Supplement to Inferring the evolutionary history of the Sino-Himalayan biodiversity hotspot using a Bayesian birth-death skyline model

This repository contains the supplementary files for:

Allen BJ, Vaughan TG, du Plessis L, Schouten TLA, Yuan Z, Willett SD, Stadler T. 2024. Inferring the evolutionary history of the Sino-Himalayan biodiversity hotspot using a Bayesian birth-death skyline model. Geological Society of London Special Publications, 549.

Description of files

This repository contains the cleaned tree file, raw log files, simulated trees, XML files for running the analyses in BEAST2, and R code to process the datasets.

Liu_et_al_SinoHimalayan.nex - the phylogeny inferred by Liu et al. (2021), trimmed to only include the 8864 tips associated with genetic data

Skyline_logs.zip - skyline logs produced by BEAST2 analyses (see below for naming convention)

Regression_results.zip - results of the linear modelling between global palaeotemperature and diversification estimates

Sim_trees.trees - the phylogenies simulated by ReMASTER

Adequacy_logs.zip - skyline logs produced from the analyses using the simulated phylogenies

Description of BEAST2 XMLs

The XML files contain the BEAST2 configurations for:

Liu_et_al_bd.xml, Liu_et_al_bd_high.xml, Liu_et_al_bd_mid.xml, Liu_et_al_bd_low.xml - skyline analyses using equal length time bins, with beta sampling prior, high fixed sampling, mid fixed sampling, and low fixed sampling respectively

Liu_et_al_bd_geol.xml, Liu_et_al_bd_geol_high.xml, Liu_et_al_bd_geol_mid.xml, Liu_et_al_bd_geol_low.xml - skyline analyses using geological time bins, with beta sampling prior, high fixed sampling, mid fixed sampling, and low fixed sampling respectively

Remaster_simulation.xml - simulating new phylogenies based on the inferred skylines using ReMASTER

Sim_trees.xml - skyline analyses conducted on the simulated phylogenies

Description of R code

The R code is subdivided into the following files:

BDSKY_skylines.R - code for processing and plotting skyline data from the BEAST2 log files

BDSKY_adjacent_bins.R - code for the analyses examining the increase or decrease in evolutionary rates between adjacent skyline bins

Plot_palaeotemp_comparison.R - code for plotting the diversification estimates against global palaeotemperature, as taken from Scotese et al. (2021)

Palaeotemperature_regressions.R - code for linear modelling between global palaeotemperature and diversification estimates

Remaster_processing.R - code for processing and plotting inferred skylines from the simulated datasets