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Volumn 32, Issue 9, 2015, Pages 2469-2482

Species tree inference using a mixture model

Author keywords

Expectation maximization; Mammalian phylogeny; Mixture model; Phylogenetics; Species trees

Indexed keywords

BIOINFORMATICS; CONTROLLED STUDY; DNA STRUCTURE; EXPECTATION; GENE DUPLICATION; GENE LOSS; GENOME; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY; PROBABILITY; SPECIES; TARGET ORGANISM; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; CLUSTER ANALYSIS; GENE; HUMAN;

EID: 84944765813     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msv115     Document Type: Article
Times cited : (10)

References (65)
  • 1
    • 65249107239 scopus 로고    scopus 로고
    • Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
    • Akerborg O, Sennblad B, Arvestad L, Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci USA. 106(14)5714-5719.
    • (2009) Proc Natl Acad Sci USA. , vol.106 , Issue.14 , pp. 5714-5719
    • Akerborg, O.1    Sennblad, B.2    Arvestad, L.3    Lagergren, J.4
  • 3
    • 0141609704 scopus 로고    scopus 로고
    • A new phylogenetic marker, apolipoprotein b, provides compelling evidence for eutherian relationships
    • Amrine-Madsen H, Koepfli K-P, Wayne RK, Springer MS. 2003. A new phylogenetic marker, apolipoprotein b, provides compelling evidence for eutherian relationships. Mol Phylogenet Evol. 28(2):225-240.
    • (2003) Mol Phylogenet Evol. , vol.28 , Issue.2 , pp. 225-240
    • Amrine-Madsen, H.1    Koepfli, K.-P.2    Wayne, R.K.3    Springer, M.S.4
  • 6
    • 70349414048 scopus 로고    scopus 로고
    • The gene evolution model and computing its associated probabilities
    • Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM. 56(2):1-44.
    • (2009) J ACM. , vol.56 , Issue.2 , pp. 1-44
    • Arvestad, L.1    Lagergren, J.2    Sennblad, B.3
  • 8
    • 84873326063 scopus 로고    scopus 로고
    • Genome-scale coestimation of species and gene trees
    • Boussau B, Szollosi GJ, Duret L, et al. 2013. Genome-scale coestimation of species and gene trees. Genome Res. 23(2)323-330.
    • (2013) Genome Res. , vol.23 , Issue.2 , pp. 323-330
    • Boussau, B.1    Szollosi, G.J.2    Duret, L.3
  • 9
    • 84864697376 scopus 로고    scopus 로고
    • Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis
    • Bryant D, Bouckaert R, Felsenstein J, Rosenber NA, RoyChoudhury A. 2012. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol. 29(8):1917-1932.
    • (2012) Mol Biol Evol. , vol.29 , Issue.8 , pp. 1917-1932
    • Bryant, D.1    Bouckaert, R.2    Felsenstein, J.3    Rosenber, N.A.4    RoyChoudhury, A.5
  • 10
    • 78549247493 scopus 로고    scopus 로고
    • IGTP: A software package for large-scale gene tree parsimony analysis
    • Chaudhary R, Bansal M, Wehe A et al. 2010. iGTP: a software package for large-scale gene tree parsimony analysis. BMC Bioinformatics 11(1):574.
    • (2010) BMC Bioinformatics , vol.11 , Issue.1 , pp. 574
    • Chaudhary, R.1    Bansal, M.2    Wehe, A.3
  • 11
    • 33845335476 scopus 로고    scopus 로고
    • Finding a maximum likelihood tree is hard
    • Chor B, Tuller T. 2006. Finding a maximum likelihood tree is hard. J ACM. 53(5)722-744.
    • (2006) J ACM. , vol.53 , Issue.5 , pp. 722-744
    • Chor, B.1    Tuller, T.2
  • 12
    • 84980104550 scopus 로고
    • The myology of the tree-shrew (Tupaia minor)
    • Clark WELG. 1924. The myology of the tree-shrew (Tupaia minor). Proc Zool Soc Lond. 94(2):461-497
    • (1924) Proc Zool Soc Lond. , vol.94 , Issue.2 , pp. 461-497
    • Clark, W.E.L.G.1
  • 13
    • 84874229463 scopus 로고    scopus 로고
    • Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants
    • De Smet R, Adams KL, Vandepoele K, et al. 2013. Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc Natl Acad Sci USA. 110(8):2898-2903.
    • (2013) Proc Natl Acad Sci USA. , vol.110 , Issue.8 , pp. 2898-2903
    • De Smet, R.1    Adams, K.L.2    Vandepoele, K.3
  • 16
    • 4043093120 scopus 로고
    • The reconstruction of evolution
    • Edwards A, Cavalli-Sforza L 1963. The reconstruction of evolution. Ann Hum Genet 18(27):105-106.
    • (1963) Ann Hum Genet , vol.18 , Issue.27 , pp. 105-106
    • Edwards, A.1    Cavalli-Sforza, L.2
  • 17
    • 34347256397 scopus 로고    scopus 로고
    • High-resolution species trees without concatenation
    • Edwards SV, Liu L, Pearl DK. 2007. High-resolution species trees without concatenation. Proc Natl Acad Sci USA. 104(14):5936-5941.
    • (2007) Proc Natl Acad Sci USA. , vol.104 , Issue.14 , pp. 5936-5941
    • Edwards, S.V.1    Liu, L.2    Pearl, D.K.3
  • 18
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17(6)368-376.
    • (1981) J Mol Evol. , vol.17 , Issue.6 , pp. 368-376
    • Felsenstein, J.1
  • 19
    • 84959747425 scopus 로고
    • Toward defining the course of evolution: Minimum change for a specific tree topology
    • Fitch WM. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool. 20(4):406-416.
    • (1971) Syst Zool. , vol.20 , Issue.4 , pp. 406-416
    • Fitch, W.M.1
  • 21
    • 0032269108 scopus 로고    scopus 로고
    • How many clusters? Which clustering method? Answers via model-based cluster analysis
    • Fraley C 1998. How many clusters? Which clustering method? Answers via model-based cluster analysis. Comput J. 41(8)578-588.
    • (1998) Comput J. , vol.41 , Issue.8 , pp. 578-588
    • Fraley, C.1
  • 22
    • 0036110773 scopus 로고    scopus 로고
    • A structural em algorithm for phylogenetic inference
    • Friedman N, Ninio M, Pe'er I, Pupko T 2002. A structural EM algorithm for phylogenetic inference. J Comput Biol. 9(2)331-353
    • (2002) J Comput Biol. , vol.9 , Issue.2 , pp. 331-353
    • Friedman, N.1    Ninio, M.2    Pe'Er, I.3    Pupko, T.4
  • 24
    • 38549097058 scopus 로고    scopus 로고
    • OPTIC: Orthologous and paralogous transcripts in clades
    • Heger A Ponting CP. 2008. OPTIC: orthologous and paralogous transcripts in clades. Nucleic Acids Res. 36(database issue):D267-D270.
    • (2008) Nucleic Acids Res. , vol.36 , pp. D267-D270
    • Heger, A.1    Ponting, C.P.2
  • 25
    • 77249086587 scopus 로고    scopus 로고
    • Bayesian inference of species trees from multilocus data
    • Heled J, Drummond AJ. 2010. Bayesian inference of species trees from multilocus data. Mol Biol Evol. 27(3)570-580.
    • (2010) Mol Biol Evol. , vol.27 , Issue.3 , pp. 570-580
    • Heled, J.1    Drummond, A.J.2
  • 26
    • 33846906954 scopus 로고    scopus 로고
    • Site specific rates of mitochondrial genomes and the phylogeny of eutheria
    • Kjer K, Honeycutt R. 2007. Site specific rates of mitochondrial genomes and the phylogeny of eutheria. BMC Evol Biol. 7(1):8.
    • (2007) BMC Evol Biol. , vol.7 , Issue.1 , pp. 8
    • Kjer, K.1    Honeycutt, R.2
  • 27
    • 16444381885 scopus 로고    scopus 로고
    • A comprehensive evolutionary classification of proteins encoded in complete eukary-otic genomes
    • Koonin EV, Fedorova ND, Jackson JD, et al. 2004. A comprehensive evolutionary classification of proteins encoded in complete eukary-otic genomes. Genome Biol. 5(2):R7
    • (2004) Genome Biol. , vol.5 , Issue.2 , pp. R7
    • Koonin, E.V.1    Fedorova, N.D.2    Jackson, J.D.3
  • 28
    • 78650202986 scopus 로고    scopus 로고
    • Phylogeny and conservation priorities of afrotherian mammals (afrotheria, mammalia)
    • Kuntner M, May-Collado LJ, Agnarsson I. 2011. Phylogeny and conservation priorities of afrotherian mammals (afrotheria, mammalia). Zool Scr. 40(1):1-15
    • (2011) Zool Scr. , vol.40 , Issue.1 , pp. 1-15
    • Kuntner, M.1    May-Collado, L.J.2    Agnarsson, I.3
  • 29
    • 78149256307 scopus 로고    scopus 로고
    • BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
    • Larget BR, Kotha SK, Dewey CN, Ane C. 2010. BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26(22):2910-2911.
    • (2010) Bioinformatics , vol.26 , Issue.22 , pp. 2910-2911
    • Larget, B.R.1    Kotha, S.K.2    Dewey, C.N.3    Ane, C.4
  • 31
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison WP. 1997. Gene trees in species trees. Syst Biol. 46(3)523
    • (1997) Syst Biol. , vol.46 , Issue.3 , pp. 523
    • Maddison, W.P.1
  • 32
    • 0035252569 scopus 로고    scopus 로고
    • Parallel adaptive radiations in two major clades of placental mammals
    • Madsen O, Scally M, Douady CJ, et al. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409(6820):610-614.
    • (2001) Nature , vol.409 , Issue.6820 , pp. 610-614
    • Madsen, O.1    Scally, M.2    Douady, C.J.3
  • 33
    • 84901266509 scopus 로고    scopus 로고
    • Genome-wide probabilistic reconciliation analysis across vertebrates
    • Mahmudi O, Sjostrand J, Sennblad B, Lagergren J. 2013. Genome-wide probabilistic reconciliation analysis across vertebrates. BMC Bioinformatics 14(Suppl. 15):S10.
    • (2013) BMC Bioinformatics , vol.14 , pp. S10
    • Mahmudi, O.1    Sjostrand, J.2    Sennblad, B.3    Lagergren, J.4
  • 35
    • 0000028423 scopus 로고
    • A quantitative approach to a problem in classification
    • Michener CD, Sokal RR. 1957. A quantitative approach to a problem in classification. Evolution 11(2):130-162.
    • (1957) Evolution , vol.11 , Issue.2 , pp. 130-162
    • Michener, C.D.1    Sokal, R.R.2
  • 36
    • 84917708481 scopus 로고    scopus 로고
    • Statistical binning enables an accurate coalescent-based estimation of the avian tree
    • Mirarab S, Bayzid MS, Boussau B, Warnow T 2014. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 346(6215):1250463-1-1250463-9
    • (2014) Science , vol.346 , Issue.6215 , pp. 12504631-12504639
    • Mirarab, S.1    Bayzid, M.S.2    Boussau, B.3    Warnow, T.4
  • 37
    • 84978808477 scopus 로고    scopus 로고
    • Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting
    • Advance Access published August 26, 2014
    • Mirarab S, Bayzid MS, Warnow T. 2014. Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting. Syst Biol. Advance Access published August 26, 2014, doi:10.1093/sysbio/syu063.
    • (2014) Syst Biol
    • Mirarab, S.1    Bayzid, M.S.2    Warnow, T.3
  • 39
    • 0035252080 scopus 로고    scopus 로고
    • Molecular phylogenetics and the origins of placental mammals
    • Murphy WJ, Eizirik E, Johnson WE, et al. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409(6820):614-618.
    • (2001) Nature , vol.409 , Issue.6820 , pp. 614-618
    • Murphy, W.J.1    Eizirik, E.2    Johnson, W.E.3
  • 40
    • 0035861441 scopus 로고    scopus 로고
    • Resolution of the early placental mammal radiation using Bayesian phylogenetics
    • Murphy WJ, Eizirik E, O'Brien SJ, et al. 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294(5550):2348-2351.
    • (2001) Science , vol.294 , Issue.5550 , pp. 2348-2351
    • Murphy, W.J.1    Eizirik, E.2    O'Brien, S.J.3
  • 41
    • 84888137812 scopus 로고    scopus 로고
    • Computational approaches to species phylogeny inference and gene tree reconciliation
    • Nakhleh L. 2013. Computational approaches to species phylogeny inference and gene tree reconciliation. Trends Ecol Evol. 28(12):719-728.
    • (2013) Trends Ecol Evol. , vol.28 , Issue.12 , pp. 719-728
    • Nakhleh, L.1
  • 43
    • 84885371732 scopus 로고    scopus 로고
    • Tupaiine tree shrews (Scandentia, Mammalia) from the Yuanmou Lufengpithecus locality of Yunnan, China
    • Ni X, Qiu Z. 2012. Tupaiine tree shrews (Scandentia, Mammalia) from the Yuanmou Lufengpithecus locality of Yunnan, China. Swiss J Palaeontol. 131(1):51-60.
    • (2012) Swiss J Palaeontol. , vol.131 , Issue.1 , pp. 51-60
    • Ni, X.1    Qiu, Z.2
  • 44
    • 0031110886 scopus 로고    scopus 로고
    • From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem
    • Page RD, Charleston MA. 1997. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol Phylogenet Evol. 7(2):231-240.
    • (1997) Mol Phylogenet Evol. , vol.7 , Issue.2 , pp. 231-240
    • Page, R.D.1    Charleston, M.A.2
  • 46
    • 0041817551 scopus 로고    scopus 로고
    • Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    • Rannala B, Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164(4):1645-1656.
    • (2003) Genetics , vol.164 , Issue.4 , pp. 1645-1656
    • Rannala, B.1    Yang, Z.2
  • 47
    • 38849160068 scopus 로고    scopus 로고
    • Accurate gene-tree reconstruction by learning gene-and species-specific substitution rates across multiple complete genomes
    • Rasmussen MD, Kellis M. 2007. Accurate gene-tree reconstruction by learning gene-and species-specific substitution rates across multiple complete genomes. Genome Res. 17(12):1932-1942.
    • (2007) Genome Res. , vol.17 , Issue.12 , pp. 1932-1942
    • Rasmussen, M.D.1    Kellis, M.2
  • 48
    • 78650481676 scopus 로고    scopus 로고
    • A Bayesian approach for fast and accurate gene tree reconstruction
    • Rasmussen MD, Kellis M. 2011. A Bayesian approach for fast and accurate gene tree reconstruction. Mol Biol Evol. 28(1):273-290.
    • (2011) Mol Biol Evol. , vol.28 , Issue.1 , pp. 273-290
    • Rasmussen, M.D.1    Kellis, M.2
  • 49
    • 58149357704 scopus 로고    scopus 로고
    • A two-stage pruning algorithm for likelihood computation for a population tree
    • RoyChoudhury A, Felsenstein J, Thompson EA. 2008. A two-stage pruning algorithm for likelihood computation for a population tree. Genetics 180(2):1095-1105.
    • (2008) Genetics , vol.180 , Issue.2 , pp. 1095-1105
    • RoyChoudhury, A.1    Felsenstein, J.2    Thompson, E.A.3
  • 51
    • 70349413154 scopus 로고    scopus 로고
    • Probabilistic orthology analysis
    • Sennblad B, Lagergren J. 2009. Probabilistic orthology analysis. Syst Biol. 58(4):411-424.
    • (2009) Syst Biol. , vol.58 , Issue.4 , pp. 411-424
    • Sennblad, B.1    Lagergren, J.2
  • 53
    • 84899553363 scopus 로고    scopus 로고
    • Raxml version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis A. 2014. Raxml version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312-1313.
    • (2014) Bioinformatics , vol.30 , Issue.9 , pp. 1312-1313
    • Stamatakis, A.1
  • 54
    • 84867904826 scopus 로고    scopus 로고
    • Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
    • Szöllosi GJ, Boussau B, Abby SS, et al. 2012. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proc Natl Acad Sci USA. 109(43):17513-17518.
    • (2012) Proc Natl Acad Sci USA. , vol.109 , Issue.43 , pp. 17513-17518
    • Szöllosi, G.J.1    Boussau, B.2    Abby, S.S.3
  • 55
    • 40949096949 scopus 로고    scopus 로고
    • Afrotherian mammals: A review of current data
    • Tabuce R, Asher RJ, Lehmann T. 2008. Afrotherian mammals: a review of current data. Mammalia 72(1):2-14.
    • (2008) Mammalia , vol.72 , Issue.1 , pp. 2-14
    • Tabuce, R.1    Asher, R.J.2    Lehmann, T.3
  • 56
    • 0021066244 scopus 로고
    • Evolutionary relationship of DNA sequences in finite populations
    • Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105(2):437-460.
    • (1983) Genetics , vol.105 , Issue.2 , pp. 437-460
    • Tajima, F.1
  • 57
    • 0017465744 scopus 로고
    • Finding optimum branchings
    • Tarjan RE. 1977. Finding optimum branchings. Networks 7(1):25-35.
    • (1977) Networks , vol.7 , Issue.1 , pp. 25-35
    • Tarjan, R.E.1
  • 58
    • 70349658769 scopus 로고    scopus 로고
    • Species tree inference by minimizing deep coalescences
    • Than C, Nakhleh L. 2009. Species tree inference by minimizing deep coalescences. PLoS Comput Biol. 5(9):e1000501.
    • (2009) PLoS Comput Biol. , vol.5 , Issue.9 , pp. e1000501
    • Than, C.1    Nakhleh, L.2
  • 61
    • 0035752767 scopus 로고    scopus 로고
    • A phylogenetic foundation for comparative mammalian genomics
    • Waddell PJ, Kishino H, Ota R. 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Inform. 12:141-154.
    • (2001) Genome Inform. , vol.12 , pp. 141-154
    • Waddell, P.J.1    Kishino, H.2    Ota, R.3
  • 62
    • 79953324603 scopus 로고    scopus 로고
    • Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi
    • Waterhouse RM, Zdobnov EM, Kriventseva EV. 2011. Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi. Genome Biol Evol. 3:75-86.
    • (2011) Genome Biol Evol. , vol.3 , pp. 75-86
    • Waterhouse, R.M.1    Zdobnov, E.M.2    Kriventseva, E.V.3
  • 63
    • 46249126320 scopus 로고    scopus 로고
    • Duptree: A program for large-scale phylogenetic analyses using gene tree parsimony
    • Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24(13):1540-1541.
    • (2008) Bioinformatics , vol.24 , Issue.13 , pp. 1540-1541
    • Wehe, A.1    Bansal, M.S.2    Burleigh, J.G.3    Eulenstein, O.4
  • 64
    • 0026031181 scopus 로고
    • Inferences of species phylogeny in relation to segregation of ancient polymorphisms
    • Wu CI. 1991. Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127(2):429-435.
    • (1991) Genetics , vol.127 , Issue.2 , pp. 429-435
    • Wu, C.I.1
  • 65
    • 80955136714 scopus 로고    scopus 로고
    • Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles
    • Yu Y, Warnow T, Nakhleh L. 2011. Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles. J Comput Biol. 18(11):1543-1559.
    • (2011) J Comput Biol. , vol.18 , Issue.11 , pp. 1543-1559
    • Yu, Y.1    Warnow, T.2    Nakhleh, L.3


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