. Author manuscript; available in PMC: 2017 Oct 10.

Published in final edited form as: Nat Ecol Evol. 2017 Apr 10;1(5):126. doi: 10.1038/s41559-017-0126

Table 1.

The 17 contentious branches and 6 well-established branches (controls) as well as their alternative hypotheses in three phylogenomic data matrices from plants, animals, and fungi.

Kingdom	Branch	Maximum likelihood tree (T1)	Alternative hypothesis (T2)	P-value of AU^& test
Plants	Amborella	Amborella as sister to all other flowering plants	Amborella + Nuphar as sister to all other flowering plants	0.001*
	Angiosperm	Magnoliids as sister to Eudicots + Chloranthales	Magnoliids + Chloranthales as sister to Eudicots	0.030*
	Bryophyte	Hornworts as sister to all other land plants	Hornworts as sister to mosses + liverworts	0.012*
	Gymnosperm	Gnetales as sister to the Pinaceae, nested within the Coniferales	Gnetales as sister to the Coniferales	2e-06*
	Land plant	Zygnematophyceae as sister to all land plants	Charales as sister to all land plants	0.003*
	Control: Seed plant	Seed plants are monophyletic	Seed plants are paraphyletic	3e-99*
	Control: Moss	Mosses are monophyletic	Mosses are paraphyletic	1e-43*
Animals	Amphibian	Gymnophiona as sister to all other amphibians	Anura as sister to all other amphibians	6e-13*
	Eutherian	Xenarthra + Afrotheria as sister to all other placental mammals	Afrotheria as sister to all other placental mammals	0.036*
	Lungfish	Lungfishes as sister to all tetrapods	Lungfishes + coelacanths as sister to all tetrapods	7e-41*
	Neoavian	Pigeons as sister to all other Neoaves	Falcons as sister to all other Neoaves	0.322
	Teleost	Elopomorpha + Osteoglossomorpha as sister to all other teleosts	Osteoglossomorpha alone as sister to all other teleosts	2e-05*
	Turtle	Turtles as sister to archosaurs (birds + crocodiles)	Turtles as sister to crocodiles	1e-29*
	Control: Amniote	Amniotes are monophyletic	Amniotes are paraphyletic	2e-05*
	Control: Mammal	Mammals are monophyletic	Mammals are paraphyletic	1e-06*
Fungi	Ascoideaceae	Ascoideaceae as sister to Phaffomycetaceae + Saccharomycodaceae + Saccharomycetaceae	Ascoideaceae as sister to Pichiaceae + CUG-Ser clade + Phaffomycetaceae + Saccharomycodaceae + Saccharomycetaceae	0.005*
	Candida glabrata	Candida glabrata + Nakaseomyces as sister to Saccharomyces	Kazachstania + Naumovozyma as sister to Saccharomyces	1e-07*
	Candida tanzawaensis	Candida tanzawaensis as sister to Scheffersomyces stipitis + Candida	Candida tanzawaensis + Scheffersomyces stipiti as sister to Candida	0.012*
	Candida tenuis	Candida tenuis as sister to all other CUG-Ser yeasts	Candida tenuis as sister to Debaryomyces +Meyerozyma + Candida	2e-59*
	Hyphopichia	Hyphopichia burtonii as sister to Candida auris + Metschnikowia	Hyphopichia burtonii as sister to Debaryomyces + Meyerozyma	1e-53*
	WGD clade	Yeasts of the WGD clade are monophyletic	Yeasts of the WGD clade are paraphyletic	0.002*
	Control: Saccharomycetaceae	Yeasts of the family Saccharomycetaceae are monophyletic	Yeasts of the family Saccharomycetaceae are paraphyletic	2e-05*
	Control: Pichiaceae	Yeasts of the family Pichiaceae are paraphyletic	Yeasts of the family Pichiaceae are monophyletic	7e-05*

For each branch, the topological test between T1 and T2 was conducted using the approximately unbiased (AU)¹⁹ test, as implemented in the CONSEL software, version 2.0²⁰, with 1000 bootstrap replicates. Star symbols (*) indicate cases where T1 is significantly better than T2 (P-value < 0.05).