鸟类基因组核苷酸频数的进化模型
|
摘要
鸟类是四足类动物中最丰富的一类脊椎动物,本研究以12种鸟类的全基因组核苷酸序列数据为研究对象,建立核苷酸频数进化方程,研究了鸟类基因组核苷酸频数的进化机制和规律。通过拟合基因组数据确定了方程中的进化惯性参数、耗散参数和环境参数,估算出进化速率,得到了基因组长度随时间的演化曲线,解出了基因组在短时间内快速增加,信息快速积累,然后进入进化停滞阶段,核苷酸频数不再明显变化。本研究的方法为定量研究鸟类和一般物种的进化提供了新的思路。
Birds are the most abundant group of vertebrates among the tetrapods. In this study, the nucleotide sequence data of the whole genome of 12 species of birds were taken as the research object, and the evolution equation of nucleotide frequency was established to study the evolution mechanism and rule of nucleotide frequency in the bird genome. The evolutionary inertia parameters, dissipation parameters and environmental parameters in the equation were determined by fitting the genome data. This study estimated the evolution rate and obtained the evolution curve of genome length over time. The results showed that the genome increased rapidly in a short time, the information accumulated rapidly as well, and then entered the stage of evolutionary stagnation,and the frequency of nucleotides no longer changed significantly. The method of this study provides a new way to quantitatively study the evolution of birds and general species.
Birds are the most abundant group of vertebrates among the tetrapods. In this study, the nucleotide sequence data of the whole genome of 12 species of birds were taken as the research object, and the evolution equation of nucleotide frequency was established to study the evolution mechanism and rule of nucleotide frequency in the bird genome. The evolutionary inertia parameters, dissipation parameters and environmental parameters in the equation were determined by fitting the genome data. This study estimated the evolution rate and obtained the evolution curve of genome length over time. The results showed that the genome increased rapidly in a short time, the information accumulated rapidly as well, and then entered the stage of evolutionary stagnation,and the frequency of nucleotides no longer changed significantly. The method of this study provides a new way to quantitatively study the evolution of birds and general species.
引文
Cooper A.,and Penny D.,1997,Mass survival of birds across the Cretaceous-Tertiary boundary:molecular evidence,Science,275(5303):1109-1113
Ericson P.G.,Anderson C.L.,Britton T.,Elzanowski A.,Johansson U.S.,Kallersjo M.,Ohlson J.I.,Parsons T.J.,Zuccon D.,and Mayr G.,2006,Diversification of Neoaves:integration of molecular sequence data and fossils,Biology Letters,2(4):543-547
Feduccia A.,1995,Explosive evolution in Tertiary birds and mammals,Science,267(5198):637-638
Gregory T.R.,2005,The evolution of the genome,Elsevier Academic Press,London,UK,2(3):1-5
Hedges S.B.,Parker P.H.,Sibley C.G.,and Kumar S.,1996,Continental breakup and the ordinal diversification of birds and mammals,Nature,381(6579):226-229
Jarvis E.D.,Mirarab S.,Aberer A.J.,Li B.,Houde P.,Li C.,Ho S.Y.W.,Faircloth B.C.,Nabholz B.,Howard J.T.,Suh A.,Weber C.C.,da Fonseca R.R.,Li J.W.,Zhang F.,Li H.,Zhou L.,Narula N.,Liu L.,Ganapathy G.,Boussau B.,Bayzid M.S.,Zavidovych V.,Subramanian S.,Gabaldon T.,Capella-Gutierrez S.,Huerta-Cepas J.,Rekepalli B.,Munch K.,Schierup M.,Lindow B.,Warren W.C.,Ray D.,Green R.E.,Bruford M.W.,Zhan X.J.,Dixon A.,Li S.B.,Li N.,Huang Y.H.,Derryberry E.P.,Bertelsen M.F.,Sheldon F.H.,Brumfield R.T.,Mello C.V.,Lovell P.V.,Wirthlin M.,Schneider M.P.C.,Prosdocimi F.,Samaniego J.A.,Vela zquez A.M.V.,Alfaro-Nunez A.,Campos P.F.,Petersen B.,Sicheritz-Ponten T.,Pas A.,Bailey T.,Scofield P.,Bunce M.,Lambert D.M.,Zhou Q.,Perelman P.,Driskell A.C.,Shapiro B.,Xiong Z.J.,Zeng Y.L.,Liu S.P.,Li Z.Y.,Liu B.H.,Wu K.,Xiao J.,Yinqi X.,Zheng Q.M.,Zhang Y.,Yang H.M.,Wang J.,Smeds L.,Rheindt F.E.,Braun M.,Fjeldsa J.,Orlando L.,Barker F.K.,Jonsson K.A.,Johnson W.,Koepfli K.P.,O'Brien S.,Haussler D.,Ryder O.A.,Rahbek C.,Willerslev E.,Graves G.R.,Glenn T.C.,McCormack J.,Burt D.,Ellegren H.,Alstrom P.,Edwards S.V.,Stamatakis A.,Mindell D.P.,Cracraft J.,Braun E.L.,Warnow T.,Jun W.,Gilbert M.T.P.,and Zhang G.J.,2014,Whole-genome analyses resolve early branches in the tree of life of modern birds,Science,346(6215):1320-1331
Jarvis E.D.,Mirarab S.,Aberer A.J.,Li B.,Houde P.,Li C.,Ho SY.W.,Faircloth B.C.,Nabholz B.,Howard J.T.,Suh A.,Weber C.C.,da Fonseca R.R.,Alfaro-Nunez A.,Narula N.,Liu L.Burt D.,Ellegren H.,Edwards S.V.,Stamatakis A.,Mindell DP.,Cracraft J.,Braun E.L.,Warnow T.,Jun W.,Gilbert M.T.P.and Zhang G.J.,2015,Phylogenomic analyses data of the bird phylogenomics project,Giga Science,4(1):4-12
Jiang X.M.,Niu Y.L.,and Xu X.Y.,2016,Phylogenetic evolutionand expression analysis of NAC gene family in tomato(Solanum lycopersicum),Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(8):1948-1964(姜秀明,牛义岭,许向阳,2016,番茄NAC基因家族的系统进化及表达分析,分子植物育种,14(8):1948-1964)
Ksepka D.T.,and Boyd C.A.,2012,Quantifying historical trends in the completeness of the fossil record and the contributing factors:an example using Aves,Paleobiology,38(1):112-125
Longrich N.R.,Tokaryk T.,and Field D.J.,2011,Mass extinction of birds at the Cretaceous-Paleogene(K-Pg)boundary,Proc Natl.Acad.Sci.USA,108(37):15253-15257
Prum R.O.,Berv J.S.,Dornburg A.,Field D.J.,Townsend J.P.Lemmon E.M.,and Lemmon A.R.,2015,A comprehensive phylogeny of birds(Aves)using targeted next-generation DNAsequencing,Nature,526(7574):569-573
Romanov M.N.,Farre M.,Lithgow P.E.,Fowler K.E.,Skinner BM.,O'Connor R.,Fonseka G.,Backstrom N.,Matsuda Y.Nishida C.,Houde P.,Jarvis E.D.,Ellegren H.,Burt D.W.Larkin D.M.,and Griffin D.K.,2014,Reconstruction of gross bird genome structure,organization and evolution suggests that the chicken lineage most closely resembles the dinosaur bird ancestor,BMC Genomics,15(1):1060-1065
Schulte P.,Alegret L.,Arenillas I.,Arz J.A.,Barton P.J.,Bown PR.,Bralower T.J.,Christeson G.L.,Claeys P.,Cockell C.S.Collins G.S.,Deutsch A.,Goldin T.J.,Goto K.,Grajales-Nishimura J.M.,Grieve R.A.,Gulick S.P.,Johnson KR.,Kiessling W.,Koeberl C.,Kring D.A.,MacLeod K.G.,Matsui T.,Melosh J.,Montanari A.,Morgan J.V.,Neal C.R.,Nichols D.J.,Norris R.D.,Pierazzo E.,Ravizza G.,Rebolledo-Vieyra M.,Reimold W.U.,Robin E.,Salge T.,Speijer R.P.,Sweet A.R.,Urrutia-Fucugauchi J.,Vajda V.,Whalen M.T.,and Willumsen P.S.,2010,The Chicxulub asteroid impact and mass extinction at the Cretaceous-Paleogene boundary,Science,327(5970):1214-1218
Simon Y.H.,and Matthew J.P.,2009,Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times,Systematic Biology,58(3):367-380
Zhang G.J.,Li C.,Li Q.,Li B.,Larkin D.M.,Lee C.,Storz J.F.,Antunes A.,Greenwold M.J.,Meredith R.W.,Odeen A.,Cui J.,Zhou Q.,Xu L.,Pan H.,Wang Z.,Jin L.,Zhang P.,Hu H.,Yang W.,Hu J.,Xiao J.,Yang Z.,Liu Y.,Xie Q.,Yu H.,Lian J.,Wen P.,Zhang F.,Li H.,Zeng Y.,Xiong Z.,Liu S.,Zhou L.,Huang Z.,An N.,Wang J.,Zheng Q.,Xiong Y.,Wang G.,Wang B.,Wang J.,Fan Y.,da Fonseca R.R.,Alfaro-Nunez A.,Schubert M.,Or lando L.,Mourier T.,Howard J.T.,Ganapathy G.,Pfenning A.,Whitney O.,Rivas M.V.,Hara E.,Smith J.,Farre M.,Narayan J.,Slavov G.,Romanov M.N.,Borges R.,Machado J.P.,Khan I.,Springer M.S.,Gatesy J.,Hoffmann F.G.,Opazo J.C.,Hastad O.,Sawyer R.H.,Kim H.,Kim K.W.,Kim H.J.,Cho S.,Li N.,Huang Y.,Bruford M.W.,Zhan X.,Dixon A.,Bertelsen M.F.,Derryberry E.,Warren W.,Wilson R.K.,Li S.,Ray D.A.,Green R.E.,O'Brien S.J.,Griffin D.,Johnson W.E.,Haussler D.,Ryder O.A.,Willerslev E.,Graves G.R.,Alstrom P.,Fjeldsa J.,Mindell D.P.,Edwards S.V.,Braun E.L.,Rahbek C.,Burt D.W.,Houde P.,Zhang Y.,Yang H.,and Wang J.,2014,Comparative genomics reveals insights into bird genome evolution and adaptation,Science,346(6215):1311-1320
Zhang Y.F.,Zhou X.,Luo L.F.,and Zhang L.R.,2017,Construction and analysis of the avian phylogenetic tree,Jisuan Shengwuxue(Hans Journal of Computational Biology),7(1):1-11(张永芬,周勋,罗辽复,张利绒,2017,鸟类基因组进化树的构建与分析,计算生物学,7(1):1-11)
Ericson P.G.,Anderson C.L.,Britton T.,Elzanowski A.,Johansson U.S.,Kallersjo M.,Ohlson J.I.,Parsons T.J.,Zuccon D.,and Mayr G.,2006,Diversification of Neoaves:integration of molecular sequence data and fossils,Biology Letters,2(4):543-547
Feduccia A.,1995,Explosive evolution in Tertiary birds and mammals,Science,267(5198):637-638
Gregory T.R.,2005,The evolution of the genome,Elsevier Academic Press,London,UK,2(3):1-5
Hedges S.B.,Parker P.H.,Sibley C.G.,and Kumar S.,1996,Continental breakup and the ordinal diversification of birds and mammals,Nature,381(6579):226-229
Jarvis E.D.,Mirarab S.,Aberer A.J.,Li B.,Houde P.,Li C.,Ho S.Y.W.,Faircloth B.C.,Nabholz B.,Howard J.T.,Suh A.,Weber C.C.,da Fonseca R.R.,Li J.W.,Zhang F.,Li H.,Zhou L.,Narula N.,Liu L.,Ganapathy G.,Boussau B.,Bayzid M.S.,Zavidovych V.,Subramanian S.,Gabaldon T.,Capella-Gutierrez S.,Huerta-Cepas J.,Rekepalli B.,Munch K.,Schierup M.,Lindow B.,Warren W.C.,Ray D.,Green R.E.,Bruford M.W.,Zhan X.J.,Dixon A.,Li S.B.,Li N.,Huang Y.H.,Derryberry E.P.,Bertelsen M.F.,Sheldon F.H.,Brumfield R.T.,Mello C.V.,Lovell P.V.,Wirthlin M.,Schneider M.P.C.,Prosdocimi F.,Samaniego J.A.,Vela zquez A.M.V.,Alfaro-Nunez A.,Campos P.F.,Petersen B.,Sicheritz-Ponten T.,Pas A.,Bailey T.,Scofield P.,Bunce M.,Lambert D.M.,Zhou Q.,Perelman P.,Driskell A.C.,Shapiro B.,Xiong Z.J.,Zeng Y.L.,Liu S.P.,Li Z.Y.,Liu B.H.,Wu K.,Xiao J.,Yinqi X.,Zheng Q.M.,Zhang Y.,Yang H.M.,Wang J.,Smeds L.,Rheindt F.E.,Braun M.,Fjeldsa J.,Orlando L.,Barker F.K.,Jonsson K.A.,Johnson W.,Koepfli K.P.,O'Brien S.,Haussler D.,Ryder O.A.,Rahbek C.,Willerslev E.,Graves G.R.,Glenn T.C.,McCormack J.,Burt D.,Ellegren H.,Alstrom P.,Edwards S.V.,Stamatakis A.,Mindell D.P.,Cracraft J.,Braun E.L.,Warnow T.,Jun W.,Gilbert M.T.P.,and Zhang G.J.,2014,Whole-genome analyses resolve early branches in the tree of life of modern birds,Science,346(6215):1320-1331
Jarvis E.D.,Mirarab S.,Aberer A.J.,Li B.,Houde P.,Li C.,Ho SY.W.,Faircloth B.C.,Nabholz B.,Howard J.T.,Suh A.,Weber C.C.,da Fonseca R.R.,Alfaro-Nunez A.,Narula N.,Liu L.Burt D.,Ellegren H.,Edwards S.V.,Stamatakis A.,Mindell DP.,Cracraft J.,Braun E.L.,Warnow T.,Jun W.,Gilbert M.T.P.and Zhang G.J.,2015,Phylogenomic analyses data of the bird phylogenomics project,Giga Science,4(1):4-12
Jiang X.M.,Niu Y.L.,and Xu X.Y.,2016,Phylogenetic evolutionand expression analysis of NAC gene family in tomato(Solanum lycopersicum),Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(8):1948-1964(姜秀明,牛义岭,许向阳,2016,番茄NAC基因家族的系统进化及表达分析,分子植物育种,14(8):1948-1964)
Ksepka D.T.,and Boyd C.A.,2012,Quantifying historical trends in the completeness of the fossil record and the contributing factors:an example using Aves,Paleobiology,38(1):112-125
Longrich N.R.,Tokaryk T.,and Field D.J.,2011,Mass extinction of birds at the Cretaceous-Paleogene(K-Pg)boundary,Proc Natl.Acad.Sci.USA,108(37):15253-15257
Prum R.O.,Berv J.S.,Dornburg A.,Field D.J.,Townsend J.P.Lemmon E.M.,and Lemmon A.R.,2015,A comprehensive phylogeny of birds(Aves)using targeted next-generation DNAsequencing,Nature,526(7574):569-573
Romanov M.N.,Farre M.,Lithgow P.E.,Fowler K.E.,Skinner BM.,O'Connor R.,Fonseka G.,Backstrom N.,Matsuda Y.Nishida C.,Houde P.,Jarvis E.D.,Ellegren H.,Burt D.W.Larkin D.M.,and Griffin D.K.,2014,Reconstruction of gross bird genome structure,organization and evolution suggests that the chicken lineage most closely resembles the dinosaur bird ancestor,BMC Genomics,15(1):1060-1065
Schulte P.,Alegret L.,Arenillas I.,Arz J.A.,Barton P.J.,Bown PR.,Bralower T.J.,Christeson G.L.,Claeys P.,Cockell C.S.Collins G.S.,Deutsch A.,Goldin T.J.,Goto K.,Grajales-Nishimura J.M.,Grieve R.A.,Gulick S.P.,Johnson KR.,Kiessling W.,Koeberl C.,Kring D.A.,MacLeod K.G.,Matsui T.,Melosh J.,Montanari A.,Morgan J.V.,Neal C.R.,Nichols D.J.,Norris R.D.,Pierazzo E.,Ravizza G.,Rebolledo-Vieyra M.,Reimold W.U.,Robin E.,Salge T.,Speijer R.P.,Sweet A.R.,Urrutia-Fucugauchi J.,Vajda V.,Whalen M.T.,and Willumsen P.S.,2010,The Chicxulub asteroid impact and mass extinction at the Cretaceous-Paleogene boundary,Science,327(5970):1214-1218
Simon Y.H.,and Matthew J.P.,2009,Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times,Systematic Biology,58(3):367-380
Zhang G.J.,Li C.,Li Q.,Li B.,Larkin D.M.,Lee C.,Storz J.F.,Antunes A.,Greenwold M.J.,Meredith R.W.,Odeen A.,Cui J.,Zhou Q.,Xu L.,Pan H.,Wang Z.,Jin L.,Zhang P.,Hu H.,Yang W.,Hu J.,Xiao J.,Yang Z.,Liu Y.,Xie Q.,Yu H.,Lian J.,Wen P.,Zhang F.,Li H.,Zeng Y.,Xiong Z.,Liu S.,Zhou L.,Huang Z.,An N.,Wang J.,Zheng Q.,Xiong Y.,Wang G.,Wang B.,Wang J.,Fan Y.,da Fonseca R.R.,Alfaro-Nunez A.,Schubert M.,Or lando L.,Mourier T.,Howard J.T.,Ganapathy G.,Pfenning A.,Whitney O.,Rivas M.V.,Hara E.,Smith J.,Farre M.,Narayan J.,Slavov G.,Romanov M.N.,Borges R.,Machado J.P.,Khan I.,Springer M.S.,Gatesy J.,Hoffmann F.G.,Opazo J.C.,Hastad O.,Sawyer R.H.,Kim H.,Kim K.W.,Kim H.J.,Cho S.,Li N.,Huang Y.,Bruford M.W.,Zhan X.,Dixon A.,Bertelsen M.F.,Derryberry E.,Warren W.,Wilson R.K.,Li S.,Ray D.A.,Green R.E.,O'Brien S.J.,Griffin D.,Johnson W.E.,Haussler D.,Ryder O.A.,Willerslev E.,Graves G.R.,Alstrom P.,Fjeldsa J.,Mindell D.P.,Edwards S.V.,Braun E.L.,Rahbek C.,Burt D.W.,Houde P.,Zhang Y.,Yang H.,and Wang J.,2014,Comparative genomics reveals insights into bird genome evolution and adaptation,Science,346(6215):1311-1320
Zhang Y.F.,Zhou X.,Luo L.F.,and Zhang L.R.,2017,Construction and analysis of the avian phylogenetic tree,Jisuan Shengwuxue(Hans Journal of Computational Biology),7(1):1-11(张永芬,周勋,罗辽复,张利绒,2017,鸟类基因组进化树的构建与分析,计算生物学,7(1):1-11)
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |