INTEGRATING FOSSILS WITH MOLECULAR PHYLOGENIES IMPROVES INFERENCE OF TRAIT EVOLUTION
Article first published online: 10 JUL 2012
© 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.
Volume 66, Issue 12, pages 3931–3944, December 2012
How to Cite
Slater, G. J., Harmon, L. J. and Alfaro, M. E. (2012), INTEGRATING FOSSILS WITH MOLECULAR PHYLOGENIES IMPROVES INFERENCE OF TRAIT EVOLUTION. Evolution, 66: 3931–3944. doi: 10.1111/j.1558-5646.2012.01723.x
- Issue published online: 3 DEC 2012
- Article first published online: 10 JUL 2012
- Accepted manuscript online: 25 JUN 2012 09:10AM EST
- Received February 1, 2012 Accepted May 24, 2012 Data Archived: Dryad repository: doi:10.5061/dryad.q96d7
Figure S1. Histogram showing the sum distance of fossil taxa from their associated nodes under the simulated sampling scheme.
Figure S2. Akaike weights relative to extinction rate for each of the four models fitted to datasets simulated under BM, Trend, DC, AC, and SSP (columns).
Figure S3. Bayes factors with informative node priors derived from simulated fossil records.
Figure S4. Histogram of fossil taxa numbers used to define node priors based on the simulated fossil record.
Figure S5. Plot of the gamma statistic against extinction rate for a sample of simulated trees.
Figure S6. Median Akaike weights for each of four candidate models fitted to 500 datasets (see main text) simulated under BM (A–D), Trend (E–H), DC (I–L), AC (M–P), and SSP (Q–T).
Figure S7. Median Akaike weights for each of four candidate models fitted to 500 simulated datasets (see main text).
Figure S8. Time-calibrated phylogeny of the Canidae reconstructed and used for this analysis.
Figure S9. Time-calibrated phylogeny of the Otariidae reconstructed and used for this analysis.
Figure S10. Majority rule consensus trees from Bayesian analyses of molecular and morphological data for living and fossil Mephitids with (A) Mk+G and (B) Mk + unequal state frequencies for the morphological partition.
Figure S11. Time-calibrated phylogeny of Mephitidae reconstructed and used in this analysis.
Figure S12. Majority rule consensus trees from Bayesian analyses of molecular and morphological data for living and fossil Procyonids with (A) Mk+G and (B) Mk + unequal state frequencies for the morphological partition.
Figure S13. Time-calibrated phylogeny of Procyonidae reconstructed and used in this analysis.
Table S1. Correlation coefficients between Akaike weights for the true model of trait evolution and extinction rates of the phylogenies on which traits were simulated.
Table S2. False-positive rates for Bayesian model selection using node value priors derived from a simulated fossil record.
Table S3. Median Akaike weights over all parameter values under each fossil sampling level for the five sets of simulations.
Table S5. Sampled loci and Genbank accession numbers for the otariid analysis
Table S6. Sampled loci and Genbank accession numbers for the Mephitid analysis
Table S7. Fossil taxa used to define informative priors on node states when fitting models of quantitative trait evolution to the caniform dataset.
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