The effects of cryptic diversity on diversification dynamics analyses in Crocodylia

Incomplete taxon sampling due to underestimation of present-day biodiversity biases diversification analysis by favouring slowdowns in speciation rates towards recent time. For instance, in diversification dynamics studies in Crocodylia, long-term low net-diversification rates and slowdowns in speciation rates have been suggested to characterise crocodylian evolution. However, crocodylian cryptic diversity has never been considered. Here, we explore the effects of incorporating cryptic diversity into a diversification dynamics analysis of extant crocodylians. We inferred a time-calibrated cryptic-species-level phylogeny using cytochrome b sequences of 45 lineages compared with the formally recognized 26 crocodylian species. Diversification rate estimates using the cryptic-species-level phylogeny show increasing speciation and net-diversification rates towards the present time, which is contrasting to previous findings. Cryptic diversity should be considered in future macroevolutionary a..., , , # Data from: The effects of cryptic diversity on diversification dynamics analyses in Crocodylia

Authors: Gustavo Darlim and Sebastian Höhna

# Summary of the study

In this manuscript, we present an original study exploring how a more comprehensive sampling of crocodylian extant diversity
– by including cryptic species – affects outcomes of diversification dynamics analyses.

This compressed file archive contains all data and scripts used for the phylogenetic and diversification dynamics analyses in RevBayes.

# Description of data files and file structure are indicateded by an asterisk.

`Darlim_Höhna_electronic_supp_mat.pdf`: this file includes:

* Extended methods: explanation for the use of different calibration sets for time-estimating the species-level and cryptic-species-level crocodylian topology
* Results of the phylogenetic inferences and diversification analyses using calibration sets 1 and 2.
The following supplementary figures and tables can be found in the electronic s...