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

Genome-wide 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 Southeast Asia and Australia/Papua New Guinea. Using 32433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between Southeast Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. FST and principle component analysis revealed striking divergence between Southeast 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 Southeast Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from Southeast 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.

全基因组范围的遗传分化分析，对于解析异域物种形成（allopatric speciation）的遗传进程具有至关重要的意义。本研究对来自东南亚、澳大利亚及巴布亚新几内亚的6个种群共131尾亚洲海鲈（Asian seabass）样本的RAD标签（RAD tags）进行了测序。依托32433个单核苷酸多态性（Single Nucleotide Polymorphism，SNP）位点，本研究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。澳大利亚及巴布亚新几内亚种群的遗传多样性水平相对偏低。FST值与主成分分析（Principal Component Analysis，PCA）结果均显示，两类种群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。本研究进一步基于折叠联合位点频率谱（folded joint site frequency spectrum），对亚洲海鲈的种群历史动态展开了检验。带有历史种群规模变化的古老基因流模型，被证实为最适配东南亚与澳大利亚/巴布亚新几内亚亚洲海鲈遗传分化的最优演化模型。该模型同时揭示：澳大利亚及巴布亚新几内亚种群的祖先源自东南亚种群，分化事件发生于中更新世；且在末次冰期消退后，这些种群便与祖先种群完全隔离。本研究还检测到了局部选择的印迹，其可能与种群间的差异化生态适应相关。研究对古老基因流进行了评估，结果显示其强度不足以抵消遗传漂变所引发的遗传分化。本研究观测到的基因组分化模式，与"基因组岛（genomic islands）"假说存在冲突。综上，自中更新世与祖先种群分化以来，亚洲海鲈大概率正朝着异域物种形成的方向演化。