Phylogeographic history of Japanese macaques
Phylogeographic history of Japanese macaques
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DOI：
10.1111/jbi.14087
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发表时间：
2021-04-15
影响因子：
3.9
通讯作者：
Kawamoto, Yoshi
中科院分区：
文献类型：
--
作者：
Ito, Tsuyoshi;Hayakawa, Takashi;Kawamoto, Yoshi
目的 了解密切相关的物种内部和之间的地理遗传变异的模式和过程是系统发育地理学的本质。日本猕猴，也称为雪猴，已被广泛研究，特别是在社会生物学、生态学和实验生物学领域；然而，我们对其进化历史的了解相对有限。在这项研究中，我们旨在阐明日本猕猴遗传变异的地理模式及其背后的过程。地点日本。恒河猴，M. mulatta；台湾猕猴，M. cyclopis。方法采用双酶切限制性位点相关DNA (RAD) 测序来鉴定全基因组单核苷酸变异。我们使用精细RAD结构、ADMIXTURE和主成分分析来估计遗传群体结构。然后根据邻居网络、邻居连接、最大似然和 SVDquartets 算法推断系统发育关系。我们使用人口统计推断和 ABBA-BABA 测试评估了基因流，并使用生态位模型估计了末次盛冰期 (LGM) 期间的过去分布。结果日本猕猴显示出与中国恒河猴、印度恒河猴和台湾猕猴组成的进化枝的姐妹群关系。日本猕猴由东北部和西南部的主要分支组成，其边界位于日本中部附近，并且检测到东北部和西南部系之间的基因流。据估计，末次盛冰期的避难所分布在日本列岛南部海岸的有限区域。 主要结论 日本猕猴的系统发育地理变异可能主要是由于在冰期期间退回避难所以及随后的基因流动而导致的东北-西南分歧。
Aim Understanding patterns and processes of geographic genetic variation within and among closely related species is the essence of phylogeography. Japanese macaques, also called snow monkeys, have been extensively studied, particularly in the fields of sociobiology, ecology and experimental biology; however, our knowledge of their evolutionary history is relatively limited. In this study we aimed to elucidate the geographic patterns of genetic variation in Japanese macaques and the processes that underlie them.Location Japan.Taxa Japanese macaque, Macaca fuscata; rhesus macaque, M. mulatta; Taiwanese macaque, M. cyclopis.Methods Double-digest restriction site-associated DNA (RAD) sequencing was used to identify genome-wide single nucleotide variants. We used fineRADstructure, ADMIXTURE and principal component analyses to estimate the genetic population structure. Phylogenetic relationships were then inferred based on neighbour-net, neighbour-joining, maximum likelihood and SVDquartets algorithms. We assessed gene flow using demographic inference and ABBA-BABA tests, and estimated past distributions during the Last Glacial Maximum (LGM) using ecological niche modelling.Results Japanese macaques show a sister group relationship with a clade comprising Chinese rhesus, Indian rhesus and Taiwanese macaques. Japanese macaques comprise major north-eastern and south-western clades, with a boundary located near central Japan, and gene flow between the north-eastern and south-western lineages was detected. Refugia during the LGM were estimated to be distributed in limited areas along the south coasts of the Japanese archipelago.Main conclusions Phylogeographic variation of Japanese macaques is likely due mainly to northeast-southwest divergence, which resulted from withdrawal into refugia during the glacial period, and subsequent gene flow.