Bi Changwei, Lu Na, Huang Zhen, Chen Junyuan, He Chunpeng, Lu Zuhong
State Key Laboratory of Bioelectronics School of Biological Science and Medical Engineering Southeast University Nanjing China.
The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration College of Life Sciences Fujian Normal University Fuzhou China.
Ecol Evol. 2020 Jul 20;10(15):8210-8224. doi: 10.1002/ece3.6527. eCollection 2020 Aug.
Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 individuals by whole-genome resequencing strategy. We detected over 140 million genomic variations for each individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size ( ) of population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long-term population dynamics of . The inferred ancestral of the populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10) or third glaciation (mutation rate = 9 × 10) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long-term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of and make full use of these detected genetic variations to facilitate the functional study of for adaptation to local environments.
全球气候波动支配着物种的祖先种群历史，并有助于将当前的种群状况置于更广泛的生态和进化背景中。由于每个个体的基因组都是祖先基因组的不完美镶嵌体，遗传变异将在现存物种的种内遗传变异模式中留下明确的印记。在这里，我们通过全基因组重测序策略报告了20个个体的基因组序列。我们在每个个体中检测到超过1.4亿个基因组变异。特别是，我们应用了成对顺序马尔可夫合并（PSMC）方法来估计更新世期间种群有效种群大小（ ）的变化轨迹。我们评估了使用PSMC正确推断种群历史的测序深度阈值为≥25×。PSMC结果突出了历史全球气候波动在种群长期动态中的作用。推断来自中国湛江和厦门海水的种群在更新世第一次（突变率 = 3×10）或第三次冰期（突变率 = 9×10）之前的祖先种群大小在幅度上有所不同，这表明这两个种群很可能在更新世第一次或第三次冰期之后在各自海域开始独立进化。在所有个体中都观察到与末次盛冰期同时出现的明显种群瓶颈，随后在晚更新世发生了种群扩张。经历长期衰退的物种可能特别容易受到近期人为活动的影响。最近，工业污染和海砂开采破坏了文昌鱼物种和谐的生存环境。未来，我们需要保护文昌鱼的栖息地，并充分利用这些检测到的遗传变异来促进文昌鱼适应当地环境的功能研究。
