Extreme heat and chronic water scarcity present formidable challenges to large desert-dwelling mammals.In addition to camels,antelopes within the Hippotraginae and Alcelaphinae subfamilies also exhibit remarkable phys...Extreme heat and chronic water scarcity present formidable challenges to large desert-dwelling mammals.In addition to camels,antelopes within the Hippotraginae and Alcelaphinae subfamilies also exhibit remarkable physiological and genetic specializations for desert survival.Among them,the critically endangered addax(Addax nasomaculatus)represents the most desert-adapted antelope species.However,the evolutionary and molecular mechanisms underlying desert adaptations remain largely unexplored.Herein,a high-quality genome assembly of the addax was generated to investigate the molecular evolution of desert adaptation in camels and desert antelopes.Comparative genomic analyses identified 136 genes harboring convergent amino acid substitutions implicated in crucial biological processes,including water reabsorption,fat metabolism,and stress response.Notably,a convergent R146S amino acid mutation in the prostaglandin EP2 receptor gene PTGER2 significantly reduced receptor activity,potentially facilitating large-mammal adaptation to arid environments.Lineage-specific innovations were also identified in desert antelopes,including previously uncharacterized conserved non-coding elements.Functional assays revealed that several of these elements exerted significant regulatory effects in vitro,suggesting potential roles in adaptive gene expression.Additionally,signals of introgression and variation in genetic load were observed,indicating their possible influence on desert adaptation.These findings provide insights into the sequential evolutionary processes that drive physiological resilience in arid environments and highlight the importance of convergent evolution in shaping adaptive traits in large terrestrial mammals.展开更多
The matrilineal genealogy of the genus Paramesotriton is hypothesized based on DNA sequences from mitochondrial NADH subunit two （ND2） and its flanking tRNAs （tRN^Arp and a partial tRNA^Ala）. The genealogy identif...The matrilineal genealogy of the genus Paramesotriton is hypothesized based on DNA sequences from mitochondrial NADH subunit two （ND2） and its flanking tRNAs （tRN^Arp and a partial tRNA^Ala）. The genealogy identifies a highly divergent, unnamed lineage from Qixiling Nature Reserve, Jiangxi, China and places it as the sister taxon of P. chinensis. The newly discovered population differs from other congeners by several features of external morphology including having large clusters of dark brown conical warts on the dorsum of the head, lateral surface of the body and dorsolateral ridges. Its intermittent dorsal vertebral ridge is the same color as other parts of the dorsum and tail narrows gradually from the base to the tip. Further, the new population differs from all congeners by an uncorrected P-distance of more than 9.38% in ND2. Consequently, we describe the new species of Asian warty newt （Salamandridae） as Paramesotriton qixilingensis sp. nov.展开更多
DEAR EDITOR,Cavefish are of considerable interest due to the remarkable morphological changes that occurred during their adaptation to cave or subterranean river habitats.These changes are thought to involve trade-off...DEAR EDITOR,Cavefish are of considerable interest due to the remarkable morphological changes that occurred during their adaptation to cave or subterranean river habitats.These changes are thought to involve trade-offs in metabolic requirements and energy utilization.Mitochondria play a vital role in oxygen use and energy metabolism;thus,mitochondrial genes are likely to have experienced specific selective pressures during cavefish evolution.In this study,we assembled and annotated the mitogenome of Sinocyclocheilus sanxiaensis,a typical cavefish species in China.Using this sequence and other available mitogenomes from the NCBI database,we reconstructed an updated phylogeny of Sinocyclocheilus based on 29 species.Five species groups were revealed,with the recently erected S.microphthalmus species group supported.To determine whether divergent selective pressures have acted on the protein-coding genes(PCGs)of the 29 Sinocyclocheilus species exhibiting different morphological features(including eye shape and body color),the fish were classified into three groups according to their cave-related traits.The branch model test revealed higher nonsynonymous/synonymous substitution ratios(ω)in the cave-dwelling groups,potentially resulting from a balance between adaptive selection and relaxed functional constraints.Sophisticated analysis using site and branch-site models identified 24 highly credible positive selection sites located on nine PCGs,with most sites also showing radical changes in amino acid properties.This study sheds light on the phylogeny and mitogenomic evolution of Sinocyclocheilus cavefish,highlighting their successful adaptation and survival in subterranean environments.展开更多
MicroRNAs （miRNAs） are endogenous -22 nucleotide noncoding RNAs that regulate the expression of complementary messenger RNAs （mRNAs）. Thousands of miRNA genes have been found in diverse species, and many of them a...MicroRNAs （miRNAs） are endogenous -22 nucleotide noncoding RNAs that regulate the expression of complementary messenger RNAs （mRNAs）. Thousands of miRNA genes have been found in diverse species, and many of them are highly conserved. With the miRNA roles identified in nearly all aspects of biological processes, evidence is mounting that miRNAs could represent a new layer of regulatory network, and their regulatory effect might be much more pervasive than previously suspected. Here we focus on the posttranscriptional level gene regulation of miRNAs in animals and review how the miRNAs act to sustain and shape up the expression profiles of specific cell types; how the miRNAs integrate into the existing gene regulatory networks; and how the miRNAs influence the evolution of 3＇UTR of mammalian mRNAs.展开更多
Why humans have large brains with higher cognitive abilities is a question long asked by scientjsts.However,much remains unknown,especially the underlying genetic mechanisms.With the use of a transgenic mon key model,...Why humans have large brains with higher cognitive abilities is a question long asked by scientjsts.However,much remains unknown,especially the underlying genetic mechanisms.With the use of a transgenic mon key model,we showed that human-specific sequenee changes of a key brain development gene(Primary microcephaly 1,MCPH7)could result in detectable molecularand cognitive changes resembling human neoteny,a no table characteristic developed during human evolution.This study was published in National Science Review(Shi et al.,2019).展开更多
South China and Indochina host striking species diversity and endemism. Complex tectonic and climatic evolutions appear to be the main drivers of the biogeographic patterns. In this study, based on the geologic histor...South China and Indochina host striking species diversity and endemism. Complex tectonic and climatic evolutions appear to be the main drivers of the biogeographic patterns. In this study, based on the geologic history of this region, we test 2 hypotheses using the evolutionary history of Microhyla fissipes species complex. Using DNA sequence data from both mitochondrial and nuclear genes, we first test the hypothesis that the Red River is a barrier to gene flow and dispersal. Second, we test the hypothesis that Pleistocene climatic cycling affected the genetic structure and population history of these frogs. We detect 2 major genetic splits that associate with the Red River. Time estimation suggests that late Miocene tectonic movement associated with the Red River drove their diversification. Species distribution modeling （SDM） resolves significant ecolo- gical differences between sides of the Red River. Thus, ecological divergence also probably promoted and maintained the diversification. Genogeography, historical demography, and SDM associate patterns in southern China with climate changes of the last glacial maximum （LGM）, but not Indochina. Differences in geography and climate between the 2 areas best explain the discovery. Responses to the Pleistocene glacial-interglacial cycling vary among species and regions.展开更多
The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on...The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved young genes. Two indispensible steps are involved in this process： origin of new gene copies through various mutational mechanisms and evolution of novel functions, which fur- ther more leads to fixation of the new copies within populations. The theoretical framework for the former step formed in 1970s. Ohno proposed gene duplication as the most important mechanism producing new gene copies. He also believed that the most common fate for new gene copies is to become pseudogenes. This classical view was validated and was also challenged by the characterization of the first functional young gene jingwei in Drosophila. Recent genome-wide comparison on young genes of Drosophila has elucidated a compre- hensive picture addressing remarkable roles of various mechanisms besides gene duplication during origin of new genes. Case surveys revealed it is not rare that new genes would evolve novel structures and functions to contribute to the adaptive evolution of organisms. Here, we review recent advances in understanding how new genes originated and evolved on the basis of genome-wide results and ex- perimental efforts on cases. We would finally discuss the future directions of this fast-growing research field in the context of functional genomics era.展开更多
Effective conservation of threatened biota relies on accurate assessments and scientific guidance.As an unfortunate example,Chinese giant salamanders(Andrias,CGS)remain critically endangered in nature.Misguided conser...Effective conservation of threatened biota relies on accurate assessments and scientific guidance.As an unfortunate example,Chinese giant salamanders(Andrias,CGS)remain critically endangered in nature.Misguided conservation efforts,e.g.,commercial propagation and releasing of millions of likely non-indigenous or interspecific hybrids,have further compromised conservation initiatives.Limited information on wild populations of CGS poses a significant conservation challenge.Following 18-month long field monitoring,we now report the discovery of a wild population of CGS in a closed nature reserve in Jiangxi Province,China.Genomic assessments reveal its genetic distinctiveness and do not detect genetic admixture with other species.Based on morphological and molecular evidences,we describe this CGS as a new species Andrias jiangxiensis sp.nov.This is the only known species of CGS today with a genetically pure,reproducing,in situ population.This discovery emphasizes the important role that closed nature reserves play in protecting species,and the necessity of integrating long-term field monitoring and genetic assessments.It sets a new pathway for discovering and conserving endangered species,especially for those biotas that are similarly being extirpated by anthropogenic translocations and overexploitation.展开更多
Gamma-aminobutyric acid(GABA)and glutamate are two important amino acid neurotransmitters widely present in the nervous systems of mammals,insects,round worm,and platyhelminths,while their receptors are quite diversif...Gamma-aminobutyric acid(GABA)and glutamate are two important amino acid neurotransmitters widely present in the nervous systems of mammals,insects,round worm,and platyhelminths,while their receptors are quite diversified across different animal phyla.However,the evolutionary mechanisms between the two conserved neurotransmitters and their diversified receptors remain elusive,and antagonistic interactions between GABA and glutamate signal transduction systems,in particular,have begun to attract significant attention.In this review,we summarize the extant results on the origin and evolution of GABA and glutamate,as well as their receptors,and analyze possible evolutionary processes and phylogenetic relationships of various GABAs and glutamate receptors.We further discuss the evolutionary history of Excitatory/Neutral Amino Acid Transporter(EAAT),a transport protein,which plays an important role in the GABA-glutamate“yin and yang”balanced regulation.Finally,based on current advances,we propose several potential directions of future research.展开更多
Formyl peptide receptors (FPRs) were observed to expand in rodents and were recently suggested as candidate vomeronasal chemo-sensory receptors. Since vomeronasal chemosensory receptors usually underwent positive sele...Formyl peptide receptors (FPRs) were observed to expand in rodents and were recently suggested as candidate vomeronasal chemo-sensory receptors. Since vomeronasal chemosensory receptors usually underwent positive selection and evolved concordantly with the vomeronasal organ (VNO) morphology, we surveyed FPRs in primates in which VNO morphology is greatly diverse and thus it would provide us a clearer view of VNO-FPRs evolution. By screening available primate genome sequences, we obtained the FPR repertoires in representative primate species. As a result, we did not find FPR family size expansion in primates. Further analyses showed no evolution-ary force variance between primates with or without VNO structure, which indicated that there was no functional divergence among pri-mates FPRs. Our results suggest that primates lack the VNO-specific FPRs and the FPR expansion is not a common phenomenon in mammals outside rodent lineage, regardless of VNO complexity.展开更多
The flying squirrels(Pteromyini,Rodentia)are the most diverse and widely distributed group of gliding mammals.Taxonomic boundaries and relationships within flying squirrels remain an area of active research in mammalo...The flying squirrels(Pteromyini,Rodentia)are the most diverse and widely distributed group of gliding mammals.Taxonomic boundaries and relationships within flying squirrels remain an area of active research in mammalogy.The discovery of new specimens of Pteromys(Hylopetes)leonardi Thomas,1921,previously considered a synonym of Hylopetes alboniger,in Yunnan Province,China allowed a morphological and genetic reassessment of the status of this taxon.Phylogenetic reconstruction was implemented using sequences of two mitochondrial(12S ribosomal RNA and 16S ribosomal RNA)and one nuclear(interphotoreceptor retinoid-binding protein)gene fragments.Morphological assessments involved examinations of features preserved on skins,skulls,and penises of museum specimens,supplemented with principal component analysis of craniometric data.Together these assessments revealed that this taxon should be recognized not only as a distinct species,but should also be placed within a new genus,described here as Priapomys gen.nov.展开更多
Abstract The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about l...Abstract The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about labeonines have been undertaken the results have been inconsistent and a comprehensive phylogeny is needed. Further, an incongruence between morphological and molecular phylogeny requires a systematic exploration of the significance of morphological characters on the basis of the molecular phylogeny. In this study, a total of 292 nucleotide sequences from 73 individuals （representing 24 genera and 73 species） of Labeoninae were analyzed. The results of the phylogenetic analysis indicate that there are four major clades within Labeoninae and three monophyletic lineages within the fourth clade. Results of the character evolution show that all oromandibular morphological characters are homoplastically distributed on the molecular phylogenetic tree and suggests that these characters evolved several times during the history of labeonines. In particular, the labeonine, a specific disc on the lower lip, has been acquired three times and reversed twice. These morphological characters do not have systematic significance but can be useful for taxonomy. The results of biogeography suggest that the Labeoninae originated from Southeast Asia and separately dispersed to Africa, East Asia and South Asia.展开更多
Six main mitochondrial DNA （mtDNA） lineages have been described in minnow （Zacco platypus） samples obtained from northern, western and southern China Perdices et al. （2004） predicted that further sampling of oth...Six main mitochondrial DNA （mtDNA） lineages have been described in minnow （Zacco platypus） samples obtained from northern, western and southern China Perdices et al. （2004） predicted that further sampling of other tributaries might discover more lineages of this species. In this study, we collected 26 Zacco platypus individuals in the Huangshan area of eastern China and determined the cytochrome b （cytb） sequence variations. Combined with reported data in GenBank, we identified ten matrilines （Zacco A-J） in a total of 169 samples, with relatively high molecular divergence found among them. The Huangshan population had the greatest genetic variation among all sampled regions and hosted six of the ten matrilines. Our results highlight the significance of the Huangshan area for the conservation of Zacco platypus.展开更多
Gamma-aminobutyric acid （GABA） and glutamate are two important amino acid neurotransmitters widely present in the nervous systems of mammals, insects, round worm, and platyhelminths, while their receptors are quite ...Gamma-aminobutyric acid （GABA） and glutamate are two important amino acid neurotransmitters widely present in the nervous systems of mammals, insects, round worm, and platyhelminths, while their receptors are quite diversified across different animal phyla. However, the evolutionary mechanisms between the two conserved neurotransmitters and their diversified receptors remain elusive, and antagonistic interactions between GABA and glutamate signal transduction systems, in particular, have began to attract significant attention. In this review, we summarize the extant results on the origin and evolution of GABA and glutamate, as well as their receptors, and analyze possible evolutionary processes and phylogenetic relationships of various GABAs and glutamate receptors. We further discuss the evolutionary history of Excitatory/Neutral Amino Acid Transporter （EAAT）, a transport protein, which plays an important role in the GABA-glutamate ＂yin and yang＂ balanced regulation. Finally, based on current advances, we propose several potential directions of future research.展开更多
The secreted Wnt signaling inhibitor Dickkopfl （Dkkl） plays key role in vertebrate head induction. Its receptor Kremen synergizes with Dkkl in Wnt inhibition. Here we have carried out expression and functional studi...The secreted Wnt signaling inhibitor Dickkopfl （Dkkl） plays key role in vertebrate head induction. Its receptor Kremen synergizes with Dkkl in Wnt inhibition. Here we have carried out expression and functional studies of the Dkk and Kremen genes in amphioxus （Branchiostoma belcheri）. During embryonic and larval development, BbDkkl/2/4 is expressed in the posterior mesoendoderm, anterior somatic mesoderm and the pharyngeal regions. Its expression becomes restricted to the pharyngeal region on the left side at larval stages. In 45 h larvae, BbDkkl/2/4 is expressed specifically in the cerebral vesicle. BbDkk3 was only detected at larval stages in the mid-intestine region. Seven Kremen related genes were identified in the genome of the Florida amphioxus （Branchiostoma floridae）, clustered in 4 scaffolds, and are designated Kremenl-4 and Kremen-like 1-3, respectively. In B. belcheri, Kremenl is strongly expressed in the mesoendoderm during early development and Kremen3 is expressed asymmetrically in spots in the larval pharyngeal region. In luciferase reporter assays, BbDkkl/2/4 can strongly inhibit Wnt signaling, while BbDkk3, BbKremenl and BbKremen3 can not. No co-operative effect was observed between amphioxus Dkkl/2/4 and Kremens, suggesting that the interaction between Dkk and Kremen likely originated later during evolution.展开更多
Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories...Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories,which are presently unknown.We found that most species showed a reduction of population size since the beginning of the last glacial period,except for those species distributed in Australasia and in the far south of South America.Different degrees of contraction and expansion of transposable elements(TE)have shaped the paleognathous genome architecture,with a higher transposon removal rate in tinamous than in ratites.One repeat family,AviRTE,likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago.Our analysis of gene families identified rapid turnover of immune and reproductionrelated genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites.We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites,with the former also showing more degenerated W chromosomes.This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria.Overall,we reconstructed the evolutionary history of the Palaeognathae populations,genes,and TEs.Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.展开更多
DEAR EDITOR,In this study, we sequenced the complete mitochondrial genome （mitogenome） of the Thai Red Junglefowl （RJF; Gallus gallus） using the next-generation sequencing （NGS） platform of the Ion Torrent PGM. ...DEAR EDITOR,In this study, we sequenced the complete mitochondrial genome （mitogenome） of the Thai Red Junglefowl （RJF; Gallus gallus） using the next-generation sequencing （NGS） platform of the Ion Torrent PGM. Samples were taken from Mae Wang District, Chiang Mai Province, northern Thailand Our data showed the complete mitogenome to be 16 785 bp in length, composed by 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The genome nucleotide composition was 30.3% A, 23.7% T, 32.5% C, and 13.5% G, resulting in a high percentage of A＋T （50.4%）. Phylogenetic analysis revealed that the mitogenome belonged to haplogroup X, whereas those of all domestic chickens belong to haplogroups A to G. This newly released mitogenome sequence will advance further evolutionary and population genetics study of the RJF and domestic chicken The availability of the G. gallus mitogenome will also contribute to further conservation genetics research of a unique species, listed as ＇data deficient＇ in Thailand.展开更多
Many paleognaths(ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for the differen...Many paleognaths(ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for the different tempos of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes.We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of “evolutionary strata”. Nine of the 15 studied species’ sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending more than half of the entire chromosome length. We found that in the older strata, the W chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared with other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly expressed progenitors. We speculate such “defeminization” of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females rather than males, which evolved in their common ancestors.展开更多
Pygmy lorises are arboreal primates primarily found in forest environments across Southeast Asia(Nekaris 2014).Theyhave a diverse diet,including plant secretions,nectar,fruits,invertebrates,tree bark,and bird eggs.All...Pygmy lorises are arboreal primates primarily found in forest environments across Southeast Asia(Nekaris 2014).Theyhave a diverse diet,including plant secretions,nectar,fruits,invertebrates,tree bark,and bird eggs.All 9 known speciesof pygmy lorises are listed as globally endangered species(Nekaris 2014).Pygmy lorises exhibit a range of unique phenotypic characteristics rarely seen among primates.展开更多
Shandong province,located in the Lower Yellow River,is one of the birthplaces of ancient Chinese civilization.However,the comprehensive genetic histories of this region have remained largely unknown until now due to a...Shandong province,located in the Lower Yellow River,is one of the birthplaces of ancient Chinese civilization.However,the comprehensive genetic histories of this region have remained largely unknown until now due to a lack of ancient human genomes.Here,we present 21 ancient genomes from Shandong dating from the Warring States period to the Northern Dynasties.Unlike the early Neolithic samples from Shandong,the historical samples are most closely related to post-Late Neolithic populations of the Middle Yellow River Basin,suggesting a population turnover in Shandong from the Neolithic Age to the Historical era.In addition,we detect a close genetic affinity between the historical samples in Shandong and present-day Han Chinese,showing long-term genetic stability in Han Chinese,at least since the Warring States period.展开更多
基金supported by the National Key R&D Program of China(2022YFF1000100)Shaanxi Program for Support of Top-notch Young ProfessionalsFundamental Research Funds for the Central Universities。
文摘Extreme heat and chronic water scarcity present formidable challenges to large desert-dwelling mammals.In addition to camels,antelopes within the Hippotraginae and Alcelaphinae subfamilies also exhibit remarkable physiological and genetic specializations for desert survival.Among them,the critically endangered addax(Addax nasomaculatus)represents the most desert-adapted antelope species.However,the evolutionary and molecular mechanisms underlying desert adaptations remain largely unexplored.Herein,a high-quality genome assembly of the addax was generated to investigate the molecular evolution of desert adaptation in camels and desert antelopes.Comparative genomic analyses identified 136 genes harboring convergent amino acid substitutions implicated in crucial biological processes,including water reabsorption,fat metabolism,and stress response.Notably,a convergent R146S amino acid mutation in the prostaglandin EP2 receptor gene PTGER2 significantly reduced receptor activity,potentially facilitating large-mammal adaptation to arid environments.Lineage-specific innovations were also identified in desert antelopes,including previously uncharacterized conserved non-coding elements.Functional assays revealed that several of these elements exerted significant regulatory effects in vitro,suggesting potential roles in adaptive gene expression.Additionally,signals of introgression and variation in genetic load were observed,indicating their possible influence on desert adaptation.These findings provide insights into the sequential evolutionary processes that drive physiological resilience in arid environments and highlight the importance of convergent evolution in shaping adaptive traits in large terrestrial mammals.
基金supported by grants from the Ministry of Science and Technology of China (MOST Grant 2011FY120200)the National Natural Science Foundation of China (31090250)+5 种基金the Chinese Academy of Sciences (CAS KSCX2-EW-Z-2 KSCX2-EW-Q-9 KSCX2-YW-Z-0807)the Bureau of Science and Technology of Yunnan ProvinceNatural Sciences and Engineering Research Council (NSERC) Discovery Grant 3148 supported preparation of the manuscript
文摘The matrilineal genealogy of the genus Paramesotriton is hypothesized based on DNA sequences from mitochondrial NADH subunit two （ND2） and its flanking tRNAs （tRN^Arp and a partial tRNA^Ala）. The genealogy identifies a highly divergent, unnamed lineage from Qixiling Nature Reserve, Jiangxi, China and places it as the sister taxon of P. chinensis. The newly discovered population differs from other congeners by several features of external morphology including having large clusters of dark brown conical warts on the dorsum of the head, lateral surface of the body and dorsolateral ridges. Its intermittent dorsal vertebral ridge is the same color as other parts of the dorsum and tail narrows gradually from the base to the tip. Further, the new population differs from all congeners by an uncorrected P-distance of more than 9.38% in ND2. Consequently, we describe the new species of Asian warty newt （Salamandridae） as Paramesotriton qixilingensis sp. nov.
基金supported by the Key R&D Project of Hubei Provincial Science and Technology Department(2020BBB076)Talent Project of Hunan Provincial Science and Technology Department(2020RC3057)National Natural Science Foundation of China(32060128)。
文摘DEAR EDITOR,Cavefish are of considerable interest due to the remarkable morphological changes that occurred during their adaptation to cave or subterranean river habitats.These changes are thought to involve trade-offs in metabolic requirements and energy utilization.Mitochondria play a vital role in oxygen use and energy metabolism;thus,mitochondrial genes are likely to have experienced specific selective pressures during cavefish evolution.In this study,we assembled and annotated the mitogenome of Sinocyclocheilus sanxiaensis,a typical cavefish species in China.Using this sequence and other available mitogenomes from the NCBI database,we reconstructed an updated phylogeny of Sinocyclocheilus based on 29 species.Five species groups were revealed,with the recently erected S.microphthalmus species group supported.To determine whether divergent selective pressures have acted on the protein-coding genes(PCGs)of the 29 Sinocyclocheilus species exhibiting different morphological features(including eye shape and body color),the fish were classified into three groups according to their cave-related traits.The branch model test revealed higher nonsynonymous/synonymous substitution ratios(ω)in the cave-dwelling groups,potentially resulting from a balance between adaptive selection and relaxed functional constraints.Sophisticated analysis using site and branch-site models identified 24 highly credible positive selection sites located on nine PCGs,with most sites also showing radical changes in amino acid properties.This study sheds light on the phylogeny and mitogenomic evolution of Sinocyclocheilus cavefish,highlighting their successful adaptation and survival in subterranean environments.
基金supported by the National Basic Research Program of China (973 Program) (No. 2006CB701506 and 2007CB815705)the Chinese Academy of Sciences (No. KSCX1-YW-R-34)+1 种基金the National Natural Science Foundation of China (No. 30525028, 30630013 and 30871343)the Natural Science Foundation of Yunnan Province of China.
文摘MicroRNAs （miRNAs） are endogenous -22 nucleotide noncoding RNAs that regulate the expression of complementary messenger RNAs （mRNAs）. Thousands of miRNA genes have been found in diverse species, and many of them are highly conserved. With the miRNA roles identified in nearly all aspects of biological processes, evidence is mounting that miRNAs could represent a new layer of regulatory network, and their regulatory effect might be much more pervasive than previously suspected. Here we focus on the posttranscriptional level gene regulation of miRNAs in animals and review how the miRNAs act to sustain and shape up the expression profiles of specific cell types; how the miRNAs integrate into the existing gene regulatory networks; and how the miRNAs influence the evolution of 3＇UTR of mammalian mRNAs.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB13000000)the National Natural Science Foundation of China(31730088)the Youth Innovation Promotion Association of CAS
文摘Why humans have large brains with higher cognitive abilities is a question long asked by scientjsts.However,much remains unknown,especially the underlying genetic mechanisms.With the use of a transgenic mon key model,we showed that human-specific sequenee changes of a key brain development gene(Primary microcephaly 1,MCPH7)could result in detectable molecularand cognitive changes resembling human neoteny,a no table characteristic developed during human evolution.This study was published in National Science Review(Shi et al.,2019).
基金Acknowledgments We thank Sheng-guo Fang, Hal-tan Shi, Li-jun Wang, Li-min Ding, Yun-yu Wang, Ban-ling Zhang, Hai-peng Zhao, Jin-ming Chen, Jun-xiao Yang, Jia-jun Zhou, Gang Yao, Nikolai L. Orlov, Son Nguyen Truong, Tao Thien Nguyen, Truong Quang Nguyen, Tran Ngoc Ninh, Ba Dinh Vo, Andrei N. Kuznetsov, Leonid P. Korzoun, Anna B. Vassilieva, Eduard A. Galoyan, Igor V. Palko, Suwat Seaya, and Prakayjit Saengham for helping with sample col- lections. We thank the local Forestry Department and National reserve helped for the fieldworks in China. We thank the Forestry Department of Thailand and Vietnam for permissions to undertake field survey, specimen collections and local national park for helping. The Institute of Animal for Scientific Purposes Development （IAD） issued permission （No.U1-01205-2558） in Thailand. The Department of Forestry, Ministry of Agriculture and Rural Development of Vietnam issued permission （permits No. 170/TCLN-BTI＇N, 982/TCLN-BTTN and 831/TCLN-BTTN） in Vietnam. For loans of tissues, we thank Amy Lathrop from the Royal Ontario Museum （ROM）, Toronto, Canada. We gratefully acknowledge Wei-wei Zhou and Yong-jie Wu for providing thoughtful comments during preparation of the previous version of this manuscript.This work was supported by the program of Chinese Academy of Sciences （2015CASEABRI002）, the Ministry of Science and Technology of China （2011FY120200）, the National Natural Science Foundation of China （31090250）, and the Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences （the Large Research Infrastructure Funding） to J. C. the Chinese Academy of Sciences Visiting Fellowship for Researchers （Postdoc） from Developing Countries （2013FFS130015） to C. S.+2 种基金 the National Natural Science Foundation of China （31501843） to H. M. C. the Russian Foundation of Basic Research （Grant No. RFBR Taiwan No. 14-04- 92000, 15-29-02771 and 15-04-02029） and the Russian Science Foundation （RSF grant No 14-50-00029） to N. A. P. NSERC Discovery Grant （3148）, the ROM Foundation, and the ROM Members Volunteer Committee to R. W. M.
文摘South China and Indochina host striking species diversity and endemism. Complex tectonic and climatic evolutions appear to be the main drivers of the biogeographic patterns. In this study, based on the geologic history of this region, we test 2 hypotheses using the evolutionary history of Microhyla fissipes species complex. Using DNA sequence data from both mitochondrial and nuclear genes, we first test the hypothesis that the Red River is a barrier to gene flow and dispersal. Second, we test the hypothesis that Pleistocene climatic cycling affected the genetic structure and population history of these frogs. We detect 2 major genetic splits that associate with the Red River. Time estimation suggests that late Miocene tectonic movement associated with the Red River drove their diversification. Species distribution modeling （SDM） resolves significant ecolo- gical differences between sides of the Red River. Thus, ecological divergence also probably promoted and maintained the diversification. Genogeography, historical demography, and SDM associate patterns in southern China with climate changes of the last glacial maximum （LGM）, but not Indochina. Differences in geography and climate between the 2 areas best explain the discovery. Responses to the Pleistocene glacial-interglacial cycling vary among species and regions.
基金a CAS-Max Planck Society Fellowship, an award （No. 30325016）；the National Science Foundation of China （NSFC）,two NSFC key grants （No. 30430400 and 30623007）the National Basic Research Program of China （973 Program）（No. 2007CB815703-5）W.W., and a NSFC grant(No.30500283）for junior researchers to S.Y.
文摘The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved young genes. Two indispensible steps are involved in this process： origin of new gene copies through various mutational mechanisms and evolution of novel functions, which fur- ther more leads to fixation of the new copies within populations. The theoretical framework for the former step formed in 1970s. Ohno proposed gene duplication as the most important mechanism producing new gene copies. He also believed that the most common fate for new gene copies is to become pseudogenes. This classical view was validated and was also challenged by the characterization of the first functional young gene jingwei in Drosophila. Recent genome-wide comparison on young genes of Drosophila has elucidated a compre- hensive picture addressing remarkable roles of various mechanisms besides gene duplication during origin of new genes. Case surveys revealed it is not rare that new genes would evolve novel structures and functions to contribute to the adaptive evolution of organisms. Here, we review recent advances in understanding how new genes originated and evolved on the basis of genome-wide results and ex- perimental efforts on cases. We would finally discuss the future directions of this fast-growing research field in the context of functional genomics era.
基金equally supported by the STS Program of Chinese Academy of Sciencesand the Strategic Priority Research Program of Chinese Academy of Sciences(XDB31000000)+1 种基金The Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(Large Research Infrastructure Funding)Jiangxi Academy of Sciences(2021YSBG50008)partially supported it。
文摘Effective conservation of threatened biota relies on accurate assessments and scientific guidance.As an unfortunate example,Chinese giant salamanders(Andrias,CGS)remain critically endangered in nature.Misguided conservation efforts,e.g.,commercial propagation and releasing of millions of likely non-indigenous or interspecific hybrids,have further compromised conservation initiatives.Limited information on wild populations of CGS poses a significant conservation challenge.Following 18-month long field monitoring,we now report the discovery of a wild population of CGS in a closed nature reserve in Jiangxi Province,China.Genomic assessments reveal its genetic distinctiveness and do not detect genetic admixture with other species.Based on morphological and molecular evidences,we describe this CGS as a new species Andrias jiangxiensis sp.nov.This is the only known species of CGS today with a genetically pure,reproducing,in situ population.This discovery emphasizes the important role that closed nature reserves play in protecting species,and the necessity of integrating long-term field monitoring and genetic assessments.It sets a new pathway for discovering and conserving endangered species,especially for those biotas that are similarly being extirpated by anthropogenic translocations and overexploitation.
文摘Gamma-aminobutyric acid(GABA)and glutamate are two important amino acid neurotransmitters widely present in the nervous systems of mammals,insects,round worm,and platyhelminths,while their receptors are quite diversified across different animal phyla.However,the evolutionary mechanisms between the two conserved neurotransmitters and their diversified receptors remain elusive,and antagonistic interactions between GABA and glutamate signal transduction systems,in particular,have begun to attract significant attention.In this review,we summarize the extant results on the origin and evolution of GABA and glutamate,as well as their receptors,and analyze possible evolutionary processes and phylogenetic relationships of various GABAs and glutamate receptors.We further discuss the evolutionary history of Excitatory/Neutral Amino Acid Transporter(EAAT),a transport protein,which plays an important role in the GABA-glutamate“yin and yang”balanced regulation.Finally,based on current advances,we propose several potential directions of future research.
基金supported by grants from National Natural Science Foundation of China (No. 30900793)a grant from Key Project from National Natural Science Foundation of China (No. 30930015) to P.S.+1 种基金West Light Foundation of the Chinese Academy of Sciences to H.Y.by a start-up fund of "Hundreds Talent Program" from Chinese Academy of Sciences
文摘Formyl peptide receptors (FPRs) were observed to expand in rodents and were recently suggested as candidate vomeronasal chemo-sensory receptors. Since vomeronasal chemosensory receptors usually underwent positive selection and evolved concordantly with the vomeronasal organ (VNO) morphology, we surveyed FPRs in primates in which VNO morphology is greatly diverse and thus it would provide us a clearer view of VNO-FPRs evolution. By screening available primate genome sequences, we obtained the FPR repertoires in representative primate species. As a result, we did not find FPR family size expansion in primates. Further analyses showed no evolution-ary force variance between primates with or without VNO structure, which indicated that there was no functional divergence among pri-mates FPRs. Our results suggest that primates lack the VNO-specific FPRs and the FPR expansion is not a common phenomenon in mammals outside rodent lineage, regardless of VNO complexity.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research Program(STEP,2019QZKK0501)National Natural Science Foundation of China(32000304)+4 种基金Yunnan Fundamental Research Projects(202101AT070294)National Key Research and Development Program of China(2017YFC0505200)Strategic Priority Research Program of Chinese Academy of Sciences(XDA20050202)Biodiversity Survey,Monitoring and Assessment(2019HB2096001006)Kadoorie Farm&Botanic Garden。
文摘The flying squirrels(Pteromyini,Rodentia)are the most diverse and widely distributed group of gliding mammals.Taxonomic boundaries and relationships within flying squirrels remain an area of active research in mammalogy.The discovery of new specimens of Pteromys(Hylopetes)leonardi Thomas,1921,previously considered a synonym of Hylopetes alboniger,in Yunnan Province,China allowed a morphological and genetic reassessment of the status of this taxon.Phylogenetic reconstruction was implemented using sequences of two mitochondrial(12S ribosomal RNA and 16S ribosomal RNA)and one nuclear(interphotoreceptor retinoid-binding protein)gene fragments.Morphological assessments involved examinations of features preserved on skins,skulls,and penises of museum specimens,supplemented with principal component analysis of craniometric data.Together these assessments revealed that this taxon should be recognized not only as a distinct species,but should also be placed within a new genus,described here as Priapomys gen.nov.
基金Great thanks to Rick Winterbottom for his hard work on improving this manuscript and Abebe Getahun for graciously providing a part of his dissertation. We thank LN Du, MN He, WS Jiang, JH Lan, R Min, B Yang and J Yang for sample collection. GH Cui provided information on collection localities. L Jia and WY Wang helped with laboratory work. GH Yu and YF Huang provided advice on the study. This study was supported by the National Natural Science Foundation of China （30730017, 31201707）, National Basic Research Program of China （2007CB411600, 2008GA001）, Western Light Doctor Programme of Chinese Academy of Sciences, and Yunnan Provincial Science and Technology Program （2009CC008）.
文摘Abstract The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about labeonines have been undertaken the results have been inconsistent and a comprehensive phylogeny is needed. Further, an incongruence between morphological and molecular phylogeny requires a systematic exploration of the significance of morphological characters on the basis of the molecular phylogeny. In this study, a total of 292 nucleotide sequences from 73 individuals （representing 24 genera and 73 species） of Labeoninae were analyzed. The results of the phylogenetic analysis indicate that there are four major clades within Labeoninae and three monophyletic lineages within the fourth clade. Results of the character evolution show that all oromandibular morphological characters are homoplastically distributed on the molecular phylogenetic tree and suggests that these characters evolved several times during the history of labeonines. In particular, the labeonine, a specific disc on the lower lip, has been acquired three times and reversed twice. These morphological characters do not have systematic significance but can be useful for taxonomy. The results of biogeography suggest that the Labeoninae originated from Southeast Asia and separately dispersed to Africa, East Asia and South Asia.
基金Foundation items： This research was funded by the National Natural Science Foundation of China （NSFC 30870290, 31071891 and 31471968）ACKNOWLEDGEMENTS We extend our thanks to Dr. Robert W. MURPHY for his valuable comments on this manuscript. We thank Jin-Min CHEN （Yunnan University）, Bao-Lin ZHANG （Kunming Institute of Zoology, CAS） and Li-Fang PENG （Nanjing Forestry University） for their help in data processing. We further thank Dian- Cheng YANG （Nanjing Forestry University） and Jun-Sheng CUI （Anhui Agricultural University） for sampling.
文摘Six main mitochondrial DNA （mtDNA） lineages have been described in minnow （Zacco platypus） samples obtained from northern, western and southern China Perdices et al. （2004） predicted that further sampling of other tributaries might discover more lineages of this species. In this study, we collected 26 Zacco platypus individuals in the Huangshan area of eastern China and determined the cytochrome b （cytb） sequence variations. Combined with reported data in GenBank, we identified ten matrilines （Zacco A-J） in a total of 169 samples, with relatively high molecular divergence found among them. The Huangshan population had the greatest genetic variation among all sampled regions and hosted six of the ten matrilines. Our results highlight the significance of the Huangshan area for the conservation of Zacco platypus.
文摘Gamma-aminobutyric acid （GABA） and glutamate are two important amino acid neurotransmitters widely present in the nervous systems of mammals, insects, round worm, and platyhelminths, while their receptors are quite diversified across different animal phyla. However, the evolutionary mechanisms between the two conserved neurotransmitters and their diversified receptors remain elusive, and antagonistic interactions between GABA and glutamate signal transduction systems, in particular, have began to attract significant attention. In this review, we summarize the extant results on the origin and evolution of GABA and glutamate, as well as their receptors, and analyze possible evolutionary processes and phylogenetic relationships of various GABAs and glutamate receptors. We further discuss the evolutionary history of Excitatory/Neutral Amino Acid Transporter （EAAT）, a transport protein, which plays an important role in the GABA-glutamate ＂yin and yang＂ balanced regulation. Finally, based on current advances, we propose several potential directions of future research.
基金supported by the grant from the Innovation Project of Chinese Academy of Sciences (No. KSCX2-YW-R-090)
文摘The secreted Wnt signaling inhibitor Dickkopfl （Dkkl） plays key role in vertebrate head induction. Its receptor Kremen synergizes with Dkkl in Wnt inhibition. Here we have carried out expression and functional studies of the Dkk and Kremen genes in amphioxus （Branchiostoma belcheri）. During embryonic and larval development, BbDkkl/2/4 is expressed in the posterior mesoendoderm, anterior somatic mesoderm and the pharyngeal regions. Its expression becomes restricted to the pharyngeal region on the left side at larval stages. In 45 h larvae, BbDkkl/2/4 is expressed specifically in the cerebral vesicle. BbDkk3 was only detected at larval stages in the mid-intestine region. Seven Kremen related genes were identified in the genome of the Florida amphioxus （Branchiostoma floridae）, clustered in 4 scaffolds, and are designated Kremenl-4 and Kremen-like 1-3, respectively. In B. belcheri, Kremenl is strongly expressed in the mesoendoderm during early development and Kremen3 is expressed asymmetrically in spots in the larval pharyngeal region. In luciferase reporter assays, BbDkkl/2/4 can strongly inhibit Wnt signaling, while BbDkk3, BbKremenl and BbKremen3 can not. No co-operative effect was observed between amphioxus Dkkl/2/4 and Kremens, suggesting that the interaction between Dkk and Kremen likely originated later during evolution.
基金This study was supported by the National Natural Science Foundation of China(31671319,31722050,32061130208)Natural Science Foundation of Zhejiang Province(LD19C190001)+5 种基金European Research Council Starting Grant(grant agreement 677696)to Q.Z.the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31020000,XDB13000000)International Partnership Program of Chinese Academy of Sciences(152453KYSB20170002)Carlsberg Foundation(CF16-0663)Villum Foundation(25900)to G.J.ZWe thank China National Genebank at BGI for contributing to the sequencing.We would like to thank Christopher C.Witt,Mariel L.Campbell and Ariel M.Gaffney from the Museum of Southwestern Biology,Gary Graves from Smithsonian Institute,Robb T.Brumfield and Donna L.Dittman from Louisiana State University Museum of Natural Science,Jack Withrow and Andy Kratter from Florida Museum of Natural History,University of New Mexico for providing bird DNA samples for this work.
文摘Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories,which are presently unknown.We found that most species showed a reduction of population size since the beginning of the last glacial period,except for those species distributed in Australasia and in the far south of South America.Different degrees of contraction and expansion of transposable elements(TE)have shaped the paleognathous genome architecture,with a higher transposon removal rate in tinamous than in ratites.One repeat family,AviRTE,likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago.Our analysis of gene families identified rapid turnover of immune and reproductionrelated genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites.We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites,with the former also showing more degenerated W chromosomes.This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria.Overall,we reconstructed the evolutionary history of the Palaeognathae populations,genes,and TEs.Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.
基金supported by the National Key Research and Development Program(2016YFC1200705)Southeast Asia Biodiversity Research Institute,Chinese Academy of Sciences(Y4ZK111B01:2015CASEABR1002)+2 种基金Ministry of Science and Technology of China(2012FY110800)Chinese Academy of Sciences(KFZD-SW-208)Yunnan Provincial Science and Technology Department
文摘DEAR EDITOR,In this study, we sequenced the complete mitochondrial genome （mitogenome） of the Thai Red Junglefowl （RJF; Gallus gallus） using the next-generation sequencing （NGS） platform of the Ion Torrent PGM. Samples were taken from Mae Wang District, Chiang Mai Province, northern Thailand Our data showed the complete mitogenome to be 16 785 bp in length, composed by 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The genome nucleotide composition was 30.3% A, 23.7% T, 32.5% C, and 13.5% G, resulting in a high percentage of A＋T （50.4%）. Phylogenetic analysis revealed that the mitogenome belonged to haplogroup X, whereas those of all domestic chickens belong to haplogroups A to G. This newly released mitogenome sequence will advance further evolutionary and population genetics study of the RJF and domestic chicken The availability of the G. gallus mitogenome will also contribute to further conservation genetics research of a unique species, listed as ＇data deficient＇ in Thailand.
基金supported by the National Natural Science Foundation of China (32061130208, 32170415)the Natural Science Foundation of Zhejiang Province (LD19C190001)+4 种基金the European Research Council Starting Grant (grant agreement 677696)supported by Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31020000, XDB13000000)International Partnership Program of Chinese Academy of Sciences (152453KYSB20170002)Carlsberg foundation (CF16-0663)Villum Foundation (25900)。
文摘Many paleognaths(ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for the different tempos of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes.We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of “evolutionary strata”. Nine of the 15 studied species’ sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending more than half of the entire chromosome length. We found that in the older strata, the W chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared with other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly expressed progenitors. We speculate such “defeminization” of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females rather than males, which evolved in their common ancestors.
基金supported by the Shaanxi FundamentalScience Research Project for Chemistry&Biology(grant no.22JHQ049)Basic Research Program of Natural Sciencesof Shaanxi Province(2019JM-339).
文摘Pygmy lorises are arboreal primates primarily found in forest environments across Southeast Asia(Nekaris 2014).Theyhave a diverse diet,including plant secretions,nectar,fruits,invertebrates,tree bark,and bird eggs.All 9 known speciesof pygmy lorises are listed as globally endangered species(Nekaris 2014).Pygmy lorises exhibit a range of unique phenotypic characteristics rarely seen among primates.
基金funded by the Shandong Province Humanities and Social Sciences Project“Sorting and Research on Human Bones of Han Dynasty Excavated from the Medical Center Cemetery in Linzi”granted to Zhigang Wu(2022-JCLS-12)the National Key Research and Development Program(2023YFC3303701-02)+5 种基金the National Natural Science Foundation of China(32270667)the Natural Science Foundation of Fujian Province of China(2023J06013)the Major Project of the National Social Science Foundation of China granted to Chuan-Chao Wang(21&ZD285)Open Research Fund of State Key Laboratory of Genetic Engineering at Fudan University(No.SKLGE-2310)Open Research Fund of Forensic Genetics Key Laboratory of the Ministry of Public Security(2023FGKFKT07)Major Special Project of Philosophy and Social Sciences Research of the Ministry of Education(2022JZDZ023).
文摘Shandong province,located in the Lower Yellow River,is one of the birthplaces of ancient Chinese civilization.However,the comprehensive genetic histories of this region have remained largely unknown until now due to a lack of ancient human genomes.Here,we present 21 ancient genomes from Shandong dating from the Warring States period to the Northern Dynasties.Unlike the early Neolithic samples from Shandong,the historical samples are most closely related to post-Late Neolithic populations of the Middle Yellow River Basin,suggesting a population turnover in Shandong from the Neolithic Age to the Historical era.In addition,we detect a close genetic affinity between the historical samples in Shandong and present-day Han Chinese,showing long-term genetic stability in Han Chinese,at least since the Warring States period.
