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Volumn 109, Issue 37, 2012, Pages 14942-14947

Erratum: Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model (Proceedings of the National Academy of Sciences of the United States of America (2012) 109 (14942-14947) (DOI:10.1073/pnas.1211733109));Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Author keywords

Gene tree heterogeneity; Incomplete lineage sorting; Multispecies coalescent model; Phylogenetic incongruence

Indexed keywords

ARTICLE; ATLANTOGENATA; BOREOEUTHERIA; COALESCENT METHOD; CONCATENATION METHOD; EUARCHONTOGLIRES; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; LAURASIATHERIA; NONHUMAN; PHYLOGENETIC TREE ROOT; PHYLOGENOMICS; PLACENTAL MAMMALS; PRIMATE; PRIORITY JOURNAL; SCANDENTIA; TAXON;

EID: 84866289853     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1518753112     Document Type: Erratum
Times cited : (353)

References (46)
  • 1
    • 33845627286 scopus 로고    scopus 로고
    • The supermatrix approach to systematics
    • de Queiroz A, Gatesy J (2007) The supermatrix approach to systematics. Trends Ecol Evol 22(1):34-41.
    • (2007) Trends Ecol Evol , vol.22 , Issue.1 , pp. 34-41
    • De Queiroz, A.1    Gatesy, J.2
  • 2
    • 0012871763 scopus 로고    scopus 로고
    • Combining data in phylogenetic analysis
    • William J, Ballard O (1996) Combining data in phylogenetic analysis. Trends Ecol Evol 11:334.
    • (1996) Trends Ecol Evol , vol.11 , pp. 334
    • William, J.1    Ballard, O.2
  • 3
    • 52149099649 scopus 로고    scopus 로고
    • Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae)
    • Belfiore NM, Liu L, Moritz C (2008) Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae). Syst Biol 57(2):294-310.
    • (2008) Syst Biol , vol.57 , Issue.2 , pp. 294-310
    • Belfiore, N.M.1    Liu, L.2    Moritz, C.3
  • 4
    • 58249100073 scopus 로고    scopus 로고
    • Is a new and general theory of molecular systematics emerging?
    • Edwards SV (2009) Is a new and general theory of molecular systematics emerging? Evolution 63(1):1-19.
    • (2009) Evolution , vol.63 , Issue.1 , pp. 1-19
    • Edwards, S.V.1
  • 5
    • 33847302458 scopus 로고    scopus 로고
    • Inconsistency of phylogenetic estimates from concatenated data under coalescence
    • Kubatko LS, Degnan JH (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 56(1):17-24.
    • (2007) Syst Biol , vol.56 , Issue.1 , pp. 17-24
    • Kubatko, L.S.1    Degnan, J.H.2
  • 6
    • 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
  • 7
    • 47749093183 scopus 로고    scopus 로고
    • Estimating species trees using multiple-allele DNA sequence data
    • Liu L, Pearl DK, Brumfield RT, Edwards SV (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    Brumfield, R.T.3    Edwards, S.V.4
  • 8
    • 77957686501 scopus 로고    scopus 로고
    • A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
    • Liu L, Yu L, Edwards SV (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
  • 9
    • 70349425459 scopus 로고    scopus 로고
    • Estimating species phylogenies using coalescence times among sequences
    • Liu L, Yu L, Pearl DK, Edwards SV (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    Yu, L.2    Pearl, D.K.3    Edwards, S.V.4
  • 10
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference and the multispecies coalescent
    • Degnan JH, Rosenberg NA (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
  • 11
    • 0035252080 scopus 로고    scopus 로고
    • Molecular phylogenetics and the origins of placental mammals
    • Murphy WJ, et al. (2001) Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
    • (2001) Nature , vol.409 , pp. 614-618
    • Murphy, W.J.1
  • 12
    • 0035861441 scopus 로고    scopus 로고
    • Resolution of the early placental mammal radiation using Bayesian phylogenetics
    • Murphy WJ, 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
  • 13
    • 80055070300 scopus 로고    scopus 로고
    • Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification
    • Meredith RW, et al. (2011) Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334:521-524.
    • (2011) Science , vol.334 , pp. 521-524
    • Meredith, R.W.1
  • 15
    • 33846552919 scopus 로고    scopus 로고
    • Early history of mammals is elucidated with the ENCODE multiple species sequencing data
    • NISC Comparative Sequencing Program
    • Nikolaev S, et al. NISC Comparative Sequencing Program (2007) Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet 3:e2.
    • (2007) PLoS Genet , vol.3
    • Nikolaev, S.1
  • 16
    • 35448956570 scopus 로고    scopus 로고
    • Genomics, biogeography, and the diversification of placental mammals
    • Wildman DE, et al. (2007) Genomics, biogeography, and the diversification of placental mammals. Proc Natl Acad Sci USA 104:14395-14400.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 14395-14400
    • Wildman, D.E.1
  • 17
    • 49749129961 scopus 로고    scopus 로고
    • Confirming the phylogeny of mammals by use of large comparative sequence data sets
    • NISC Comparative Sequencing Program
    • Prasad AB, Allard MW, Green ED, Green ED, NISC Comparative Sequencing Program (2008) Confirming the phylogeny of mammals by use of large comparative sequence data sets. Mol Biol Evol 25:1795-1808.
    • (2008) Mol Biol Evol , vol.25 , pp. 1795-1808
    • Prasad, A.B.1    Allard, M.W.2    Green, E.D.3    Green, E.D.4
  • 18
    • 33646255212 scopus 로고    scopus 로고
    • Retroposed elements as archives for the evolutionary history of placental mammals
    • Kriegs JO, et al. (2006) Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol 4:e91.
    • (2006) PLoS Biol , vol.4
    • Kriegs, J.O.1
  • 19
    • 34548448442 scopus 로고    scopus 로고
    • Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups
    • Hallström BM, Kullberg M, Nilsson MA, Janke A (2007) Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups. Mol Biol Evol 24:2059-2068.
    • (2007) Mol Biol Evol , vol.24 , pp. 2059-2068
    • Hallström, B.M.1    Kullberg, M.2    Nilsson, M.A.3    Janke, A.4
  • 20
    • 70349973873 scopus 로고    scopus 로고
    • The new framework for understanding placental mammal evolution
    • Asher RJ, Bennett N, Lehmann T (2009) The new framework for understanding placental mammal evolution. Bioessays 31:853-864.
    • (2009) Bioessays , vol.31 , pp. 853-864
    • Asher, R.J.1    Bennett, N.2    Lehmann, T.3
  • 22
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 23
    • 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
  • 24
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Suzuki Y, Glazko GV, Nei M (2002) Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci USA 99:16138-16143.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 16138-16143
    • Suzuki, Y.1    Glazko, G.V.2    Nei, M.3
  • 25
    • 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
  • 26
    • 79952270485 scopus 로고    scopus 로고
    • Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
    • Hobolth A, Dutheil JY, Hawks J, Schierup MH, Mailund T (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    Dutheil, J.Y.2    Hawks, J.3    Schierup, M.H.4    Mailund, T.5
  • 27
    • 79955439952 scopus 로고    scopus 로고
    • Reconstructing concordance trees and testing the coalescent model from genome-wide data sets
    • eds Knowles LL, Kubatko L, (Wiley-Blackwell, Hoboken, NJ)
    • Ané C (2010) Reconstructing concordance trees and testing the coalescent model from genome-wide data sets. Estimating Species Trees: Practical and Theoretical Aspects, eds Knowles LL, Kubatko L, (Wiley-Blackwell, Hoboken, NJ), pp 35-52.
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 35-52
    • Ané, C.1
  • 28
    • 39749188544 scopus 로고    scopus 로고
    • Rooting the eutherian tree: The power and pitfalls of phylogenomics
    • Nishihara H, Okada N, Hasegawa M (2007) Rooting the eutherian tree: The power and pitfalls of phylogenomics. Genome Biol 8:R199.
    • (2007) Genome Biol , vol.8
    • Nishihara, H.1    Okada, N.2    Hasegawa, M.3
  • 29
    • 79955117575 scopus 로고    scopus 로고
    • Bayesian estimation of species trees: A practical guide to optimal sampling and analysis
    • eds Knowles LL, Kubatko L, (Wiley-Blackwell, Hoboken, NJ)
    • Castillo-Ramirez S, Liu L, Pearl DK, Edward SV (2010) Bayesian estimation of species trees: A practical guide to optimal sampling and analysis. Estimating Species Trees: Practical and Theoretical Aspects, eds Knowles LL, Kubatko L, (Wiley-Blackwell, Hoboken, NJ), pp 15-33.
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 15-33
    • Castillo-Ramirez, S.1    Liu, L.2    Pearl, D.K.3    Edward, S.V.4
  • 30
    • 77951961553 scopus 로고    scopus 로고
    • Phybase: An R package for species tree analysis
    • Liu L, Yu L (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
  • 31
    • 0242669921 scopus 로고    scopus 로고
    • Is sparse taxon sampling a problem for phylogenetic inference?
    • Hillis DM, Pollock DD, McGuire JA, Zwickl DJ (2003) Is sparse taxon sampling a problem for phylogenetic inference? Syst Biol 52:124-126.
    • (2003) Syst Biol , vol.52 , pp. 124-126
    • Hillis, D.M.1    Pollock, D.D.2    McGuire, J.A.3    Zwickl, D.J.4
  • 32
    • 0036699885 scopus 로고    scopus 로고
    • Increased taxon sampling is advantageous for phylogenetic inference
    • Pollock DD, Zwickl DJ, McGuire JA, Hillis DM (2002) Increased taxon sampling is advantageous for phylogenetic inference. Syst Biol 51:664-671.
    • (2002) Syst Biol , vol.51 , pp. 664-671
    • Pollock, D.D.1    Zwickl, D.J.2    McGuire, J.A.3    Hillis, D.M.4
  • 33
    • 33747339757 scopus 로고    scopus 로고
    • Resolution of phylogenetic conflict in large data sets by increased taxon sampling
    • Hedtke SM, Townsend TM, Hillis DM (2006) Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst Biol 55:522-529.
    • (2006) Syst Biol , vol.55 , pp. 522-529
    • Hedtke, S.M.1    Townsend, T.M.2    Hillis, D.M.3
  • 34
    • 79953716259 scopus 로고    scopus 로고
    • Resolving difficult phylogenetic questions: Why more sequences are not enough
    • Philippe H, et al. (2011) Resolving difficult phylogenetic questions: Why more sequences are not enough. PLoS Biol 9:e1000602.
    • (2011) PLoS Biol , vol.9
    • Philippe, H.1
  • 35
    • 85069328073 scopus 로고    scopus 로고
    • Untraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis
    • 10.1101/gr.125864.12511
    • McCormack JE, et al. (2011) Untraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis. Genome Res, 10.1101/gr.125864.12511.
    • (2011) Genome Res
    • McCormack, J.E.1
  • 36
    • 38449121762 scopus 로고    scopus 로고
    • Molecular and genomic data identify the closest living relative of primates
    • Janecka JE, et al. (2007) Molecular and genomic data identify the closest living relative of primates. Science 318:792-794.
    • (2007) Science , vol.318 , pp. 792-794
    • Janecka, J.E.1
  • 37
    • 2942627753 scopus 로고    scopus 로고
    • Mesozoic origin for West Indian insectivores
    • Roca AL, et al. (2004) Mesozoic origin for West Indian insectivores. Nature 429:649-651.
    • (2004) Nature , vol.429 , pp. 649-651
    • Roca, A.L.1
  • 38
    • 48349115697 scopus 로고    scopus 로고
    • Mitogenomic relationships of placental mammals and molecular estimates of their divergences
    • Arnason U, et al. (2008) Mitogenomic relationships of placental mammals and molecular estimates of their divergences. Gene 421(1-2):37-51.
    • (2008) Gene , vol.421 , Issue.1-2 , pp. 37-51
    • Arnason, U.1
  • 39
    • 0141609704 scopus 로고    scopus 로고
    • A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships
    • Amrine-Madsen H, Koepfli KP, Wayne RK, Springer MS (2003) A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships. Mol Phylogenet Evol 28:225-240.
    • (2003) Mol Phylogenet Evol , vol.28 , pp. 225-240
    • Amrine-Madsen, H.1    Koepfli, K.P.2    Wayne, R.K.3    Springer, M.S.4
  • 40
    • 0033085002 scopus 로고    scopus 로고
    • Towards resolving the interordinal relationships of placental mammals
    • Waddell PJ, Okada N, Hasegawa M (1999) Towards resolving the interordinal relationships of placental mammals. Syst Biol 48(1):1-5.
    • (1999) Syst Biol , vol.48 , Issue.1 , pp. 1-5
    • Waddell, P.J.1    Okada, N.2    Hasegawa, M.3
  • 41
    • 50949129519 scopus 로고    scopus 로고
    • Calculating bootstrap probabilities of phylogeny using multilocus sequence data
    • Seo TK (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
  • 43
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck JP, 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
  • 44
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson DF, Foulds LR (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
  • 45
    • 0000122573 scopus 로고
    • PHYLIP: Phylogeny Inference Package
    • Version 3.2
    • Felsenstein J (1989) PHYLIP: Phylogeny Inference Package (Version 3.2). Cladistics 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1


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