偶蹄目(Artiodactyla)动物是人类驯化物种的主要来源(如反刍动物),是研究自然选择和人工选择下染色体进化的重要模型生物。在已发表的72个染色体水平的偶蹄目动物基因组中,通过构建全基因组基因共线性的方法,建立了物种之间的直系同源...偶蹄目(Artiodactyla)动物是人类驯化物种的主要来源(如反刍动物),是研究自然选择和人工选择下染色体进化的重要模型生物。在已发表的72个染色体水平的偶蹄目动物基因组中,通过构建全基因组基因共线性的方法,建立了物种之间的直系同源基因集,并由此构建了偶蹄目物种的完整系统发育树,它与已有结果的相似性为86%。同时,通过建立基因共线性的方法,确定了7个反刍动物代表物种的染色体共线性。结合TRF(Tandem repeats finder)软件预测数据和着丝粒蛋白A抗体CUT&Tag(Cleavage under targets and tagmentation)数据定位了反刍动物代表物种--梅花鹿(Cervus nippon)、水牛(Bubalus bubalis)和黄牛(Bos taurus)的染色体着丝粒区域。结果显示,大部分染色体重排-染色体融合或断裂发生在着丝粒区域,它们的着丝粒结构具有共同的起源。同时发现在一些染色体的重排过程中,会在染色体的融合处进化出新的功能性着丝粒区域,而在染色体重排前的对应着丝粒位置仍然存在祖先着丝粒序列的痕迹。从鉴定到的染色体着丝粒区域的特征性串联重复序列结构来看,这些重复序列具有较高的鸟嘌呤和胞嘧啶(GC)含量,暗示着丝粒区域的功能活化和沉默受到了表观遗传学的调控。本研究初步揭示了物种间染色体重排的分子机制,推测由染色体重排带来的染色体多样性是驱动反刍动物物种多样性形成的重要动力。展开更多
The ancient Neo-Tethyan region underwent profound tectonic transformations,including the orogenesis of the Xizang Plateau and the westward retreat and ultimate closure of the Neo-Tethyan Ocean.These events significant...The ancient Neo-Tethyan region underwent profound tectonic transformations,including the orogenesis of the Xizang Plateau and the westward retreat and ultimate closure of the Neo-Tethyan Ocean.These events significantly influenced the diversification and biogeography of aquatic animals.However,the impact of these large-scale sea-land shifts on the long-range evolutionary history of terrestrial fauna remains unclear.This study investigated how geological changes in the Neo-Tethyan region shaped the evolutionary trajectories and dispersal patterns of Pholcus sensu lato cellar spiders across the Old World.Molecular dating,ancestral area reconstructions,and diversity analyses were conducted using sequences from seven genes across 234 samples representing 209 species.Results indicated that these spiders originated in the eastern Neo-Tethyan region during the Early Eocene,with their subsequent diversification driven by a series of concomitant geological events.The Eurasian(ER)Group dispersed into Europe following the westward retreat of the Neo-Tethyan Ocean in the Early Miocene,while the African(AF)Group migrated into Africa via the Arabian Plate land bridge following the closure of the Neo-Tethyan Ocean in the Oligocene.The East Asian(EA)Group,which expanded along the southeastern margin of the Himalayas,experienced explosive diversification in response to sustained orogenesis at the Eocene-Oligocene boundary.These findings illustrate how large-scale geological processes and sea-land changes shaped the evolutionary history of terrestrial fauna in the Neo-Tethyan region.展开更多
High-altitude and marine mammals inhabit distinct ecosystems but share a common challenge:hypoxia.To survive in low-oxygen environments,these species have evolved similar phenotypic pulmonary adaptations,characterized...High-altitude and marine mammals inhabit distinct ecosystems but share a common challenge:hypoxia.To survive in low-oxygen environments,these species have evolved similar phenotypic pulmonary adaptations,characterized by a high density of elastic fibers.In this study,we explored the molecular mechanisms underlying these adaptations,focusing on pulmonary fibrosis and hypoxia tolerance through comparative genomics and convergent evolution analyses.We observed significant expansions and contractions in certain gene families across both high-altitude and marine mammals,closely associated with processes involved in pulmonary fibrosis.Notably,members of the keratin gene family,such as KRT17 and KRT14,appear to be associated with the development of the dense elastic fiber phenotype observed in the lungs of hypoxia-tolerant mammals.Through selection pressure and amino acid substitution analyses,we identified multiple genes exhibiting convergent accelerated evolution,positive selection,and amino acid substitution in these species,associated with adaptation to hypoxic environments.Specifically,the convergent evolution of ZFP36L1,FN1,and NEDD9 was found to contribute to the high density of elastic fibers in the lungs of both high-altitude and marine mammals,facilitating their hypoxia tolerance.Additionally,we identified convergent amino acid substitutions and gene loss events associated with sperm development,differentiation,and spermatogenesis,such as amino acid substitutions in SLC26A3 and pseudogenization of CFAP47,as confirmed by PCR.These genetic alterations may be linked to changes in the reproductive capabilities of these animals.Overall,this study offers novel perspectives on the genetic and molecular adaptations of high-altitude and marine mammals to hypoxic environments,with a particular emphasis on pulmonary fibrosis.展开更多
文摘偶蹄目(Artiodactyla)动物是人类驯化物种的主要来源(如反刍动物),是研究自然选择和人工选择下染色体进化的重要模型生物。在已发表的72个染色体水平的偶蹄目动物基因组中,通过构建全基因组基因共线性的方法,建立了物种之间的直系同源基因集,并由此构建了偶蹄目物种的完整系统发育树,它与已有结果的相似性为86%。同时,通过建立基因共线性的方法,确定了7个反刍动物代表物种的染色体共线性。结合TRF(Tandem repeats finder)软件预测数据和着丝粒蛋白A抗体CUT&Tag(Cleavage under targets and tagmentation)数据定位了反刍动物代表物种--梅花鹿(Cervus nippon)、水牛(Bubalus bubalis)和黄牛(Bos taurus)的染色体着丝粒区域。结果显示,大部分染色体重排-染色体融合或断裂发生在着丝粒区域,它们的着丝粒结构具有共同的起源。同时发现在一些染色体的重排过程中,会在染色体的融合处进化出新的功能性着丝粒区域,而在染色体重排前的对应着丝粒位置仍然存在祖先着丝粒序列的痕迹。从鉴定到的染色体着丝粒区域的特征性串联重复序列结构来看,这些重复序列具有较高的鸟嘌呤和胞嘧啶(GC)含量,暗示着丝粒区域的功能活化和沉默受到了表观遗传学的调控。本研究初步揭示了物种间染色体重排的分子机制,推测由染色体重排带来的染色体多样性是驱动反刍动物物种多样性形成的重要动力。
基金supported by the Science&Technology Fundamental Resources Investigation Program of China(2023FY100200)National Natural Science Foundation of China(NSFC-32430015,32170461,31872193)。
文摘The ancient Neo-Tethyan region underwent profound tectonic transformations,including the orogenesis of the Xizang Plateau and the westward retreat and ultimate closure of the Neo-Tethyan Ocean.These events significantly influenced the diversification and biogeography of aquatic animals.However,the impact of these large-scale sea-land shifts on the long-range evolutionary history of terrestrial fauna remains unclear.This study investigated how geological changes in the Neo-Tethyan region shaped the evolutionary trajectories and dispersal patterns of Pholcus sensu lato cellar spiders across the Old World.Molecular dating,ancestral area reconstructions,and diversity analyses were conducted using sequences from seven genes across 234 samples representing 209 species.Results indicated that these spiders originated in the eastern Neo-Tethyan region during the Early Eocene,with their subsequent diversification driven by a series of concomitant geological events.The Eurasian(ER)Group dispersed into Europe following the westward retreat of the Neo-Tethyan Ocean in the Early Miocene,while the African(AF)Group migrated into Africa via the Arabian Plate land bridge following the closure of the Neo-Tethyan Ocean in the Oligocene.The East Asian(EA)Group,which expanded along the southeastern margin of the Himalayas,experienced explosive diversification in response to sustained orogenesis at the Eocene-Oligocene boundary.These findings illustrate how large-scale geological processes and sea-land changes shaped the evolutionary history of terrestrial fauna in the Neo-Tethyan region.
基金supported by the National Natural Science Foundation of China(32270442,31872219,31370401,32030011,31630071,31772448)National Key Research and Development Program of China(2022YFF1301602)Postgraduate Research&Practice Innovation Program of Jiangsu Province(KYCX23_1747,KYCX23_1740)。
文摘High-altitude and marine mammals inhabit distinct ecosystems but share a common challenge:hypoxia.To survive in low-oxygen environments,these species have evolved similar phenotypic pulmonary adaptations,characterized by a high density of elastic fibers.In this study,we explored the molecular mechanisms underlying these adaptations,focusing on pulmonary fibrosis and hypoxia tolerance through comparative genomics and convergent evolution analyses.We observed significant expansions and contractions in certain gene families across both high-altitude and marine mammals,closely associated with processes involved in pulmonary fibrosis.Notably,members of the keratin gene family,such as KRT17 and KRT14,appear to be associated with the development of the dense elastic fiber phenotype observed in the lungs of hypoxia-tolerant mammals.Through selection pressure and amino acid substitution analyses,we identified multiple genes exhibiting convergent accelerated evolution,positive selection,and amino acid substitution in these species,associated with adaptation to hypoxic environments.Specifically,the convergent evolution of ZFP36L1,FN1,and NEDD9 was found to contribute to the high density of elastic fibers in the lungs of both high-altitude and marine mammals,facilitating their hypoxia tolerance.Additionally,we identified convergent amino acid substitutions and gene loss events associated with sperm development,differentiation,and spermatogenesis,such as amino acid substitutions in SLC26A3 and pseudogenization of CFAP47,as confirmed by PCR.These genetic alterations may be linked to changes in the reproductive capabilities of these animals.Overall,this study offers novel perspectives on the genetic and molecular adaptations of high-altitude and marine mammals to hypoxic environments,with a particular emphasis on pulmonary fibrosis.
