DOI: 10.5061/dryad.8kprr4xv4
title: Diversifying in the mountains: spatio-temporal diversification of frogs in the Western Ghats biodiversity hotspot

description: Mountain ranges are hotspots of biodiversity. However, the mechanisms that
 generate biodiversity patterns in different mountainous regions and taxa
 are not apparent. The Western Ghats (WG) escarpment in India is a globally
 recognised biodiversity hotspot with high species richness and endemism.
 Most studies have either invoked paleoclimatic conditions or climatic
 stability in the southern WG refugium to explain this high diversity and
 endemism. However, the factors driving macroevolutionary change remain
 unexplored for most taxa. Here, we generated the most comprehensive dated
 phylogeny to date for ranoid frogs in the WG and tested the role of
 paleoclimatic events or climatic stability in influencing frog
 diversification. We found that the diversity of different ranoid frog
 clades in the WG either accumulated at a constant rate through time or
 underwent a decrease in speciation rates around 3–2.5 Ma during the
 Pleistocene glaciation cycles. We also find no significant difference in
 diversification rate estimates across elevational gradients and the three
 broad biogeographic zones in the WG (northern, central, and southern WG).
 However, time-for-speciation explained regional species richness within
 clades, wherein older lineages have more extant species diversity.
 Overall, we find that global paleoclimatic events have had little impact
 on WG frog diversification throughout most of its early history until the
 Quaternary and that the WG may have been climatically stable allowing
 lineages to accumulate and persist over evolutionary time.
description: # Diversifying in the mountains: spatio-temporal diversification of frogs
 in the Western Ghats biodiversity hotspot
 This repository contains
 two folders that contain all the data and scripts used to perform the
 analyses in the article.\ Details of the two folders are provided below.
 ## 1. WG\_frog\_trees folder This folder contains the dated tree of
 Ranoidea generated during this study and the pruned trees of the six
 Western Ghats clades (Nyctibatrachus, Micrixalidae, Ranixalidae,
 Raorchestes, WG-Ranidae and Uperodon) analysed individually in the paper.
 ## 2. Data\_and \_Rscript folder This folder contains all the data and R
 scripts used to run all the analyses. ### Data files control.txt This file
 contains the settings used to run the BAMM analysis. mcmc_out.txt This
 file provides the output from the BAMM analysis and contains information
 about the MCMC simulation that was used to diagnose the convergence of the
 runs. event_data.txt This file is an output from the BAMM analysis and
 contains all of the model parameters estimated by BAMM. This output file
 was used to estimate diversification rates using the R script
 WG_Frog_BAMM.R (detailed below) BAMM_WG_distribution.csv This file
 provides the distribution of all the species included in the BAMM
 analysis. Species are categorised as SWG: southern Western Ghats, CWG:
 central Western Ghats, NWG: northern Western Ghats, PI: peninsular India
 and EL: extra limital (species distributed outside India).
 WG_rates_MiSSE.csv This file contains the branch-specific diversification
 rates (turnover rates, net diversification rates, speciation rates,
 extinction rates) estimated by the MiSSE analysis.
 Misse_elevation_data.csv This file provides the distribution, median
 elevation and median latitude of all the species included in the tree and
 is used to examine diversification rate variation across regions and
 elevational gradients across the Western Ghats.
 WG_genus_divergence_data.csv This file contains the currently known
 species richness, the clade age and mean net diversification rates
 estimated for each non-monotypic genera found in the Western Ghats.
 Frog_trees.RData This file contains all the time-calibrated phylogenetic
 trees required to reproduce the analyses mentioned in the manuscript. ###
 R scripts WG_frog_div_across_clades.R This R script performs all the
 temporal diversification analyses (TESS, RPANDA and DDD) for the six
 selected clades of frogs mentioned in the paper. WG_frogs_CRABS.R This R
 script performs the CRABS analyses examining the trends within congruent
 classes constructed under alternative hypotheses for all the six frog
 clades. WG_Frog_BAMM.R This R script reproduces the analyses examining the
 variation in diversification rates estimates by BAMM across families and
 regions. essim.R R script provided by Harvey & Rabosky (2018)
 (available at ) used to run the
 simulation-based test on the log-transformed equal split (ES) measure (DR
 statistic). WG_Frog_MiSSE.R R script for reproducing the analyses
 examining the variation in diversification rates estimated by MiSSE,
 ClaDS2 and DR statistics across regions and elevation in the western
 Ghats. Species_richness_patterns.R R script for reproducing the
 correlation analyses testing for the association of diversification rates
 and clade age with species richness.