Nayfa Maria G, Zenger Kyall R
Centre for Sustainable Tropical Fisheries and Aquaculture, College of Marine and Environmental Sciences, James Cook University, Townsville 4811, QLD, Australia.
Mar Genomics. 2016 Aug;28:99-106. doi: 10.1016/j.margen.2016.02.005. Epub 2016 Feb 28.
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 Fst values for directional outliers (0.348) were up to eight times greater than for neutral markers (0.043). Pairwise Fst 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 (MAFavg=0.144, Ho=0.238 and MAFavg=0.232, Ho=0.369, respectively) compared to Aru (MAFavg=0.292, Ho=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 Fst 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.
由于环境特征（如洋流）和生活史特征（如广泛扩散的浮游幼虫阶段）维持着高水平的基因流动，许多海洋生物的种群遗传结构往往表现出较弱的水平。这可能导致一种假设，即基于高水平的种群连通性，可以将这些生物作为一个单一的种群进行管理。然而，这忽略了其他微进化力量，如选择，而选择也会塑造这些种群。本研究利用1130个全基因组SNP位点，来揭示基因流动和选择对印度洋 - 太平洋地区（阿鲁、巴厘岛和西巴布亚）生态和经济上重要的银唇珠母贝（大珠母贝）三个高度连通的种群的影响。在这些种群中鉴定出22个受定向选择的位点，为该地区种群之间强烈的局部适应性（即G×E效应）提供了进一步的支持证据。定向异常值的全局Fst值（0.348）比中性标记的Fst值（0.043）高出八倍。阿鲁和巴厘岛之间的成对Fst比较显示出最大的定向差异（0.488），而巴厘岛和西巴布亚之间的差异最小（0.062）。未加权邻接法（NJ）距离树和定向异常值的遗传多样性指数表明，与阿鲁（MAFavg = 0.292，Ho = 0.412）相比，来自巴厘岛和西巴布亚的个体等位基因变异减少（MAFavg分别为0.144，Ho = 0.238和MAFavg = 0.232，Ho = 0.369）。这表明定向选择最有可能作用于巴厘岛和西巴布亚种群内的遗传变异。NJ距离树、主成分判别分析和定向异常值的Fst分析揭示了两个以前未被识别的不同群体（“巴厘岛/西巴布亚”；“阿鲁”）。本研究不仅表明尽管基因流动水平很高，但相对较强的局部适应力仍在发生，而且确定了最有可能经历选择的种群。此外，本研究强调在解决种群结构问题时，需要了解作用于种群的所有微进化力量。
