Wang Le, Wan Zi Yi, Lim Huan Sein, Yue Gen Hua
Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
Marine Aquaculture Center, Agri-Food & Veterinary Authority of Singapore, 5 Maxwell Road, Singapore, 069110, Singapore.
Mol Ecol. 2016 Aug;25(15):3605-21. doi: 10.1111/mec.13714. Epub 2016 Jul 9.
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的遗传过程至关重要。我们对来自东南亚以及澳大利亚/巴布亚新几内亚的六个种群的131个亚洲海鲈个体的RAD标签进行了测序。利用32433个单核苷酸多态性（SNP），我们研究了所有种群的遗传多样性和种群分化模式。我们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证据。澳大利亚/巴布亚新几内亚种群的遗传多样性水平相对较低。FST和主成分分析揭示了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分化。有趣的是，未观察到当代基因流的证据。基于折叠后的联合位点频率谱对种群历史进行了进一步检验。古代迁移伴随历史种群大小变化的情景被认为是解释东南亚与澳大利亚/巴布亚新几内亚亚洲海鲈遗传分化的最佳拟合模型。该情景还表明，澳大利亚/巴布亚新几内亚种群是在更新世中期由来自东南亚的祖先建立的，并且在末次冰期消退后与祖先种群完全隔离。我们还检测到了局部选择的痕迹，这可能与不同的生态适应性有关。对古代基因流进行了检验，认为其可能不足以抵消遗传漂变导致的遗传分化。观察到的基因组分化模式与“基因组岛”情景相冲突。总之，自更新世中期与祖先种群分离以来，亚洲海鲈可能一直在朝着异域物种形成的方向进化。
