Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family-level tree for Mammalia

Cladistics

Volumn 33, Issue 3, 2017, Pages 295-332

  Gatesy, John ^a   Meredith, Robert W ^b   Janecka, Jan E ^c   Simmons, Mark P ^d   Murphy, William J ^e   Springer, Mark S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MONTCLAIR STATE UNIVERSITY   (United States)

^c DUQUESNE UNIVERSITY   (United States)

^d Department of Environmental and Radiological Health Sciences   (United States)

^e TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOGEOGRAPHY; COALESCENCE; DATA SET; GENOMICS; MAMMAL; PHYLOGENETICS; SPATIAL DISTRIBUTION; SPATIAL RESOLUTION; TAXONOMY;

MAMMALIA;

ARTICLE; CLADISTICS; MAMMAL; NONHUMAN; PHYLOGENOMICS;

EID: 84981717848     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/cla.12170     Document Type: Article

References (151)

1. Agnarsson, I., Kuntner, M., Collado, L.J., 2010. Dogs, cats, and kin: a molecular species-level phylogeny of Carnivora. Mol. Phylogenet. Evol. 54, 726–745.
2. Aguirre-Fernández, G., Fordyce, R.E., 2014. Papahu taitapu, gen. et sp. nov., an early Miocene stem odontocete (Cetacea) from New Zealand. J. Vertebr. Paleontol. 34, 195–210.
3. Anderson, F., Swofford, D., 2004. Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA Mol. Phylogenet. Evol. 33, 440–451.
4. Baker, R., DeSalle, R., 1997. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst. Biol. 46, 654–673.
5. Barrett, M., Donoghue, M.J., Sober, E., 1991. Against consensus. Syst. Zool. 40, 486–493.
6. Bayzid, M.S., Mirarab, S., Boussau, B., Warnow, T., 2015. Weighted statistical binning: enabling statistically consistent genome-scale phylogenetic analyses. PLoS ONE 10, e0129183.
7. Bergsten, J., 2005. A review of long-branch attraction. Cladistics 21, 163–193.
8. Betancur-R, R., Li, C., Munroe, T.A., Ballesteros, J.A., Ortí, G., 2013. Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). Syst. Biol. 62, 763–785.
9. Bininda-Emonds, O.R.P., Gittleman, J.L., Purvis, A., 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biol. Rev. 74, 143–175.
10. 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., 2007. The delayed rise of present-day mammals. Nature 446, 507–512.
11. Bremer, K., 1994. Branch support and tree stability. Cladistics 10, 295–304.
12. Bromham, L., 2011. The genome as a life-history character: why rate of molecular evolution varies between mammal species. Phil. Trans. R. Soc. B 366, 2503–2513.
13. Cassens, I., Vicario, S., Waddell, V.G., Balchowsky, H., Van Belle, D., Ding, W., Fan, C., Lal Mohan, R.S., Simões-Lopes, P.C., Bastida, R., Meyer, A., Stanhope, M.J., Milinkovitch, M.C., 2000. Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages. Proc. Natl Acad. Sci. USA 97, 11343–11347.
14. Chiari, Y., Cahais, V., Galtier, N., Delsuc, F., 2012. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol. 10, 65.
15. Chippindale, P., Wiens, J., 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 43, 278–287.
16. Chou, J., Gupta, A., Yaduvanshi, S., Davidson, R., Nute, M., Mirarab, S., Warnow, T., 2015. A comparative study of SVDquartets and other coalescent-based species tree estimation methods. BMC Genom. 16, S2.
17. Collins, T., Fedrigo, O., Naylor, G., 2005. Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenies. Syst. Biol. 54, 493–500.
18. Delsuc, F., Scally, M., Madsen, O., Stanhope, M.J., de Jong, W.W., Catzeflis, F.M., Springer, M.S., Douzery, E.J.P., 2002. Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting. Mol. Biol. Evol. 19, 1656–1671.
19. Doronina, L., Churakov, G., Shi, J., Brosius, J., Baertsch, R., Clawson, H., Schmitz, J., 2015. Exploring massive incomplete lineage sorting in arctoids (Laurasiatheria, Carnivora). Mol. Biol. Evol. 32, 3194–3204.
20. Douady, C.J., Douzery, E.J.P. 2009. Hedgehogs, shrews, moles, and solenodons (Eulipotyphla). In: Hedges, S.B., Kumar, S. (Eds.), The Timetree of Life, Oxford University Press, Oxford, pp. 495–498.
21. Douady, C.J., Chatelier, P.I., Madsen, O., de Jong, W.W., Catzeflis, F., Springer, M.S., Stanhope, M.J., 2002. Molecular phylogenetic evidence confirming the Eulipotyphla concept and in support of hedgehogs as the sister group to shrews. Mol. Phylogenet. Evol. 25, 200–209.
22. Douady, C.J., Scally, M., Springer, M.S., Stanhope, M.J., 2004. “Lipotyphlan” phylogeny based on the growth hormone receptor gene: a reanalysis. Mol. Phylogenet. Evol. 30, 778–788.
23. Edwards, S.V., 2009. Is a new and general theory of molecular systematics merging? Evolution 63, 1–19.
24. Edwards, S.V., Xi, Z., Janke, A., Faircloth, B.C., McCormack, J.E., Glenn, T.C., Zhong, B., Wu, S., Lemmon, E.M., Lemmon, A.R., Leaché, A.D., Liu, L., Davis, C.C., 2016. Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics. Mol. Phylogenet. Evol. 94, 447–462.
25. Eizirik, E., Murphy, W.J., Koepfli, K.-P., Johnson, W.E., Dragoo, J.W., Wayne, R.K., O'Brien, S.J., 2010. Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Mol. Phylogenet. Evol. 56, 49–63.
26. Emerling, C.A., Huynh, H.T., Nguyen, M.A., Meredith, R.W., Springer, M.S., 2015. Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution. Proc. R. Soc. B 282, 20151817.
27. Farris, J.S., Albert, V.A., Källersjö, M., Lipscomb, D., Kluge, A.G., 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12, 99–124.
28. Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.
29. Flynn, J.J., Finarelli, J.A., Zehr, S., Hsu, J., Nedbal, M.A., 2005. Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst. Biol. 54, 317–337.
30. Fordyce, R.E., 1994. Waipatia maerewhenua, new genus and new species (Waipatiidae, new family), an archaic late Oligocene dolphin (Cetacea: Odontoceti: Platanistoidea) from New Zealand. In: Berta, A., Deméré, T.A. (Eds.), Contributions in Marine Mammal Paleontology Honoring Frank Whitmore Jr. Proc. San Diego Soc. Nat. Hist. 29, 147–176.
31. Gatesy, J., Baker, R.H., 2005. Hidden likelihood support in genomic data: can forty-five wrongs make a right? Syst. Biol. 54, 483–492.
32. Gatesy, J., Springer, M.S., 2013. Concatenation versus coalescence versus “concatalescence”. Proc. Natl Acad. Sci. USA 110, E1179.
33. Gatesy, J., Springer, M.S., 2014. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol. Phylogenet. Evol. 80, 231–266.
34. Gatesy, J., O'Grady, P., Baker, R., 1999. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 15, 271–313.
35. Gatesy, J., Amato, G., Norell, M., DeSalle, R., Hayashi, C., 2003. Combined support for wholesale taxic atavism in gavialine crocodylians. Syst. Biol. 52, 403–422.
36. Gatesy, J., Geisler, J.H., Chang, J., Buell, C., Berta, A., Meredith, R.W., Springer, M.S., McGowen, M., 2013. A phylogenetic blueprint for a modern whale. Mol. Phylogenet. Evol. 66, 479–506.
37. Geisler, J.H., Sanders, A.E., 2003. Morphological evidence for the phylogeny of Cetacea. J. Mammal. Evol. 10, 23–129.
38. Geisler, J.H., McGowen, M.R., Yang, G., Gatesy, J., 2011. A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea. BMC Evol. Biol. 11, 112.
39. Goloboff, P.A., 1993. Estimating character weights during tree search. Cladistics 9, 83–91.
40. Goloboff, P.A., Farris, J.S., 2001. Methods for quick consensus estimation. Cladistics 17, S26–S34.
41. Goloboff, P.A., Carpenter, J.M., Arias, J.S., Miranda Esquivel, D.R., 2008. Weighting against homoplasy improves phylogenetic analysis of morphological data sets. Cladistics 24, 1–16.
42. Guindon, S., Gascuel, O., 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696–704.
43. Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., Gascuel, O., 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321.
44. Hallström, B.M., Janke, A., 2010. Mammalian evolution may not be strictly bifurcating. Mol. Biol. Evol. 27, 2804–2816.
45. Hallström, B., Schneider, A., Zoller, S., Janke, A., 2011. A genomic approach to examine the complex evolution of laurasiatherian mammals. PLoS ONE 6, e28199.
46. Hamilton, H., Caballero, S., Collins, A.G., Brownell, R.L., 2001. Evolution of river dolphins. Proc. R. Soc. Lond. B 268, 549–556.
47. Hartig, G., Churakov, G., Warren, W., Brosius, J., Makalowski, W., Schmitz, J., 2013. Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids. Sci. Rep. 3, 1756.
48. 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., 2012. Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C. R. Biol. 335, 32–50.
49. Heled, J., Drummond, A.J., 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27, 570–580.
50. Heyning, J.E., 1989. Comparative facial anatomy of beaked whales (Ziphiidae) and a systematic revision among the families of extant Odontoceti. Nat. Hist. Mus. Los Angeles Cty. Contrib. Sci. 405, 1–64.
51. Heyning, J.E., 1997. Sperm whale phylogeny revisited: analysis of the morphological evidence. Mar. Mammal Sci. 13, 596–613.
52. Hou, Z., Romero, R., Wildman, D.E., 2009. Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data. Mol. Phylogenet. Evol. 52, 660–664.
53. Huang, H., He, Q., Kubatko, L.S., Knowles, L.L., 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.
54. Huelsenbeck, J., Hillis, D., 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42, 247–264.
55. Jameson, N.M., Hou, Z.-C., Sterner, K.N., Weckle, A., Goodman, M., Steiper, M.E., Wildman, D.E., 2011. Genomic data reject the hypothesis of a prosimian primate clade. J. Hum. Evol. 61, 295–305.
56. Kimball, R.T., Wang, N., Heimer-McGinn, V., Ferguson, C., Braun, E.L., 2013. Identifying localized biases in large datasets: a case study using the avian tree of life. Mol. Phylogenet. Evol. 69, 1021–1032.
57. Kluge, A.G., 1989. A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38, 7–25.
58. Kubatko, L., Carstens, B.C., Knowles, L.L., 2009. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25, 971–973.
59. Kumar, V., Hallström, B.M., Janke, A., 2013. Coalescent-based genome analyses resolve the early branches of the Euarchontoglires. PLoS ONE 8, e60019.
60. Kuntner, M., May-Collado, L.J., Agnarsson, I., 2011. Phylogeny and conservation priorities of afrotherian mammals (Afrotheria, Mammalia). Zool. Scr. 40, 1–15.
61. Lambert, O., 2005. Phylogenetic affinities of the long-snouted dolphin Eurhinodelphis (Cetacea, Odontoceti) from the Miocene of Antwerp, Belgium. Palaeontology 48, 653–679.
62. Lee, M., Hugall, A., 2003. Partitioned likelihood support and the evaluation of data set conflict. Syst. Biol. 52, 15–22.
63. Leffler, E., Gao, Z., Pfeifer, S., Ségurel, L., Auton, A., Venn, O., Bowden, R., Bontrop, R., Wall, J., Sella, G., Donnelly, P., McVean, G., Przeworski, M., 2013. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 339, 1578–1582.
64. Liu, L., Yu, L., Pearl, D.K., Edwards, S.V., 2009. Estimating species phylogenies using coalescence times among sequences. Syst. Biol. 58, 468–477.
65. Liu, L., Yu, L., Edwards, S.V., 2010. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 10, 302.
66. Liu, L., Xi, Z., Wu, S., Davis, C.C., Edwards, S.V., 2015. Estimating phylogenetic trees from genome-scale data. Ann. N. Y. Acad. Sci. 1360, 36–53.
67. Maddison, W.P., 1997. Gene trees in species trees. Syst. Biol. 46, 523–536.
68. 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., 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409, 610–614.
69. May-Collado, L., Agnarsson, I., 2006. Cytochrome b and Bayesian inference of whale phylogeny. Mol. Phylogenet. Evol. 38, 2344–2354.
70. McCormack, J.E., Faircloth, B.C., Crawford, N.G., Gowaty, P.A., Brumfield, R.T., Glenn, T.C., 2012. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res. 22, 746–754.
71. McGowen, M.R., Spaulding, M., Gatesy, J., 2009. Divergence date estimation and a comprehensive molecular tree of extant cetaceans. Mol. Phylogenet. Evol. 53, 891–906.
72. McVay, J., Carstens, B., 2013. Phylogenetic model choice: justifying a species tree or concatenation analysis. J. Phylogenetics. Evol. Biol. 1, 114.
73. Meredith, R.W., Janecka, J.E., Gatesy, J., Ryder, O.A., Fisher, C.A., Teeling, E.C., Goodbla, A., Eizirik, E., Simão, T.L.L., Stadler, T., Rabosky, D.L., Honeycutt, R.L., Flynn, J.J., Ingram, C.M., Steiner, C., Williams, T.L., Robinson, T.J., Burk-Herrick, A., Westerman, M., Ayoub, N.A., Springer, M.S., Murphy, W.J., 2011. Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334, 521–524.
74. Messenger, S.L., McGuire, J.A., 1998. Morphology, molecules, and the phylogenetics of cetaceans. Syst. Biol. 47, 90–124.
75. Mirarab, S., Warnow, T., 2015. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31, i44–i52.
76. Mirarab, S., Reaz, R., Bayzid, M.S., Zimmermann, T., Swenson, M.S., Warnow, T., 2014. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30, i541–i548.
77. Miyamoto, M., 1985. Consensus cladograms and general classifications. Cladistics 1, 186–189.
78. Morgan, C., Foster, P., Webb, A., Pisani, D., McInerney, J., O'Connell, M., 2013. Heterogeneous models place the root of the placental mammal phylogeny. Mol. Biol. Evol. 30, 2145–2156.
79. Murphy, W.J., Eizirik, E., Johnson, W.E., Zhang, Y.P., Ryder, O.A., O'Brien, S.J., 2001a. Molecular phylogenetics and the origins of placental mammals. Nature 409, 614–618.
80. 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., Springer, M.S., 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294, 2348–2351.
81. Murphy, W.J., Pringle, T.H., Crider, T.A., Springer, M.S., Miller, W., 2007. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res. 17, 413–421.
82. Nikaido, M., Rooney, A.P., Okada, N., 1999. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: hippopotamuses are the closest extant relatives of whales. Proc. Natl Acad. Sci. USA 96, 10261–10266.
83. Nikaido, M., Matsuno, F., Hamilton, H., Brownell, R.L., Cao, Y., Ding, W., Zuoyan, Z., Shedlock, A.M., Fordyce, R.E., Hasegawa, M., Okada, N., 2001. Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins. Proc. Natl Acad. Sci. USA 98, 7384–7389.
84. Nikaido, M., Hamilton, H., Makino, H., Sasaki, T., Takahashi, K., Goto, M., Kanda, N., Pastene, L.A., Okada, N., 2006. Baleen whale phylogeny and a past extensive radiation event revealed by SINE insertion analysis. Mol. Biol. Evol. 23, 866–873.
85. Nikaido, M., Piskurek, O., Okada, N., 2007. Toothed whale monophyly reassessed by SINE insertion analysis: the absence of lineage sorting effects suggests a small population of a common ancestral species. Mol. Phylogenet. Evol. 40, 216–224.
86. Nikolaev, S., Montoya-Burgos, J., Margulies, E., Rougemont, J., Nyffeler, B., Antonarakis, S., 2007. Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet. 3, e2.
87. Nishihara, H., Hasegawa, M., Okada, N., 2006. Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proc. Natl Acad. Sci. USA 103, 9929–9934.
88. Nishihara, H., Maruyama, S., Okada, N., 2009. Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals. Proc. Natl Acad. Sci. USA 106, 5235–5240.
89. Nixon, K., Carpenter, J., 1996. On simultaneous analysis. Cladistics, 12, 221–241.
90. Nowak, R.M., 1991. Walker's Mammals of the World, 5th edn. The Johns Hopkins University Press, Baltimore.
91. Nyakatura, K., Bininda-Emonds, O.R.P., 2012. Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates. BMC Biol. 10, 12.
92. Ogawa, L.M., Vallender, E.J., 2014. Evolutionary conservation in genes underlying human psychiatric disorders. Front. Hum. Neurosci. 8, 283.
93. 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., Ni, X., Novacek, M.J., Perini, F.A., Randall, Z.S., Rougier, G.W., Sargis, E.J., Silcox, M.T., Simmons, N.B., Spaulding, M., Velazco, P.M., Weksler, M., Wible, J.R., Cirranello, A.L., 2013. The placental mammal ancestor and the post-K-Pg radiation of placentals. Science 339, 662–667.
94. Patel, S., Kimball, R., Braun, E., 2013. Error in phylogenetic estimation for bushes in the tree of life. J. Phylogenetics. Evol. Biol. 1, 110.
95. Perelman, P., Johnson, W.E., Roos, C., Seuánez, H.N., Horvath, J.E., Moreira, M.A.M., Kessing, B., Pontius, J., Roelke, M., Rumpler, Y., Schneider, M.P.C., Silva, A., O'Brien, S.J., Pecon-Slattery, J., 2011. A molecular phylogeny of living primates. PLoS Genet. 7, e1001342.
96. Plyusnin, A., Sironen, T., 2014. Evolution of hantaviruses: co-speciation with reservoir hosts for more than 100 MYR. Virus Res. 187, 22–26.
97. Prasad, A.B., Allard, M.W., The NISC Comparative Sequencing Program, Green, E.D., 2008. Confirming the phylogeny of mammals by use of large comparative sequence datasets. Mol. Biol. Evol. 25, 1795–1808.
98. Price, S.A., Bininda-Emonds, O.R.P., Gittleman, J.L., 2005. A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla). Biol. Rev. 80, 1–29.
99. Prum, R.O., Berv, J.S., Dornburg, A., Field, D.J., Townsend, J.P., Lemmon, E.M., Lemmon, A.R., 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526, 569–573.
100. de Queiroz, A., Gatesy, J., 2007. The supermatrix approach to systematics. Trends Ecol. Evol. 22, 34–41.
101. dos Reis, M., Inoue, J., Hasegawa, M., Asher, R., Donoghue, P., Yang, Z., 2012. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. R. Soc. B 279, 3491–3500.
102. Robinson, D.F., Foulds, L.R., 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131–147.
103. Roca, A.L., Bar-Gal, G.K., Eizirik, E., Helgen, K.M., Maria, R., Springer, M.S., O'Brien, S.J., Murphy, W.J., 2004. Mesozoic origin for West Indian insectivores. Nature 429, 649–651.
104. Roch, S., Warnow, T., 2015. On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods. Syst. Biol. 64, 663–676.
105. Rokas, A., Holland, P., 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15, 454–459.
106. Romiguier, J., Ranwez, V., Delsuc, F., Galtier, N., Douzery, E., 2013. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. Mol. Biol. Evol. 30, 2124–2144.
107. Rosenberg, M.S., Kumar, S., 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl Acad. Sci. USA 98, 10751–10756.
108. Rosenfeld, J.A., Payne, A., DeSalle, R., 2012. Random roots and lineage sorting. Mol. Phylogenet. Evol. 64, 12–20.
109. Salichos, L., Rokas, A., 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497, 327–331.
110. Salichos, L., Stamatakis, A., Rokas, A., 2014. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol. Biol. Evol. 31, 1261–1271.
111. Sayyari, E., Mirarab, S., 2016. Fast coalescent-based computation of local branch support from quartet frequencies. Mol. Biol. Evol. 33, 1654–1668.
112. Scally, M., Madsen, O., Douady, C.J., de Jong, W.W., Stanhope, M.J., Springer, M.S., 2001. Molecular evidence for the major clades of placental mammals. J. Mammal. Evol. 8, 239–277.
113. Seiffert, E.R., 2010. The oldest and youngest records of afrosoricid placentals from the Fayum Depression of northern Egypt. Acta Palaeontol. Pol. 55, 599–616.
114. Seiffert, E.R., Simons, E.L., Ryan, T.M., Bown, T.M., Attia, Y., 2007. New remains of Eocene and Oligocene Afrosoricida (Afrotheria) from Egypt, with implications for the origin(s) of afrosoricid zalambdondonty. J. Vertebr. Paleontol. 27, 963–972.
115. Shaw, T.I., Ruan, Z., Glenn, T.C., Liu, L., 2013. STRAW: Species TRee Analysis Web server. Nucleic Acids Res. 41, W238–W241.
116. Shedlock, A.M., Okada, N., 2000. SINE insertions: powerful tools for molecular systematics. BioEssays 22, 148–160.
117. Simmons, M.P., Freudenstein, J.V., 2011. Spurious 99% bootstrap and jackknife support for unsupported clades. Mol. Phylogenet. Evol. 61, 177–191.
118. Simmons, M.P., Gatesy, J., 2015. Coalescence vs. concatenation: sophisticated analyses vs. first principles applied to rooting the angiosperms. Mol. Phylogenet. Evol. 91, 98–122.
119. Simmons, M.P., Sloan, D.B., Gatesy, J., 2016. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Mol. Phylogenet. Evol. 97, 76–89.
120. Slater, G.J., 2013. Integrating fossils with molecular phylogenies improves inference of trait evolution. Meth. Ecol. Evol. 4, 734–744.
121. Song, S., Liu, L., Edwards, S.V., Wu, S., 2012. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc. Natl Acad. Sci. USA 109, 14942–14947.
122. Sorenson, M.D., 1999. TreeRot, Version 2. Boston University, Boston.
123. Springer, M.S., Gatesy, J., 2014. Land plant origins and coalescence confusion. Trends Plant Sci. 19, 267–269.
124. Springer, M.S., Gatesy, J., 2016. The gene tree delusion. Mol. Phylogenet. Evol. 94, 1–33.
125. Springer, M.S., Murphy, W.J., Eizirik, E., O'Brien, S.J., 2003. Placental mammal diversification and the Cretaceous–Tertiary boundary. Proc. Natl Acad. Sci. USA 100, 1056–1061.
126. Springer, M.S., Stanhope, M.J., Madsen, O., de Jong, W.W., 2004. Molecules consolidate the placental mammal tree. Trends Ecol. Evol. 19, 430–438.
127. Springer, M.S., Murphy, W.J., Eizirik, E., O'Brien, S.J. 2005. Molecular evidence for major placental clades. In: Rose, K.D., Archibald, J.D. (Eds.), The Rise of Placental Mammals: Origins and Relationships of the Major Extant Clades. The Johns Hopkins University Press, Baltimore, pp. 37–49.
128. Springer, M.S., Burk-Herrick, A., Meredith, R., Eizirik, E., Teeling, E., O'Brien, S.J., Murphy, W.J., 2007a. The adequacy of morphology for reconstructing the early history of placental mammals. Syst. Biol. 56, 673–684.
129. Springer, M.S., Murphy, W.J., Eizirik, E., Madsen, O., Scally, M., Douady, C.J., Teeling, E.C., Stanhope, M.J., de Jong, W.W., O'Brien, S.J., 2007b. A molecular classification for the living orders of placental mammals and the phylogenetic placement of primates. In: Ravosa, M.J., Dagosto, M. (Eds.), Primate Origins: Adaptations and Evolution. Springer, New York, pp. 1–28.
130. 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., 2012. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS ONE 7, e49521.
131. Stamatakis, A., 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690.
132. Stamatakis, A., Hoover, P., Rougemont, J., 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 57, 758–771.
133. Stanhope, M.J., Madsen, O., Waddell, V.G., Cleven, G.C., de Jong, W.W., Springer, M.S., 1998a. Highly congruent molecular support for a diverse superordinal clade of endemic African mammals. Mol. Phylogenet. Evol. 9, 501–508.
134. Stanhope, M.J., Waddell, V.G., Madsen, O., de Jong, W.W., Hedges, S.B., Cleven, G.C., Kao, D., Springer, M.S., 1998b. Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals. Proc. Natl Acad. Sci. USA 95, 9967–9972.
135. Steeman, M.E., Hebsgaard, M.B., Fordyce, R.E., Ho, S.Y.W., Rabosky, D.L., Nielsen, R., Rahbek, C., Glenner, H., Sørensen, M.V., Willerslev, E., 2009. Radiation of extant cetaceans driven by restructuring of the oceans. Syst. Biol. 58, 573–585.
136. Sullivan, J., Swofford, D., 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics J. Mammal. Evol. 4, 77–86.
137. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland, MA.
138. Teeling, E.C., Hedges, S.B., 2013. Making the impossible possible: rooting the tree of placental mammals. Mol. Biol. Evol. 30, 1999–2000.
139. Townsend, T.M., Mulcahy, D.G., Noonan, B.P., Sites, J.W., Kuczynski, C.A., Wiens, J.J., Reeder, T.W., 2011. 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. 61, 363–380.
140. Tsagkogeorga, G., Parker, J., Stupka, E., Cotton, J.A., Rossiter, S.J., 2013. Phylogenomic analyses elucidate the evolutionary relationships of bats. Curr. Biol. 23, 2262–2267.
141. Vachaspati, P., Warnow, T., 2015. ASTRID: Accurate Species TRees from Internode Distances. BMC Genom. 16, S3.
142. Vrana, P.B., Milinkovitch, M.C., Powell, J.R., Wheeler, W.C., 1994. Higher level relationships of the arctoid Carnivora based on sequence data and “total evidence”. Mol. Phylogenet. Evol. 3, 47–58.
143. Wickett, N.J, Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E, Matasci, N, Ayyampalayam, S., Barker, M.S., Burleigh, J.G., Gitzendanner, M.A., Ruhfel, B.R., Wafula, E., Der, J.P., Graham, SW, Mathews, S., Melkonian, M., Soltis, D.E., Soltis, P.S., Miles, N.W., Rothfels, C.J., Pokorny, L., Shaw, A.J., DeGironimo, L., Stevenson, D.W., Surek, B., Villarreal, J.C., Roure, B., Philippe, H, dePamphilis, C.W., Chen, T., Deyholos, M.K., Baucom, R.S., Kutchan, T.M., Augustin, M.M., Wang, J., Zhang, Y., Tian, Z., Yan, Z., Wu, X., Sun, X., Wong, G.K., Leebens-Mack, J., 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc. Natl Acad. Sci. USA 111, E4859–E4868.
144. Wildman, D., Uddin, M., Opazo, J., Liu, G., Lefort, V., Guindon, S., Gascuel, O., Grossman, G., Romero, R., Goodman, M., 2007. Genomics, biogeography, and the diversification of placental mammals. Proc. Natl Acad. Sci. USA 104, 14395–14400.
145. Wu, S., Song, S., Liu, L., Edwards, S., 2013. Reply to Gatesy and Springer: the multispecies coalescent model can effectively handle recombination and gene tree heterogeneity. Proc. Natl Acad. Sci. USA 110, E1180.
146. Wyss, A.R., Flynn, J.J. 1993. A phylogenetic analysis and definition of the Carnivora. In: Szalay, F., Novacek, M., McKenna, M. (Eds.), Mammal Phylogeny: Placentals, Vol. 1. Springer-Verlag, New York, pp. 32–52.
147. Xi, Z., Liu, L., Rest, J.S., Davis, C.C., 2014. Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies. Syst. Biol. 63, 919–932.
148. Xi, Z., Liu, L., Davis, C.C., 2016. The Impact of missing data on species tree estimation. Mol. Biol. Evol. 33, 838–860.
149. Zhong, B., Liu, L., Yan, Z., Penny, D., 2013. Origin of land plants using the multispecies coalescent model. Trends Plant Sci. 18, 492–495.
150. Zhong, B., Liu, L., Penny, D., 2014. The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy. Trends Plant Sci. 19, 270–272.
151. Zhou, X., Xu, S., Xu, J., Chen, B., Zhou, K., Yang, G., 2011. Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals. Syst. Biol. 61, 150–164.