Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China.
Center of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, China.
BMC Genomics. 2021 Jun 30;22(1):490. doi: 10.1186/s12864-021-07816-7.
Global climate oscillation, as a selection dynamic, is an ecologically important element resulting in global biodiversity. During the glacial geological periods, most organisms suffered detrimental selection pressures (such as food shortage and habitat loss) and went through population declines. However, during the mild interglacial periods, many species re-flourished. These temporal dynamics of effective population sizes (N) provide essential information for understanding and predicting evolutionary outcomes during historical and ongoing global climate changes.
Using high-quality genome assemblies and corresponding sequencing data, we applied the Pairwise Sequentially Markovian Coalescent (PSMC) method to quantify N changes of twelve representative teleost species from approximately 10 million years ago (mya) to 10 thousand years ago (kya). These results revealed multiple rounds of population contraction and expansion in most of the examined teleost species during the Neogene and the Quaternary periods. We observed that 83% (10/12) of the examined teleosts had experienced a drastic decline in N before the last glacial period (LGP, 110-12 kya), slightly earlier than the reported pattern of N changes in 38 avian species. In comparison with the peaks, almost all of the examined teleosts maintained long-term lower N values during the last few million years. This is consistent with increasingly dramatic glaciation during this period.
In summary, these findings provide a more comprehensive understanding of the historical N changes in teleosts. Results presented here could lead to the development of appropriate strategies to protect species in light of ongoing global climate changes.
全球气候波动是一种选择动态，是导致全球生物多样性的生态重要因素。在冰川地质时期，大多数生物经历了不利的选择压力（如食物短缺和栖息地丧失），导致种群数量下降。然而，在温和的间冰期，许多物种再次繁荣。有效种群大小（N）的这些时间动态为理解和预测历史和当前全球气候变化期间的进化结果提供了重要信息。
我们使用高质量的基因组组装和相应的测序数据，应用成对顺序马尔可夫合并（PSMC）方法来量化 12 种代表性硬骨鱼类物种从大约 1000 万年前（mya）到 10000 年前（kya）的 N 变化。这些结果表明，在新近纪和第四纪期间，大多数检查的硬骨鱼类物种经历了多次种群收缩和扩张。我们观察到，在末次冰期（LGP，110-12 kya）之前，83%（10/12）的检查硬骨鱼类经历了 N 的急剧下降，略早于 38 种鸟类 N 变化的报告模式。与峰值相比，在过去的几百万年中，几乎所有检查的硬骨鱼类都保持了长期的低 N 值。这与该时期冰川作用日益剧烈一致。
总之，这些发现提供了对硬骨鱼类历史 N 变化的更全面理解。这里呈现的结果可以为根据正在发生的全球气候变化制定保护物种的适当策略提供指导。
