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 supplementary material:
  Figure S1: Convergence assessment of the phylogenetic inferences including and excluding cryptic species under the calibration set 1
  Figure S2: Time-calibrated species-level crocodylian phylogeny using calibration set 1
  Figure S3: Time-calibrated cryptic-species-level crocodylian phylogeny using calibration set 1
  Figure S4: Diversification dynamics analyses in Crocodylia based on data sets excluding and including cryptic diversity under calibration set 1
  Figure S5: Convergence assessment of the phylogenetic inferences including and excluding cryptic species under the calibration set 2
  Figure S6: Time-calibrated species-level crocodylian phylogeny using calibration set 2
  Figure S7: Time-calibrated cryptic-species-level crocodylian phylogeny using calibration set 2
  Figure S8: Diversification dynamics analyses in Crocodylia based on data sets excluding and including cryptic diversity under calibration set 2

  Table S1: GenBank accession numbers for CYTB sequences for the cryptic-species-level analysis
  Table S2: List of fossil calibrations and calibration densities for calibration sets 1 and 2
  Table S3:agee age estimates of the time-calibrated crocodylian tree using calibration set 1.
  Table S4:agee age estimates of the time-calibrated crocodylian tree using calibration set 2.

• data folder: contains files for performing the phylogenetic analysis, in addition to the tree files for the diversification dynamics analyses:

  crocs_species.tre : maximum a posteriori (MAP) phylogeny of the phylogenetic analysis excluding cryptic species used for the diversification dynamics analysis
  crocs_subspecies.tre: maximum a posteriori (MAP) phylogeny of the phylogenetic analysis including cryptic species used for the diversification dynamics analysis

  • cryptic_speceis_level folder: a folder containing the alignment of the mitochondrial gene cytochrome b (CYTB) in nexus file for 45 crocodylian lineages used in the phylogenetic analyFolderfoa lder: a folder containing alignments for mitochondrial genes for the species-level phylogenetic analysis. All files are in .nex format. This folder includes the following files:
  • 12s.nex, 16s.nex, ATP6.nex, ATP8.nex, COI.nex, COII.nex, COIII.nex, CYTB.nex, ``ND1.nex, ND2.nex`, `ND3.nex`, `ND4.nex`, `ND4L.nex`, `ND5.nex`, `ND6.nex`

• scripts folder: contains the scripts for performing phylogenetic analyses, and diversification dynamics analyses using the sourced data files described above.
  Please refer to our analysis pipeline for proper use of the following scripts:

  clock_relaxed_mixture.Rev : script to run the mixture model for relaxed clocks on molecular branch rates
  map_tree.Rev : script for computing the MAP tree
  mcmc_crocs.Rev : script for analysis settings & MCMC
  mcmc_EBD.Rev : script to run Bayesian inference of diversification rates under an episodic birth-death model (EBD) in RevBayes
  mcmc.Rev : script containing analysis settings & Markov chain Monte Carlo (MCMC) for divergence time estimation using a relaxed clock and node calibration in RevBayes
  model.Rev : general model settings for Divergence time estimation using a relaxed clock and node calibration in RevBayes
  node_calibrations_older.Rev : script containing node calibrations and calibration density settings for divergence time estimation using the calibration set 2
  node_calibrations_younger.Rev : script containing node calibrations and calibration density settings for divergence time estimation using the calibration set 1
  plot_EBD.R : script to plot diversification rates through time using the package RevGadgets in R
  plot_helper.R : script containing the function to plot the split frequencies of different runs using the package RevGadgets in R
  plot_MAP_trees.R : script for plotting the MAP trees from the partitioned UCE analyses using the package RevGadgets in R
  plot_split_frequencies.R : script containing the function to plot the split frequencies of different runs using the package RevGadgets in R
  read_data_cryptic.Rev : script containing the commands to read the molecular data for the cryptic-species-level phylogenetic analysis
  read_data_species.Rev : script containing the commands to read the molecular data for the species-level phylogenetic analysis
  root_calibrations_older.Rev : script containing the settings for root calibration based on calibration set 2. Explanations fcalibrationion sets used are found in the Darlim_Höhna_electronic_supp_mat.pdf file
  root_calibrations_younger.Rev : script containing the settings for root calibration based on calibration set 1. Explanations fcalibrationion sets used are found in the Darlim_Höhna_electronic_supp_mat.pdf file
  sub_GTRG_partitioned.Rev : script for partitions for each dsubsetsets
  sub_GTRG.Rev : script containing the settings for the general time reversible substitution model with gamma distribution for phylogenetic analysis and divergence time estimation
  tree_BD_mix.Rev : script containing the settings for the mixture models of tree priors
  tree_BD.Rev : script containing settings for the Birth-Death Process toior on the topology and speciation times
  tree_EBD.Rev : script containing settings for estimating the episodic diversification rates

Analysis pipeline

We assume you have RevBayes installed with the name rb. Note that you can also use the MPI version of RevBayes instead.

To run the divergence time estimation with the cryptic-species level data, run:

rb --file scripts/mcmc_crocs.Rev --args 500000 4

To compute the maximum a posteriori phylogeny from the posterior samples, run

rb --file scripts/map_tree.Rev --args 4

Next, to plot the MAP trees and check for convergence, run

Rscript scripts/plot_MAP_trees.R
Rscript scripts/plot_split_frequencies.R 4 output crocs_all_subspecies

To run the diversification rate analysis under the EBD model in RevBayes, run

rb --file scripts/mcmc_EBD.Rev --args species 500000 4
rb --file scripts/mcmc_EBD.Rev --args subspecies 500000 4

To plot the diversification rates, run

Rscript scripts/plot_EBD.R