Data from: Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass

Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South-East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South-East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. FST and principal components analysis revealed striking divergence between South-East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South-East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South-East Asia during mid-Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the ‘genomic islands’ scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid-Pleistocene.

全基因组遗传分化分析对于理解异域成种（allopatric speciation）的遗传进程至关重要。我们对采自东南亚、澳大利亚/巴布亚新几内亚的6个种群共131尾亚洲海鲈个体的限制性位点关联DNA标签（RAD tags）进行了测序。利用32433个单核苷酸多态性位点（SNPs），我们分析了所有种群的遗传多样性与种群分化模式。研究发现，东南亚种群与澳大利亚/巴布亚新几内亚种群之间存在显著的遗传异质性。澳大利亚/巴布亚新几内亚种群的遗传多样性水平显著偏低。固定指数（FST）与主成分分析结果显示，东南亚种群与澳大利亚/巴布亚新几内亚种群之间存在显著的遗传分化。值得注意的是，未检测到当代基因流的存在。我们基于折叠联合位点频率频谱进一步检验了种群的历史动态。带有历史种群规模变化的远古基因流模型被推断为最契合解释亚洲海鲈在东南亚与澳大利亚/巴布亚新几内亚之间遗传分化的最优模型。该模型同时揭示，澳大利亚/巴布亚新几内亚种群的祖先源于更新世中期的东南亚种群，并在末次冰期退却后与祖先种群完全隔离。我们还检测到了局部选择的印迹，其可能与差异化的生态适应相关。对远古基因流的分析显示，其强度不足以抵消遗传漂变引发的遗传分化。观测到的基因组分化模式与"基因组岛"假说相悖。综上，亚洲海鲈自更新世中期与祖先种群分化以来，大概率正朝着异域成种的方向演化。