메뉴 건너뛰기




Volumn 70, Issue 1, 2014, Pages 112-119

How low can you go? The effects of mutation rate on the accuracy of species-tree estimation

Author keywords

BEAST; Locus variability; Multispecies coalescent; Phylogenetic accuracy; Sampling effort; STEM

Indexed keywords

(*)BEAST; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; DNA SEQUENCE; GENE LOCUS; LOCUS VARIABILITY; MULTISPECIES COALESCENT; MUTATION RATE; PHYLOGENETIC ACCURACY; PHYLOGENY; SAMPLING EFFORT; STATISTICAL MODEL; STEM; UNCERTAINTY;

EID: 84888140829     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.09.006     Document Type: Article
Times cited : (53)

References (48)
  • 2
    • 0037329391 scopus 로고    scopus 로고
    • Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confindence
    • Alfaro M.E., Zoller S., François L. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confindence. Mol. Biol. Evol. 2003, 20:255-266.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 255-266
    • Alfaro, M.E.1    Zoller, S.2    François, L.3
  • 3
    • 34548591633 scopus 로고    scopus 로고
    • The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes
    • Althoff D.M., Althoff M.A., Gitzendanner M.A., Segraves K.A. The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes. Syst. Biol. 2007, 56:477-484.
    • (2007) Syst. Biol. , vol.56 , pp. 477-484
    • Althoff, D.M.1    Althoff, M.A.2    Gitzendanner, M.A.3    Segraves, K.A.4
  • 5
    • 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
  • 6
    • 0036623259 scopus 로고    scopus 로고
    • Model misspecification and probabilistic tests of topology: evidence from empirical data sets
    • Buckley T.R. Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst. Biol. 2002, 51:509-523.
    • (2002) Syst. Biol. , vol.51 , pp. 509-523
    • Buckley, T.R.1
  • 7
    • 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
  • 9
    • 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
  • 10
    • 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
  • 11
  • 12
  • 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
    • 53849131729 scopus 로고    scopus 로고
    • A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics
    • Holder M., Sukumaran J., Lewis P. A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics. Syst. Biol. 2008, 57:814-821.
    • (2008) Syst. Biol. , vol.57 , pp. 814-821
    • Holder, M.1    Sukumaran, J.2    Lewis, P.3
  • 15
    • 70450237691 scopus 로고    scopus 로고
    • What is the danger of the anomaly zone for empirical phylogenetics?
    • Huang H., Knowles L.L. What is the danger of the anomaly zone for empirical phylogenetics?. Syst. Biol. 2009, 58:527-536.
    • (2009) Syst. Biol. , vol.58 , pp. 527-536
    • Huang, H.1    Knowles, L.L.2
  • 16
    • 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
  • 17
    • 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
  • 18
    • 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
  • 21
    • 34447620474 scopus 로고    scopus 로고
    • Delimiting species without monophyletic gene trees
    • Knowles L.L., Carstens B.C. Delimiting species without monophyletic gene trees. Syst. Biol. 2007, 56:887-895.
    • (2007) Syst. Biol. , vol.56 , pp. 887-895
    • Knowles, L.L.1    Carstens, B.C.2
  • 23
    • 84866147332 scopus 로고    scopus 로고
    • Full modeling versus summarizing phylogenetic uncertainty: method choice and species-tree accuracy
    • 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) Mol. Phylogenet. Evol. , vol.65 , pp. 501-509
    • Knowles, L.L.1    Lanier, H.C.2    Kilmov, P.3    He, Q.4
  • 24
    • 33847302458 scopus 로고    scopus 로고
    • Inconsistency of phylogenetic estimates from concatenated data under coalescence
    • Kubatko L.S., Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 2007, 56:17-24.
    • (2007) Syst. Biol. , vol.56 , pp. 17-24
    • Kubatko, L.S.1    Degnan, J.H.2
  • 25
    • 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. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009, 25:971-973.
    • (2009) Bioinformatics , vol.25 , pp. 971-973
    • Kubatko, L.S.1    Carstens, B.C.2    Knowles, L.L.3
  • 26
    • 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
  • 27
    • 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
  • 28
    • 19044373497 scopus 로고    scopus 로고
    • Polytomies and Bayesian phylogenetic inference
    • Lewis P.O., Holder M.T., Holsinger K.E. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 2005, 54:241-253.
    • (2005) Syst. Biol. , vol.54 , pp. 241-253
    • Lewis, P.O.1    Holder, M.T.2    Holsinger, K.E.3
  • 30
    • 79957648061 scopus 로고    scopus 로고
    • PhyDesign: an online application for profiling phylogenetic informativeness
    • López-Giráldez F., Townsend J.P. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evol. Biol. 2011, 11:152.
    • (2011) BMC Evol. Biol. , vol.11 , pp. 152
    • López-Giráldez, F.1    Townsend, J.P.2
  • 31
    • 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
  • 32
    • 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
  • 34
    • 84860153849 scopus 로고    scopus 로고
    • Recurrent introgression of mitochondrial DNA among hares (Lepus spp.) revealed by species-tree inference and coalescent simulations
    • Melo-Ferreira J., Boursot P., Carneiro M., Esteves P.J., Farelo L., Alves P.C. Recurrent introgression of mitochondrial DNA among hares (Lepus spp.) revealed by species-tree inference and coalescent simulations. Syst. Biol. 2012, 61:367-381.
    • (2012) Syst. Biol. , vol.61 , pp. 367-381
    • Melo-Ferreira, J.1    Boursot, P.2    Carneiro, M.3    Esteves, P.J.4    Farelo, L.5    Alves, P.C.6
  • 35
    • 79957893436 scopus 로고    scopus 로고
    • Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates
    • Moeller A.H., Townsend J.P. Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates. Mol. Phylogenet. Evol. 2011, 60:271-272.
    • (2011) Mol. Phylogenet. Evol. , vol.60 , pp. 271-272
    • Moeller, A.H.1    Townsend, J.P.2
  • 36
    • 25844516325 scopus 로고    scopus 로고
    • Phylogenetic MCMC algorithms are misleading on mixtures of trees
    • Mossel E., Vigoda E. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 2005, 309:2207-2209.
    • (2005) Science , vol.309 , pp. 2207-2209
    • Mossel, E.1    Vigoda, E.2
  • 37
    • 84856846459 scopus 로고    scopus 로고
    • Evolution in Australasian mangrove forests: Multilocus phylogenetic analysis of the Gerygone Warblers (Aves: Acanthizidae)
    • Nyári Á.S., Joseph L. Evolution in Australasian mangrove forests: Multilocus phylogenetic analysis of the Gerygone Warblers (Aves: Acanthizidae). PLoS ONE 2012, 7:e31840.
    • (2012) PLoS ONE , vol.7
    • Nyári Á, S.1    Joseph, L.2
  • 38
    • 75149123416 scopus 로고    scopus 로고
    • Testing for biogeographic mechanisms promoting divergence in Caribbean crickets (genus Amphiacusta)
    • Oneal E., Otte D., Knowles L.L. Testing for biogeographic mechanisms promoting divergence in Caribbean crickets (genus Amphiacusta). J. Biogeogr. 2010, 37:530-540.
    • (2010) J. Biogeogr. , vol.37 , pp. 530-540
    • Oneal, E.1    Otte, D.2    Knowles, L.L.3
  • 39
    • 84857482775 scopus 로고    scopus 로고
    • Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history
    • Peters J.L., Roberts T.E., Winker K., McCracken K.G. Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history. PLoS ONE 2012, 7:e31972.
    • (2012) PLoS ONE , vol.7
    • Peters, J.L.1    Roberts, T.E.2    Winker, K.3    McCracken, K.G.4
  • 40
    • 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
  • 42
    • 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
  • 43
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Suzuki Y., Glazko G.V., Nei M. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci., USA 2002, 99:16138-16143.
    • (2002) Proc. Natl. Acad. Sci., USA , vol.99 , pp. 16138-16143
    • Suzuki, Y.1    Glazko, G.V.2    Nei, M.3
  • 44
    • 34447279942 scopus 로고    scopus 로고
    • Profiling phylogenetic informativeness
    • Townsend J.P. Profiling phylogenetic informativeness. Syst. Biol. 2007, 56:222-231.
    • (2007) Syst. Biol. , vol.56 , pp. 222-231
    • Townsend, J.P.1
  • 45
    • 79955371078 scopus 로고    scopus 로고
    • Taxon sampling and the optimal rates of evolution for phylogenetic inference
    • Townsend J.P., Leuenberger C. Taxon sampling and the optimal rates of evolution for phylogenetic inference. Syst. Biol. 2011, 60:358-365.
    • (2011) Syst. Biol. , vol.60 , pp. 358-365
    • Townsend, J.P.1    Leuenberger, C.2
  • 46
    • 77953763243 scopus 로고    scopus 로고
    • Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships
    • Townsend J.P., Lopez-Giraldez F. Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships. Syst. Biol. 2010, 59:446-457.
    • (2010) Syst. Biol. , vol.59 , pp. 446-457
    • Townsend, J.P.1    Lopez-Giraldez, F.2
  • 47
    • 56149119671 scopus 로고    scopus 로고
    • The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree
    • Townsend J.P., López-Giráldez F., Friedman R. The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. J. Mol. Evol. 2008, 67:437-447.
    • (2008) J. Mol. Evol. , vol.67 , pp. 437-447
    • Townsend, J.P.1    López-Giráldez, F.2    Friedman, R.3
  • 48
    • 80052752932 scopus 로고    scopus 로고
    • Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation
    • Townsend T.M., Mulcahy D.G., Noonan B.P., Sites J.W., Kuczynski C.A., Wiens J.J., Reeder T.W. Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation. Mol. Phylogenet. Evol. 2011, 61:363-380.
    • (2011) Mol. Phylogenet. Evol. , vol.61 , pp. 363-380
    • Townsend, T.M.1    Mulcahy, D.G.2    Noonan, B.P.3    Sites, J.W.4    Kuczynski, C.A.5    Wiens, J.J.6    Reeder, T.W.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.