Diversifying in the mountains: spatio-temporal diversification of frogs in the Western Ghats biodiversity hotspot
Data files
Jan 19, 2024 version files 6.51 MB
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Data_and__Rscript.zip
6.49 MB
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README.md
3.42 KB
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WG_frog_trees.zip
19.91 KB
Abstract
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.
https://doi.org/10.5061/dryad.8kprr4xv4
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 https://github.com/mgharvey/ES-sim) 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.