Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using amplicon sequencing
Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using amplicon sequencing
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使用扩增子测序推断日本雪松、日本柳杉的种群历史
DOI：
10.1038/s41437-019-0198-y
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发表时间：
2019
期刊：
影响因子：
3.8
通讯作者：
Kusumi Junko
中科院分区：
文献类型：
--
作者：
Moriguchi Natsuki;Uchiyama Kentaro;Miyagi Ryutaro;Moritsuka Etsuko;Takahashi Aya;Tamura Koichiro;Tsumura Yoshihiko;Teshima Kosuke M.;Tachida Hidenori;Kusumi Junko
一个物种的进化取决于多种力量，如人口统计学和自然选择。要了解一个目标物种的进化轨迹和驱动力，首先需要利用适当的遗传标记揭示该物种的种群历史，如过去和现在的种群规模、亚群和基因流。日本柳杉（Cryptomeria japonicae）是分布于日本的一种长寿雌雄同株针叶树种。有两个主要的线（omote-sugi和ura-sugi），这是区分的形态特征，可能有助于他们的地方适应明显的差异。这些形态特征的进化似乎与东亚过去的气候变化有关，但这两个线的分歧时间和随后的种群动态没有精确的估计。在这里，我们分析了120个核基因的核苷酸变异，在94个人使用扩增子测序结合高通量测序技术。分析表明，屋久岛种群数量最多，是我国南方分布区的界限。japonicain日本，从其他人群0.85万年前（MYA）分歧。日本大陆其他种群的分歧时间估计为0.32 MYA，这表明表杉和浦杉的分歧可能发生在末次盛冰期之前。虽然我们发现目前的人口之间的基因流的适度水平，长期隔离和气候变化造成的环境异质性可能有助于线的分化和当地的适应。
The evolution of a species depends on multiple forces, such as demography and natural selection. To understand the trajectory and driving forces of evolution of a target species, it is first necessary to uncover that species’ population history, such as past and present population sizes, subdivision and gene flow, by using appropriate genetic markers.Cryptomeria japonicais a long-lived monoecious conifer species that is distributed in Japan. There are two main lines (omote-sugi and ura-sugi), which are distinguished by apparent differences in morphological traits that may have contributed to their local adaptation. The evolution of these morphological traits seems to be related to past climatic changes in East Asia, but no precise estimate is available for the divergence time of these two lines and the subsequent population dynamics in this species. Here, we analyzed the nucleotide variations at 120 nuclear genes in 94 individuals by using amplicon sequencing in combination with high-throughput sequencing technologies. Our analysis indicated that the population on Yakushima Island, the southern distribution limit ofC. japonicain Japan, diverged from the other populations 0.85 million years ago (MYA). The divergence time of the other populations on mainland Japan was estimated to be 0.32 MYA suggesting that the divergence of omote-sugi and ura-sugi might have occurred before the last glacial maximum. Although we found modest levels of gene flow between the present populations, the long-term isolation and environmental heterogeneity caused by climatic changes might have contributed to the differentiation of the lines and their local adaptation.
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影响因子：
3.3
作者：
J. K. Pritchard;Matthew Stephens;Peter Donnelly
通讯作者：
J. K. Pritchard;Matthew Stephens;Peter Donnelly
影响因子：
7
作者：
Miller, Michael R.;Dunham, Joseph P.;Johnson, Eric A.
通讯作者：
Johnson, Eric A.
影响因子：
3.3
作者：
R. Hudson;M. Slatkint;W. Maddison
通讯作者：
R. Hudson;M. Slatkint;W. Maddison
日本近2万年来柳杉的海拔和纬度迁移
影响因子：
2.3
作者：
M. Tsukada
通讯作者：
M. Tsukada
影响因子：
4.9
作者：
Ewing, Gregory B.;Jensen, Jeffrey D.
通讯作者：
Jensen, Jeffrey D.