A novel RNA virus,the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is responsible for the ongoing outbreak of coronavirus disease 2019(COVID-19).Population genetic analysis could be useful for investiga...A novel RNA virus,the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is responsible for the ongoing outbreak of coronavirus disease 2019(COVID-19).Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19.However,due to extensive sampling bias and existence of infection clusters during the epidemic spread,direct applications of existing approaches can lead to biased parameter estimations and data misinterpretation.In this study,we first present robust estimator for the time to the most recent common ancestor(TMRCA)and the mutation rate,and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2.The mutation rate is inferred to be 8.69×10^(−4) per site per year with a 95%confidence interval(CI)of[8.61×10^(−4),8.77×10^(−4)],and the TMRCA of the samples inferred to be Nov 28,2019 with a 95%CI of[Oct 20,2019,Dec 9,2019].The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market.We further demonstrate that genetic polymorphism patterns,including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters,are similar to those caused by evolutionary forces such as natural selection.Our results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism of SARS-CoV-2.Software for implementing VirusMuT can be downloaded at https://bigd.big.ac.cn/biocode/tools/BT007081.展开更多
The small dwarf honey bee, Apis andreniformis, is a rare and patchily distributed Apis spp. and is one of the native Thai honey bees, yet little is known about its biodiversity. Thirty （27 Thai and 3 Malaysian） and ...The small dwarf honey bee, Apis andreniformis, is a rare and patchily distributed Apis spp. and is one of the native Thai honey bees, yet little is known about its biodiversity. Thirty （27 Thai and 3 Malaysian） and 37 （32 Thai and 5 Malaysian） colonies of A. andreniformis were sampled for morphometric and genetic analysis, respectively. For morphometric analysis, 20 informative characters were used to determine the variation. After plotting the factor scores, A. andreniformis from across Thailand were found to belong to one group, a notion further supported by a cluster analysis generated dendrogram. However, clinal pattems in groups of bee morphometric characters were revealed by linear regression analysis. The body size of bees increases from South to North but decreases from West to East, although this may reflect altitude rather than longitude. Genetic variation was determined by sequence analysis of a 520 bp fragment of the mitochondrial cytochrome oxidase subunit b （cytb）. DNA polymorphism among bees from the mainland of Thailand is lower than that from Phuket Island and Chiang Mal. Although two main different groups of bees were obtained from phylogenetic trees constructed by neighbor-joining and unweighted pair-group method using arithmetic averages programs, no clear geographic signal was present. Thus, while the minor group （B） contained all of the samples from the only island sampled （Phuket in the south）, but not the southem mainland colonies, it also contained samples from the far northem inland region of Chiang Mai, other samples of which were firmly rooted in the major group （A）.展开更多
Further geometric morphometric analysis of the genus Eysarcoris was done based on the former studies to classified the nine Eysarcoris species from China. In this study, six characters, such as forewing, hindwing, pyg...Further geometric morphometric analysis of the genus Eysarcoris was done based on the former studies to classified the nine Eysarcoris species from China. In this study, six characters, such as forewing, hindwing, pygophore, head, pronotum and scutellum, were selected to investigate the shape variation of Eysarcoris. Significant divergence in the shapes of the six characters was observed among the species（p 〈 0.05）. For all methods, phenetic similarity based on the six characters agrees with the current status of the genus. The cluster analysis of eight species are consistent with the traditional morphological studies. CVA analysis also shows that the values of the six characters are not equal in taxonomy. Pygophore, forewing, hindwing and pronotum play more important roles in the classification.展开更多
基金This study was supported by the National Key R&D Program of China(Grant No.2020YFC0847000)the National Natural Science Foundation of China(Grant Nos.31571370,91731302,and 31772435).
文摘A novel RNA virus,the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is responsible for the ongoing outbreak of coronavirus disease 2019(COVID-19).Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19.However,due to extensive sampling bias and existence of infection clusters during the epidemic spread,direct applications of existing approaches can lead to biased parameter estimations and data misinterpretation.In this study,we first present robust estimator for the time to the most recent common ancestor(TMRCA)and the mutation rate,and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2.The mutation rate is inferred to be 8.69×10^(−4) per site per year with a 95%confidence interval(CI)of[8.61×10^(−4),8.77×10^(−4)],and the TMRCA of the samples inferred to be Nov 28,2019 with a 95%CI of[Oct 20,2019,Dec 9,2019].The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market.We further demonstrate that genetic polymorphism patterns,including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters,are similar to those caused by evolutionary forces such as natural selection.Our results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism of SARS-CoV-2.Software for implementing VirusMuT can be downloaded at https://bigd.big.ac.cn/biocode/tools/BT007081.
文摘The small dwarf honey bee, Apis andreniformis, is a rare and patchily distributed Apis spp. and is one of the native Thai honey bees, yet little is known about its biodiversity. Thirty （27 Thai and 3 Malaysian） and 37 （32 Thai and 5 Malaysian） colonies of A. andreniformis were sampled for morphometric and genetic analysis, respectively. For morphometric analysis, 20 informative characters were used to determine the variation. After plotting the factor scores, A. andreniformis from across Thailand were found to belong to one group, a notion further supported by a cluster analysis generated dendrogram. However, clinal pattems in groups of bee morphometric characters were revealed by linear regression analysis. The body size of bees increases from South to North but decreases from West to East, although this may reflect altitude rather than longitude. Genetic variation was determined by sequence analysis of a 520 bp fragment of the mitochondrial cytochrome oxidase subunit b （cytb）. DNA polymorphism among bees from the mainland of Thailand is lower than that from Phuket Island and Chiang Mal. Although two main different groups of bees were obtained from phylogenetic trees constructed by neighbor-joining and unweighted pair-group method using arithmetic averages programs, no clear geographic signal was present. Thus, while the minor group （B） contained all of the samples from the only island sampled （Phuket in the south）, but not the southem mainland colonies, it also contained samples from the far northem inland region of Chiang Mai, other samples of which were firmly rooted in the major group （A）.
基金anoperatinggrantfromtheMedicalResearchCouncilofCanada (MRC Grant #GOP 3 810 6)toLiuShu Lin +2 种基金anoperatinggrantfromtheNaturalSciencesandEngineeringResearchCouncilofCanada (NSERC Grant #2 16912 0 0 )toLiuShu Lin anoperatinggrantfromtheCanadi an
基金benefited from the National Natural Sciences Foundation of China(31440078,31501840)Shanxi Province Programs for Science and Technology Development(20150311010-7)+1 种基金Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi(2017169)Graduate Innovation Project in Shanxi Province(2016BY067)
文摘Further geometric morphometric analysis of the genus Eysarcoris was done based on the former studies to classified the nine Eysarcoris species from China. In this study, six characters, such as forewing, hindwing, pygophore, head, pronotum and scutellum, were selected to investigate the shape variation of Eysarcoris. Significant divergence in the shapes of the six characters was observed among the species（p 〈 0.05）. For all methods, phenetic similarity based on the six characters agrees with the current status of the genus. The cluster analysis of eight species are consistent with the traditional morphological studies. CVA analysis also shows that the values of the six characters are not equal in taxonomy. Pygophore, forewing, hindwing and pronotum play more important roles in the classification.
