DOI: 10.5061/dryad.xwdbrv1pn
title: Data from: The effects of cryptic diversity on diversification dynamics analyses in Crocodylia

description: 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 analyses, however representation of cryptic extinct taxa
 represents a major challenge. Additionally, further investigation of
 crocodylian diversification dynamics under different underlying genomic
 data is encouraged upon advances in population genetics. Our case study
 adds to diversification dynamics knowledge of extant taxa and demonstrates
 that cryptic species and robust taxonomic assessment are essential to
 study recent biodiversity dynamics with broad implications for
 evolutionary biology and ecology.
description: # 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 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: &gt; rb --file scripts/mcmc_crocs.Rev --args 500000 4 To compute the
 maximum a posteriori phylogeny from the posterior samples, run &gt; rb
 --file scripts/map_tree.Rev --args 4 Next, to plot the MAP trees and check
 for convergence, run &gt; Rscript scripts/plot_MAP_trees.R &gt; Rscript
 scripts/plot_split_frequencies.R 4 output crocs_all_subspecies To run the
 diversification rate analysis under the EBD model in RevBayes, run &gt; rb
 --file scripts/mcmc_EBD.Rev --args species 500000 4 &gt; rb --file
 scripts/mcmc_EBD.Rev --args subspecies 500000 4 To plot the
 diversification rates, run &gt; Rscript scripts/plot_EBD.R