Skip to main content
Dryad

Speciation across the Earth driven by global cooling in terrestrial Orchids

Thompson, Jamie1; Davis, Katie E.2; Dodd, Harry O.1; Wills, Matthew A.1; Priest, Nicholas K.1

Published Aug 31, 2023 on Dryad. https://doi.org/10.5061/dryad.fttdz08rv

Cite this dataset

Thompson, Jamie et al. (2023). Speciation across the Earth driven by global cooling in terrestrial Orchids [Dataset]. Dryad. https://doi.org/10.5061/dryad.fttdz08rv

Abstract

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 >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.

README: 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

Methods

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

Usage notes

RAxML, Figtree, Excel, Notepad, R packages including BAMMtools and RPANDA

All details and sources are available in the README

Funding

Roger and Sue Whorrod Studentship

John Templeton Foundation, Award: 61408

Research England, Award: QR GCRF