Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

Molecular Phylogenetics and Evolution

Volumn 80, Issue 1, 2014, Pages 231-266

  Gatesy, John ^a   Springer, Mark S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Deep coalescence; Gene tree; Mammalia; Species tree; Supermatrix

Indexed keywords

ANIMAL; BIOLOGICAL MODEL; CLASSIFICATION; DNA SEQUENCE; GENETICS; MAMMAL; PHYLOGENY;

ANIMALS; MAMMALS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84908162664     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2014.08.013     Document Type: Article

References (175)

1. Aguiar B.O., Schrago C.G. Conventional simulation of biological sequences leads to a biased assessment of multi-loci phylogenetic analysis. Evol. Bioinform. 2013, 9:317-325.
2. Anderson F.E., Swofford D.L. Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. Mol. Phylogenet. Evol. 2004, 33:440-451.
3. Ané C. Reconstructing concordance trees and testing the coalescent model from genome-wide data sets. Estimating Species Trees: Practical and Theoretical Aspects 2010, 35-52. Wiley-Blackwell, Hoboken, New Jersey. L.L. Knowles, L.S. Kubatko (Eds.).
4. Ané C., Larget B., Baum D.A., Smith S.D., Rokas A. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 2007, 24:412-426.
5. Arnason U., Adegoke J.A., Gullberg A., Harley E.H., Janke A., Kullberg M. Mitogenomic relationships of placental mammals and molecular estimates of their divergences. Gene 2008, 421:37-51.
6. Asher R.J., Novacek M.J., Geisler J.H. Relationships of endemic African mammals and their fossil relatives based on morphological and molecular evidence. J. Mamm. Evol. 2003, 10:131-194.
7. Asher R.J., Emry R.J., McKenna M.C. New material of Centetodon (Mammalia, Lipotyphla) and the importance of (missing) DNA sequences in systematic paleontology. J. Vertebr. Paleontol. 2005, 25:911-923.
8. Asher R.J., Hofreiter M. Tenrecid phylogeny and the noninvasive extraction of nuclear DNA. Syst. Biol. 2006, 55:181-194.
9. Avise J.D., Robinson T. Hemiplasy: a new term in the lexicon of phylogenetics. Syst. Biol. 2008, 57:503-507.
10. Baker R.H., DeSalle R. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst. Biol. 1997, 46:654-673.
11. Barrett M., Donoghue M.J., Sober E. Against consensus. Syst. Zool. 1991, 40:486-493.
12. Bayzid M.S., Warnow T. Naive binning improves phylogenomic analyses. Bioinformatics 2013, 29:2277-2284.
13. Bergsten J. A review of long-branch attraction. Cladistics 2005, 21:163-193.
14. Bibi F., Fack F., Vrba E. A new fossil caprin and a combined molecular and morphological Bayesian analysis of Caprini (Mammalia: Bovidae). J. Evol. Biol. 2012, 25:1843-1854.
15. Bininda-Emonds O.R.P., Cardillo M., Jones K.E., MacPhee R.D.E., Beck R.M.D., Grenyer R., Price S.A., Vos R.A., Gittleman J.L., Purvis A. The delayed rise of present-day mammals. Nature 2007, 446:507-512.
16. Bryant D., Bouckaert R., Felsenstein J., Rosenberg N.A., Roy-Choudhury A. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 2012, 29:1917-1932.
17. Bull J.J., Huelsenbeck J.P., Cunningham C.W., Swofford D.L., Waddell P.J. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 1993, 42:384-397.
18. 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.
19. Chiari Y., Cahais V., Galtier N., Delsuc F. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol. 2012, 10:65.
20. Chippindale P.T., Wiens J.J. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 1994, 43:278-287.
21. Chung Y., Ané C. Comparing two Bayesian methods for gene tree/species tree reconstruction: a simulation with incomplete lineage sorting and horizontal gene transfer. Syst. Biol. 2011, 60:261-275.
22. Collins T.M., Fedrigo O., Naylor G.J.P. Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenies. Syst. Biol. 2005, 54:493-500.
23. Decker J.E., Pires J.C., Conant G.C., McKay S.D., Heaton M.P., Chen K., Cooper A., Vilkki J., Seabury C.M., Caetano A.R., et al. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc. Natl. Acad. Sci. USA 2009, 106:18644-18649.
24. DeGiorgio M., Degnan J.H. Robustness to divergence time underestimation when inferring species trees from estimated gene trees. Syst. Biol. 2014, 63:66-82.
25. Degnan J.H. Anomalous unrooted gene trees. Syst. Biol. 2013, 62:574-590.
26. Degnan J.H., Rosenberg N.A. Discordance of species trees with their most likely gene trees. PLoS Genet. 2006, 2:762-768.
27. Degnan J.H., Rosenberg N.A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 2009, 24:332-340.
28. Degnan J.H., Salter L.A. Gene tree distributions under the coalescent process. Evolution 2005, 59:24-37.
29. Deméré T.A., McGowen M.R., Berta A., Gatesy J. Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales. Syst. Biol. 2008, 57:15-37.
30. Dunn C.W., Hejnol A., Matus D.Q., Pang K., Browne W.E., Smith S.A., Seaver E., Rouse G.W., Obst M., Edgecombe G.D., et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452:745-749.
31. de Queiroz A., Gatesy J. The supermatrix approach to systematics. Trends Ecol. Evol. 2007, 22:34-41.
32. de Queiroz A., Donoghue M.J., Kim J. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 1995, 26:657-681.
33. dos Reis M., Inoue J., Hasegawa M., Asher R.J., Donoghue P.C.J., Yang Z. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. Roy. Soc. B 2012, 279:3491-3500.
34. dos Reis M., Donoghue P.C.J., Yang Z. Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biol. Lett. 2014, 10:20131003.
35. Doyle J.J. Gene trees and species trees: molecular systematics as one character taxonomy. Syst. Bot. 1992, 17:144-163.
36. Doyle J.J. Trees within trees: genes and species, molecules and morphology. Syst. Biol. 1997, 46:537-553.
37. Dutheil J.Y., Ganapathy G., Hobolth A., Mailund T., Uyenoyama M.K., Schierup M.H. Ancestral population genomics: the coalescent hidden Markov model approach. Genetics 2009, 183:259-274.
38. Edwards S.V. Is a new and general theory of molecular systematics merging?. Evolution 2009, 63:1-19.
39. Edwards S.V., Liu L., Pearl D.K. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA 2007, 104:5936-5941.
40. Eernisse D.J., Kluge A.G. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol. Biol. Evol. 1993, 10:1170-1195.
41. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 1978, 27:401-410.
42. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 1981, 17:368-376.
43. Gatesy J. Molecular evidence for the phylogenetic affinities of Cetacea. The Emergence of Whales 1998, 63-111. Plenum, New York. J.G.M. Thewissen (Ed.).
44. Gatesy J. Linked branch support and tree stability. Syst. Biol. 2000, 49:800-807.
45. Gatesy J., Arctander P. Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: a combined analysis of gross anatomical evidence and DNA sequences from five genes. Syst. Biol. 2000, 49:515-538.
46. Gatesy J., Baker R.H. Hidden likelihood support in genomic data: can forty-five wrongs make a right?. Syst. Biol. 2005, 54:483-492.
47. Gatesy J., Springer M.S. A critique of matrix representation with parsimony supertrees. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Computational Biology 2004, vol. 4:369-388. Kluwer Academic Publishers.
48. Gatesy J., Springer M.S. Concatenation versus coalescence versus "concatalescence". Proc. Natl. Acad. Sci. USA 2013, 110:E1179.
49. Gatesy J., O'Grady P., Baker R.H. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 1999, 15:271-313.
50. Gatesy J., Matthee C., DeSalle R., Hayashi C. Resolution of a supertree/supermatrix paradox. Syst. Biol. 2002, 51:652-664.
51. Gatesy J., Amato G., Norell M., DeSalle R., Hayashi C. Combined support for wholesale taxic atavism in gavialine crocodylians. Syst. Biol. 2003, 52:403-422.
52. Gatesy J., Baker R.H., Hayashi C. Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia. Syst. Biol. 2004, 53:342-355.
53. Gatesy J., DeSalle R., Wahlberg N. How many genes should a systematist sample? conflicting insights from a phylogenomic matrix characterized by replicated incongruence. Syst. Biol. 2007, 56:355-363.
54. Gatesy J., Geisler J.H., Chang J., Buell C., Berta A., Meredith R.W., Springer M.S., McGowen M.R. A phylogenetic blueprint for a modern whale. Mol. Phylogenet. Evol. 2013, 66:479-506.
55. Geisler J.H., Theodor J.M. Brief communications arising: hippo and whale phylogeny. Nature 2009, 458:E1-E4.
56. Geisler J.H., McGowen M.R., Yang G., Gatesy J. A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea. BMC Evol. Biol. 2011, 11:112.
57. GoloboffP., Pol D. Semi-strict supertrees. Cladistics 2002, 18:514-525.
58. Guindon S., Dufayard J.-F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010, 59:307-321.
59. Hartig G., Churakov G., Warren W.C., Brosius J., Makalowski W., Schmitz J. Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids. Sci. Rep. 2013, 3:1756.
60. Hallström B.M., Schneider A., Zoller S., Janke A. A genomic approach to examine the complex evolution of laurasiatherian mammals. PLoS ONE 2011, 6:e28199.
61. Hassanin A., Delsuc F., Ropiquet A., Hammer C., van Vuuren B.J., Matthee C., Ruiz-Garcia M., Catzeflis F., Areskoug V., Nguyen T.T., Couloux A. Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. CR. Biol. 2012, 335:32-50.
62. Hedtke S.M., Townsend T.M., Hillis D.M. Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst. Biol. 2006, 55:522-529.
63. Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
64. Hillis D.M. Molecular versus morphological approaches to systematics. Annu. Rev. Syst. 1987, 18:23-42.
65. Hobolth A., Christensen O.F., Mailund T., Schierup M.H. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet. 2007, 3:e7.
66. Hobolth A., Dutheil J.Y., Hawks J., Schierup M.H., Mailund T. Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res. 2011, 21:349-356.
67. Horovitz I. A phylogenetic study of living and fossil platyrrhines. Am. Mus. Novit. 1999, 3269:1-40.
68. Hovmöller R., Knowles L.L., Kubatko L.S. Effects of missing data on species tree estimation under the coalescent. Mol. Phylogenet. Evol. 2013, 69:1057-1062.
69. Huang H., Knowles L.L. What is the danger of the anomaly zone for empirical phylogenetics?. Syst. Biol. 2009, 58:527-536.
70. 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.
71. Hudson R.R. Gene genealogies and the coalescent process. Ox. Surv. Evol. Biol. 1990, 7:1-44.
72. Huelsenbeck J.P., Hillis D.M. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 1993, 42:247-264.
73. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:254-267.
74. Janies D.A., Studer J., Handelman S.K., Linchangco G. A comparison of supermatrix and supertree methods for multilocus phylogenetics using organismal datasets. Cladistics 2013, 29:560-566.
75. Kimball R.T., Wang N., Heimer-McGinn V., Ferguson C., Braun E.L. Identifying localized biases in large datasets: a case study using the avian tree of life. Mol. Phylogenet. Evol. 2013, 69:1021-1032.
76. Kluge A.G. A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 1989, 38:7-25.
77. Estimating Species Trees: Practical and Theoretical Aspects 2010, Wiley & Sons, Hoboken, New Jersey. L.L. Knowles, L.S. Kubatko (Eds.).
78. Knowles L.L. Sampling strategies for species tree estimation. Estimating Species Trees: Practical and Theoretical Aspects 2010, 163-173. Wiley-Blackwell, Hoboken, New Jersey. L.L. Knowles, L.S. Kubatko (Eds.).
79. 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.
80. Kubatko L.S. Identifying hybridization events in the presence of coalescence via model selection. Syst. Biol. 2009, 58:478-488.
81. Kubatko L.S., Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 2007, 56:17-24.
82. 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.
83. Kumar V., Hallström B.M., Janke A. Coalescent-based genome analyses resolve the early branches of the euarchontoglires. PLoS ONE 2013, 8:e60019.
84. Lanier H.C., Knowles L.L. Is recombination a problem for species-tree analyses?. Syst. Biol. 2012, 61:691-701.
85. Lanier H.C., Huang H., Knowles L.L. How low can you go? the effects of mutation rate on the accuracy of species-tree estimation. Mol. Phylogenet. Evol. 2014, 70:112-119.
86. Lambkin C. Partitioned Bremer support localizes significant conflict in bee flies (Diptera: Bombyliidae: Anthracinae). Invert. Syst. 2004, 18:351-360.
87. Leaché A.D., Rannala B. The accuracy of species tree estimation under simulation: a comparison of methods. Syst. Biol. 2011, 60:126-137.
88. Lee M., Hugall A. Partitioned likelihood support and the evaluation of data set conflict. Syst. Biol. 2003, 52:15-22.
89. Leffler E.M., Gao Z., Pfeifer S., Ségurel L., Auton A., Venn O., Bowden R., Bontrop R., Wall J.D., Sella G., et al. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 2013, 339:1578-1582.
90. Lemmon A.R., Brown J.M., Stanger-Hall K., Lemmon E.M. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst. Biol. 2009, 58:130-145.
91. Lindblad-Toh K., Garber M., Zuk O., Lin M.F., Parker B.J., Washietl S., Kheradpour P., Ernst J., Jordan G., Mauceli E., et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 2011, 478:476-482.
92. Liu L. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 2008, 24:2542-2543.
93. Liu L., Edwards S.V. Phylogenetic analysis in the anomaly zone. Syst. Biol. 2009, 58:452-460.
94. Liu L., Pearl D.K. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 2007, 56:504-514.
95. Liu L., Yu L., Kubatko L.S., Pearl D.K., Edwards S.V. Coalescent methods for estimating phylogenetic trees. Mol. Phylogenet. Evol. 2009, 53:320-328.
96. Liu L., Yu L., Pearl D.K., Edwards S.V. Estimating species phylogenies using coalescence times among sequences. Syst. Biol. 2009, 58:468-477.
97. Liu L., Yu L., Edwards S.V. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 2010, 10:302.
98. Luo Z.-X., Yuan C.-X., Meng Q.-J., Ji Q. A Jurassic eutherian mammal and divergence of marsupials and placentals. Nature 2011, 476:442-445.
99. Maddison W.P. Gene trees in species trees. Syst. Biol. 1997, 46:523-536.
100. Maddison W.P., Knowles L.L. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 2006, 55:21-30.
101. Madsen O., Scally M., Douady C.J., Kao D.J., DeBry R.W., Adkins R., Amrine H.M., Stanhope M.J., de Jong W.W., Springer M.S. Parallel adaptive radiations in two major clades of placental mammals. Nature 2001, 409:610-614.
102. McCormack J.E., Faircloth B.C., Crawford N.G., Gowaty P.A., Brumfield R.T., Glenn T.C. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res. 2012, 22:746-754.
103. McCormack J., Harvey M., Faircloth B., Crawford N., Glenn T., et al. A phylogeny of birds based on over 1500 loci collected by target enrichment and high-throughput sequencing. PLoS ONE 2013, 8:e54848.
104. McKenna M.C., Bell S.K. Classification of Mammals Above the Species Level 1997, Columbia University Press, New York.
105. McVay J., Carstens B. Phylogenetic model choice: justifying a species tree or concatenation analysis. J. Phylogenet. Evol. Biol. 2013, 1:114.
106. Meng J., Hu Y., Li C. The osteology of Rhombomylus (Mammalia: Glires): implications for the phylogeny and evolution of Glires. Bull. Am. Mus. Nat. Hist. 2003, 275:1-247.
107. Meredith R.W., Janečka J.E., Gatesy J., Ryder O.A., Fisher C.A., Teeling E.C., Goodbla A., Eizirik E., Simão T.L.L., Stadler T., et al. Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 2011, 334:521-524.
108. Miller M.A., Pfeiffer W., Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop 2010, 1-8.
109. Miyamoto M. Consensus cladograms and general classifications. Cladistics 1985, 1:186-189.
110. Miyamoto M.M., Fitch W.M. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 1995, 44:64-76.
111. Morgan C.C., Foster P.G., Webb A.E., Pisani D., McInerney J.O., O'Connell M.J. Heterogeneous models place the root of the placental mammal phylogeny. Mol. Biol. Evol. 2013, 30:2145-2156.
112. Murphy W.J., Eizirik E., Johnson W.E., Zhang Y.P., Ryder O.A., O'Brien S.J. Molecular phylogenetics and the origins of placental mammals. Nature 2001, 409:614-618.
113. Murphy W.J., Eizirik E., O'Brien S.J., Madsen O., Scally M., Douady C.J., Teeling E., Ryder O.A., Stanhope M.J., de Jong W.W., et al. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 2001, 294:2348-2351.
114. Murphy W.J., Pringle T.H., Crider T.A., Springer M.S., Miller W. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res. 2007, 17:413-421.
115. Narechania A., Baker R.H., Sit R., Kolokotronis S., DeSalle R., Planet P.J. Random addition concatenation analysis: a novel approach to the exploration of phylogenomic signal reveals strong agreement between core and shell genomic partitions in the cyanobacteria. Genome Biol. Evol. 2012, 4:30-43.
116. Nelson G. Cladistic analysis and synthesis: principles and definitions, with a historical note on Adanson's Familles des Plantes (1763-1764). Syst. Zool. 1979, 28:1-21.
117. Nikolaev S., Montoya-Burgos J.I., Margulies E.H., NISC Comparative Sequencing Program, Rougemont J., Nyffeler B., Antonarakis S.E. Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet. 2007, 3:e2.
118. Nishihara H., Hasegawa M., Okada N. Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proc. Natl. Acad. Sci. USA 2006, 103:9929-9934.
119. Nishihara H., Maruyama S., Okada N. Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals. Proc. Natl. Acad. Sci. USA 2009, 106:5235-5240.
120. Nixon K.C., Carpenter J.M. On simultaneous analysis. Cladistics 1996, 12:221-241.
121. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 2004, 53:47-67.
122. Oaks J.R. A time-calibrated species tree of Crocodylia reveals a recent radiation of the true Crocodiles. Evolution 2011, 65:3285-3297.
123. O'Brien S.J., Menotti-Raymond M., Murphy W.J., Nash W.G., Wienberg J., Stanyon R., Copeland N.G., Jenkins N.A., Womack J.E., Marshall Graves J.A. The promise of comparative genomics in mammals. Science 1999, 286:458-480.
124. O'Leary M.A. Parsimony analysis of total evidence from extinct and extant taxa, and the cetacean-artiodactyl question. Cladistics 1999, 15:315-330.
125. O'Leary M.A. The phylogenetic position of cetaceans: further combined data analyses, comparisons with the stratigraphic record and a discussion of character optimization. Am. Zool. 2001, 41:487-506.
126. O'Leary M.A., Allard M., Novacek M.J., Meng J., Gatesy J. Building the mammalian sector of the tree of life. Assembling the Tree of Life 2004, 490-516. Oxford University Press, New York. J. Cracraft, M.J. Donoghue (Eds.).
127. O'Leary M.A., Gatesy J. Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): combined analysis including fossils. Cladistics 2008, 24:397-442.
128. O'Leary M.A., Bloch J.I., Flynn J.J., Gaudin T.J., Giallombardo A., Giannini N.P., Goldberg S.L., Kraatz B.P., Luo Z.-X., Meng J., et al. The placental mammal ancestor and the post-K-Pg radiation of placentals. Science 2013, 339:662-667.
129. Oliver J.C. Microevolutionary processes generate phylogenomic discordance at ancient divergences. Evolution 2013, 67:1823-1830.
130. Patel S., Kimball R.T., Braun E.L. Error in phylogenetic estimation for bushes in the tree of life. J. Phylogenet. Evol. Biol. 2013, 1:110.
131. Pérez M.E., Pol D. Major radiations in the evolution of caviid rodents: reconciling fossils, ghost lineages, and relaxed molecular clocks. PLoS ONE 2012, 7:e48380.
132. Piertney S.B., Oliver M.K. The evolutionary ecology of the major histocompatibility complex. Heredity 2006, 96:7-21.
133. Pisani D., Wilkinson M. Matrix representation with parsimony, taxonomic congruence, and total evidence. Syst. Biol. 2002, 51:151-155.
134. Pollard D., Iyer V.N., Moses A.M., Eisen M.B. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet. 2006, 2:e173.
135. Ranwez V., Delsuc F., Ranwez S., Belkhir K., Tilak M., Douzery E.J.P. OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics. BMC Evol. Biol. 2007, 7:241.
136. Ren F., Tanaka H., Yang Z. An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst. Biol. 2005, 54:808-818.
137. Rodrigo A.G. A comment on Baum's method for combining phylogenetic trees. Taxon 1993, 42:631-636.
138. Romiguier J., Ranwez V., Delsuc F., Galtier N., Douzery E.J.P. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. Mol. Biol. Evol. 2013, 30:2124-2144.
139. Ronquist F., Klopfstein S., Vilhelmsen L., Schulmeister S., Murray D.L., Rasnitsyn A.P. A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst. Biol. 2012, 61:973-999.
140. Rosenberg N.A. Discordance of species trees with their most likely gene trees: a unifying principle. Mol. Biol. Evol. 2013, 30:2709-2713.
141. Rosenberg N.A., Tao R. Discordance of species trees with their most likely gene trees: the case of five taxa. Syst. Biol. 2008, 57:131-140.
142. Rosenfeld J.A., Payne A., DeSalle R. Random roots and lineage sorting. Mol. Phylogenet. Evol. 2012, 64:12-20.
143. Salichos L., Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 2013, 497:327-331.
144. Sanderson M.J. Confidence limits on phylogenies: the bootstrap revisited. Cladistics 1989, 5:113-129.
145. Shaw T.I., Ruan Z., Glenn T.C., Liu L. STRAW: Species TRee Analysis Web server. Nucleic Acids Res. 2013, 41(Web Server issue):W238-W241.
146. Simmons M.P. Misleading results of likelihood-based phylogenetic analyses in the presence of missing data. Cladistics 2012, 28:208-222.
147. Simmons M.P., GoloboffP.A. An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters. Mol. Phylogenet. Evol. 2013, 69:265-275.
148. Simmons M.P., Norton A.P. Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example. Mol. Phylogenet. Evol. 2013, 67:277-296.
149. Simmons N.B., Geisler J.H. Phylogenetic relationships of Icaronycteris, Archaeonycteris, Hassianycteris, and Palaeochiropteryx to extant bat lineages, with comments on the evolution of echolocation and foraging strategies in Microchiroptera. Bull. Am. Mus. Nat. Hist. 1998, 235:4-182.
150. Slowinski J.B., Page R.D.M. How should species phylogenies be inferred from sequence data?. Syst. Biol. 1999, 48:814-825.
151. Song S., Liu L., Edwards S.V., Wu S. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc. Natl. Acad. Sci. USA 2012, 109:14942-14947.
152. Spaulding M., O'Leary M.A., Gatesy J. Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution. PLoS ONE 2009, 4:e7062.
153. Springer M.S., de Jong W.W. Which mammalian supertree to bark up?. Science 2001, 291:1709-1711.
154. Springer M.S., Gatesy J. Land plant origins and coalescence confusion. Trends Plant Sci. 2014, 19:267-269.
155. Springer M.S., Murphy W.J., Eizirik E., O'Brien S.J. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. USA 2003, 100:1056-1061.
156. Springer M.S., Stanhope M.J., Madsen O., de Jong W.W. Molecules consolidate the placental mammal tree. Trends Ecol. Evol. 2004, 19:430-438.
157. Springer M.S., Meredith R.W., Gatesy J., Emerling C.A., Park J., Rabosky D.L., Stadler T., Steiner C., Ryder O.A., Janečka J.E., Fisher C.A., Murphy W.J. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS ONE 2012, 7:e49521.
158. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
159. Struck T.H., Purschke G., Halanych K.M. Phylogeny of Eunicida (Annelida) and exploring data congruence using a partition addition bootstrap alteration (PABA) approach. Syst. Biol. 2006, 55:1-20.
160. Sullivan J., Swofford D.L. Are guinea pigs rodents? the importance of adequate models in molecular phylogenetics. J. Mamm. Evol. 1997, 4:77-86.
161. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Sinauer Associates, Sunderland, Massachusetts.
162. Swofford D.L., Waddell P.J., Huelsenbeck J.P., Foster P.G., Lewis P.O., Rogers J.S. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 2001, 50:525-539.
163. 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.
164. Tsagkogeorga G., Parker J., Stupka E., Cotton J.A., Rossiter S.J. Phylogenomic analyses elucidate the evolutionary relationships of bats. Curr. Biol. 2013, 23:2262-2267.
165. Underhill P.A., Kivisild T. Use of Y chromosome and mitochondrial DNA population structure in tracing human migrations. Annu. Rev. Genet. 2007, 41:539-564.
166. Wahlberg N., Braby M.F., Brower A.V.Z., de Jong R., Lee M.-M., Nylin S., Pierce N.E., Sperling F.A.H., Vila R., Warren A.D., Zakharov E. Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proc. Biol. Sci. 2005, 272:1577-1586.
167. Wildman D.E., Uddin M., Opazo J.C., Liu G., Lefort V., Guindon S., Gascuel O., Grossman L.I., Romero R., Goodman M. Genomics, biogeography, and the diversification of placental mammals. Proc. Natl. Acad. Sci. USA 2007, 104:14395-14400.
168. Wolsan M., Sato J.J. Effects of data incompleteness on the relative performance of parsimony and Bayesian approaches in a supermatrix phylogenetic reconstruction of Mustelidae and Procyonidae (Carnivora). Cladistics 2010, 26:168-194.
169. Wu S., Song S., Liu L., Edwards S. Reply to Gatesy and Springer: the multispecies coalescent model can effectively handle recombination and gene tree heterogeneity. Proc. Natl. Acad. Sci. USA 2013, 110:E1180.
170. Xi Z., Rest J.S., Davis C.C. Phylogenomics and coalescent analyses resolve extant seed plant relationships. PLoS ONE 2013, 8:e80870.
171. Yu Y., Warnow T., Nakhleh L. Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles. J. Comput. Biol. 2011, 18:1543-1559.
172. Zhong B., Liu L., Yan Z., Penny D. Origin of land plants using the multispecies coalescent model. Trends Plant Sci. 2013, 18:492-495.
173. Zhong B., Liu L., Penny D. The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy. Trends Plant Sci. 2014, 19:270-272.
174. Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion. Ph. D. Dissertation, The University of Texas at Austin.
175. Zwickl D.J., Hillis D.M. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 2002, 51:588-598.