Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages

Lancaster, Lesley T

doi:10.1186/1471-2148-10-162

BMC Ecology and Evolution

Table 3 Nucleotide substitution models and calibration dates for each of the 13 clades under consideration.

From: Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages

Clade	Substitution model	Calibration Priors
		Node	age (mya)	source	citation	distribution *
Antirrhineae	GTR+I+Γ	Ingroup	38-48	previous estimate	[39]	Normal, 43, 3
		Acanthorrhinum, Albraunia, Antirrhinum, Chaenorhhinum, Galvezia, Holzneria, Misopates, Mohavea, and Pseudomisopates	21.49 ± 4.27	previous estimate	[39]	Normal, 21.49, 6
Artemisia	GTR+Γ	Ingroup	34 - 45	fossil and previous estimate	[40–42]	Uniform, 34, 45
		A. canariensis - A. arborescens split	17.1	vicariance event	[43]	Uniform, 0, 17.1
Chironiinae	GTR+Γ	Ingroup	54.8	fossil - earliest Gentianaceae	[44]	Uniform, 0, 54.8
		Mexican species of Zeltnera	5	vicariance event	[45]	Normal, 5, 0.2
		Z. trichantha - Z. namophila split	2	vicariance event	[45]	Normal, 2, 0.2
Ericameria	GTR+Γ	Ingroup	5-26	previous estimate	[46]	Uniform, 5, 26
		E. ophitidis - E. gilmanii split	5	vicariance event	[47]	Normal, 5, 1.0
Lepidium	GTR+Γ			ITS rate for Brassicaceae	[48]	Uniform, 4.5E-3, 8.3E-3 subst/site/my
Lotus	GTR+Γ	Ingroup	65	fossil	[49]	Lognormal, 65, 0, 1
		Canary Island clade	0-21	vicariance event	[50]	Normal, 12, 3
Lupinus	GTR+I+Γ	Ingroup	18	previous estimate	[51]	Normal, 18, 2.5
Lycieae	GTR+I+Γ	Ingroup	86-20	previous estimate	[52, 53]	Uniform, 20, 86
		Lycium	29.4 ± 9.7	previous estimate	[52]	Normal, 29.5, 5.9
		Australian-Eurasian split	14.1 ± 3.2	previous estimate	[52]	Normal, 14.1, 1.945
Phrymoideae	GTR+I+Γ	Ingroup + Verbina	49.4	previous estimate - minimum	[54]	Lognormal, 49.4, 0, 1
		Phryma	3.93	previous estimate	[54]	Normal, 3.93, 2.46
Polemoniaceae	GTR+I+Γ	Ingroup	41.3 - 91.2	previous estimate	[55, 56]	Normal, 50, 5
		Giliae	41.3	fossil	[55]	Lognormal, 41.3, 0, 1
Salvia	GTR+I+Γ	Ingroup	25	fossil	[57, 58]	Lognormal, 25, 0, 1
		S. glutinosa - (S. digitaloidies, S. robrowskii, S. cynica, S. przewalskii) split	11.61 - 3.6	fossil	[59]	Lognormal, 3.6, 2, 1
		S. officinalis - S. aucheri split	3.6 - 2.59	fossil	[60]	Lognormal, 2.69, 2, 1
Saniculoideae	GTR+Γ	Ingroup	33.7 - 69	fossil and previous estimate	[53, 61, 62]	Lognormal, 33.7, 2, 1
		Sanicula	33.7	fossil	[61]	Lognormal, 33.7, 0, 1
Sidalcea, etc.	GTR+Γ	Ingroup	34 - 69.7	fossil and previous estimate	[56, 63]	Uniform, 34, 70
		Malvastrum	34	fossil	[63]	Lognormal, 0, 1

*Values separated by commas represent the following parameters: Normal, mean, standard deviation (s.d.); Uniform, lower bound, upper bound; or Lognormal, zero offset, mean, s.d.
Units are in m.y. (millions of years) unless otherwise indicated.

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