DEAR EDITOR,A new bush frog species, Raorchestes cangyuanensis sp. nov., from Cangyuan, Yunnan Province, China, is described based on morphological and molecular analyses. It differs from all known congeners by a comb...DEAR EDITOR,A new bush frog species, Raorchestes cangyuanensis sp. nov., from Cangyuan, Yunnan Province, China, is described based on morphological and molecular analyses. It differs from all known congeners by a combination of the following characters: body size small, adult snout-vent length (SVL) 16.1–20.0 mm in males (n=3);tympanum indistinct;tips of all fingers and toes expanded into discs with circummarginal grooves;rudimentary webbing between toes;fingers and toes with lateral dermal fringes;inner and outer metacarpal tubercles present;heels meeting when limbs held at right angles to body;crotch with a distinct black patch;discs of fingers and toes orange;male with external single subgular vocal sac and reddish nuptial pad at the base of first finger.展开更多
DEAR EDITOR,Species of Xenophrys are conserved morphologically and live primarily in forests. In Thailand, the genus harbors many cryptic species. Herein we report the collection of specimens from Doi Inthanon, Chiang...DEAR EDITOR,Species of Xenophrys are conserved morphologically and live primarily in forests. In Thailand, the genus harbors many cryptic species. Herein we report the collection of specimens from Doi Inthanon, Chiang Mai Province, northern Thailand, which were identified previously as X. minor. Molecular and morphological analyses find that these specimens differ significantly from other known congeners, and therefore we describe a new species. Further, our phylogenetic analyses indicate that X. latidactyla is a junior synonym of X. palpebralespinosa.展开更多
Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation （OXPHOS） is the only process under...Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation （OXPHOS） is the only process under control of both nuclear and mitochondrial genomes. Although factors affecting codon usage in a single genome have been studied, this has not occurred when both interactional genomes are involved. Consequently, we investigated whether or not other factors influence codon usage of coevolved genes. We used Drosophila melanogaster as a model organism. Our χ^2 test on the number of codons of nuclear and mitochondrial genes involved in the OXPHOS system was significantly different （χ^2= 7945.16, P 〈 0.01）. A plot of effective number of codons against GC3s content of nuclear genes showed that few genes lie on the expected curve, indicating that codon usage was random. Correspondence analysis indicated a significant correlation between axis 1 and codon adaptation index （R = 0.947, P 〈 0.01） in every nuclear gene sequence. Thus, codon usage bias of nuclear genes appeared to be affected by translational selection. Correlation between axis 1 coordinates and GC content （R = 0.814, P 〈 0.01） indicated that the codon usage of nuclear genes was also affected by GC composition. Analysis of mitochondrial genes did not reveal a significant correlation between axis 1 and any parameter. Statistical analyses indicated that codon usages of both nDNA and mtDNA were subjected to context-dependent mutations.展开更多
Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. Howeve...Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.展开更多
Orogenesis of the Qinghai-Tibetan Plateau,which occurred in a stepwise manner,contributed to the extreme aridity of the Tarim Basin,resulting in vulnerable and unstable ecosystems.Quaternary climatic oscillations may ...Orogenesis of the Qinghai-Tibetan Plateau,which occurred in a stepwise manner,contributed to the extreme aridity of the Tarim Basin,resulting in vulnerable and unstable ecosystems.Quaternary climatic oscillations may have affected the ecosystems and,consequently,the distributions and genetic structuring of the Tarim Basin's biota.We used nucleotide sequence data from 2 mitochondrial (mt) DNA genes (Cyt b and the D-loop) to test hypotheses associated with the matrilineal and demographical histories of the Tarim Basin's endemic Yarkand hare (Lepus yarkandensis).Range-wide sampling involving 20 populations and 224 individuals detected 126 haplotypes that clustered into 5 major lineages in both the phylogenetic tree and median-joining network.Populations from the northern and eastern Tarim Basin shared a similar history,as did those from the western and southern regions.Demographical analysis and genetic diversity estimations suggested that the western and southern regions might have served as glacial refugia for the Yarkand hare during Quaternary climatic oscillations.The distribution of the Yarkand hare,especially in the northern and eastern parts,probably represented 3 postglacial colonization events,dated to 0.21,0.090 and 0.054 MYA,which corresponded to known interglacial periods.Given the relatively complete geographic isolation between the eastern and southern populations,the Yarkand hare likely dispersed during postglacial periods from the southwest to the north,and then onward to the east.The absence of water likely forced the species into refugia,and this differed from other Pleistocene biogeographical drivers.The demographical and historical patterns have important implications for conservation.展开更多
Based on molecular phylogeny of the Chinese white cross-band krait, Bungarus multicinctus, several individuals from southwestern and southern China were found to be nested within putative species B. candidus（Linnaeus...Based on molecular phylogeny of the Chinese white cross-band krait, Bungarus multicinctus, several individuals from southwestern and southern China were found to be nested within putative species B. candidus（Linnaeus, 1758） with high support values. Morphological examination also indicated these specimens were identical to B. candidus. We concluded that the Chinese white cross-band krait, previously identified as B. multicinctus in southwest and south China, should be recognized as B. candidus, a new record in China, and B. m. wanghaoti should be invalid. B. multicinctus is recurrently limited to southern China within China.展开更多
基金supported by the National Natural Science Foundation of China(31622052,31501843)Southeast Asia Biodiversity Research Institute,Chinese Academy of Sciences(CAS)(Y4ZK111B01:2017CASSEABRIQG002)+4 种基金International Partnership Program of CAS(152453KYSB20170033)Youth Innovation Promotion Association CAS,and Animal Branch of the Germplasm Bank of Wild Species,CAS(Large Research Infrastructure Funding)to J.C.,CAS President’s International Fellowship Initiative(PIFI)NSERC Discovery Grant(3148)ROM Foundation,and ROM Members Volunteer Committee to R.W.M.,Unit of Excellence 2019 on Biodiversity and Natural Resources Management,University of Phayao(UoE62005)Thailand Research Fund:DBG6180001,and Plant Genetic Conservation Project under the Royal Initiative of Her Royal Highness Princess Maha Chakri Sirindhorn,University of Phayao(RS013)to C.S
文摘DEAR EDITOR,A new bush frog species, Raorchestes cangyuanensis sp. nov., from Cangyuan, Yunnan Province, China, is described based on morphological and molecular analyses. It differs from all known congeners by a combination of the following characters: body size small, adult snout-vent length (SVL) 16.1–20.0 mm in males (n=3);tympanum indistinct;tips of all fingers and toes expanded into discs with circummarginal grooves;rudimentary webbing between toes;fingers and toes with lateral dermal fringes;inner and outer metacarpal tubercles present;heels meeting when limbs held at right angles to body;crotch with a distinct black patch;discs of fingers and toes orange;male with external single subgular vocal sac and reddish nuptial pad at the base of first finger.
基金supported by the Strategic Priority Research Program A of the Chinese Academy of Science(CAS)(No.XDA19050303)Southeast Asia Biodiversity Research Institute(Y4ZK111B01:2017CASSEABRIQG002)+5 种基金the International Partnership Program(152453KYSB20170033)the Youth Innovation Promotion Association,and the Animal Branch of the Germplasm Bank of Wild Species,CAS(Large Research Infrastructure Funding)to J.C.the CAS President’s International Fellowship Initiative(PIFI),NSERC Discovery Grant(3148),ROM Foundation,and ROM Members Volunteer Committee to R.W.M.Unit of Excellence 2019 on Biodiversity and Natural Resources Management,University of Phayao(UoE62005)Thailand Research Fund:DBG6180001 and the Plant Genetic Conservation Project under the Royal Initiative of Her Royal Highness Princess Maha Chakri Sirindhorn,University of Phayao(RS013)to C.Sthe Russian Science Foundation grant No.19-14-00050 to N.A.P
文摘DEAR EDITOR,Species of Xenophrys are conserved morphologically and live primarily in forests. In Thailand, the genus harbors many cryptic species. Herein we report the collection of specimens from Doi Inthanon, Chiang Mai Province, northern Thailand, which were identified previously as X. minor. Molecular and morphological analyses find that these specimens differ significantly from other known congeners, and therefore we describe a new species. Further, our phylogenetic analyses indicate that X. latidactyla is a junior synonym of X. palpebralespinosa.
基金The Third Phase of the Innovation Program in the Chinese Academy of SciencesGrants from the National Natural Science Foundation of China (Grant Nos.30670242 and 30500056)the Major Program from the Natural Science Foundation,Beijing(6081002)
基金supported by the National Natural Science Foundation of China (No.30770302 and 30570970)the Program of Ministry of Science and Technology of the Republic of China (No.2006FY110500)partially by the National Science Fund for Fostering Talents in Basic Research (NSFC-J0630964/J0109)
文摘Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation （OXPHOS） is the only process under control of both nuclear and mitochondrial genomes. Although factors affecting codon usage in a single genome have been studied, this has not occurred when both interactional genomes are involved. Consequently, we investigated whether or not other factors influence codon usage of coevolved genes. We used Drosophila melanogaster as a model organism. Our χ^2 test on the number of codons of nuclear and mitochondrial genes involved in the OXPHOS system was significantly different （χ^2= 7945.16, P 〈 0.01）. A plot of effective number of codons against GC3s content of nuclear genes showed that few genes lie on the expected curve, indicating that codon usage was random. Correspondence analysis indicated a significant correlation between axis 1 and codon adaptation index （R = 0.947, P 〈 0.01） in every nuclear gene sequence. Thus, codon usage bias of nuclear genes appeared to be affected by translational selection. Correlation between axis 1 coordinates and GC content （R = 0.814, P 〈 0.01） indicated that the codon usage of nuclear genes was also affected by GC composition. Analysis of mitochondrial genes did not reveal a significant correlation between axis 1 and any parameter. Statistical analyses indicated that codon usages of both nDNA and mtDNA were subjected to context-dependent mutations.
文摘Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.
基金supported by the National Key Basic Research Program of China (2007CB411600)the National Natural Science Foundation of China (30500061 and 31060152)+1 种基金the Research Start-up Fund of Xinjiang Uighur Autonomous Region for Young Teachers in University (XJEDU2008S03)the College-University United Project of Xinjiang University (XY080117)
文摘Orogenesis of the Qinghai-Tibetan Plateau,which occurred in a stepwise manner,contributed to the extreme aridity of the Tarim Basin,resulting in vulnerable and unstable ecosystems.Quaternary climatic oscillations may have affected the ecosystems and,consequently,the distributions and genetic structuring of the Tarim Basin's biota.We used nucleotide sequence data from 2 mitochondrial (mt) DNA genes (Cyt b and the D-loop) to test hypotheses associated with the matrilineal and demographical histories of the Tarim Basin's endemic Yarkand hare (Lepus yarkandensis).Range-wide sampling involving 20 populations and 224 individuals detected 126 haplotypes that clustered into 5 major lineages in both the phylogenetic tree and median-joining network.Populations from the northern and eastern Tarim Basin shared a similar history,as did those from the western and southern regions.Demographical analysis and genetic diversity estimations suggested that the western and southern regions might have served as glacial refugia for the Yarkand hare during Quaternary climatic oscillations.The distribution of the Yarkand hare,especially in the northern and eastern parts,probably represented 3 postglacial colonization events,dated to 0.21,0.090 and 0.054 MYA,which corresponded to known interglacial periods.Given the relatively complete geographic isolation between the eastern and southern populations,the Yarkand hare likely dispersed during postglacial periods from the southwest to the north,and then onward to the east.The absence of water likely forced the species into refugia,and this differed from other Pleistocene biogeographical drivers.The demographical and historical patterns have important implications for conservation.
基金supported by the National Natural Science Foundation of China(31071892,31372152)Department of Education of Sichuan Province(13TD0027)to PGSoutheast Asia Biodiversity Research Institute,Chinese Academy of Sciences(Y4ZK111B01)to JC
文摘Based on molecular phylogeny of the Chinese white cross-band krait, Bungarus multicinctus, several individuals from southwestern and southern China were found to be nested within putative species B. candidus（Linnaeus, 1758） with high support values. Morphological examination also indicated these specimens were identical to B. candidus. We concluded that the Chinese white cross-band krait, previously identified as B. multicinctus in southwest and south China, should be recognized as B. candidus, a new record in China, and B. m. wanghaoti should be invalid. B. multicinctus is recurrently limited to southern China within China.
