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物种形成（allopatric speciation）的遗传进程至关重要。本研究对来自东南亚以及澳大利亚/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酶切位点相关DNA（RAD, Restriction-site Associated DNA）标签进行了测序。依托32433个单核苷酸多态性（SNP, Single Nucleotide Polymorphism）位点，本研究分析了所有种群的遗传多样性水平及种群分化模式。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, Fixation Index）分析与主成分分析结果均显示，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，本研究未检测到当代基因交流的迹象。研究基于折叠联合位点频率谱进一步推断了种群的演化历史。结合历史种群规模变化的古基因交流模型被认为是最契合东南亚与澳大利亚/巴布亚新几内亚亚洲海鲈遗传分化的演化模型。该模型同时显示，澳大利亚/巴布亚新几内亚种群的祖先源自更新世中期的东南亚种群，并在末次冰期消退后与祖先种群完全隔离。本研究还检测到了局部选择的印迹，其可能与种群间差异化的生态适应相关。研究对古基因交流进行了分析，结果显示其强度不足以抵消遗传漂变引发的遗传分化。本研究观测到的基因组分化模式与“基因组岛”（genomic islands）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，大概率正朝着异域物种形成的方向演化。