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Volumn 83, Issue , 2015, Pages 191-199

Applying species-tree analyses to deep phylogenetic histories: Challenges and potential suggested from a survey of empirical phylogenetic studies

Author keywords

*BEAST; Coalescent variance; Data sufficiency; Incomplete lineage sorting; Mutational variance; Tree of Life (ToL) studies

Indexed keywords

BIOLOGICAL MODEL; DNA SEQUENCE; EVOLUTION; MUTATION; PHYLOGENY;

EID: 84922680916     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2014.10.022     Document Type: Article
Times cited : (37)

References (47)
  • 1
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. A new look at the statistical model identification. IEEE T. Automat. Contr. 1974, 19:716-723.
    • (1974) IEEE T. Automat. Contr. , vol.19 , pp. 716-723
    • Akaike, H.1
  • 3
    • 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. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 2007, 56:400-411.
    • (2007) Syst. Biol. , vol.56 , pp. 400-411
    • Carstens, B.C.1    Knowles, L.L.2
  • 4
    • 79955380843 scopus 로고    scopus 로고
    • Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer
    • Chung Y.J., Ané C. Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer. Syst. Biol. 2011, 60:261-275.
    • (2011) Syst. Biol. , vol.60 , pp. 261-275
    • Chung, Y.J.1    Ané, C.2
  • 5
    • 84862864097 scopus 로고    scopus 로고
    • Summarizing gene tree incongruence at multiple phylogenetic depths
    • Wiley-Blackwell, Hoboken (NJ), L.L. Knowles, L.S. Kubatko (Eds.)
    • Cranston K.A. Summarizing gene tree incongruence at multiple phylogenetic depths. Estimating Species Trees: Practical and Theoretical Aspects 2010, 129-143. Wiley-Blackwell, Hoboken (NJ). L.L. Knowles, L.S. Kubatko (Eds.).
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 129-143
    • Cranston, K.A.1
  • 6
    • 13244292527 scopus 로고    scopus 로고
    • Gene tree distributions under the coalescent process
    • Degnan J., Salter L. Gene tree distributions under the coalescent process. Evolution 2005, 59:24-37.
    • (2005) Evolution , vol.59 , pp. 24-37
    • Degnan, J.1    Salter, L.2
  • 7
    • 56549103832 scopus 로고    scopus 로고
    • Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow
    • Eckert A.J., Carstens B.C. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Mol. Phylogenet. Evol. 2008, 49:142-152.
    • (2008) Mol. Phylogenet. Evol. , vol.49 , pp. 142-152
    • Eckert, A.J.1    Carstens, B.C.2
  • 8
    • 84922623764 scopus 로고    scopus 로고
    • Global phylogenetic structure of a hyperdiverse radiation reveals the convergent evolution of macroecological patterns
    • Proc. Royal Soc. London B.
    • Economo, E.P., Klimov, P., Sarnat, E.M., Guenard, B., Weiser, M.D., Lecroq, B., Knowles, L.L., in press. Global phylogenetic structure of a hyperdiverse radiation reveals the convergent evolution of macroecological patterns. Proc. Royal Soc. London B.
    • Economo, E.P.1    Klimov, P.2    Sarnat, E.M.3    Guenard, B.4    Weiser, M.D.5    Lecroq, B.6    Knowles, L.L.7
  • 9
    • 58249100073 scopus 로고    scopus 로고
    • Is a new and general theory of molecular systematics emerging?
    • Edwards S.V. Is a new and general theory of molecular systematics emerging?. Evolution 2009, 63:1-19.
    • (2009) Evolution , vol.63 , pp. 1-19
    • Edwards, S.V.1
  • 12
    • 33751381461 scopus 로고    scopus 로고
    • TimeTree: a public knowledge-base of divergence times among organisms
    • Hedges S., Dudley J., Kumar S. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 2006, 22:2971.
    • (2006) Bioinformatics , vol.22 , pp. 2971
    • Hedges, S.1    Dudley, J.2    Kumar, S.3
  • 13
    • 77249086587 scopus 로고    scopus 로고
    • Bayesian inference of species trees from multilocus data
    • Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 570-580
    • Heled, J.1    Drummond, A.J.2
  • 14
    • 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., Knowles 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.3    Knowles, L.4
  • 15
    • 84901446644 scopus 로고    scopus 로고
    • Do estimated and actual species phylogenies match? Evaluation of African cichlid radiations
    • Huang H., Tran L.A.P., Knowles L.L. Do estimated and actual species phylogenies match? Evaluation of African cichlid radiations. Mol. Phylogenet. Evo. 2014, 78:56-65.
    • (2014) Mol. Phylogenet. Evo. , vol.78 , pp. 56-65
    • Huang, H.1    Tran, L.A.P.2    Knowles, L.L.3
  • 16
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson R.R. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18:247-264.
    • (2002) Bioinformatics , vol.18 , pp. 247-264
    • Hudson, R.R.1
  • 17
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phylogenetic trees
    • Huelsenbeck J.P., Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 18
    • 70350278632 scopus 로고    scopus 로고
    • A fossil-calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene entry into South America
    • Ickert-Bond S.M., Rydin C., Renner S.S. A fossil-calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene entry into South America. J. Syst. Evol. 2009, 47:444-456.
    • (2009) J. Syst. Evol. , vol.47 , pp. 444-456
    • Ickert-Bond, S.M.1    Rydin, C.2    Renner, S.S.3
  • 21
    • 84866147332 scopus 로고    scopus 로고
    • Full modeling versus summarizing phylogenetic uncertainty: method choice and species-tree accuracy Mol
    • Knowles L.L., Lanier H.C., Kilmov P., He Q. Full modeling versus summarizing phylogenetic uncertainty: method choice and species-tree accuracy Mol. Phylogenet. Evol. 2012, 65:501-509.
    • (2012) Phylogenet. Evol. , vol.65 , pp. 501-509
    • Knowles, L.L.1    Lanier, H.C.2    Kilmov, P.3    He, Q.4
  • 22
    • 84860552871 scopus 로고    scopus 로고
    • Is recombination a problem for species-tree analyses?
    • Lanier H.C., Knowles L.L. Is recombination a problem for species-tree analyses?. Syst. Biol. 2012, 61:691-701.
    • (2012) Syst. Biol. , vol.61 , pp. 691-701
    • Lanier, H.C.1    Knowles, L.L.2
  • 23
    • 84888140829 scopus 로고    scopus 로고
    • How low can you go? The effects of mutation rate on the accuracy of species-tree estimation
    • Lanier H.C., Huang H., Knowles L.L. How low can you go? The effects of mutation rate on the accuracy of species-tree estimation. Mol. Phylogenet. Evol. 2014, 70:112-119.
    • (2014) Mol. Phylogenet. Evol. , vol.70 , pp. 112-119
    • Lanier, H.C.1    Huang, H.2    Knowles, L.L.3
  • 24
    • 79951561454 scopus 로고    scopus 로고
    • The accuracy of species tree estimation under simulation: a comparison of methods
    • Leache A.D., Rannala B. The accuracy of species tree estimation under simulation: a comparison of methods. Syst. Biol. 2010, 60:126-137.
    • (2010) Syst. Biol. , vol.60 , pp. 126-137
    • Leache, A.D.1    Rannala, B.2
  • 25
    • 70349425459 scopus 로고    scopus 로고
    • Estimating species phylogenies using coalescence times among sequences
    • Liu L., Yu L., Pearl D.K., Edwards S.V. Estimating species phylogenies using coalescence times among sequences. Syst. Biol. 2009, 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
  • 26
    • 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
  • 27
    • 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
  • 28
    • 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., 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.1    Huang, H.2    Knowles, L.L.3
  • 29
    • 78650931246 scopus 로고    scopus 로고
    • Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma Jays
    • McCormack J., Heled J., Delaney K.S., Peterson A.T., Knowles L.L. Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma Jays. Evolution 2011, 65:184-202.
    • (2011) Evolution , vol.65 , pp. 184-202
    • McCormack, J.1    Heled, J.2    Delaney, K.S.3    Peterson, A.T.4    Knowles, L.L.5
  • 30
    • 84893740882 scopus 로고    scopus 로고
    • Phylogenetic model choice. Justifying a species tree or concatenation analysis
    • McVay J.D., Carstens B.C. Phylogenetic model choice. Justifying a species tree or concatenation analysis. Phylogenet. Evo. Biol. 2013, 1:1000114.
    • (2013) Phylogenet. Evo. Biol. , vol.1 , pp. 1000114
    • McVay, J.D.1    Carstens, B.C.2
  • 31
    • 84898996686 scopus 로고    scopus 로고
    • First steps for birds
    • Pagel M. First steps for birds. Nature 2012, 491:337.
    • (2012) Nature , vol.491 , pp. 337
    • Pagel, M.1
  • 33
    • 45849154165 scopus 로고    scopus 로고
    • JModelTest: phylogenetic model averaging
    • Posada D. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25.
    • (2008) Mol. Biol. Evol. , pp. 25
    • Posada, D.1
  • 34
    • 84884341444 scopus 로고    scopus 로고
    • Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation
    • Rabosky D.L., Santini F., Eastman J., Smith S.A., Sidlauskas B., Chang J., Alfaro M.E. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat. Comm. 2013, 4:1958.
    • (2013) Nat. Comm. , vol.4 , pp. 1958
    • Rabosky, D.L.1    Santini, F.2    Eastman, J.3    Smith, S.A.4    Sidlauskas, B.5    Chang, J.6    Alfaro, M.E.7
  • 35
    • 0030928378 scopus 로고    scopus 로고
    • SEQ-GEN: an application for the Monte Carlo simulation of DNA sequences along phylogenetic trees
    • Rambaut A., Grassly N.C. SEQ-GEN: an application for the Monte Carlo simulation of DNA sequences along phylogenetic trees. Comput. Appl. Biosci. 1997, 13:235-238.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 36
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson D.F., Foulds L.R. Comparison of phylogenetic trees. Math. Biosci. 1981, 53:131-147.
    • (1981) Math. Biosci. , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 37
    • 44449117871 scopus 로고    scopus 로고
    • Major evolutionary transitions in ant agriculture
    • Schultz T., Brady S. Major evolutionary transitions in ant agriculture. Proc. Nat. Acad. Sci. 2008, 105:5435-5440.
    • (2008) Proc. Nat. Acad. Sci. , vol.105 , pp. 5435-5440
    • Schultz, T.1    Brady, S.2
  • 39
    • 77950543389 scopus 로고    scopus 로고
    • An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants
    • Smith S.A., Beaulieu J.M., Donoghue M.J. An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:5897-5902.
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 5897-5902
    • Smith, S.A.1    Beaulieu, J.M.2    Donoghue, M.J.3
  • 43
    • 70349658769 scopus 로고    scopus 로고
    • Species tree inference by minimizing deep coalescenses
    • Than C.V., Nakhleh L.K. Species tree inference by minimizing deep coalescenses. PLoS Comput. Biol. 2009, 5:e1000501.
    • (2009) PLoS Comput. Biol. , vol.5 , pp. e1000501
    • Than, C.V.1    Nakhleh, L.K.2
  • 46
  • 47
    • 84857687426 scopus 로고    scopus 로고
    • Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood
    • Wu Y. Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution 2011, 66:763-775.
    • (2011) Evolution , vol.66 , pp. 763-775
    • Wu, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.