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Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly-dispersive mud crab Scylla olivacea in the Sulu Sea

Citation

Mendiola, Michael John; Ravago-Gotanco, Rachel (2022), Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly-dispersive mud crab Scylla olivacea in the Sulu Sea, Dryad, Dataset, https://doi.org/10.5061/dryad.3xsj3txdz

Abstract

Connectivity of marine populations is shaped by complex interactions of biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications to the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genomics approach combining larval dispersal modeling and population genomic analysis using single nucleotide polymorphisms (SNPs) obtained from RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly-dispersive mud crab, Scylla olivacea (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal across the Sulu Sea, significant genetic differentiation was detected among eight populations based on 1,655 SNPs (FST  = 0.0057, p < 0.001) and a subset of 1,643 putatively neutral SNP markers (FST = 0.0042, p < 0.001). Oceanography influences genetic structure, with redundancy analysis (RDA) indicating  significant contribution of asymmetric ocean currents to neutral genetic variation (R2adj = 0.133; p = 0.035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (Ne < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (FST = 0.2390, p < 0.001), significantly correlated with sea surface temperature variabilities during peak spawning months for S. olivacea (R2adj = 0.692-0.763; p < 0.050), suggesting putative signatures of selection and local adaptation to thermal clines. While oceanography and dispersal ability likely shape patterns of gene flow and genetic structure of S. olivacea across the Sulu Sea, the impacts of genetic drift and natural selection influenced by sea surface temperature also appear as likely drivers of population genetic structure.  This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly-dispersive marine species, and provides information useful for spatial management of the fishery resource.

Methods

Samples were collected among eight localities in the Sulu Sea and two outgroup locations in the Philippines. 146 libraries were prepared using ddRAD sequencing. The dataset was processed through the STACKSv2.2 pipeline and other SNP filtering methods in R.

Usage Notes

One R script and three GENEPOP datasets are available: all markers (1655 SNPs), neutral-only (1,643 SNPs), and outlier loci-only (12 SNPs).

Funding

DOST-PCAARRD, Award: QSR-IA-MCR.05.01

DOST-PCAARRD, Award: QSR-IA-MCR.05.01