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Volumn 1360, Issue 1, 2015, Pages 36-53

Estimating phylogenetic trees from genome-scale data

Author keywords

Anomaly zone; Bias variance dilemma; Isochore; Recombination; Transcriptome

Indexed keywords

MESSENGER RNA; MESSENGER RNA PRECURSOR; TRANSCRIPTOME;

EID: 84949317694     PISSN: 00778923     EISSN: 17496632     Source Type: Journal    
DOI: 10.1111/nyas.12747     Document Type: Article
Times cited : (140)

References (112)
  • 1
    • 52949152371 scopus 로고    scopus 로고
    • Phylogenetic inference using whole genomes
    • Rannala, B. & Z. Yang . 2008. Phylogenetic inference using whole genomes. Ann. Rev. Genomics Hum. Genet. 9: 217-231.
    • (2008) Ann. Rev. Genomics Hum. Genet , vol.9 , pp. 217-231
    • Rannala, B.1    Yang, Z.2
  • 2
    • 84888626247 scopus 로고    scopus 로고
    • High-throughput genomic data in systematics and phylogenetics
    • Lemmon, E.M. & A.R. Lemmon . 2013. High-throughput genomic data in systematics and phylogenetics. Ann. Rev. Ecol. Evol. Syst. 44: 99-121.
    • (2013) Ann. Rev. Ecol. Evol. Syst. , vol.44 , pp. 99-121
    • Lemmon, E.M.1    Lemmon, A.R.2
  • 4
    • 84902519363 scopus 로고    scopus 로고
    • Species delimitation using genome-wide SNP data
    • Leaché, A.D. et al. 2014. Species delimitation using genome-wide SNP data. Syst. Biol. 63: 534-542.
    • (2014) Syst. Biol , vol.63 , pp. 534-542
    • Leaché, A.D.1
  • 5
    • 33847253975 scopus 로고    scopus 로고
    • Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
    • Hey, J. & R. Nielsen . 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. U.S.A. 104: 2785-2790.
    • (2007) Proc. Natl. Acad. Sci. U.S.A , vol.104 , pp. 2785-2790
    • Hey, J.1    Nielsen, R.2
  • 6
    • 0036215045 scopus 로고    scopus 로고
    • Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives
    • Machado, C.A. et al. 2002. Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Mol. Biol. Evol. 19: 472-488.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 472-488
    • Machado, C.A.1
  • 7
    • 0031018637 scopus 로고    scopus 로고
    • Estimating ancestral population parameters
    • Wakeley, J. & J. Hey . 1997. Estimating ancestral population parameters. Genetics 145: 847-855.
    • (1997) Genetics , vol.145 , pp. 847-855
    • Wakeley, J.1    Hey, J.2
  • 8
    • 84872008491 scopus 로고    scopus 로고
    • A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species
    • Mailund, T. et al. 2012. A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet. 8: e1003125.
    • (2012) PLoS Genet , vol.8 , pp. e1003125
    • Mailund, T.1
  • 9
    • 84903386054 scopus 로고    scopus 로고
    • An HMM-based comparative genomic framework for detecting introgression in eukaryotes
    • Liu, K.J. et al. 2014. An HMM-based comparative genomic framework for detecting introgression in eukaryotes. PLoS Comput. Biol. 10: e1003649.
    • (2014) PLoS Comput. Biol , vol.10 , pp. e1003649
    • Liu, K.J.1
  • 10
    • 58249100073 scopus 로고    scopus 로고
    • Is a new and general theory of molecular systematics emerging?
    • Edwards, S.V. 2009. Is a new and general theory of molecular systematics emerging? Evolution 63: 1-19.
    • (2009) Evolution , vol.63 , pp. 1-19
    • Edwards, S.V.1
  • 11
    • 84928749156 scopus 로고    scopus 로고
    • The inference of gene trees with species trees
    • Szöllosi, G.J. et al. 2015. The inference of gene trees with species trees. Syst. Biol. 64: e42-e62.
    • (2015) Syst. Biol , vol.64 , pp. e42-e62
    • Szöllosi, G.J.1
  • 12
    • 84882785806 scopus 로고    scopus 로고
    • Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes)
    • Betancur-R, R. et al. 2013. Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). Syst. Biol. 62: 763-785.
    • (2013) Syst. Biol , vol.62 , pp. 763-785
    • Betancur-R, R.1
  • 13
    • 84894596325 scopus 로고    scopus 로고
    • Conserved genes, sampling error, and phylogenomic inference
    • Betancur-R, R., G.J.P. Naylor & G. Orti . 2014. Conserved genes, sampling error, and phylogenomic inference. Syst. Biol. 63: 257-262.
    • (2014) Syst. Biol , vol.63 , pp. 257-262
    • Betancur-R, R.1    Naylor, G.J.P.2    Orti, G.3
  • 14
    • 84864249563 scopus 로고    scopus 로고
    • Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)
    • Chiari, Y. et al. 2012. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol. 10: 65.
    • (2012) BMC Biol , vol.10 , pp. 65
    • Chiari, Y.1
  • 15
    • 84866289853 scopus 로고    scopus 로고
    • Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
    • Song, S. et al. 2012. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc. Natl. Acad. Sci. U.S.A. 109: 14942-14947.
    • (2012) Proc. Natl. Acad. Sci. U.S.A , vol.109 , pp. 14942-14947
    • Song, S.1
  • 16
    • 84917708482 scopus 로고    scopus 로고
    • Whole-genome analyses resolve early branches in the tree of life of modern birds
    • Jarvis, E.D. et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346: 1320-1331.
    • (2014) Science , vol.346 , pp. 1320-1331
    • Jarvis, E.D.1
  • 17
    • 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
  • 18
    • 33845627286 scopus 로고    scopus 로고
    • The supermatrix approach to systematics
    • deQueiroz, A. & J. Gatesy . 2007. The supermatrix approach to systematics. Trends Ecol. Evol. 22: 34-41.
    • (2007) Trends Ecol. Evol , vol.22 , pp. 34-41
    • de Queiroz, A.1    Gatesy, J.2
  • 19
    • 84908162664 scopus 로고    scopus 로고
    • Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
    • Gatesy, J. & M.S. Springer . 2014. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol. Phylogenet. Evol. 80: 231-266.
    • (2014) Mol. Phylogenet. Evol , vol.80 , pp. 231-266
    • Gatesy, J.1    Springer, M.S.2
  • 20
    • 84899919331 scopus 로고    scopus 로고
    • Land plant origins and coalescence confusion
    • Springer, M.S. & J. Gatesy . 2014. Land plant origins and coalescence confusion. Trends Plant Sci. 19: 267-269.
    • (2014) Trends Plant Sci , vol.19 , pp. 267-269
    • Springer, M.S.1    Gatesy, J.2
  • 21
    • 84899921887 scopus 로고    scopus 로고
    • The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy
    • Zhong, B., L. Liu & D. Penny . 2014. The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy. Trends Plant Sci. 19: 270-272.
    • (2014) Trends Plant Sci , vol.19 , pp. 270-272
    • Zhong, B.1    Liu, L.2    Penny, D.3
  • 22
    • 68049099068 scopus 로고    scopus 로고
    • Coalescent methods for estimating phylogenetic trees
    • Liu, L. et al. 2009. Coalescent methods for estimating phylogenetic trees. Mol. Phylogenet. Evol. 53: 320-328.
    • (2009) Mol. Phylogenet. Evol , vol.53 , pp. 320-328
    • Liu, L.1
  • 23
    • 84859530730 scopus 로고    scopus 로고
    • Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis
    • McCormack, J.E. et al. 2012. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis. Genome Res. 22: 746-754.
    • (2012) Genome Res , vol.22 , pp. 746-754
    • McCormack, J.E.1
  • 24
    • 34347256397 scopus 로고    scopus 로고
    • High-resolution species trees without concatenation
    • Edwards, S.V., L. Liu & D.K. Pearl . 2007. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. U.S.A. 104: 5936-5941.
    • (2007) Proc. Natl. Acad. Sci. U.S.A , vol.104 , pp. 5936-5941
    • Edwards, S.V.1    Liu, L.2    Pearl, D.K.3
  • 25
    • 84875547630 scopus 로고    scopus 로고
    • Concatenation versus coalescence versus "concatalescence
    • Gatesy, J. & M.S. Springer . 2013. Concatenation versus coalescence versus "concatalescence." Proc. Natl. Acad. Sci. U.S.A. 110: E1179.
    • (2013) Proc. Natl. Acad. Sci. U.S.A , vol.110 , pp. E1179
    • Gatesy, J.1    Springer, M.S.2
  • 26
    • 84875513968 scopus 로고    scopus 로고
    • Reply to Gatesy and Springer: the multispecies coalescent model can effectively handle recombination and gene tree heterogeneity
    • Wu, S. et al. 2013. Reply to Gatesy and Springer: the multispecies coalescent model can effectively handle recombination and gene tree heterogeneity. Proc. Natl. Acad. Sci. U.S.A. 110: E1180.
    • (2013) Proc. Natl. Acad. Sci. U.S.A , vol.110 , pp. E1180
    • Wu, S.1
  • 27
    • 84894052682 scopus 로고    scopus 로고
    • Phylogenomics and coalescent analyses resolve extant seed plant relationships
    • Xi, Z., J.S. Rest & C.C. Davis . 2013. Phylogenomics and coalescent analyses resolve extant seed plant relationships. PLoS ONE 8: e80870.
    • (2013) PLoS ONE , vol.8 , pp. e80870
    • Xi, Z.1    Rest, J.S.2    Davis, C.C.3
  • 28
    • 84919947905 scopus 로고    scopus 로고
    • Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies
    • Xi, Z. et al. 2014. Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies. Syst. Biol. 63: 919-932.
    • (2014) Syst. Biol , vol.63 , pp. 919-932
    • Xi, Z.1
  • 29
    • 84965093929 scopus 로고    scopus 로고
    • Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting
    • Liu, L., Z. Xi & C.C. Davis . 2015. Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting. Mol. Biol. Evol. 32: 791-805.
    • (2015) Mol. Biol. Evol , vol.32 , pp. 791-805
    • Liu, L.1    Xi, Z.2    Davis, C.C.3
  • 30
    • 84904370094 scopus 로고    scopus 로고
    • A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification
    • Leaché, A.D. et al. 2014. A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification. Mol. Phylogenet. Evol. 79: 215-230.
    • (2014) Mol. Phylogenet. Evol , vol.79 , pp. 215-230
    • Leaché, A.D.1
  • 31
    • 34548575126 scopus 로고    scopus 로고
    • Species trees from gene trees: reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
    • Liu, L. & D.K. Pearl . 2007. Species trees from gene trees: reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56: 504-514.
    • (2007) Syst. Biol , vol.56 , pp. 504-514
    • Liu, L.1    Pearl, D.K.2
  • 32
    • 33847302458 scopus 로고    scopus 로고
    • Inconsistency of phylogenetic estimates from concatenated data under coalescence
    • Kubatko, L.S. & J.H. Degnan . 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56: 17-24.
    • (2007) Syst. Biol , vol.56 , pp. 17-24
    • Kubatko, L.S.1    Degnan, J.H.2
  • 33
    • 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.T. et al. 2010. 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. 59: 573-583.
    • (2010) Syst. Biol , vol.59 , pp. 573-583
    • Huang, H.T.1
  • 34
    • 84883284590 scopus 로고    scopus 로고
    • Origin of land plants using the multispecies coalescent model
    • Zhong, B. et al. 2013. Origin of land plants using the multispecies coalescent model. Trends Plant Sci. 18: 492-495.
    • (2013) Trends Plant Sci , vol.18 , pp. 492-495
    • Zhong, B.1
  • 35
    • 84922680916 scopus 로고    scopus 로고
    • Applying species tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies
    • Lanier, H.C. & L.L. Knowles . 2014. Applying species tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies. Mol. Phylogenet. Evol. 83: 191-199.
    • (2014) Mol. Phylogenet. Evol , vol.83 , pp. 191-199
    • Lanier, H.C.1    Knowles, L.L.2
  • 36
    • 84885003093 scopus 로고    scopus 로고
    • Gene tree rooting methods give distributions that mimic the coalescent process
    • Tian, Y. & L.S. Kubatko . 2014. Gene tree rooting methods give distributions that mimic the coalescent process. Mol. Phylogenet. Evol. 70: 63-69.
    • (2014) Mol. Phylogenet. Evol , vol.70 , pp. 63-69
    • Tian, Y.1    Kubatko, L.S.2
  • 38
    • 84866147332 scopus 로고    scopus 로고
    • Full modeling versus summarizing gene tree uncertainty: method choice and species tree accuracy
    • Knowles, L.L. et al. 2012. Full modeling versus summarizing gene tree uncertainty: method choice and species tree accuracy. Mol. Phylogenet. Evol. 65: 501-509.
    • (2012) Mol. Phylogenet. Evol , vol.65 , pp. 501-509
    • Knowles, L.L.1
  • 39
    • 84860552871 scopus 로고    scopus 로고
    • Is recombination a problem for species tree analyses?
    • Lanier, H.C. & L.L. Knowles . 2012. Is recombination a problem for species tree analyses? Syst. Biol. 61: 691-701.
    • (2012) Syst. Biol , vol.61 , pp. 691-701
    • Lanier, H.C.1    Knowles, L.L.2
  • 40
    • 0041817551 scopus 로고    scopus 로고
    • Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    • Rannala, B. & Z. Yang . 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
  • 41
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference, and the multispecies coalescent
    • Degnan, J.H. & N.A. Rosenberg . 2009. Gene tree discordance, phylogenetic 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
  • 42
    • 84917708481 scopus 로고    scopus 로고
    • Statistical binning enables an accurate coalescent-based estimation of the avian tree
    • Mirarab, S. et al. 2014. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 346: 1250463.
    • (2014) Science , vol.346 , pp. 1250463
    • Mirarab, S.1
  • 43
    • 84883482283 scopus 로고    scopus 로고
    • Naive binning improves phylogenomic analyses
    • Bayzid, M.S. & T. Warnow . 2013. Naive binning improves phylogenomic analyses. Bioinformatics 29: 2277-2284.
    • (2013) Bioinformatics , vol.29 , pp. 2277-2284
    • Bayzid, M.S.1    Warnow, T.2
  • 44
    • 13244292527 scopus 로고    scopus 로고
    • Gene tree distributions under the coalescent process
    • Degnan, J.H. & L. Salter . 2005. Gene tree distributions under the coalescent process. Evolution 59: 24-37.
    • (2005) Evolution , vol.59 , pp. 24-37
    • Degnan, J.H.1    Salter, L.2
  • 45
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • Degnan, J.H. & N.A. Rosenberg . 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
  • 46
    • 33846277992 scopus 로고    scopus 로고
    • Model use in phylogenetics: nine key questions
    • Kelchner, S.A. & M.A. Thomas . 2007. Model use in phylogenetics: nine key questions. Trends Ecol. Evol. 22: 87-94.
    • (2007) Trends Ecol. Evol , vol.22 , pp. 87-94
    • Kelchner, S.A.1    Thomas, M.A.2
  • 47
    • 70349425459 scopus 로고    scopus 로고
    • Estimating species phylogenies using coalescence times among sequences
    • Liu, L. et al. 2009. Estimating species phylogenies using coalescence times among sequences. Syst. Biol. 58: 468-477.
    • (2009) Syst. Biol , vol.58 , pp. 468-477
    • Liu, L.1
  • 48
    • 77957686501 scopus 로고    scopus 로고
    • A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
    • Liu, L., L. Yu & S.V. Edwards . 2010. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 10: 302.
    • (2010) BMC Evol. Biol , vol.10 , pp. 302
    • Liu, L.1    Yu, L.2    Edwards, S.V.3
  • 49
    • 77249086587 scopus 로고    scopus 로고
    • Bayesian inference of species trees from multilocus data
    • Heled, J. & A.J. Drummond . 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27: 570-580.
    • (2010) Mol. Biol. Evol , vol.27 , pp. 570-580
    • Heled, J.1    Drummond, A.J.2
  • 50
    • 25644452054 scopus 로고    scopus 로고
    • Speciational history of Australian grass finches (Poephila) inferred from 30 gene trees
    • Jennings, W.B. & S.V. Edwards . 2005. Speciational history of Australian grass finches (Poephila) inferred from 30 gene trees. Evolution 59: 2033-2047.
    • (2005) Evolution , vol.59 , pp. 2033-2047
    • Jennings, W.B.1    Edwards, S.V.2
  • 51
    • 84859548731 scopus 로고    scopus 로고
    • Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales
    • Faircloth, B.C. et al. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 61: 717-726.
    • (2012) Syst. Biol , vol.61 , pp. 717-726
    • Faircloth, B.C.1
  • 52
    • 84943636475 scopus 로고    scopus 로고
    • Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae
    • Linkem, C.W., V.N. Minin & A.D. Leaché . 2014. Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae). doi: http://dx.doi.org/10.1101/012096.
    • (2014)
    • Linkem, C.W.1    Minin, V.N.2    Leaché, A.D.3
  • 53
    • 84878443264 scopus 로고    scopus 로고
    • Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae
    • Zhao, L. et al. 2013. Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae. PLoS ONE 8: e64642.
    • (2013) PLoS ONE , vol.8 , pp. e64642
    • Zhao, L.1
  • 54
    • 84909619344 scopus 로고    scopus 로고
    • Phylotranscriptomic analysis of the origin and early diversification of land plants
    • Wickett, N.J. et al. 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc. Natl. Acad. Sci. U.S.A. 111: E4859-E4868.
    • (2014) Proc. Natl. Acad. Sci. U.S.A , vol.111 , pp. E4859-E4868
    • Wickett, N.J.1
  • 55
    • 84908124067 scopus 로고    scopus 로고
    • Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics
    • Weitemier, K. et al. 2014. Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics. Appl. Plant Sci. 2: 1400042.
    • (2014) Appl. Plant Sci , vol.2 , pp. 1400042
    • Weitemier, K.1
  • 57
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27: 401-410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 58
    • 84890829647 scopus 로고    scopus 로고
    • The Amborella genome and the evolution of flowering plants
    • Amborella Genome Project
    • Amborella Genome Project. 2013. The Amborella genome and the evolution of flowering plants. Science 342: 1241089.
    • (2013) Science , vol.342 , pp. 1241089
  • 59
    • 4644250777 scopus 로고    scopus 로고
    • Amborella not a "basal angiosperm"? Not so fast
    • Soltis, D.E. & P.S. Soltis . 2004. Amborella not a "basal angiosperm"? Not so fast. Am. J. Bot. 91: 997-1001.
    • (2004) Am. J. Bot , vol.91 , pp. 997-1001
    • Soltis, D.E.1    Soltis, P.S.2
  • 60
    • 0035861441 scopus 로고    scopus 로고
    • Resolution of the early placental mammal radiation using Bayesian phylogenetics
    • Murphy, W.J. et al. 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351.
    • (2001) Science , vol.294 , pp. 2348-2351
    • Murphy, W.J.1
  • 61
    • 34147184456 scopus 로고    scopus 로고
    • Using genomic data to unravel the root of the placental mammal phylogeny
    • Murphy, W.J. et al. 2007. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res. 17: 413-421.
    • (2007) Genome Res , vol.17 , pp. 413-421
    • Murphy, W.J.1
  • 62
    • 55049088739 scopus 로고    scopus 로고
    • Developing markers for multilocus phylogenetics in non-model organisms: a test case with turtles
    • Thomson, R.C. et al. 2008. Developing markers for multilocus phylogenetics in non-model organisms: a test case with turtles. Mol. Phylogenet. Evol. 49: 514-525.
    • (2008) Mol. Phylogenet. Evol , vol.49 , pp. 514-525
    • Thomson, R.C.1
  • 63
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Suzuki, Y., G.V. Glazko & M. Nei . 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. U.S.A. 99: 16138-16143.
    • (2002) Proc. Natl. Acad. Sci. U.S.A , vol.99 , pp. 16138-16143
    • Suzuki, Y.1    Glazko, G.V.2    Nei, M.3
  • 64
    • 0344243515 scopus 로고    scopus 로고
    • Reanalysis of Murphy 's data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees
    • Misawa, K. & M. Nei . 2003. Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees. J. Mol. Evol. 57: S290-S296.
    • (2003) J. Mol. Evol , vol.57 , pp. S290-S296
    • Misawa, K.1    Nei, M.2
  • 65
    • 50949129519 scopus 로고    scopus 로고
    • Calculating bootstrap probabilities of phylogeny using multilocus sequence data
    • Seo, T.K. 2008. Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Mol. Biol. Evol. 25: 960-971.
    • (2008) Mol. Biol. Evol , vol.25 , pp. 960-971
    • Seo, T.K.1
  • 66
    • 84884589326 scopus 로고    scopus 로고
    • Effects of missing data on species tree estimation under the coalescent
    • Hovmoller, R., L.L. Knowles & L.S. Kubatko . 2013. Effects of missing data on species tree estimation under the coalescent. Mol. Phylogenet. Evol. 69: 1057-1062.
    • (2013) Mol. Phylogenet. Evol , vol.69 , pp. 1057-1062
    • Hovmoller, R.1    Knowles, L.L.2    Kubatko, L.S.3
  • 67
    • 8444222732 scopus 로고    scopus 로고
    • Prospects for building the tree of life from large sequence databases
    • Driskell, A.C. et al. 2004. Prospects for building the tree of life from large sequence databases. Science 306: 1172-1174.
    • (2004) Science , vol.306 , pp. 1172-1174
    • Driskell, A.C.1
  • 68
    • 42149157760 scopus 로고    scopus 로고
    • Broad phylogenomic sampling improves resolution of the animal tree of life
    • Dunn, C.W. et al. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745-745.
    • (2008) Nature , vol.452 , pp. 745-745
    • Dunn, C.W.1
  • 69
    • 84904622865 scopus 로고    scopus 로고
    • Dubious resolution and support from published sparse supermatrices: the importance of thorough tree searches
    • Simmons, M.P. & P.A. Goloboff . 2014. Dubious resolution and support from published sparse supermatrices: the importance of thorough tree searches. Mol. Phylogenet. Evol. 78: 334-348.
    • (2014) Mol. Phylogenet. Evol , vol.78 , pp. 334-348
    • Simmons, M.P.1    Goloboff, P.A.2
  • 70
    • 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., H. Huang & L.L. Knowles . 2014. How low can you go? The effects of mutation rate on the accuracy of species tree estimation. Mol. Phylogenet. Evol. 70: 112-119.
    • (2014) Mol. Phylogenet. Evol , vol.70 , pp. 112-119
    • Lanier, H.C.1    Huang, H.2    Knowles, L.L.3
  • 71
    • 77958056150 scopus 로고    scopus 로고
    • Estimating species trees: an introduction to concepts and models
    • L.L. Knowles & L.S. Kubatko, Eds. New York: Wiley-Blackwell.
    • Knowles, L.L. & L.S. Kubatko . 2010. "Estimating species trees: an introduction to concepts and models." In Estimating Species Trees: Practical and Theoretical Aspects. L.L. Knowles & L.S. Kubatko, Eds.: 1-14. New York: Wiley-Blackwell.
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 1-14
    • Knowles, L.L.1    Kubatko, L.S.2
  • 72
    • 84887319003 scopus 로고    scopus 로고
    • The influence of gene flow on species tree estimation: a simulation study
    • Leaché, A.D. et al. 2014. The influence of gene flow on species tree estimation: a simulation study. Syst. Biol. 63: 17-30.
    • (2014) Syst. Biol , vol.63 , pp. 17-30
    • Leaché, A.D.1
  • 73
    • 79951561454 scopus 로고    scopus 로고
    • The accuracy of species tree estimation under simulation: a comparison of methods
    • Leaché, A.D. & B. Rannala . 2011. The accuracy of species tree estimation under simulation: a comparison of methods. Syst. Biol. 60: 126-137.
    • (2011) Syst. Biol , vol.60 , pp. 126-137
    • Leaché, A.D.1    Rannala, B.2
  • 74
    • 84899669558 scopus 로고    scopus 로고
    • An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines
    • DeGiorgio, M. et al. 2014. An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines. BMC Evol. Biol. 14: 67.
    • (2014) BMC Evol. Biol , vol.14 , pp. 67
    • DeGiorgio, M.1
  • 75
    • 84934296789 scopus 로고    scopus 로고
    • Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased
    • Xi, Z., L. Liu & C.C. Davis . 2015. Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased. Mol. Phylogenet. Evol. In review.
    • (2015) Mol. Phylogenet. Evol
    • Xi, Z.1    Liu, L.2    Davis, C.C.3
  • 76
    • 84883229050 scopus 로고    scopus 로고
    • Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals
    • Romiguier, J. et al. 2013. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. Mol. Biol. Evol 30: 2134-2144.
    • (2013) Mol. Biol. Evol , vol.30 , pp. 2134-2144
    • Romiguier, J.1
  • 77
    • 84921289760 scopus 로고    scopus 로고
    • Likelihood-based tree reconstruction on a concatenation of alignments can be statistically inconsistent
    • Roch, S. & M. Steel . 2015. Likelihood-based tree reconstruction on a concatenation of alignments can be statistically inconsistent. Theor. Pop. Biol. 100: 56-62.
    • (2015) Theor. Pop. Biol. , vol.100 , pp. 56-62
    • Roch, S.1    Steel, M.2
  • 78
    • 77951961553 scopus 로고    scopus 로고
    • Phybase: an R package for species tree analysis
    • Liu, L. & L. Yu . 2010. Phybase: an R package for species tree analysis. Bioinformatics 26: 962-963.
    • (2010) Bioinformatics , vol.26 , pp. 962-963
    • Liu, L.1    Yu, L.2
  • 79
    • 84890335523 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees: a unifying principle
    • Rosenberg, N.A. 2013. Discordance of species trees with their most likely gene trees: a unifying principle. Mol. Biol. Evol. 30: 2709-2713.
    • (2013) Mol. Biol. Evol , vol.30 , pp. 2709-2713
    • Rosenberg, N.A.1
  • 80
    • 70450237691 scopus 로고    scopus 로고
    • What is the danger of the anomaly zone for empirical phylogenetics?
    • Huang, H.T. & L.L. Knowles . 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.T.1    Knowles, L.L.2
  • 81
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic frees
    • Rambaut, A. & N.C. Grassly . 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic frees. Comput. Appl. Biosci. 13: 235-238.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 82
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • H.N. Munro New York: Academic Press.
    • Jukes, T.H. & C.R. Cantor . 1969. "Evolution of protein molecules." In Mammalian Protein Metabolism. H.N. Munro, Ed.: 21-123. New York: Academic Press.
    • (1969) Mammalian Protein Metabolism , pp. 21-123
    • Jukes, T.H.1    Cantor, C.R.2
  • 83
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    • Guindon, S. et al. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59: 307-321.
    • (2010) Syst. Biol , vol.59 , pp. 307-321
    • Guindon, S.1
  • 84
    • 84930372526 scopus 로고    scopus 로고
    • ExaBayes: massively parallel Bayesian tree inference for the whole-genome era
    • Aberer, A.J., K. Kobert & A. Stamatakis . 2014. ExaBayes: massively parallel Bayesian tree inference for the whole-genome era. Mol. Biol. Evol. 31: 2553-2556.
    • (2014) Mol. Biol. Evol , vol.31 , pp. 2553-2556
    • Aberer, A.J.1    Kobert, K.2    Stamatakis, A.3
  • 85
    • 79955092139 scopus 로고    scopus 로고
    • Estimating species trees using approximate Bayesian computation
    • Fan, H.H. & L.S. Kubatko . 2011. Estimating species trees using approximate Bayesian computation. Mol. Phylogenet. Evol. 59: 354-363.
    • (2011) Mol. Phylogenet. Evol , vol.59 , pp. 354-363
    • Fan, H.H.1    Kubatko, L.S.2
  • 86
    • 76849102326 scopus 로고    scopus 로고
    • Incomplete lineage sorting: consistent phylogeny estimation from multiple loci
    • Mossel, E. & S. Roch . 2010. Incomplete lineage sorting: consistent phylogeny estimation from multiple loci. IEEE-ACM Trans. Comput. Biol. Bioinfo. 7: 166-171.
    • (2010) IEEE-ACM Trans. Comput. Biol. Bioinfo , vol.7 , pp. 166-171
    • Mossel, E.1    Roch, S.2
  • 87
    • 63549118031 scopus 로고    scopus 로고
    • STEM: species tree estimation using maximum likelihood for gene trees under coalescence
    • Kubatko, L.S., B.C. Carstens & L.L. Knowles . 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
  • 88
    • 84857687426 scopus 로고    scopus 로고
    • Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood
    • Wu, Y. 2012. Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution 66: 763-775.
    • (2012) Evolution , vol.66 , pp. 763-775
    • Wu, Y.1
  • 89
    • 84907019380 scopus 로고    scopus 로고
    • ASTRAL: genome-scale coalescent-based species tree estimation
    • Mirarab, S. et al. 2014. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30: i541-i548.
    • (2014) Bioinformatics , vol.30 , pp. i541-i548
    • Mirarab, S.1
  • 90
    • 84864697376 scopus 로고    scopus 로고
    • Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis
    • Bryant, D. et al. 2012. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 29: 1917-1932.
    • (2012) Mol. Biol. Evol , vol.29 , pp. 1917-1932
    • Bryant, D.1
  • 91
    • 84917697072 scopus 로고    scopus 로고
    • Quartet inference from SNP data under the coalescent model
    • Chifman, J. & L. Kubatko . 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics 30: 3317-3324.
    • (2014) Bioinformatics , vol.30 , pp. 3317-3324
    • Chifman, J.1    Kubatko, L.2
  • 92
    • 84928989201 scopus 로고    scopus 로고
    • A coalescent-based method for population tree inference with haplotypes
    • Wu, Y. 2015. A coalescent-based method for population tree inference with haplotypes. Bioinformatics 31: 691-698.
    • (2015) Bioinformatics , vol.31 , pp. 691-698
    • Wu, Y.1
  • 93
    • 84863230553 scopus 로고    scopus 로고
    • Insights into hominid evolution from the gorilla genome sequence
    • Scally, A. et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483: 169-175.
    • (2012) Nature , vol.483 , pp. 169-175
    • Scally, A.1
  • 94
    • 70450265498 scopus 로고    scopus 로고
    • Maximum likelihood estimates of species trees: how ccuracy of phylogenetic inference depends upon the divergence history and sampling design
    • McCormack, J.E., H.T. Huang & L.L. Knowles . 2009. Maximum likelihood estimates of species trees: how ccuracy 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.E.1    Huang, H.T.2    Knowles, L.L.3
  • 95
    • 0025133472 scopus 로고
    • Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships
    • Hedges, S.B., K.D. Moberg & L.R. Maxson . 1990. Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships. Mol. Biol. Evol. 7: 607-633.
    • (1990) Mol. Biol. Evol , vol.7 , pp. 607-633
    • Hedges, S.B.1    Moberg, K.D.2    Maxson, L.R.3
  • 96
    • 84864566049 scopus 로고    scopus 로고
    • Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca)
    • Sharma, P.P. et al. 2012. Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca). Mol. Phylogenet. Evol. 65: 64-74.
    • (2012) Mol. Phylogenet. Evol , vol.65 , pp. 64-74
    • Sharma, P.P.1
  • 97
    • 84892660736 scopus 로고    scopus 로고
    • Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data
    • Breinholt, J.W. & A.Y. Kawahara . 2013. Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data. Genome Biol. Evol. 5: 2082-2092.
    • (2013) Genome Biol. Evol , vol.5 , pp. 2082-2092
    • Breinholt, J.W.1    Kawahara, A.Y.2
  • 98
    • 70350139887 scopus 로고    scopus 로고
    • Ancestral population genomics: the coalescent hidden Markov model approach
    • Dutheil, J.Y. et al. 2009. Ancestral population genomics: the coalescent hidden Markov model approach. Genetics 183: 259-274.
    • (2009) Genetics , vol.183 , pp. 259-274
    • Dutheil, J.Y.1
  • 99
    • 79952270485 scopus 로고    scopus 로고
    • Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
    • Hobolth, A. et al. 2011. Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res. 21: 349-356.
    • (2011) Genome Res , vol.21 , pp. 349-356
    • Hobolth, A.1
  • 100
    • 73649129187 scopus 로고    scopus 로고
    • Fine-scale phylogenetic discordance across the house mouse genome
    • White, M.A. et al. 2009. Fine-scale phylogenetic discordance across the house mouse genome. PLoS Genet. 5: e1000729.
    • (2009) PLoS Genet , vol.5 , pp. e1000729
    • White, M.A.1
  • 101
    • 84890056203 scopus 로고    scopus 로고
    • The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution
    • Ryan, J.F. et al. 2013. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342: 1242592.
    • (2013) Science , vol.342 , pp. 1242592
    • Ryan, J.F.1
  • 102
    • 41849131023 scopus 로고    scopus 로고
    • Maximum likelihood supertrees
    • Steel, M. & A. Rodrigo . 2008. Maximum likelihood supertrees. Syst. Biol. 57: 243-250.
    • (2008) Syst. Biol , vol.57 , pp. 243-250
    • Steel, M.1    Rodrigo, A.2
  • 103
    • 84884681647 scopus 로고    scopus 로고
    • Analyzing and synthesizing phylogenies using tree alignment graphs
    • Smith, S.A., J.W. Brown & C.E. Hinchliff . 2013. Analyzing and synthesizing phylogenies using tree alignment graphs. PLoS Comput. Biol. 9. e1003223.
    • (2013) PLoS Comput. Biol , vol.9 , pp. e1003223
    • Smith, S.A.1    Brown, J.W.2    Hinchliff, C.E.3
  • 104
    • 84898963008 scopus 로고    scopus 로고
    • Poor fit to the multispecies coalescent is widely detectable in empirical data
    • Reid, N.H. et al. 2013. Poor fit to the multispecies coalescent is widely detectable in empirical data. Syst. Biol. 63: 322-333.
    • (2013) Syst. Biol , vol.63 , pp. 322-333
    • Reid, N.H.1
  • 105
    • 56549103832 scopus 로고    scopus 로고
    • Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presense of gene flow
    • Eckert, A.J. & B.C. Carstens . 2008. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presense of gene flow. Mol. Phylogenet. Evol. 49: 832-842.
    • (2008) Mol. Phylogenet. Evol , vol.49 , pp. 832-842
    • Eckert, A.J.1    Carstens, B.C.2
  • 106
    • 79955117575 scopus 로고    scopus 로고
    • Bayesian estimation of species trees: a practical guide to optimal sampling and analysis
    • L.L. Knowles & L.S. Kubatko, Eds New Jersey: Wiley-Blackwell.
    • Castillo-Ramírez, S. et al. 2010. "Bayesian estimation of species trees: a practical guide to optimal sampling and analysis." In Estimating Species Trees: Practical and Theoretical Aspects. L.L. Knowles & L.S. Kubatko, Eds.: 15-33. New Jersey: Wiley-Blackwell.
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 15-33
    • Castillo-Ramírez, S.1
  • 107
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 108
    • 84860109324 scopus 로고    scopus 로고
    • MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
    • Ronquist, F. et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61: 539-542.
    • (2012) Syst. Biol , vol.61 , pp. 539-542
    • Ronquist, F.1
  • 109
    • 54949090066 scopus 로고    scopus 로고
    • BEST: Bayesian estimation of species trees under the coalescent model
    • Liu, L. 2008. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24: 2542-2543.
    • (2008) Bioinformatics , vol.24 , pp. 2542-2543
    • Liu, L.1
  • 110
    • 80051975928 scopus 로고    scopus 로고
    • Estimating species trees from unrooted gene trees
    • Liu, L. & L. Yu . 2011. Estimating species trees from unrooted gene trees. Syst. Biol. 60: 661-667.
    • (2011) Syst. Biol , vol.60 , pp. 661-667
    • Liu, L.1    Yu, L.2
  • 111
    • 70350247510 scopus 로고    scopus 로고
    • Maximum tree: a consistent estimator of the species tree
    • Liu, L., L. Yu & D.K. Pearl . 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
  • 112
    • 84956878549 scopus 로고    scopus 로고
    • Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions
    • Tonini, J., A. Moore, D. Stern, et al. 2015. Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions. PLoS Currents Tree of Life. doi: 10.1371/currents.tol.34260cc27551a527b124ec5f6334b6be.
    • (2015) PLoS Currents Tree of Life
    • Tonini, J.1    Moore, A.2    Stern, D.3


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