메뉴 건너뛰기




Volumn 59, Issue 5, 2010, Pages 573-583

Sources of error inherent in species-tree estimation: Impact of mutational and coalescent effects on accuracy and implications for choosing among different methods

Author keywords

Coalescence; gene tree; lineage sorting; mutation; phylogenetics; sample design; species tree

Indexed keywords

ANALYSIS OF VARIANCE; ARTICLE; BIOLOGICAL MODEL; METHODOLOGY; MUTATION; PHYLOGENY; SPECIES DIFFERENTIATION;

EID: 77958059433     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syq047     Document Type: Article
Times cited : (120)

References (53)
  • 2
    • 53849128215 scopus 로고    scopus 로고
    • Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multi-locus sequence data
    • Brumfeld R.T., Liu L., Lum D.E., Edwards S.V. 2008. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multi-locus sequence data. Syst. Biol. 57:719-731.
    • (2008) Syst. Biol. , vol.57 , pp. 719-731
    • Brumfeld, R.T.1    Liu, L.2    Lum, D.E.3    Edwards, S.V.4
  • 3
    • 33747398245 scopus 로고    scopus 로고
    • Variable nuclear markers for Melanoplus oregonensis identifed from the screening of a genomic library
    • Carstens B.C., Knowles L.L. 2006. Variable nuclear markers for Melanoplus oregonensis identifed from the screening of a genomic library. Mol. Ecol. Notes 6:683-685.
    • (2006) Mol. Ecol. Notes , vol.6 , pp. 683-685
    • Carstens, B.C.1    Knowles, L.L.2
  • 4
    • 34249700809 scopus 로고    scopus 로고
    • Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: An example from Melanoplus grasshoppers
    • Carstens B.C., Knowles L.L. 2007. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 56:400-411.
    • (2007) Syst. Biol. , vol.56 , pp. 400-411
    • Carstens, B.C.1    Knowles, L.L.2
  • 5
    • 70450231658 scopus 로고    scopus 로고
    • Species trees from highly incongruent gene trees in rice
    • Cranston C., Hurwitz B., Ware D., Stein L., Wing R.A. 2009. Species trees from highly incongruent gene trees in rice. Syst. Biol. 58:489-500.
    • (2009) Syst. Biol. , vol.58 , pp. 489-500
    • Cranston, C.1    Hurwitz, B.2    Ware, D.3    Stein, L.4    Wing, R.A.5
  • 6
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • Degnan J.H., Rosenberg N.A. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2:762-768.
    • (2006) PLoS Genet. , vol.2 , pp. 762-768
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 7
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phyloge-netic inference and the multispecies coalescent
    • Degnan J.H., Rosenberg N.A. 2009. Gene tree discordance, phyloge-netic inference and the multispecies coalescent. Trends Ecol. Evol. 24:332-340.
    • (2009) Trends Ecol. Evol. , vol.24 , pp. 332-340
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 8
    • 56549103832 scopus 로고    scopus 로고
    • Does gene fow destroy phylogenetic signal? the performance of three methods for estimating species phylogenies in the presence of gene fow
    • Eckert A.J., Carstens B.C. 2008. Does gene fow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene fow. Mol. Phylogenet. Evol. 49:832-842.
    • (2008) Mol. Phylogenet. Evol. , vol.49 , pp. 832-842
    • Eckert, A.J.1    Carstens, B.C.2
  • 9
    • 58249100073 scopus 로고    scopus 로고
    • Is a new and general theory of molecular system-atics emerging?
    • Edwards S.V. 2009. Is a new and general theory of molecular system-atics emerging? Evolution. 63:1-19.
    • (2009) Evolution. , vol.63 , pp. 1-19
    • Edwards, S.V.1
  • 10
    • 34347256397 scopus 로고    scopus 로고
    • High-resolution species trees without concatenation
    • Edwards S.V., Liu L., Pearl D.K. 2007. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA. 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
  • 11
    • 0003437299 scopus 로고
    • Seattle (WA): Distributed by the author, Department of Genome Sciences, University of Washington.
    • Felsenstein J. 1993. Phylip (phylogeny inference package) version 3.5c. Seattle (WA): Distributed by the author, Department of Genome Sciences, University of Washington. Available from: http://evolution.genetics.washington. edu/phylip.html.
    • (1993) Phylip (Phylogeny Inference Package) Version 3.5c
    • Felsenstein, J.1
  • 12
    • 0028887457 scopus 로고
    • Success of maximum likelihood phylogeny inference in the four-taxon case
    • Gaut B.S., Lewis P.O. 1995. Success of maximum likelihood phylogeny inference in the four-taxon case. Mol. Biol. Evol. 12:152-162.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 152-162
    • Gaut, B.S.1    Lewis, P.O.2
  • 13
    • 67649464356 scopus 로고    scopus 로고
    • Gene discovery using massively parallel pyrosequencing to develop ESTs for the fesh fy Sarcophaga crassipalpis
    • Hahn D.A., Ragland G.J., Shoemaker D.D., Denlinger D.L. 2009. Gene discovery using massively parallel pyrosequencing to develop ESTs for the fesh fy Sarcophaga crassipalpis. BMC Genomics. 10:9.
    • (2009) BMC Genomics. , vol.10 , pp. 9
    • Hahn, D.A.1    Ragland, G.J.2    Shoemaker, D.D.3    Denlinger, D.L.4
  • 14
    • 0022376704 scopus 로고
    • Dating of the human ape splitting by a molecular clock of mitochondrial-DNA
    • Hasegawa M., Kishino H., Yano T.A. 1985. Dating of the human ape splitting by a molecular clock of mitochondrial-DNA. J. Mol. Evol. 22:160-174.
    • (1985) J. Mol. Evol. , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.A.3
  • 15
    • 33847253862 scopus 로고    scopus 로고
    • Ge-nomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model
    • Hobolth A., Christensen O.F., Mailund T., Schierup M.H. 2007. Ge-nomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet. 3:e7.
    • (2007) PLoS Genet. , vol.3
    • Hobolth, A.1    Christensen, O.F.2    Mailund, T.3    Schierup, M.H.4
  • 16
    • 70450237691 scopus 로고    scopus 로고
    • What is the danger of the anomaly zone for empirical phylogenetics?
    • Huang H., Knowles L.L. 2009. What is the danger of the anomaly zone for empirical phylogenetics? Syst. Biol. 58:527-536.
    • (2009) Syst. Biol. , vol.58 , pp. 527-536
    • Huang, H.1    Knowles, L.L.2
  • 17
    • 0001935493 scopus 로고
    • Gene genealogies and the coalescent process
    • Hudson R.R. 1990. Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 7:1-44.
    • (1990) Oxf. Surv. Evol. Biol. , vol.7 , pp. 1-44
    • Hudson, R.R.1
  • 18
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson R.R. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 18:337-338.
    • (2002) Bioinformatics. , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 19
    • 12044255023 scopus 로고
    • Success of phylogenetic methods in the four-taxon case
    • Huelsenbeck J.P., Hillis D.M. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-264.
    • (1993) Syst. Biol. , vol.42 , pp. 247-264
    • Huelsenbeck, J.P.1    Hillis, D.M.2
  • 21
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck J.P., Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17:754-755.
    • (2001) Bioinformatics. , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 22
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 23
    • 70450233546 scopus 로고    scopus 로고
    • Species tree estimation: Methods of phylogenetic analysis when there is incongruence across genes
    • Knowles L.L. 2009a. Species tree estimation: methods of phylogenetic analysis when there is incongruence across genes. Syst. Biol. 58:463-467.
    • (2009) Syst. Biol. , vol.58 , pp. 463-467
    • Knowles, L.L.1
  • 24
    • 70450281762 scopus 로고    scopus 로고
    • Statistical phylogeography
    • Knowles L.L. 2009b. Statistical phylogeography. Annu. Rev. Ecol. Syst. 40:593-612.
    • (2009) Annu. Rev. Ecol. Syst. , vol.40 , pp. 593-612
    • Knowles, L.L.1
  • 25
    • 77958072265 scopus 로고    scopus 로고
    • Sampling strategies for species-tree estimation
    • Knowles L.L., Kubatko L.S., editors Wiley- Blackwell.
    • Knowles L.L. 2010. Sampling strategies for species-tree estimation. In: Knowles L.L., Kubatko L.S., editors. Estimating species trees: practical and theoretical aspects. Wiley-Blackwell. p. 163-173.
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 163-173
    • Knowles, L.L.1
  • 26
    • 45849088450 scopus 로고    scopus 로고
    • Resolving species phylogenies of recent evolutionary radiations
    • Knowles L.L., Chan Y.-H. 2008. Resolving species phylogenies of recent evolutionary radiations. Ann. Missouri Bot. Gard. 95: 224-231.
    • (2008) Ann. Missouri Bot. Gard. , vol.95 , pp. 224-231
    • Knowles, L.L.1    Chan, Y.-H.2
  • 27
    • 77958056150 scopus 로고    scopus 로고
    • Estimating species trees: An introduction to concepts and models
    • Knowles L.L., Kubatko L.S., editors Wiley- Blackwell.
    • Knowles L.L., Kubatko L.S. 2010. Estimating species trees: an introduction to concepts and models. In:Knowles L.L., Kubatko L.S., editors. Estimating species trees: practical and theoretical aspects. Wiley-Blackwell. p. 1-14.
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 1-14
    • Knowles, L.L.1    Kubatko, L.S.2
  • 28
    • 63549118031 scopus 로고    scopus 로고
    • STEM: Species tree estimation using maximum likelihood for gene trees under coalescence
    • Kubatko L.S., Carstens B.C., Knowles L.L. 2009. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics. 25:971-973.
    • (2009) Bioinformatics. , vol.25 , pp. 971-973
    • Kubatko, L.S.1    Carstens, B.C.2    Knowles, L.L.3
  • 29
    • 77958032397 scopus 로고    scopus 로고
    • Estimating species relationships and taxon distinctiveness in Sistrurus rattlesnakes using multi-locus data
    • Knowles L.L., Kubatko L.S., editors Wiley- Blackwell.
    • Kubatko L.S., Gibbs H.L. 2010. Estimating species relationships and taxon distinctiveness in Sistrurus rattlesnakes using multi-locus data. In: Knowles L.L., Kubatko L.S., editors. Estimating species trees: practical and theoretical aspects. Wiley-Blackwell. p. 193-207.
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 193-207
    • Kubatko, L.S.1    Gibbs, H.L.2
  • 30
    • 77958055843 scopus 로고    scopus 로고
    • Species-tree estimation for complex divergence histories: A case study in Neodiprion sawfies
    • Knowles L.L., Kubatko L.S., editors Wiley- Blackwell.
    • Linnen C. 2010. Species-tree estimation for complex divergence histories: a case study in Neodiprion sawfies. In: Knowles L.L., Kubatko L.S., editors. Estimating species trees: practical and theoretical aspects. Wiley-Blackwell. p. 145-162.
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 145-162
    • Linnen, C.1
  • 31
    • 54949090066 scopus 로고    scopus 로고
    • BEST: Bayesian estimation of species trees under the coa-lescent model
    • Liu L. 2008. BEST: Bayesian estimation of species trees under the coa-lescent model. Bioinformatics. 24:2542-2543.
    • (2008) Bioinformatics. , vol.24 , pp. 2542-2543
    • Liu, L.1
  • 32
    • 47749093183 scopus 로고    scopus 로고
    • Estimating species trees using multiple-allele DNA sequence data
    • Liu L., Pearl D.K., Brumfeld R.T., Edwards S.V. 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution. 62:2080-2091.
    • (2008) Evolution. , vol.62 , pp. 2080-2091
    • Liu, L.1    Pearl, D.K.2    Brumfeld, R.T.3    Edwards, S.V.4
  • 33
    • 70350247510 scopus 로고    scopus 로고
    • Maximum tree: A consistent estimator of the species tree
    • Liu L., Yu L., Pearl D.K. 2010. Maximum tree: a consistent estimator of the species tree. J. Math. Biol. 60:95-106.
    • (2010) J. Math. Biol. , vol.60 , pp. 95-106
    • Liu, L.1    Yu, L.2    Pearl, D.K.3
  • 34
    • 70349425459 scopus 로고    scopus 로고
    • Estimating species phy-logenies using coalescence times among sequences
    • Liu L., Yu L., Pearl D.K., Edwards S.V. 2009. Estimating species phy-logenies using coalescence times among sequences. Syst. Biol. 58: 468-477.
    • (2009) Syst. Biol. , vol.58 , pp. 468-477
    • Liu, L.1    Yu, L.2    Pearl, D.K.3    Edwards, S.V.4
  • 35
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison W.P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
    • (1997) Syst. Biol. , vol.46 , pp. 523-536
    • Maddison, W.P.1
  • 36
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • Maddison W.P., Knowles L.L. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
    • (2006) Syst. Biol. , vol.55 , pp. 21-30
    • Maddison, W.P.1    Knowles, L.L.2
  • 38
    • 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.P., Huang H., Knowles L.L. 2009. Maximum-likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Syst. Biol. 58:501-508.
    • (2009) Syst. Biol. , vol.58 , pp. 501-508
    • McCormack, J.P.1    Huang, H.2    Knowles, L.L.3
  • 39
    • 76849102326 scopus 로고    scopus 로고
    • Incomplete lineage sorting: Consistent phy-logeny estimation from multiple loci
    • Mossel E., Roch S. 2007. Incomplete lineage sorting: consistent phy-logeny estimation from multiple loci. IEEE/ACM Trans. Comput. Biol. Bioinform. 7: 166-171.
    • (2007) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.7 , pp. 166-171
    • Mossel, E.1    Roch, S.2
  • 40
    • 25844516325 scopus 로고    scopus 로고
    • Phylogenetic MCMC algorithms are misleading on mixtures of trees
    • Mossel E., Vigoda E. 2005. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science. 309:2207-2209.
    • (2005) Science. , vol.309 , pp. 2207-2209
    • Mossel, E.1    Vigoda, E.2
  • 41
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo P., Nei M. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 42
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut A., Grassly, N.C. 1997. SEQ-GEN: an application for the monte carlo simulation of DNA sequence evolution along phylo-genetic trees. Comput. Appl. Biosci. 13:235-238. (Pubitemid 27249927)
    • (1997) Computer Applications in the Biosciences , vol.13 , Issue.3 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 43
    • 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. 164:1645-1656.
    • (2003) Genetics. , vol.164 , pp. 1645-1656
    • Rannala, B.1    Yang, Z.2
  • 44
    • 47749153850 scopus 로고    scopus 로고
    • Does choice in model selection affect maximum likelihood analysis?
    • Ripplinger J., Sullivan J. 2008. Does choice in model selection affect maximum likelihood analysis? Syst. Biol. 57:76-85.
    • (2008) Syst. Biol. , vol.57 , pp. 76-85
    • Ripplinger, J.1    Sullivan, J.2
  • 46
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson D.F., Foulds L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
    • (1981) Math. Biosci. , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 47
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas A., Williams B.L., King N., Carroll S.B. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 425:798-804.
    • (2003) Nature. , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 48
    • 67649376350 scopus 로고    scopus 로고
    • Strong evidence for lineage and sequence specifcity of substitution rates and patterns in Drosophila
    • Singh N.D., Arndt P.F., Clark A.G., Aquadro C.F. 2009. Strong evidence for lineage and sequence specifcity of substitution rates and patterns in Drosophila. Mol. Biol. Evol. 26:1591-1605.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 1591-1605
    • Singh, N.D.1    Arndt, P.F.2    Clark, A.G.3    Aquadro, C.F.4
  • 49
    • 0002618746 scopus 로고    scopus 로고
    • Are guinea pigs rodents? the importance of adequate models in molecular phylogenetics
    • Sullivan J., Swofford D.L. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mamm. Evol. 4:77-86.
    • (1997) J. Mamm. Evol. , vol.4 , pp. 77-86
    • Sullivan, J.1    Swofford, D.L.2
  • 50
    • 0035527373 scopus 로고    scopus 로고
    • Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?
    • Sullivan J., Swofford D.L. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst. Biol. 50:723-729.
    • (2001) Syst. Biol. , vol.50 , pp. 723-729
    • Sullivan, J.1    Swofford, D.L.2
  • 51
    • 0024713112 scopus 로고
    • Gene genealogy in three related populations: Consistency probability between gene and population trees
    • Takahata N. 1989. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics. 122:957-966.
    • (1989) Genetics. , vol.122 , pp. 957-966
    • Takahata, N.1
  • 52
    • 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. 5:5.
    • (2009) PLoS Comput. Biol. , vol.5 , pp. 5
    • Than, C.1    Nakhleh, L.2
  • 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. 2001. The discovery of single-nucleotide polymorphisms and inferences about human demographic history. Am. J. Hum. Genet. 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.