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Whole-genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations.
Ecology and Evolution ( IF 2.3 ) Pub Date : 2020-07-20 , DOI: 10.1002/ece3.6527 Changwei Bi 1 , Na Lu 1 , Zhen Huang 2, 3 , Junyuan Chen 4 , Chunpeng He 1 , Zuhong Lu 1
Ecology and Evolution ( IF 2.3 ) Pub Date : 2020-07-20 , DOI: 10.1002/ece3.6527 Changwei Bi 1 , Na Lu 1 , Zhen Huang 2, 3 , Junyuan Chen 4 , Chunpeng He 1 , Zuhong Lu 1
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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 Branchiostoma individuals by whole‐genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size (N e) of Branchiostoma 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 Branchiostoma . The inferred ancestral N e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10−9) or third glaciation (mutation rate = 9 × 10−9) 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 Branchiostoma 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 Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.
中文翻译：
全基因组重测序揭示了文昌鱼和佛罗里达文昌鱼种群的更新世时间动态。
全球气候波动控制着物种的祖先人口历史，并有助于将当前的人口状况置于更广泛的生态和进化背景中。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特征，因为每个个体的基因组都是祖先基因组的不完美镶嵌体。在这里，我们通过全基因组重测序策略报告了 20 个文昌鱼个体的基因组序列。我们检测到每个文昌鱼个体有超过 1.4 亿个基因组变异。特别是，我们应用成对顺序马尔可夫合并（PSMC）方法来估计更新世期间文昌鱼种群有效种群规模（ N e ）的变化轨迹。我们评估使用 PSMC 正确推断人口统计历史的测序深度阈值≥25×。 PSMC 结果强调了历史上全球气候波动对文昌鱼长期种群动态的影响。推测的湛江和厦门海水中的Branchiostoma belcheri种群的祖先Ne在第一次（突变率= 3 × 10 -9 ）或第三次冰期（突变率= 9 × 10 -9 ）之前的幅度不同。更新世，表明这两个种群很可能在更新世的第一次或第三次冰河作用之后开始在各自的海洋中独立进化。 在所有文昌鱼个体中都观察到了与末次盛冰期同时发生的明显的种群瓶颈，随后在更新世晚期发生了种群扩张。经历了长期衰退的物种可能特别容易受到近期人类活动的影响。近年来，工业污染和海砂开采破坏了文昌鱼和谐的生存环境。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。
更新日期：2020-08-11
中文翻译：
全基因组重测序揭示了文昌鱼和佛罗里达文昌鱼种群的更新世时间动态。
全球气候波动控制着物种的祖先人口历史，并有助于将当前的人口状况置于更广泛的生态和进化背景中。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特征，因为每个个体的基因组都是祖先基因组的不完美镶嵌体。在这里，我们通过全基因组重测序策略报告了 20 个文昌鱼个体的基因组序列。我们检测到每个文昌鱼个体有超过 1.4 亿个基因组变异。特别是，我们应用成对顺序马尔可夫合并（PSMC）方法来估计更新世期间文昌鱼种群有效种群规模（ N e ）的变化轨迹。我们评估使用 PSMC 正确推断人口统计历史的测序深度阈值≥25×。 PSMC 结果强调了历史上全球气候波动对文昌鱼长期种群动态的影响。推测的湛江和厦门海水中的Branchiostoma belcheri种群的祖先Ne在第一次（突变率= 3 × 10 -9 ）或第三次冰期（突变率= 9 × 10 -9 ）之前的幅度不同。更新世，表明这两个种群很可能在更新世的第一次或第三次冰河作用之后开始在各自的海洋中独立进化。 在所有文昌鱼个体中都观察到了与末次盛冰期同时发生的明显的种群瓶颈，随后在更新世晚期发生了种群扩张。经历了长期衰退的物种可能特别容易受到近期人类活动的影响。近年来，工业污染和海砂开采破坏了文昌鱼和谐的生存环境。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。
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