DOI: 10.5061/dryad.fttdz08rv
title: Speciation across the Earth driven by global cooling in terrestrial Orchids

description: Although climate change has been implicated as a major catalyst of
 diversification, its effects are thought to be inconsistent and much less
 pervasive than localized climate or the accumulation of species with time.
 Focused analyses of highly speciose clades are needed in order to
 disentangle the consequences of climate change, geography, and time. Here,
 we show that global cooling shapes the biodiversity of terrestrial
 orchids. Using a phylogeny of 1,475 species of Orchidoideae, the largest
 terrestrial orchid subfamily, we find that speciation rate is dependent on
 historic global cooling, not time, tropical distributions, elevation,
 variation in chromosome number, or other types of historic climate change.
 Relative to the gradual accumulation of species with time, models
 specifying speciation driven by historic global cooling are over 700 times
 more likely. Evidence ratios estimated for 212 other plant and animal
 groups reveal that terrestrial orchids represent one of the best-supported
 cases of temperature-spurred speciation yet reported. Employing
 &gt;2.5 million georeferenced records, we find that global cooling
 drove contemporaneous diversification in each of the seven major orchid
 bioregions of the Earth. With the current emphasis on understanding and
 predicting the immediate impacts of global warming, our study provides a
 clear case study of the long-term impacts of global climate change on
 biodiversity.
description: Accessions__alignment__trees.zip contains all the accessions, the
 alignment, and the final RelTime and TreePL timetrees
 BAMM_and_RPANDA_analyses.zip contains all the BAMM priors,
 sampling fractions and event-datas, as well as RPANDA model outputs and
 the meta-analysis of 212 other lineages Further details
 are available in the README file
description: RAxML, Figtree, Excel, Notepad, R packages including BAMMtools
 and RPANDA All details and sources are available in the
 README
description: # Speciation across the Earth driven by global cooling in terrestrial
 Orchids Speciation across the Earth driven by global cooling in
 terrestrial orchids, PNAS, 2023 ### Description of Data Files ####
 Directories **Accessions\_\_alignment\_\_trees.zip:** *
 final\_accessions.xlsx: Genbank accessions used in making the supermatrix
 * concat.fasta: The final cleaned concatenated supermatrix, in fasta
 format * dropped\_rogues.txt: Rogue taxa estimated with RogueNaRok and
 associated improvement scores, dropped from the final Maximum Likelihood
 (ML) tree search * reltime\_node\_constraints.txt : Divergence constraints
 used in dating the trees, taken from Givnish et al. (2015) *
 reltime\_ingroup.tre and treepl\_ingroup.tre: Final time trees estimated
 with RelTime and TreePL, in Newick format
 **BAMM\_and\_RPANDA\_analyses.zip** * reltime\_bamm\_priors.txt and
 treepl\_bamm\_priors.txt: Priors set by BAMMtools R package, for BAMM
 analyses of both TreePL and RelTime trees * sample\_frac.txt: Genus-level
 sampling fraction used by BAMM analyses of both trees *
 reltime\_event\_data.txt and treepl\_event\_data.txt: Event data outputs
 by BAMM for both trees, containing estimated lineage diversification rates
 and rate shifts * rpanda\_time\_dependent\_models.txt and
 rpanda\_temperature\_dependent\_models.txt: RPANDA ML model fits of time
 and temperature-dependent diversification, for the RelTime tree *
 rpanda\_evidence\_ratio\_calculations.xlsx: evidence ratios calculated for
 Orchidoideae, Pinus, Rhododendron and 210 tetrapod groups, with speciation
 and extinction rate parameter estimates, and other data necessary to
 estimate evidence rations ### Further details BAMM event data output files
 need reading with the BAMMtools function getEventData() Column names in
 this are: generation (the mcmc generation), leftchild and rightchild
 (defining a location of a rate shift), abstime (time of rate shift),
 lambdainit (initial speciation rate), lambdashift (how speciation
 changes), muinit (initial extinction rate), mushift (how extinction
 changes) RPANDA evidence ratio Excel file contains column names including
 logl (log likelihood), AICc, lambda0 and lambda (speciation parameters),
 mu0 and mu (same for extinction), delta AIC, AICw (AIC weight) and
 evidence ratio with the equation provided ### Code and software *
 OneTwoTree is available at http://onetwotree.tau.ac.il/index.html * RAxML
 v8 is available at https://www.phylo.org/ * RogueNaRok is available at
 https://github.com/aberer/RogueNaRok * TreePL is available at
 https://github.com/blackrim/treePL * BAMM is available at
 http://bamm-project.org/ * Analyses of BAMM output relies on functions in
 the R package BAMMtools, available at
 https://cran.r-project.org/web/packages/BAMMtools/index.html * RPANDA is
 available at https://github.com/hmorlon/PANDA