Unravelling the effects of gene flow and selection in highly connected populations of the silver-lip pearl oyster (Pinctada maxima)

Nayfa, Maria G., and Zenger, Kyall R. (2016) Unravelling the effects of gene flow and selection in highly connected populations of the silver-lip pearl oyster (Pinctada maxima). Marine Genomics, 28. pp. 99-106.

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Abstract

Many marine organisms often display weak levels of population genetic structuring as a result of both environmental characteristics (e.g., ocean currents) and life history traits (e.g., widely dispersed planktonic larval stages) maintaining high levels of gene flow. This can lead to the assumption that these organisms can be managed as a single stock based on high levels of population connectivity. However, this neglects to account for other micro-evolutionary forces such as selection, which also shape these populations. This study utilizes 1130 genome-wide SNP loci to unravel the effects of gene flow and selection shaping three highly connected populations of the silver-lip pearl oyster (Pinctada maxima) in the ecologically and economically important Indo-Pacific region (Aru, Bali, and West Papua). Twenty-two loci under directional selection were identified amongst the populations, providing further supporting evidence of strong local adaptation (i.e., G × E effects) among populations in this region. Global F(st) values for directional outliers (0.348) were up to eight times greater than for neutral markers (0.043). Pairwise F(st) comparisons between Aru and Bali revealed the largest directional differences (0.488), while Bali and West Papua had the least (0.062). Unrooted neighbour-joining (NJ) distance trees and genetic diversity indices of directional outliers revealed that individuals from Bali and West Papua had reduced allelic variation (MAF(avg) = 0.144, H(o) = 0.238 and MAF(avg) = 0.232, H(o) = 0.369, respectively) compared to Aru (MAF(avg) = 0.292, H(o) = 0.412). This indicates that directional selection is most likely acting upon genetic variation within the Bali and West Papua populations. NJ distance trees, discriminant analysis of principal components, and F(st) analyses of directional outliers revealed two divergent groups ("Bali/West Papua"; "Aru") that had previously gone unrecognized. This study not only illustrates that relatively strong local adaptive forces are occurring despite high gene flow, but identifies the populations that are most likely experiencing selection. Additionally, this study highlights the need to understand all micro-evolutionary forces acting on populations when resolving stock structure.

Item ID: 43197
Item Type: Article (Refereed Research - C1)
Keywords: marine stock, marine management, local adaptation, outlier loci, single nucleotide polymorphism (SNP), micro-evolutionary forces
ISSN: 1876-7478
Date Deposited: 13 Jul 2016 02:06
FoR Codes: 07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070401 Aquaculture @ 50%
07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070405 Fish Physiology and Genetics @ 50%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8301 Fisheries - Aquaculture > 830104 Aquaculture Oysters @ 100%
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