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Number Cited by Other Article(s)
51
Wen D, Nakhleh L. Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data. Syst Biol 2017;67:439-457. [DOI: 10.1093/sysbio/syx085] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 10/24/2017] [Indexed: 11/13/2022]  Open
52
Molloy EK, Warnow T. To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods. Syst Biol 2017;67:285-303. [DOI: 10.1093/sysbio/syx077] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 09/13/2017] [Indexed: 01/27/2023]  Open
53
Bhattacharyya S, Mukherjee J. IDXL: Species Tree Inference Using Internode Distance and Excess Gene Leaf Count. J Mol Evol 2017;85:57-78. [PMID: 28835989 DOI: 10.1007/s00239-017-9807-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/09/2017] [Indexed: 11/28/2022]
54
Léveillé-Bourret É, Starr JR, Ford BA, Moriarty Lemmon E, Lemmon AR. Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics. Syst Biol 2017;67:94-112. [DOI: 10.1093/sysbio/syx050] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/28/2017] [Indexed: 11/13/2022]  Open
55
Edwards SV. Phylogenomic subsampling: a brief review. ZOOL SCR 2016. [DOI: 10.1111/zsc.12210] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
56
Shen XX, Salichos L, Rokas A. A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference. Genome Biol Evol 2016;8:2565-80. [PMID: 27492233 PMCID: PMC5010910 DOI: 10.1093/gbe/evw179] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 12/13/2022]  Open
57
Foley NM, Springer MS, Teeling EC. Mammal madness: is the mammal tree of life not yet resolved? Philos Trans R Soc Lond B Biol Sci 2016;371:20150140. [PMID: 27325836 PMCID: PMC4920340 DOI: 10.1098/rstb.2015.0140] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2016] [Indexed: 11/12/2022]  Open
58
Linkem CW, Minin VN, Leaché AD. Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae). Syst Biol 2016;65:465-77. [PMID: 26738927 PMCID: PMC6383586 DOI: 10.1093/sysbio/syw001] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/29/2015] [Indexed: 01/28/2023]  Open
59
Larson ER, Castelin M, Williams BW, Olden JD, Abbott CL. Phylogenetic species delimitation for crayfishes of the genus Pacifastacus. PeerJ 2016;4:e1915. [PMID: 27114875 PMCID: PMC4841241 DOI: 10.7717/peerj.1915] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 03/18/2016] [Indexed: 12/20/2022]  Open
60
Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH. Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae). Mol Phylogenet Evol 2016;97:32-42. [DOI: 10.1016/j.ympev.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/04/2015] [Accepted: 12/23/2015] [Indexed: 02/02/2023]
61
Meiklejohn KA, Faircloth BC, Glenn TC, Kimball RT, Braun EL. Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods. Syst Biol 2016;65:612-27. [DOI: 10.1093/sysbio/syw014] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 01/25/2016] [Indexed: 01/30/2023]  Open
62
Ogilvie HA, Heled J, Xie D, Drummond AJ. Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods. Syst Biol 2016;65:381-96. [PMID: 26821913 PMCID: PMC4851174 DOI: 10.1093/sysbio/syv118] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 12/07/2015] [Indexed: 01/02/2023]  Open
63
Simmons MP, Sloan DB, Gatesy J. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Mol Phylogenet Evol 2016;97:76-89. [PMID: 26768112 DOI: 10.1016/j.ympev.2015.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/03/2015] [Accepted: 12/20/2015] [Indexed: 10/22/2022]
64
Springer MS, Gatesy J. The gene tree delusion. Mol Phylogenet Evol 2016;94:1-33. [DOI: 10.1016/j.ympev.2015.07.018] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/04/2015] [Accepted: 07/22/2015] [Indexed: 10/23/2022]
65
Richart CH, Hayashi CY, Hedin M. Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies. Mol Phylogenet Evol 2015;95:171-82. [PMID: 26691642 DOI: 10.1016/j.ympev.2015.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 09/16/2015] [Accepted: 11/13/2015] [Indexed: 11/19/2022]
66
Xi Z, Liu L, Davis CC. The Impact of Missing Data on Species Tree Estimation. Mol Biol Evol 2015;33:838-60. [DOI: 10.1093/molbev/msv266] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
67
Mallo D, De Oliveira Martins L, Posada D. SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees. Syst Biol 2015;65:334-44. [PMID: 26526427 PMCID: PMC4748750 DOI: 10.1093/sysbio/syv082] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/20/2015] [Indexed: 11/14/2022]  Open
68
Liu L, Edwards SV. Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science 2015;350:171. [PMID: 26450203 DOI: 10.1126/science.aaa7343] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
69
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 2015;526:569-73. [DOI: 10.1038/nature15697] [Citation(s) in RCA: 965] [Impact Index Per Article: 96.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 09/09/2015] [Indexed: 12/20/2022]
70
Chou J, Gupta A, Yaduvanshi S, Davidson R, Nute M, Mirarab S, Warnow T. A comparative study of SVDquartets and other coalescent-based species tree estimation methods. BMC Genomics 2015;16 Suppl 10:S2. [PMID: 26449249 PMCID: PMC4602346 DOI: 10.1186/1471-2164-16-s10-s2] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
71
Davidson R, Vachaspati P, Mirarab S, Warnow T. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. BMC Genomics 2015;16 Suppl 10:S1. [PMID: 26450506 PMCID: PMC4603753 DOI: 10.1186/1471-2164-16-s10-s1] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
72
Vachaspati P, Warnow T. ASTRID: Accurate Species TRees from Internode Distances. BMC Genomics 2015;16 Suppl 10:S3. [PMID: 26449326 PMCID: PMC4602181 DOI: 10.1186/1471-2164-16-s10-s3] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
73
Simmons MP, Gatesy J. Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms. Mol Phylogenet Evol 2015;91:98-122. [DOI: 10.1016/j.ympev.2015.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/01/2015] [Accepted: 05/14/2015] [Indexed: 11/24/2022]
74
Chen MY, Liang D, Zhang P. Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny. Syst Biol 2015;64:1104-20. [PMID: 26276158 DOI: 10.1093/sysbio/syv059] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 08/10/2015] [Indexed: 11/13/2022]  Open
75
Smith SA, Moore MJ, Brown JW, Yang Y. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evol Biol 2015;15:150. [PMID: 26239519 PMCID: PMC4524127 DOI: 10.1186/s12862-015-0423-0] [Citation(s) in RCA: 275] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/25/2015] [Indexed: 11/10/2022]  Open
76
Xi Z, Liu L, Davis CC. Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased. Mol Phylogenet Evol 2015;92:63-71. [PMID: 26115844 DOI: 10.1016/j.ympev.2015.06.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/23/2015] [Accepted: 06/16/2015] [Indexed: 11/30/2022]
77
Bayzid MS, Mirarab S, Boussau B, Warnow T. Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses. PLoS One 2015;10:e0129183. [PMID: 26086579 PMCID: PMC4472720 DOI: 10.1371/journal.pone.0129183] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 05/05/2015] [Indexed: 11/19/2022]  Open
78
Warnow T. Concatenation Analyses in the Presence of Incomplete Lineage Sorting. PLOS CURRENTS 2015;7:ecurrents.currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7. [PMID: 26064786 PMCID: PMC4450984 DOI: 10.1371/currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
79
Giarla TC, Esselstyn JA. The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews. Syst Biol 2015;64:727-40. [DOI: 10.1093/sysbio/syv029] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/07/2015] [Indexed: 01/30/2023]  Open
80
Heyduk K, Trapnell DW, Barrett CF, Leebens-Mack J. Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12551] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
81
Liu L, Xi Z, Wu S, Davis CC, Edwards SV. Estimating phylogenetic trees from genome-scale data. Ann N Y Acad Sci 2015;1360:36-53. [DOI: 10.1111/nyas.12747] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
82
Roch S, Warnow T. On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods. Syst Biol 2015;64:663-76. [PMID: 25813358 DOI: 10.1093/sysbio/syv016] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/20/2015] [Indexed: 11/13/2022]  Open
83
Tonini J, Moore A, Stern D, Shcheglovitova M, Ortí G. Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated Conditions. PLOS CURRENTS 2015;7. [PMID: 25901289 PMCID: PMC4391732 DOI: 10.1371/currents.tol.34260cc27551a527b124ec5f6334b6be] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
84
Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent. Theor Popul Biol 2015;100C:56-62. [DOI: 10.1016/j.tpb.2014.12.005] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 11/10/2014] [Accepted: 12/18/2014] [Indexed: 01/14/2023]
85
Meyer BS, Matschiner M, Salzburger W. A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach. Mol Phylogenet Evol 2015;83:56-71. [PMID: 25433288 PMCID: PMC4334724 DOI: 10.1016/j.ympev.2014.10.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 10/05/2014] [Accepted: 10/08/2014] [Indexed: 11/14/2022]
86
Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T. ASTRAL: genome-scale coalescent-based species tree estimation. ACTA ACUST UNITED AC 2015;30:i541-8. [PMID: 25161245 PMCID: PMC4147915 DOI: 10.1093/bioinformatics/btu462] [Citation(s) in RCA: 776] [Impact Index Per Article: 77.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
87
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, et alJarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 2014;346:1320-31. [PMID: 25504713 PMCID: PMC4405904 DOI: 10.1126/science.1253451] [Show More Authors] [Citation(s) in RCA: 1171] [Impact Index Per Article: 106.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
88
Mirarab S, Bayzid MS, Boussau B, Warnow T. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 2014;346:1250463. [PMID: 25504728 DOI: 10.1126/science.1250463] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
89
Liu L, Xi Z, Davis CC. Coalescent Methods Are Robust to the Simultaneous Effects of Long Branches and Incomplete Lineage Sorting. Mol Biol Evol 2014;32:791-805. [DOI: 10.1093/molbev/msu331] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
90
Gatesy J, Springer MS. Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol Phylogenet Evol 2014;80:231-66. [DOI: 10.1016/j.ympev.2014.08.013] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/26/2014] [Accepted: 08/10/2014] [Indexed: 11/16/2022]
91
Bayzid MS, Hunt T, Warnow T. Disk covering methods improve phylogenomic analyses. BMC Genomics 2014;15 Suppl 6:S7. [PMID: 25572610 PMCID: PMC4239662 DOI: 10.1186/1471-2164-15-s6-s7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
92
Zimmermann T, Mirarab S, Warnow T. BBCA: Improving the scalability of *BEAST using random binning. BMC Genomics 2014;15 Suppl 6:S11. [PMID: 25572469 PMCID: PMC4239591 DOI: 10.1186/1471-2164-15-s6-s11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
93
A time-calibrated, multi-locus phylogeny of piranhas and pacus (Characiformes: Serrasalmidae) and a comparison of species tree methods. Mol Phylogenet Evol 2014;81:242-57. [PMID: 25261120 DOI: 10.1016/j.ympev.2014.06.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 12/13/2022]
94
Mirarab S, Bayzid MS, Warnow T. Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting. Syst Biol 2014;65:366-80. [PMID: 25164915 DOI: 10.1093/sysbio/syu063] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 08/18/2014] [Indexed: 12/13/2022]  Open
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Huang H, Tran LAP, Knowles LL. Do estimated and actual species phylogenies match? Evaluation of East African cichlid radiations. Mol Phylogenet Evol 2014;78:56-65. [PMID: 24837624 DOI: 10.1016/j.ympev.2014.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/02/2014] [Accepted: 05/06/2014] [Indexed: 10/25/2022]
96
Zhong B, Liu L, Penny D. The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy. TRENDS IN PLANT SCIENCE 2014;19:270-272. [PMID: 24641876 DOI: 10.1016/j.tplants.2014.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 02/20/2014] [Indexed: 06/03/2023]
97
Springer MS, Gatesy J. Land plant origins and coalescence confusion. TRENDS IN PLANT SCIENCE 2014;19:267-269. [PMID: 24641875 DOI: 10.1016/j.tplants.2014.02.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 01/30/2014] [Accepted: 02/20/2014] [Indexed: 06/03/2023]
98
Molecular evidence for the monophyly of flatfishes (Carangimorpharia: Pleuronectiformes). Mol Phylogenet Evol 2014;73:18-22. [DOI: 10.1016/j.ympev.2014.01.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 01/07/2014] [Accepted: 01/09/2014] [Indexed: 11/18/2022]
99
Capella-Gutierrez S, Kauff F, Gabaldón T. A phylogenomics approach for selecting robust sets of phylogenetic markers. Nucleic Acids Res 2014;42:e54. [PMID: 24476915 PMCID: PMC3985644 DOI: 10.1093/nar/gku071] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
100
Betancur-R. R, Naylor GJ, Ortí G. Conserved Genes, Sampling Error, and Phylogenomic Inference. Syst Biol 2014;63:257-62. [DOI: 10.1093/sysbio/syt073] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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