Sandfish generations: Loss of genetic diversity due to hatchery practices in the sea cucumber Holothuria (Metriatyla) scabra

DataSheet_2.csv

“…In Fiji, Brown et al (2022) reported the presence of three genetic stocks at 6,896 selectively-neutral and 186 putatively-adaptive SNPs across ~600 km, and Lal et al ( 2021) at 8,725 selectively neutral SNPs reported substantial differentiation between Fiji and San Esteban, the Philippines (pairwise F st =0.325, ~7,500 km apart). This variability in genetic structure may be explained by potential vs. realised dispersal of H. scabra larvae, as its 14-21 day pelagic larval duration (PLD) permits widespread dispersal over large distances (Altamirano and Rodriguez, 2022;Brown et al, 2024). However, complex geomorphology (as in the Philippines), habitat heterogeneity, ocean current pathways and the availability of suitable habitat for settlement all influence the degree of connectivity, and consequently population divergence and fragmentation (Ravago-Gotanco and Kim, 2019;Brown et al, 2022).…”

“…However, complex geomorphology (as in the Philippines), habitat heterogeneity, ocean current pathways and the availability of suitable habitat for settlement all influence the degree of connectivity, and consequently population divergence and fragmentation (Ravago-Gotanco and Kim, 2019;Brown et al, 2022). Sandfish also have a biphasic settlement process, recruiting from plankton to seagrass leaves first upon completing larval development, and thereafter to sandy substrates where they become deposit feeders (Mercier et al, 2000b;Sinsona and Juinio-Meñez, 2019;Brown et al, 2024). This biological attribute is likely to contribute to the generation and maintenance of genetic structure in this species, as habitats without seagrass may not support recruitment of sandfish larvae, while population expansion may not be possible in areas with poor seagrass coverage.…”

“…Estimates of genomic diversity were largely consistent among 15 sites surveyed, with the exception of AND which exhibited a slightly lower mean number of alleles per locus (A=1.697) compared to other sites (range A=1.758-1.804, Table 3). This latter observation may be a result of extensive sea ranching activities in and around AND, which utilise hatchery-produced juveniles (Juinio-Meñez et al, 2017) that are now known to be less genetically diverse compared to wild conspecifics (Riquet et al, 2022;Brown et al, 2024). Within biogeographic regions, sites sampled along eastern coastlines (Eastern Visayas and Mindanao) were slightly more genetically diverse (observed heterozygosity, mean numbers of alleles, locally common alleles and percentages of polymorphic loci) compared to western sites (Luzon and Mindoro).…”

“…Assessment of a suitable nextgeneration sequencing approach (DArTseq) for sandfish was reported by Lal et al (2021), and used to investigate population genomic diversity and structure in Fiji (Brown et al, 2022) and the Philippines (this study). Genome-wide SNPs were also employed to examine loss of genetic diversity in hatchery-produced sandfish (Brown et al, 2024), examine growth rate variability (Ordoñez et al, 2021) and assign populations of origin for traceability studies (Ordoñez and Ravago-Gotanco, 2024).…”

“…Consequently, a high-resolution genomic audit of wild Philippine sandfish was conducted, employing a proven genotyping-by-sequencing approach (DArTseq) and genome-wide SNP markers for this species (Lal et al, 2021;Brown et al, 2022Brown et al, , 2024. Genomic data were used to examine fine-scale genetic structure, genomic diversity, relatedness population connectivity and local adaptation at both broad (biogeographic region) and local (within-biogeographic region) scales.…”