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

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.