Genomic analysis of a reef‐building coral, <i>Acropora digitifera</i> , reveals complex population structure and a migration network in the Nansei Islands, Japan
Genomic analysis of a reef‐building coral, <i>Acropora digitifera</i> , reveals complex population structure and a migration network in the Nansei Islands, Japan
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对造礁珊瑚<i>Acropora digitalifera</i>的基因组分析揭示了日本南西群岛复杂的种群结构和迁徙网络
DOI：
10.1111/mec.16665
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发表时间：
2022
影响因子：
4.9
通讯作者：
Shinzato Chuya
中科院分区：
文献类型：
--
作者：
Tsuchiya Kojin;Zayasu Yuna;Nakajima Yuichi;Arakaki Nana;Suzuki Go;Satoh Noriyuki;Shinzato Chuya
了解珊瑚种群的结构和连通性对于制定海洋保护政策至关重要，特别是在群岛等零散环境中。南西群岛位于日本西南部，绵延 1000 多公里，以珊瑚礁为支撑，具有高度的生物多样性和特有性，这使得该地区成为评估珊瑚种群遗传属性的理想选择。在这项研究中，我们基于南西群岛常见物种鹿角珊瑚的全基因组单核苷酸多态性 (SNP) 进行了群体基因组分析。通过将新获得的基因组重测序数据与之前发布的数据合并，我们在22个地点收集的303个菌落中鉴定出了超过400万个全基因组SNP，测序覆盖范围为3.91×至27.41×。虽然种群结构分析揭示了相距 >1000 公里的最南端和最北端之间的遗传相似性，但中间位置的几个亚种群表明遗传混合有限，表明南西群岛存在相互冲突的迁徙倾向。尽管迁徙网络揭示了沿着黑潮向北迁徙的总体趋势，但也发现了大量向南迁徙，这表明小型洋流对珊瑚幼虫的扩散做出了重要贡献。此外，不同地点之间有效种群规模转变的异质性表明各个亚种群的历史不同。南西群岛过去和现在的种群动态的意外复杂性意味着，过去和现在洋流和当地环境的异质性影响了该物种的种群结构，并且具有相似繁殖模式的其他海洋物种也可能出现类似的意外种群复杂性。
Understanding the structure and connectivity of coral populations is fundamental for developing marine conservation policies, especially in patchy environments such as archipelagos. The Nansei Islands, extending more than 1000 km in southwestern Japan, are characterized by high levels of biodiversity and endemism, supported by coral reefs, which make this region ideal for assessing genetic attributes of coral populations. In this study, we conducted population genomic analyses based on genome‐wide, single‐nucleotide polymorphisms (SNPs) ofAcropora digitifera, a common species in the Nansei Islands. By merging newly obtained genome resequencing data with previously published data, we identified more than 4 million genome‐wide SNPs in 303 colonies collected at 22 locations, with sequencing coverage ranging from 3.91× to 27.41×. While population structure analyses revealed genetic similarities between the southernmost and northernmost locations, separated by >1000 km, several subpopulations in intermediate locations suggested limited genetic admixture, indicating conflicting migration tendencies in the Nansei Islands. Although migration networks revealed a general tendency of northward migration along the Kuroshio Current, a substantial amount of southward migration was also detected, indicating important contributions of minor ocean currents to coral larval dispersal. Moreover, heterogeneity in the transition of effective population sizes among locations suggests different histories for individual subpopulations. The unexpected complexity of both past and present population dynamics in the Nansei Islands implies that heterogeneity of ocean currents and local environments, past and present, have influenced the population structure of this species, and similar unexpected population complexities may be expected for other marine species with similar reproductive modes.