Codes and data linked to the paper:
A flexible method for estimating tip diversification rates across a range of speciation and extinction scenarios
Thais Vasconcelos, Brian C. O’Meara, Jeremy M. Beaulieu
Empirical_example-Eucalypts
Tip-rate comparisons between plant height and net-turnover rates in Eucalypteae (Myrtaceae).
Data from:
Thornhill, A. H., Crisp, M. D., Külheim, C., Lam, K. E., Nelson, L. A., Yeates, D. K., & Miller, J. T. (2019). A dated molecular perspective of eucalypt taxonomy, evolution and diversification. Australian Systematic Botany, 32(1), 29-48. 10.1071/SB18015
EUCLID Eucalypts of Australia Edition 4 (2015, internet based, hosted by the Identic Pty Ltd, Brisbane.) link
Example_code-Lupinus_quick_run
A quick example of how MiSSE works using the genus Lupinus (Fabaceae).
Data from:
Drummond, C. S., Eastwood, R. J., Miotto, S. T., & Hughes, C. E. (2012). Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling. Systematic biology, 61(3), 443-460. 10.1093/sysbio/syr126
Simulation_study
Codes to compare MiSSE to other diversification methods based on trees from Title and Rabosky (2019) and Maliet et al. (2019).
Title, P. O., & Rabosky, D. L. (2019). Tip rates, phylogenies and diversification: what are we estimating, and how good are the estimates?. Methods in Ecology and Evolution, 10(6), 821-834. 10.1111/2041-210X.13153
Maliet, O., Hartig, F., & Morlon, H. (2019). A model with many small shifts for estimating species-specific diversification rates. Nature ecology & evolution, 3(7), 1086-1092. 10.1038/s41559-019-0908-0