and connectivity in six wild populations. Three genetically distinct populations were identified with shallow but significant differentiation (average Fst = 0.034, p≤0.05), comprising (1) Lakeba island (Lau archipelago), (2) Macuata (Vanua Levu), and (3) individuals from Yasawa, Ra, Serua island and Kadavu comprising the final unit. Small reductions in allelic diversity were observed in marginal populations in eastern Fiji (overall mean A = 1.956 vs. Lau, A = 1.912 and Macuata, A = 1.939). Signatures of putative local adaptation were also discovered in individuals from Lakeba island, suggesting that they be managed as a discrete unit. An isolation-by-distance model of genetic structure for Fijian sandfish is apparent, with population fragmentation occurring towards the east. Hatchery-based production of juveniles is promising for stock replenishment, however great care is required during broodstock source population selection and juvenile releases into source areas only. The successful use of genomic data here has the potential to be applied to other sea cucumber species in Fiji, and other regions involved in the global BDM trade. While preliminary insights into the genetic structure and connectivity of sandfish in Fiji have been obtained, further local, regional and distribution-wide investigations are required to better inform conservation efforts, wild stock management and hatchery-based restocking interventions for this valuable invertebrate.

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Section: Plos Onementioning

confidence: 99%