The fungus Ophiocordyceps sinensis is endemic to the vast region of the Qinghai-Tibetan plateau(QTP).The unique and complex geographical environmental conditions have led to the "sky island" distribution str...The fungus Ophiocordyceps sinensis is endemic to the vast region of the Qinghai-Tibetan plateau(QTP).The unique and complex geographical environmental conditions have led to the "sky island" distribution structure of O.sinensis.Due to limited and unbalanced sample collections,the previous data on O.sinensis regarding its genetic diversity and spatial structure have been deemed insufficient.In this study,we analyzed the diversity and phylogeographic structures of O.sinensis using internally transcribed spacer region(ITS) and 5-locus datasets by a large-scale sampling.A total of 111 haplotypes of ITS sequences were identified from 948 samples data of the fungus O.sinensis,with representing high genetic diversity,and 8 phylogenetic clades were recognized in O.sinensis.Both the southeastern Tibet and the northwestern Yunnan were the centers of genetic diversity and genetic differentiation of the fungus,and they were inferred as the glacial refugia in the Quaternary.Three distribution patterns were identified to correspond to the 8 clades,including but not limited to the coexistence of widely and specific local distributive structures.It also revealed that the differentiation pattern of O.sinensis did not fit for the isolation-by-distance model.The differentiation into the 8 clades occurred between 1.56 Myr and6.62 Myr.The ancestor of O.sinensis most likely originated in the late Miocene(6.62 Myr) in the northwestern Yunnan,and the Scene A-C of the Qinghai-Tibetan movements may have played an important role in the differentiation of O.sinensis during the late Miocene-Pliocene periods.Our current results provide a much clearer and detailed understanding of the genetic diversity and geographical spatial distribution of the endemic alpine fungus O.sinensis.It also revealed that the geochronology resulting from paleogeology could be cross-examined with biomolecular clock at a finer scale.展开更多
The large yellow croaker(Larimichthys crocea)is one of the most economically valuable marine fsh in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few de...The large yellow croaker(Larimichthys crocea)is one of the most economically valuable marine fsh in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades.The stock division and species distribution,which have important implications for ecological protection,germplasm recovery,and fshery resource management,have been debated since the 1960s.However,it is still uncertain even how many stocks exist in this species.To address this,we evaluated the fne-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers.Compared with the widely accepted stock boundaries proposed in the 1960s,our results revealed that a climate-driven habitat change probably occurred between the Naozhou(Nanhai)Stock and the Ming-Yuedong(Mindong)Stock.The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait,accompanied by highly asymmetric introgression.In addition,we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas.The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes,whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations.These fndings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker,providing a basis for conservation,fsheries management and further evolutionary biology studies.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.31870017,31760011)the Science and Technology Development Fund of Guidance from the Central Government to Locals(KC1610530)+2 种基金the Department of Science and Technology of Yunnan Province(Grant Nos.2018IA075,2018FY001006)the Biodiversity Survey,the Assessment Project of the Ministry of Ecology and Environment,China(Grant No.2019HJ2096001006)the China Postdoctoral Science Foundation(Grant No.2017M613017)。
文摘The fungus Ophiocordyceps sinensis is endemic to the vast region of the Qinghai-Tibetan plateau(QTP).The unique and complex geographical environmental conditions have led to the "sky island" distribution structure of O.sinensis.Due to limited and unbalanced sample collections,the previous data on O.sinensis regarding its genetic diversity and spatial structure have been deemed insufficient.In this study,we analyzed the diversity and phylogeographic structures of O.sinensis using internally transcribed spacer region(ITS) and 5-locus datasets by a large-scale sampling.A total of 111 haplotypes of ITS sequences were identified from 948 samples data of the fungus O.sinensis,with representing high genetic diversity,and 8 phylogenetic clades were recognized in O.sinensis.Both the southeastern Tibet and the northwestern Yunnan were the centers of genetic diversity and genetic differentiation of the fungus,and they were inferred as the glacial refugia in the Quaternary.Three distribution patterns were identified to correspond to the 8 clades,including but not limited to the coexistence of widely and specific local distributive structures.It also revealed that the differentiation pattern of O.sinensis did not fit for the isolation-by-distance model.The differentiation into the 8 clades occurred between 1.56 Myr and6.62 Myr.The ancestor of O.sinensis most likely originated in the late Miocene(6.62 Myr) in the northwestern Yunnan,and the Scene A-C of the Qinghai-Tibetan movements may have played an important role in the differentiation of O.sinensis during the late Miocene-Pliocene periods.Our current results provide a much clearer and detailed understanding of the genetic diversity and geographical spatial distribution of the endemic alpine fungus O.sinensis.It also revealed that the geochronology resulting from paleogeology could be cross-examined with biomolecular clock at a finer scale.
基金We acknowledge financial support from the National Key R&D Program of China(no.2022YFD2401002)the National Science Fund for Distinguished Young Scholars(no.32225049)+5 种基金the National Natural Science Foundation of China(no.U21A20264)the Special Foundation for Major Research Program of Fujian Province(no.2020NZ08003)the Major Special Funding for"Science and Technology Innovation 2025"in Ningbo(no.2021Z002)the Local Science and Technology Development Project Guide by The Central Government(no.2019L3032)the China Agriculture Research System(no.CARS-47)the Alliance of International Science Organizations(ANSO-CR-PP-2021-03).
文摘The large yellow croaker(Larimichthys crocea)is one of the most economically valuable marine fsh in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades.The stock division and species distribution,which have important implications for ecological protection,germplasm recovery,and fshery resource management,have been debated since the 1960s.However,it is still uncertain even how many stocks exist in this species.To address this,we evaluated the fne-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers.Compared with the widely accepted stock boundaries proposed in the 1960s,our results revealed that a climate-driven habitat change probably occurred between the Naozhou(Nanhai)Stock and the Ming-Yuedong(Mindong)Stock.The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait,accompanied by highly asymmetric introgression.In addition,we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas.The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes,whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations.These fndings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker,providing a basis for conservation,fsheries management and further evolutionary biology studies.
