메뉴 건너뛰기




Volumn 58, Issue 2, 2011, Pages 297-303

Reconstructing the phylogeny of " Buarremon" brush-finches and near relatives (Aves, Emberizidae) from individual gene trees

Author keywords

Anomalous genes trees; BEST; COAL; Minimizing deep coalescences; Species tree; Topological incongruence

Indexed keywords

MITOCHONDRIAL DNA;

EID: 79951577346     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.11.012     Document Type: Article
Times cited : (15)

References (55)
  • 1
    • 65449133181 scopus 로고    scopus 로고
    • Multilocus phylogeography and phylogenetics using sequence-based markers
    • Brito P., Edwards S.V. Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 2009, 135:439-455.
    • (2009) Genetica , vol.135 , pp. 439-455
    • Brito, P.1    Edwards, S.V.2
  • 2
    • 53849128215 scopus 로고    scopus 로고
    • Comparison of species tree methods for reconstructing the phylogeny of bearded Manakins (Aves: Pipridae, Manacus) from multilocus sequence data
    • Brumfield R.T., Liu L., Lum D.E., Edwards S.V. Comparison of species tree methods for reconstructing the phylogeny of bearded Manakins (Aves: Pipridae, Manacus) from multilocus sequence data. Syst. Biol. 2008, 57:719-731.
    • (2008) Syst. Biol. , vol.57 , pp. 719-731
    • Brumfield, R.T.1    Liu, L.2    Lum, D.E.3    Edwards, S.V.4
  • 3
    • 73349094371 scopus 로고    scopus 로고
    • Molecules, morphology, ecology, and songs in concert: How many species is " Arremon torquatus" (Aves, Emberizidae)?
    • Cadena C.D., Cuervo A.M. Molecules, morphology, ecology, and songs in concert: How many species is " Arremon torquatus" (Aves, Emberizidae)?. Biol. J. Linn. Soc. 2010, 99:152-176.
    • (2010) Biol. J. Linn. Soc. , vol.99 , pp. 152-176
    • Cadena, C.D.1    Cuervo, A.M.2
  • 4
    • 34547936546 scopus 로고    scopus 로고
    • Evolutionary differentiation in the Neotropical montane region: molecular phylogenetics and phylogeography of Buarremon brush-finches (Aves, Emberizidae)
    • Cadena C.D., Klicka J., Ricklefs R.E. Evolutionary differentiation in the Neotropical montane region: molecular phylogenetics and phylogeography of Buarremon brush-finches (Aves, Emberizidae). Mol. Phylogent. Evol. 2007, 44:993-1016.
    • (2007) Mol. Phylogent. Evol. , vol.44 , pp. 993-1016
    • Cadena, C.D.1    Klicka, J.2    Ricklefs, R.E.3
  • 5
    • 40849120246 scopus 로고    scopus 로고
    • Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypothesis in passerina buntings
    • Carling M.D., Brumfield R.T. Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypothesis in passerina buntings. Genetics 2008, 178:363-377.
    • (2008) Genetics , vol.178 , pp. 363-377
    • Carling, M.D.1    Brumfield, R.T.2
  • 6
    • 34249700809 scopus 로고    scopus 로고
    • Estimating phylogeny from gene tree probabilities in Melanoplus grasshoppers despite incomplete lineage sorting
    • Carstens B.C., Knowles L.L. Estimating phylogeny from gene tree probabilities in Melanoplus grasshoppers despite incomplete lineage sorting. Syst. Biol. 2007, 56:400-411.
    • (2007) Syst. Biol. , vol.56 , pp. 400-411
    • Carstens, B.C.1    Knowles, L.L.2
  • 7
    • 0028065747 scopus 로고
    • Transmission patterns of eukaryotic transposable elements: arguments for and against horizontal transfer
    • Cummings M.P. Transmission patterns of eukaryotic transposable elements: arguments for and against horizontal transfer. Trends Ecol. Evol. 1994, 9:141-145.
    • (1994) Trends Ecol. Evol. , vol.9 , pp. 141-145
    • Cummings, M.P.1
  • 8
    • 12044251056 scopus 로고
    • For consensus (sometimes)
    • De Queiroz A. For consensus (sometimes). Syst. Biol. 1993, 42:368-372.
    • (1993) Syst. Biol. , vol.42 , pp. 368-372
    • De Queiroz, A.1
  • 10
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • Degnan J.H., Rosenberg N.A. Discordance of species trees with their most likely gene trees. PLoS Genet. 2006, 2:762-768.
    • (2006) PLoS Genet. , vol.2 , pp. 762-768
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 11
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference, and the multispecies coalescent
    • Degnan J.H., Rosenberg N.A. Gene tree discordance, phylogenetic inference, and the multispecies coalescent. Trends Ecol. Evol. 2009, 24:332-340.
    • (2009) Trends Ecol. Evol. , vol.24 , pp. 332-340
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 12
    • 13244292527 scopus 로고    scopus 로고
    • Gene tree distributions under the coalescent process
    • Degnan J.H., Salter L.A. Gene tree distributions under the coalescent process. Evolution 2005, 59:24-37.
    • (2005) Evolution , vol.59 , pp. 24-37
    • Degnan, J.H.1    Salter, L.A.2
  • 13
    • 67449167484 scopus 로고    scopus 로고
    • Properties of consensus methods for inferring species trees from gene trees
    • Degnan J.H., De Giorgio M., Bryant D., Rosenberg N.A. Properties of consensus methods for inferring species trees from gene trees. Syst. Biol. 2009, 58:35-54.
    • (2009) Syst. Biol. , vol.58 , pp. 35-54
    • Degnan, J.H.1    De Giorgio, M.2    Bryant, D.3    Rosenberg, N.A.4
  • 15
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 16
    • 34347256397 scopus 로고    scopus 로고
    • High-resolution species tree without concatenation
    • Edwards S.V., Liu L., Pearl D.K. High-resolution species tree without concatenation. Proc. Natl. Acad. Sci. USA 2007, 104:5936-5941.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 5936-5941
    • Edwards, S.V.1    Liu, L.2    Pearl, D.K.3
  • 17
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • Fitch W.M. Distinguishing homologous from analogous proteins. Syst. Zool. 1970, 19:99-113.
    • (1970) Syst. Zool. , vol.19 , pp. 99-113
    • Fitch, W.M.1
  • 18
    • 14844313275 scopus 로고    scopus 로고
    • Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree
    • Gadagkar S., Rosenberg S., Kumar S. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J. Exp. Zool. 2005, 304B:64-74.
    • (2005) J. Exp. Zool. , vol.304 B , pp. 64-74
    • Gadagkar, S.1    Rosenberg, S.2    Kumar, S.3
  • 19
    • 78049390225 scopus 로고    scopus 로고
    • Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling
    • Hird S., Kubatko L.S., Carstens B.C. Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling. Mol. Phylogent. Evol. 2010, 57:888-898.
    • (2010) Mol. Phylogent. Evol. , vol.57 , pp. 888-898
    • Hird, S.1    Kubatko, L.S.2    Carstens, B.C.3
  • 20
    • 77958059433 scopus 로고    scopus 로고
    • Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods
    • Huang H., He Q., Kubatko L.S., Knowles L.L. Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Syst. Biol. 2010, 59:573-583.
    • (2010) Syst. Biol. , vol.59 , pp. 573-583
    • Huang, H.1    He, Q.2    Kubatko, L.S.3    Knowles, L.L.4
  • 21
    • 12044255616 scopus 로고
    • Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis?
    • Huelsenbeck J.P., Swofford D.L., Cunningham C.W., Bull J.J., Waddell P. Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis?. Syst. Biol. 1994, 43:288-291.
    • (1994) Syst. Biol. , vol.43 , pp. 288-291
    • Huelsenbeck, J.P.1    Swofford, D.L.2    Cunningham, C.W.3    Bull, J.J.4    Waddell, P.5
  • 22
    • 25644452054 scopus 로고    scopus 로고
    • Speciational history of Australian grass finches (Poephila) inferred from 30 gene trees
    • Jennings W.B., Edwards S.V. Speciational history of Australian grass finches (Poephila) inferred from 30 gene trees. Evolution 2005, 59:2033-2047.
    • (2005) Evolution , vol.59 , pp. 2033-2047
    • Jennings, W.B.1    Edwards, S.V.2
  • 24
    • 70450233546 scopus 로고    scopus 로고
    • Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes
    • Knowles L.L. Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Syst. Biol. 2009, 58:463-467.
    • (2009) Syst. Biol. , vol.58 , pp. 463-467
    • Knowles, L.L.1
  • 25
    • 77958072265 scopus 로고    scopus 로고
    • Sampling strategies for species-tree estimation
    • Wiley-Blackwell, L.L. Knowles, L.S. Kubatko (Eds.)
    • Knowles L.L. Sampling strategies for species-tree estimation. Estimating Species Trees: Practical and Theoretical Aspects 2010, 163-173. Wiley-Blackwell. L.L. Knowles, L.S. Kubatko (Eds.).
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 163-173
    • Knowles, L.L.1
  • 27
    • 70649110122 scopus 로고    scopus 로고
    • Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus)
    • Leaché A.D. Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus). Syst. Biol. 2009, 58:547-559.
    • (2009) Syst. Biol. , vol.58 , pp. 547-559
    • Leaché, A.D.1
  • 28
    • 0002948868 scopus 로고    scopus 로고
    • Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data
    • Kluwer, Boston, D.E. Soltis, P.S. Soltis, J.J. Doyle (Eds.)
    • Lewis P.O. Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data. Molecular Systematics of Plants II 1998, 132-163. Kluwer, Boston. D.E. Soltis, P.S. Soltis, J.J. Doyle (Eds.).
    • (1998) Molecular Systematics of Plants II , pp. 132-163
    • Lewis, P.O.1
  • 29
    • 58149239783 scopus 로고    scopus 로고
    • Comparison of methods for species-tree inference in the sawfly genus neodiprion (hymenoptera: Diprionidae)
    • Linnen C., Farrell B. Comparison of methods for species-tree inference in the sawfly genus neodiprion (hymenoptera: Diprionidae). Syst. Biol. 2008, 57:876-890.
    • (2008) Syst. Biol. , vol.57 , pp. 876-890
    • Linnen, C.1    Farrell, B.2
  • 30
    • 70349417912 scopus 로고    scopus 로고
    • Phylogenetic analysis in the anomaly zone
    • Liu L., Edwards S.V. Phylogenetic analysis in the anomaly zone. Syst. Biol. 2009, 58:452-460.
    • (2009) Syst. Biol. , vol.58 , pp. 452-460
    • Liu, L.1    Edwards, S.V.2
  • 31
    • 34548575126 scopus 로고    scopus 로고
    • Species tree from gene trees: reconstructing bayesian posterior distribution of species phylogeny using estimated gene tree distributions
    • Liu L., Pearl D. Species tree from gene trees: reconstructing bayesian posterior distribution of species phylogeny using estimated gene tree distributions. Syst. Biol. 2007, 56:504-514.
    • (2007) Syst. Biol. , vol.56 , pp. 504-514
    • Liu, L.1    Pearl, D.2
  • 32
    • 47749093183 scopus 로고    scopus 로고
    • Estimating species trees using multiple-allele DNA sequence data
    • Liu L., Pearl D., Brumfield R., Edwards S.V. Estimating species trees using multiple-allele DNA sequence data. Evolution 2008, 62:2080-2091.
    • (2008) Evolution , vol.62 , pp. 2080-2091
    • Liu, L.1    Pearl, D.2    Brumfield, R.3    Edwards, S.V.4
  • 33
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison W.P. Gene trees in species trees. Syst. Biol. 1997, 46:523-536.
    • (1997) Syst. Biol. , vol.46 , pp. 523-536
    • Maddison, W.P.1
  • 34
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • Maddison W.P., Knowles L.L. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 2006, 55:21-30.
    • (2006) Syst. Biol. , vol.55 , pp. 21-30
    • Maddison, W.P.1    Knowles, L.L.2
  • 35
    • 79951578278 scopus 로고    scopus 로고
    • Mesquite: A Modular System for Evolutionary Analysis, Version 1.01.
    • Maddison, W.P., Maddison, D.R., 2004. Mesquite: A Modular System for Evolutionary Analysis, Version 1.01. http://mesquiteproject.org.
    • (2004)
    • Maddison, W.P.1    Maddison, D.R.2
  • 36
    • 70450265498 scopus 로고    scopus 로고
    • Maximum-likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design
    • McCormack J.E., Huang H., Knowles L.L. Maximum-likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Syst. Biol. 2009, 58:501-508.
    • (2009) Syst. Biol. , vol.58 , pp. 501-508
    • McCormack, J.E.1    Huang, H.2    Knowles, L.L.3
  • 37
    • 58249136809 scopus 로고    scopus 로고
    • Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model
    • Meng C., Kubatko L.S. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model. Theor. Pop. Biol. 2009, 75:35-45.
    • (2009) Theor. Pop. Biol. , vol.75 , pp. 35-45
    • Meng, C.1    Kubatko, L.S.2
  • 38
    • 0035400648 scopus 로고    scopus 로고
    • Gene trees and species trees are not the same
    • Nichols R. Gene trees and species trees are not the same. Trends Ecol. Evol. 2001, 16:358-364.
    • (2001) Trends Ecol. Evol. , vol.16 , pp. 358-364
    • Nichols, R.1
  • 40
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo P., Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 1988, 5:568-583.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 42
    • 8444235408 scopus 로고    scopus 로고
    • A broad survey of recombination in animal mitochondrial
    • Piganeau G.V., Gardner M., Eyre-Walker A. A broad survey of recombination in animal mitochondrial. Mol. Biol. Evol. 2004, 21:2319-2325.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 2319-2325
    • Piganeau, G.V.1    Gardner, M.2    Eyre-Walker, A.3
  • 43
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: testing the model of DNA substitution
    • Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 44
    • 79951581427 scopus 로고    scopus 로고
    • Tracer v1.4 2003-2008. Mcmc Trace.
    • Rambaut, A., Drummond, A., 2007. Tracer v1.4 2003-2008. Mcmc Trace.
    • (2007)
    • Rambaut, A.1    Drummond, A.2
  • 46
    • 0042313795 scopus 로고    scopus 로고
    • Conflicting phylogenetic signals at the base of the metazoan tree
    • Rokas A., King N., Finnerty J., Carroll S.B. Conflicting phylogenetic signals at the base of the metazoan tree. Evol. Dev. 2003, 5:346-359.
    • (2003) Evol. Dev. , vol.5 , pp. 346-359
    • Rokas, A.1    King, N.2    Finnerty, J.3    Carroll, S.B.4
  • 47
    • 0041386108 scopus 로고    scopus 로고
    • MRBAYES 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F., Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 48
    • 0027739757 scopus 로고
    • Rapid assessment of single-copy nuclear DNA variation in diverse species
    • Slade R.W., Moritz C., Heideman A. Rapid assessment of single-copy nuclear DNA variation in diverse species. Mol. Ecol. 1993, 2:359-373.
    • (1993) Mol. Ecol. , vol.2 , pp. 359-373
    • Slade, R.W.1    Moritz, C.2    Heideman, A.3
  • 49
    • 0033161156 scopus 로고    scopus 로고
    • Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates
    • Sorenson M.D., Ast J.C., DimcheV D.E., Yuri T., Mindell D.P. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol. Phylogenet. Evol. 1999, 12:105-114.
    • (1999) Mol. Phylogenet. Evol. , vol.12 , pp. 105-114
    • Sorenson, M.D.1    Ast, J.C.2    DimcheV, D.E.3    Yuri, T.4    Mindell, D.P.5
  • 50
    • 63049121388 scopus 로고    scopus 로고
    • Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles
    • Spinks P.Q., Thomson R.C., Lovely G.A., Shaffer H.B. Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles. BMC Evol. Biol. 2009, 9:56.
    • (2009) BMC Evol. Biol. , vol.9 , pp. 56
    • Spinks, P.Q.1    Thomson, R.C.2    Lovely, G.A.3    Shaffer, H.B.4
  • 52
    • 0024713112 scopus 로고
    • Gene genealogy in three related populations: consistency probability between gene and population trees
    • Takahata N. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 1989, 122:957-966.
    • (1989) Genetics , vol.122 , pp. 957-966
    • Takahata, N.1
  • 53
    • 0035205317 scopus 로고    scopus 로고
    • The discovery of single-nucleotide polymorphisms and inferences about human demographic history
    • Wakeley J., Nielsen R., Liu-Cordero S.N., Ardlie K. The discovery of single-nucleotide polymorphisms and inferences about human demographic history. Am. J. Hum. Genet. 2001, 69:1332-1347.
    • (2001) Am. J. Hum. Genet. , vol.69 , pp. 1332-1347
    • Wakeley, J.1    Nielsen, R.2    Liu-Cordero, S.N.3    Ardlie, K.4
  • 54
    • 77958055335 scopus 로고    scopus 로고
    • Gene trees versus species trees: reassessing life-history evolution in a freshwater fish radiation
    • Waters J.M., Rowe D.L., Burridge C.P., Wallis G.P. Gene trees versus species trees: reassessing life-history evolution in a freshwater fish radiation. Syst. Biol. 2010, 59:504-517.
    • (2010) Syst. Biol. , vol.59 , pp. 504-517
    • Waters, J.M.1    Rowe, D.L.2    Burridge, C.P.3    Wallis, G.P.4
  • 55
    • 79951578934 scopus 로고    scopus 로고
    • AWTY: A System for Graphical Exploration of MCMC Convergence in Bayesian Phylogenetic Inference.
    • Wilgenbusch, J.C., Warren, D.L., Swofford, D.L., 2004. AWTY: A System for Graphical Exploration of MCMC Convergence in Bayesian Phylogenetic Inference. http://ceb.csit.fsu.edu/awt.
    • (2004)
    • Wilgenbusch, J.C.1    Warren, D.L.2    Swofford, D.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.