基于线粒体COX1基因探讨夜鹭的分歧时间
|
摘要
物种分化过程与原因是进化生物学和生态学研究的热点问题之一,分化的本质为基因的分化。研究采用全球分布的夜鹭作为研究对象,基于线粒体COX1基因,分别采用贝叶斯法和最大似然法构建其系统发育树;采用放松分子钟的方法,利用鹳形目与鹈形目的分歧时间结点68. 92百万年,与企鹅目的分歧时间67. 12百万年,及鹈形目与企鹅目的分歧时间72. 25百万年作为校正点,使用BEAST软件构建其分歧时间树,目的是利用分子手段探究夜鹭的分歧时间,并尝试推测其可能的分化因素。结果表明:夜鹭可依分布区域而分为两个支系,亚洲支系和美洲支系;距今56. 74百万年左右,两支系分开;分歧原因可能与亚洲大陆和美洲大陆的分离有关。
The process and reason of species divergence is one of the hot issues in evolutionary biology and ecology field,the nature of species divergence is the gene differentiation. This research studied the globally distributed black-crowned night heron. A phylogenetic tree was constructed by using the method of bayesian and maximum likelihood based on mitochondrial COX1 gene. A time tree was built by the BEAST software using a relaxed molecular clock and three calibration points from the divergence time 68. 92 million years between Ciconiiformes and Pelecaniformes,67. 12 million years between Ciconiiformes and Sphenisciformes,72. 25 million years between Ciconiiformes and Sphenisciformes. The purpose of this study is to use molecular methods to evaluate the divergence time of blackcrowned night heron and infer the divergence factors. The results showed that the night heron could be divided into two lineages according to their distribution areas,the Americas lineage and Asia lineage. The divergence of the two lineages approximately happened56. 74 million years ago. The separation of the Asian continent and America caused this divergence.
The process and reason of species divergence is one of the hot issues in evolutionary biology and ecology field,the nature of species divergence is the gene differentiation. This research studied the globally distributed black-crowned night heron. A phylogenetic tree was constructed by using the method of bayesian and maximum likelihood based on mitochondrial COX1 gene. A time tree was built by the BEAST software using a relaxed molecular clock and three calibration points from the divergence time 68. 92 million years between Ciconiiformes and Pelecaniformes,67. 12 million years between Ciconiiformes and Sphenisciformes,72. 25 million years between Ciconiiformes and Sphenisciformes. The purpose of this study is to use molecular methods to evaluate the divergence time of blackcrowned night heron and infer the divergence factors. The results showed that the night heron could be divided into two lineages according to their distribution areas,the Americas lineage and Asia lineage. The divergence of the two lineages approximately happened56. 74 million years ago. The separation of the Asian continent and America caused this divergence.
引文
[1]刘红云,刘四凤,张晓强,等.郑州市夜鹭的越冬生态研究[J].安徽农业科学,2017,45(25):125-127.
[2]ASHOORI A,MORADI HV,REZAIEE H R,et al.Nest position,breeding success and diet of the black-crowned night heron,Nycticorax nycticorax in the anzali wetland,northern iran(aves:ardeidae)[J].Zoology in the Middle East,2017,63(4):283-290.
[3]BRIANNE E,BRUSSEE P S,COATES R L,et al.Nest survival is influenced by parental behaviour and hetero specifics in a mixed‐species colony[J].Ibis,2016,158(2):315-326.
[4]MATEUSZ L,JACEK B.Post-breeding migration of night herons nycticorax nycticorax tracked by GPS/GSM transmitters[J].Journal of Ornithology,2015,156(1):1-4.
[5]ZHOU Y,YIN G,ASPLUND L,et al.A novel pollution pattern:highly chlorinated biphenyls retained in black-crowned night heron(Nycticorax nycticorax)and whiskered tern(Chlidonias hybrida)from the yangtze river delta[J].Chemosphere,2016,150:491-498.
[6]KIM J,KOO T H.Heavy metal concentrations in diet and livers of blackcrowned night heron Nycticorax nycticorax and grey heron ardea cinerea chicks from pyeongtaek korea[J].Ecotoxicology,2007,16(5):411-416.
[7]BURGER E.Metal levels in eggs of waterbirds in the new york harbor(USA):trophic relationships and possible risk to human consumers[J].Journal of Toxicology and Environmental Health,Part A,2015,78(2):78-91.
[8]GRASMAN K A,ECHOLS K R,MAY T M,et al.Immunological and reproductive health assessment in herring gulls and black-crowned night herons in the Hudson-Raritan Estuary[J].Environmental Toxicology and Chemistry,2013,32(3):548-561.
[9]PACHECO M A,BATTISTUZZI F U,Lentino M,et al.Evolution of modern birds revealed by mitogenomics:timing the radiation and origin of major orders[J].Molecular Biology&Evolution,2011,28(6):19-27.
[10]马婷婷.糙颈露螽属和华绿露螽属的分子系统学研究[D].长春:吉林农业大学,2011.
[11]FOLMER O,BLACK M,HOEH W,et al.DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates[J].Molecular Marine Biology and Biotechnology,1994,3(5):294-299.
[12]XIA X.DAMBE5:A comprehensive software package for data analysis in molecular biology and evolution[J].Molecular Biology&Evolution,2013,30(7):1720-1728.
[13]ZHOU X,LIN Q,FANG W,et al.The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements[J].BMC Genomics,2014,15(1):1-9.
[14]SAITOH T,SUGITA N,SOMEYA S,et al.DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago[J].Molecular Ecology Resources[J],2015,15(1):177-86.
[15]YOO H S,EAH J Y,KIM J S,et al.Dna barcoding korean birds[J].Molecules&Cells,2006,22(3):323-327.
[16]HEBERT P D N,STOECKLE M Y,ZEMLAK T S,et al.Identification of birds through DNA barcodes[J].PLo S Biology,2004,2(10):e312.
[17]HIEMANN T C,BRAULT A C,EMEST H B,et al.Development of a high-throughput microsphere-based molecular assay to identify 15 common bloodmeal hosts of culex,mosquitoes[J].Molecular Ecology Resources,2012,12(2):238-246.
[18]TAVARES E S,GONCALVES P,MIYAKI C Y,et al.Dna barcode detects high genetic structure within neotropical bird species[J].PLo S One,2011,6(12):e28543.
[19]KERR K C,BIRKS S M,KALYAKIN M V,et al.Filling the gap-coi barcode resolution in eastern palearctic birds[J].Frontiers in Zoology,2009,6(1):1-13.
[20]Zhou X,Wang Y,Chen X,et al.Permanent genetic resources:a set of primer pairs for amplifying the complete mitochondrial DNA of endangered Chinese egret(Aves,Ardeidae,Egretta eulophotes)[J].Molecular Ecology Resources,2008,8(2):412-414.
[21]Baker A J,Tavares E S,Elbourne R F.Countering criticisms of single mitochondrial DNA gene barcoding in birds[J].Molecular Ecology Resources,2009,9(s1):257-268.
[22]SANTORUM J M,DARRIBA D,TABOADA G L,et al.Jmodeltest.org:selection of nucleotide substitution models on the cloud[J].Bioinformatics,2014,30(9):1310-1311.
[23]KUMAR S,STECHER G,TAMURA K.MEGA7:Molecular evolutionary genetics analysis version 7.0 for bigger datasets[J].Molecular Biology and Evolution,2016,33(7):1870-1874.
[24]DRUMMOND A J,SUCHARD M A,XIE D,et al.Bayesian phylogenetics with BEAUti and the BEAST 1.7[J].Molecular Biology and Evolution,2012,29:1969-1973.
[25]PATON T,HADDRATH O,BAKER A J.Complete mitochondrial dna genome sequences show that modern birds are not descended from transitional shorebirds[J].Proceedings of the Royal Society B Biological Sciences,2002,269(1493):839-846.
[26]PEREIRA S L,JOHNSON K P,CLAYTON D H,et al.Mitochondrial and nuclear DNA sequences support a Cretaceous origin of Columbiformes and a dispersal-driven radiation in the Paleogene[J].Systematic Biology,2007,56:656-672.
[27]WANG X L,QU J Y,LIU N F,et al.Limited gene flow and partial isolation phylogeography of Himalayan snowcock Tetraogallus himalayensis based on part mitochondrial D-loop sequences[J].Current Zoology,2011,57(6):758-767.
[28]QU J,LIU N,BAO X,et al.Phylogeography of the ring-necked pheasant(Phasianus colchicus)in China[J].Molecular Phylogenetics Evollution,2009,52(1):125-132.
[29]ZHAO N,DAI C Y,WANG W J,et al.Pleistocene climate changes shaped the divergence and demography of Asian populations of the great tit Parus major:evidence from phylogeographic analysis and ecological niche models[J].Journal of Avian Biology,2012,43(4):297-310.
[30]CRACRAFT J.Avian evolution,Gondwana biogeography and the Cretaceous Tertiary mass extinction event[J].Proceedings of the Royal Society B,2001,268:459-469.
[2]ASHOORI A,MORADI HV,REZAIEE H R,et al.Nest position,breeding success and diet of the black-crowned night heron,Nycticorax nycticorax in the anzali wetland,northern iran(aves:ardeidae)[J].Zoology in the Middle East,2017,63(4):283-290.
[3]BRIANNE E,BRUSSEE P S,COATES R L,et al.Nest survival is influenced by parental behaviour and hetero specifics in a mixed‐species colony[J].Ibis,2016,158(2):315-326.
[4]MATEUSZ L,JACEK B.Post-breeding migration of night herons nycticorax nycticorax tracked by GPS/GSM transmitters[J].Journal of Ornithology,2015,156(1):1-4.
[5]ZHOU Y,YIN G,ASPLUND L,et al.A novel pollution pattern:highly chlorinated biphenyls retained in black-crowned night heron(Nycticorax nycticorax)and whiskered tern(Chlidonias hybrida)from the yangtze river delta[J].Chemosphere,2016,150:491-498.
[6]KIM J,KOO T H.Heavy metal concentrations in diet and livers of blackcrowned night heron Nycticorax nycticorax and grey heron ardea cinerea chicks from pyeongtaek korea[J].Ecotoxicology,2007,16(5):411-416.
[7]BURGER E.Metal levels in eggs of waterbirds in the new york harbor(USA):trophic relationships and possible risk to human consumers[J].Journal of Toxicology and Environmental Health,Part A,2015,78(2):78-91.
[8]GRASMAN K A,ECHOLS K R,MAY T M,et al.Immunological and reproductive health assessment in herring gulls and black-crowned night herons in the Hudson-Raritan Estuary[J].Environmental Toxicology and Chemistry,2013,32(3):548-561.
[9]PACHECO M A,BATTISTUZZI F U,Lentino M,et al.Evolution of modern birds revealed by mitogenomics:timing the radiation and origin of major orders[J].Molecular Biology&Evolution,2011,28(6):19-27.
[10]马婷婷.糙颈露螽属和华绿露螽属的分子系统学研究[D].长春:吉林农业大学,2011.
[11]FOLMER O,BLACK M,HOEH W,et al.DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates[J].Molecular Marine Biology and Biotechnology,1994,3(5):294-299.
[12]XIA X.DAMBE5:A comprehensive software package for data analysis in molecular biology and evolution[J].Molecular Biology&Evolution,2013,30(7):1720-1728.
[13]ZHOU X,LIN Q,FANG W,et al.The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements[J].BMC Genomics,2014,15(1):1-9.
[14]SAITOH T,SUGITA N,SOMEYA S,et al.DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago[J].Molecular Ecology Resources[J],2015,15(1):177-86.
[15]YOO H S,EAH J Y,KIM J S,et al.Dna barcoding korean birds[J].Molecules&Cells,2006,22(3):323-327.
[16]HEBERT P D N,STOECKLE M Y,ZEMLAK T S,et al.Identification of birds through DNA barcodes[J].PLo S Biology,2004,2(10):e312.
[17]HIEMANN T C,BRAULT A C,EMEST H B,et al.Development of a high-throughput microsphere-based molecular assay to identify 15 common bloodmeal hosts of culex,mosquitoes[J].Molecular Ecology Resources,2012,12(2):238-246.
[18]TAVARES E S,GONCALVES P,MIYAKI C Y,et al.Dna barcode detects high genetic structure within neotropical bird species[J].PLo S One,2011,6(12):e28543.
[19]KERR K C,BIRKS S M,KALYAKIN M V,et al.Filling the gap-coi barcode resolution in eastern palearctic birds[J].Frontiers in Zoology,2009,6(1):1-13.
[20]Zhou X,Wang Y,Chen X,et al.Permanent genetic resources:a set of primer pairs for amplifying the complete mitochondrial DNA of endangered Chinese egret(Aves,Ardeidae,Egretta eulophotes)[J].Molecular Ecology Resources,2008,8(2):412-414.
[21]Baker A J,Tavares E S,Elbourne R F.Countering criticisms of single mitochondrial DNA gene barcoding in birds[J].Molecular Ecology Resources,2009,9(s1):257-268.
[22]SANTORUM J M,DARRIBA D,TABOADA G L,et al.Jmodeltest.org:selection of nucleotide substitution models on the cloud[J].Bioinformatics,2014,30(9):1310-1311.
[23]KUMAR S,STECHER G,TAMURA K.MEGA7:Molecular evolutionary genetics analysis version 7.0 for bigger datasets[J].Molecular Biology and Evolution,2016,33(7):1870-1874.
[24]DRUMMOND A J,SUCHARD M A,XIE D,et al.Bayesian phylogenetics with BEAUti and the BEAST 1.7[J].Molecular Biology and Evolution,2012,29:1969-1973.
[25]PATON T,HADDRATH O,BAKER A J.Complete mitochondrial dna genome sequences show that modern birds are not descended from transitional shorebirds[J].Proceedings of the Royal Society B Biological Sciences,2002,269(1493):839-846.
[26]PEREIRA S L,JOHNSON K P,CLAYTON D H,et al.Mitochondrial and nuclear DNA sequences support a Cretaceous origin of Columbiformes and a dispersal-driven radiation in the Paleogene[J].Systematic Biology,2007,56:656-672.
[27]WANG X L,QU J Y,LIU N F,et al.Limited gene flow and partial isolation phylogeography of Himalayan snowcock Tetraogallus himalayensis based on part mitochondrial D-loop sequences[J].Current Zoology,2011,57(6):758-767.
[28]QU J,LIU N,BAO X,et al.Phylogeography of the ring-necked pheasant(Phasianus colchicus)in China[J].Molecular Phylogenetics Evollution,2009,52(1):125-132.
[29]ZHAO N,DAI C Y,WANG W J,et al.Pleistocene climate changes shaped the divergence and demography of Asian populations of the great tit Parus major:evidence from phylogeographic analysis and ecological niche models[J].Journal of Avian Biology,2012,43(4):297-310.
[30]CRACRAFT J.Avian evolution,Gondwana biogeography and the Cretaceous Tertiary mass extinction event[J].Proceedings of the Royal Society B,2001,268:459-469.