title: Swept away: ocean currents and seascape features influence genetic structure across the 18,000 Km Indo-Pacific distribution of a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera.
abstract: Genetic structure in many widely-distributed broadcast spawning marine invertebrates remains poorly understood, posing substantial challenges for their fishery management, conservation and aquaculture. Under the Core-Periphery Hypothesis (CPH), genetic diversity is expected to be highest at the centre of a species' distribution, progressively decreasing with increased differentiation towards outer range limits, as populations become increasingly isolated, fragmented and locally adapted. The unique life history characteristics of many marine invertebrates such as high dispersal rates, stochastic survival and variable recruitment are also likely to influence how populations are organised. To examine the microevolutionary forces influencing population structure, connectivity and adaptive variation in a highly-dispersive bivalve, populations of the black-lip pearl oyster Pinctada margaritifera were examined across its ~18,000 km Indo-Pacific distribution.
  
  
  
  Analyses utilising 9,624 genome-wide SNPs and 580 oysters, discovered differing patterns of significant and substantial broad-scale genetic structure between the Indian and Pacific Ocean basins. Indian Ocean populations were markedly divergent (Fst= 0.2534-0.4177, p < 0.001), compared to Pacific Ocean oysters, where basin-wide gene flow was much higher (Fst= 0.0007-0.1090, p < 0.001). Partitioning of genetic diversity (hierarchical AMOVA) attributed 18.1% of variance between ocean basins, whereas greater proportions were resolved within samples and populations (45.8% and 35.7% respectively). Visualisation of population structure at selectively neutral loci resolved three and five discrete genetic clusters for the Indian and Pacific Oceans respectively. Evaluation of genetic structure at adaptive loci for Pacific populations (89 SNPs under directional selection; Fst= 0.1012-0.4371, FDR = 0.05), revealed five clusters identical to those detected at neutral SNPs, suggesting environmental heterogeneity within the Pacific. Patterns of structure and connectivity were supported by Mantel tests of isolation by distance (IBD) and independent hydrodynamic particle dispersal simulations.
  
  
  
  It is evident that genetic structure and connectivity across the natural range of P. margaritifera is highly complex, and produced by the interaction of ocean currents, IBD and seascape features at a broad scale, together with habitat geomorphology and local adaptation at regional levels. Overall population organisation is far more elaborate than generalised CPH predictions, however valuable insights for regional fishery management, and a greater understanding of range-wide genetic structure in a highly-dispersive marine invertebrate have been gained.
authors.affiliation: Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811, QLD, Australia. monal.lal@my.jcu.edu.au.
authors.forename: Monal M
authors.initials: MM
authors.lastname: Lal
authors.affiliation: Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811, QLD, Australia.|Australian Centre for Pacific Islands Research, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, QLD, Australia.
authors.forename: Paul C
authors.initials: PC
authors.lastname: Southgate
authors.affiliation: Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811, QLD, Australia.
authors.forename: Dean R
authors.initials: DR
authors.lastname: Jerry
authors.affiliation: Geoscience Division, Secretariat of the Pacific Community, 241 Mead Road, Nabua, Suva, Fiji Islands.
authors.forename: Cyprien
authors.initials: C
authors.lastname: Bosserelle
authors.affiliation: Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811, QLD, Australia.
authors.forename: Kyall R
authors.initials: KR
authors.lastname: Zenger
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D063147:Animal Distribution; D025041:Animal Migration; D000818:Animals; D014644:Genetic Variation; D019156:Indian Ocean; D010140:Pacific Ocean; D049911:Pinctada / Q000235:genetics* / Q000502:physiology; D020641:Polymorphism, Single Nucleotide
keywords: Aquaculture; Core-periphery hypothesis; Hydrodynamic dispersal; Population genomics; SNP; Species distribution