Supplementary material previous estimates



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SUPPLEMENTARY MATERIAL




Previous estimates




Table S1.1 Previously published dates for the origin of Lepidosauria (tuatara-lizard divergence).


Reference

Date (Mya)

Context

Evans 1991

“By the end of the early Triassic” [247]


Inferred from the fossil record.

Gorr et al. 1998

230

Inferred from the fossil record as discussed in Benton 1985, 1990 and Evans 1988. Used as a calibration point.


Gorr et al. 1998

233

Date calculated from rate changes in α hemoglobin chains. Rate calibrated using tuatara-lizard divergence (230 Mya) and three divergence dates of clades within snakes.


Gorr et al. 1998

226

Date calculated from rate changes in β hemoglobin chains. Rate calibrated using tuatara-lizard divergence (230 Mya) and three divergence dates of clades within snakes.


Kumar and Hedges 1998

276±54.4

Estimated from gene-specific substitution rates in separate gene trees averaged over the trees (after exclusion of outliers and genes with extensive heterogeneity)


Evans 2003

“Early-Middle Triassic”

[= 235-252]




Inferred from the fossil record.

Rest et al. 2003

230

Inferred from the fossil record based on Benton (1993) and Carroll (1988). Used as a calibration point.


Wiens et al. 2006

227

Inferred from the fossil record based on Sues and Olsen 1990. Used as a calibration point.


Kumazawa, 2007

260 – 290

Molecular divergence date obtained from a Bayesian autocorrelated clock “multidivtime”, using mitochondrial DNA and four fossil constraints including a lizard-bird divergence date of 255-305.


Hugall et al. 2007

268 – 275

Molecular divergence date obtained using a RAG-1 phylogeny obtained by MrBayes and five fossil calibration dates spread around the tetrapod tree including 99 Mya for the Heloderma-Elgaria split, 245 Mya for the bird-crocodile divergence date and 315 Mya for the origin of Amniota. Results obtained from penalized likelihood (r8s) were 268 ± 12 based on nucleotides and 275 ± 17 based on amino acids.


Hipsley et al. 2009

238 ± 10

Several clock models were compared using the Bayesian TreeTime software and the uncorrelated lognormal model was found to best fit the

data. Median date obtained using a mixture of mitochondrial and nuclear genes and a minimum constraint of 228 Mya (inferred from the fossil record of Sues and Olsen 1990).




Jones et al. 2009


240 – 250

Inferred from the fossil record.

Albert et al. 2009

272 (255-290)

Molecular divergence estimates based on complete mitochondrial genomes and penalized likelihood. A date of 227 Mya used as a minimum age for the origin of Lepidosauria based on Sues and Olsen (1990).


Albert et al. 2009

289 (282-293)

Molecular divergence estimates based on complete mitochondrial genomes and Bayesian autocorrelated clock “multidivtime”. A date of 227 Mya used as a minimum age for the origin of Lepidosauria based on Sues and Olsen (1990).


Pyron 2010

236 (212-253)

BEAST, Bayesian uncorrelated lognormal clock using 4 fossil constraints from Müller and Reisz (2005).


Pyron 2010

265 (240-290)

BEAST, Bayesian uncorrelated lognormal clock using 5 fossil constraints from Hugall et al. (2007).


Mulcahy et al. 2012

~233 (223-243)


BEAST, Bayesian uncorrelated lognormal clock (discussed further below)

Mulcahy et al. 2012

~275 (na)

r8s, Penalized Likelihood (discussed further below)


Table S1.2 Previously published dates for the origin of Squamata (shared common ancestor of all snakes and lizards).


Reference

Date (Mya)

Context

Janke et al. 2001


294

Rate changes in mitochondrial DNA


Vidal & Hedges 2005

240

(221–251)



Inferred from the fossil record. Molecular clock date obtained from Bayesian autocorrelated clock “multidivtime”, nuclear gene data and a constraint bracket of 200 - 251 Mya based on the fossil record.


Wiens et al. 2006

178.7 ± 5.5

Molecular clock date obtained using the RAG-1 nuclear gene and 11 calibration dates including 228 Mya for the tuatara-lizard split (inferred from the fossil record based on Sues and Olsen 1990).


Hugall et al. 2007

190 - 201

Molecular clock date obtained using a RAG-1 phylogeny obtained by MrBayes and five fossil calibration dates spread around the tetrapod tree including 99 Mya for the Heloderma-Elgaria split, 245 Mya for the bird-crocodile divergence date and 315 Mya for the origin of Amniota. Results obtained from penalized likelihood (r8s) were 190 ± 14 based on nucleotides and 201 ± 19 based on amino acids.


Alfaro et al. 2009

246 (208 -275)


BEAST, Bayesian uncorrelated lognormal clock, multiple calibration points with lognormal distribution and hard younger bounds.

Albert et al., 2009

259 (240–278)

Molecular clock estimates based on complete mitochondrial genomes and penalized likelihood. A date of 227 Mya used as a minimum age for the origin of Lepidosauria based on Sues and Olsen (1990).


Albert et al., 2009

281 (289–299)

Molecular clock estimates based on complete mitochondrial genomes and Bayesian autocorrelated clock “multidivtime”. A date of 227 Mya used as a minimum age for the origin of Lepidosauria based on Sues and Olsen (1990).


Okajima & Kumazawa 2009


240 (220-260)

“multidivtime”, Bayesian autocorrelated clock

Pyron 2010

189 (163-213)

BEAST, Bayesian uncorrelated lognormal clock using 4 fossil constraints from Müller and Reisz (2005).


Pyron 2010

208 (179-234)

BEAST, Bayesian uncorrelated lognormal clock using 5 fossil constraints from Hugall et al. (2007).


Shen et al. 2011


205 (180-228)

“multidivtime”, Bayesian autocorrelated clock. Three nodes constrained using dates from Müller and Reisz (2005) and Benton and Donoghue (2007).


Mulcahy et al. 2012


180 (160-198)

BEAST, Bayesian uncorrelated lognormal clock (discussed further below)

Mulcahy et al. 2012

191.8 (186-194)

r8s, Penalized Likelihood (discussed further below)











Table S1.3 Previously published dates for the divergence of Lepidosauromorpha and Archosauromorpha (bird-lizard split).


Reference

Date (Mya)

Context

Reisz and Müller 2004

252–257

Proposed calibration date inferred from the fossil record.


Benton & Donoghue 2007

259.7–299.8

Proposed calibration date inferred from the fossil record.



Hugall et al. 2007

285–289

Molecular clock date obtained using the RAG-1 nuclear gene and five fossil calibration dates spread around the tetrapod tree including 99 Ma for the Heloderma-Elgaria split, 245 Mya for the bird-crocodile divergence date and 315 Mya for the origin of Amniota. 285 ± 11 Mya obtain with nucleotide Bayesian analysis and 289 ± 13 Mya obtain with an amino acid Bayesian analysis.


Sanders and Lee 2007

282.8 (263–303.9)

Estimate using a relaxed clock analysis with lognormal calibration points.


Sanders and Lee 2007

261.1 (249.5–269.1)

Estimate using a global clock analysis.


Alfaro et al. 2009

270 (257–292)

Node used as a calibration point with reference to Müller and Reisz (2005) and Reisz et al. (2007).: 255 Mya with a soft upper bound set to 282 Mya.


J Müller in San Mauro 2010: 556


271–259.7

Proposed calibration date inferred from the fossil record.



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