Data for: Global diversity patterns are explained by diversification rates and dispersal at ancient, not shallow, timescales

Data files

Apr 17, 2025 version files 36.31 MB

README.md

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Supplementary_Datasets_Feb_21_2025v2.zip

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May 22, 2025 version files 37.34 MB

README.md

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Supplementary_Datasets_Feb_21_2025v3.zip

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Abstract

Online supplementary materials and datasets for "Global diversity patterns are explained by diversification rates at ancient, not shallow, timescales. The online supplemental materials include Appendices S1–S5, Figures S1–S6, andTables S1–S12. Dataset S1 contains R code for all analyses conducted in the study. The other files contain the raw data used for spatial analyses. Datasets S2–S5, S9, and S10 contain squamate phylogenies used for analyses. Datasets S6–S8, S13, and S14 contain diversification rates for various clades estimated using various methods. Dataset S15 contains files needed for a phylogenetic reconstruction of past patterns of squamate dispersal among nine biogeographic realms, including additional R code both for conducting the analysis and parsing the output. Datasets S16 and S17 contain estimates of the colonization times of realms by various species. Dataset S18 contains 100 replicates of an analysis confirming that there is no relationship between diversification rates and species richness. Finally, Dataset S19 contains a global squamate presence-absence matrix for 10,213 species of squamates and 14800 terrestrial grid cells.

Dryad DOI: https://doi.org/10.5061/dryad.0zpc8671s

README for Dryad data files associated with:

Patrick R. Stephens*, Maxwell J. Farrell, T. Jonathan Davies, John L. Gittleman, Shai Meiri, Mathew O. Moreira, Uri Roll, John J. Wiens. Global diversity patterns are explained by diversification rates and dispersal at ancient, not shallow, timescales. Systematic Biology 74: https://doi.org/10.1093/sysbio/syaf018.\

*corresponding author: patrick.stephens@okstate.edu

Version change log

22 May 2025: Added missing file and updated the file name to reflect the version of it that I uploaded: “Supp_Mat_21Feb2025_clean.pdf”

This archive contains:

Supplementary Datasets Feb 21.zip

Inside this zip archive are the following files:

Supp_Mat_21Feb2025_clean.pdf : Contains online supplemental materials including Appendices S1-S6, Figures S1-S5, and Tables S1-S12.

Dataset_S1_R_Code_Dec_22_2024.R: R script file containing code for analyses we present. The code includes the version numbers of all libraries used for analyses.

Dataset_S2_zw2016.nexus: Time-calibrated tree from Zheng and Wiens (2016).

Dataset_S3_Ton_2016_consensus.zip: Zip file containing Newick-formatted consensus tree from Tonini et al. (2016). Unaltered from the original publication.

Original downloaded from: https://doi.org/10.5061/dryad.db005

Dataset_S4_100_trees.tre: Contains 100 trees chosen at random from the Bayesian posterior distribution of 10,000 potential fully resolved trees published by Tonini et al. (2016).

Dataset_S5_TNN_et_al_mol_contree.tre: Nexus formatted consensus tree of 10,000 molecular trees published by Tonini et al. (2016). See the methods of the main paper for additional details.

Dataset_S6_BAMM_tip_speciation_rates.xlsx: Speciation rate for tips (species) calculated using BAMM. See the Methods of the main paper for additional details.

Contains the following variables:

Variable	Explanation
Binomial	Species bionimial from tree of Tonini et al. (2016)
tip_rates	BAMM speciation rate for tip species. See the Methods of the main paper for additional details.

Dataset_S7_ClaDS_tip_speciation_rates.xlsx: Speciation rate for tips (species) calculated using ClaDS. See the Methods of the main paper for additional details.

Contains the following variables

Variable	Explanation
Binomial	Species bionimial from tree of Tonini et al. (2016)
tip_rates	ClaDS speciation rate for tip species. See the Methods of the main paper for additional details.

Dataset_S8_Squamate_diversification_rates.xlsx: All genus and family-level diversification rates used for global squamate analyses, for each species. Also contains stem ages of genera and families used to assign species to bins, and lists the taxa these represent.

Contains the following variables:

Variable	Explanation
RN	reference number assigned during merge
RDB 2017 binomial	SIC binomial from reptile database (2017_10)
Tree_Binom	same but with spaces replaced with underscore for easier alignment with trees
Genus	genus
Family	family
Ton_fam	family names used to match to "Ton_family_16Jan2020_v2.csv" and to "family_rates_ClaDS.csv"
Ton_F_stem_age	stem age from "Ton_family_16Jan2020_v2.csv"
Ton_FDR_log_e5	log10 diversification rate using an extinction exponent of 5 from "Ton_family_16Jan2020_v2.csv"
ZW_family	family names used to match "ZW_family_16Jan2020_v2.xls"
ZW_F_stem_age	stem age from "ZW_family_16Jan2020_v2.xls"
ZW_FDR_log_e5	log10 diversification rate estimated using an extinction exponent of 5 from "ZW_family_16Jan2020_v2.xls"
Ton_genus	genus name used to match "Tonini_genus_rates_16Jan2020.xls"
Ton_genus_note	notes on why name differs from RDB name
Ton_G_stem_age	stem age from "Tonini_genus_rates_16Jan2020.xls"
Ton_GDR_log_e5	log10 diversification rate using an extinction exponent of 5 from "Tonini_genus_rates_16Jan2020.xls"
Family_and_higher_taxa	notes on higher taxa in RDB
ZW_genus	genus names used to match to "ZW_family_16Jan2020_v2.xls"
ZW_genus_notes	notes on why name differs from RDB name
ZW_G_stem_age	stem age from "ZW_genus_rates_16Jan2020.xls"
ZW_GDR_log_e5	log10 diversification rate estimated using an extinction exponent of 5 from "ZW_genus_rates_16Jan2020.xls"
CLADn	number of species assumed to be in the family for ClaDS rate estimates
CLADmean	mean diversification rate of family estimated using the ClaDS method
CLADmedian	median diversification rate of the family using the ClaDS method
CLADsd	standard deviation of diversification rate of family using the ClaDS method
CLADmin	minimum diversification rate of clade included in family using ClaDS method
CLADmax	maximum diversification rate of clade included in family using ClaDS method

Dataset_S9_Tonini_et_al_tree_MoM_Genera.xlsx: Contains additional information on genera from the tree of Tonini et al. (2016) used for analyses (number of species, stem ages, and MoM rate estimates using three values for extinction fraction)

Contains the following variables

Variable	Explanation
number of species	total number of described species in genus (from Reptile Database)
stem age	stem age of genus in millions of years
stem diversification rate (e=0)	stem diversification rate with an assumed relative extinction fraction of 0
stem diversification rate (e=0.5)	stem diversification rate with an assumed relative extinction fraction of 0.5
stem diversification rate (e=0.9)	stem diversification rate with an assumed relative extinction fraction of 0.9

Dataset_S10_Zheng_Wiens_tree_MoM_Genera.xlsx: Contains additional information on genera from the tree of Zheng and Wiens (2016) used for analyses (number of species, stem ages, and MoM rate estimates using three values for extinction fraction)

Contains the following variables:

Variable	Explanation
Genus	Squamate genus
ZW stem age	clade's stem age in millions of years
RDB 2017 species	number of described species (from Reptile Database)
notes	notes
Family	Squamate family
log10-e0	stem diversification rate with an assumed relative extinction fraction of 0
log10-e5	stem diversification rate with an assumed relative extinction fraction of 0.5
log10-e9	stem diversification rate with an assumed relative extinction fraction of 0.9

Dataset_S11_Tonini_et_al_tree_MoM_Families.xlsx: Contains additional information on families from the tree of Tonini et al. (2016) used for analyses (number of species, stem ages, and MoM rate estimates using three values for extinction fraction)

Contains the following variables:

Variable	Explanation
Family	Squamate family
number of described species	number of described species (from Reptile Database)
stem age	clade's stem age in millions of years
crown age	clade's crown age in millions of years
ln_species described	natural logarithm of number of described species (from Reptile Database)
stem diversification rate (e=0)	stem diversification rate with an assumed relative extinction fraction of 0
stem diversification rate (e=0.5)	stem diversification rate with an assumed relative extinction fraction of 0.5
stem diversification rate (e=0.9)	stem diversification rate with an assumed relative extinction fraction of 0.9
crown diversification rate (e=0)	crown diversification rate with an assumed relative extinction fraction of 0
crown diversification rate (e=0.5)	crown diversification rate with an assumed relative extinction fraction of 0.5
crown diversification rate (e=0.9)	crown diversification rate with an assumed relative extinction fraction of 0.9

Dataset_S12_Zheng_Wiens_tree_MoM_Families.xlsx: Contains additional information on families from the tree of Zheng and Wiens (2016) used for analyses (number of species, stem ages, and MoM rate estimates using three values for extinction fraction)

Contains the following variables:

Variable	Explanation
Family	Squamate family
number of described species	number of described species (from Reptile Database)
stem age	clade's stem age in millions of years
crown age	clade's crown age in millions of years
ln_species described	natural logarithm of number of described species (from Reptile Database)
stem diversification rate (e=0)	stem diversification rate with an assumed relative extinction fraction of 0
stem diversification rate (e=0.5)	stem diversification rate with an assumed relative extinction fraction of 0.5
stem diversification rate (e=0.9)	stem diversification rate with an assumed relative extinction fraction of 0.9
crown diversification rate (e=0)	crown diversification rate with an assumed relative extinction fraction of 0
crown diversification rate (e=0.5)	crown diversification rate with an assumed relative extinction fraction of 0.5
crown diversification rate (e=0.9)	crown diversification rate with an assumed relative extinction fraction of 0.9

Dataset_S13_Snake_diversification_rates.xlsx: Contains diversification rates for snake families estimated using MoM, BAMM, RPANDA, and ClaDS.

Contains the following variables:

Variable	Explanation
Family	Family designation used to match to family level diversification rates from Dataset_S1
BAMM whole tree	BAMM rates calculated from the whole tree in: A. L. Meyer, J. J. Wiens, Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts. Evolution 72, 39-53 (2018).
BAMM individual clades	BAMM rates calculated for clades in isolation in: A. L. Meyer, J. J. Wiens, Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts. Evolution 72, 39-53 (2018).
TNN MoM	Methods of Moments estimates of diversification rates based on the tree of: J. F. R. Tonini, K. H. Beard, R. B. Ferreira, W. Jetz, R. A. Pyron, Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status. Biological Conservation 204, 23-31 (2016).
ZW MoM	Methods of Moments estimates of diversification rates based on the tree of: Y. Zheng, J. J. Wiens, Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Molecular Phylogenetics and Evolution 94, 537-547 (2016).
RPANDA Stem	Rates estimated from RPANDA using absolute values of speciation and extinction rates. Rates were obtained from: M. Bars‐Closel, T. Kohlsdorf, D. S. Moen, J. J. Wiens. Diversification rates are more strongly related to microhabitat than climate in squamate reptiles (lizards and snakes). Evolution 71, 2243-2261 (2017).
ClaDS	Rates estimated using ClaDS method

Dataset_S14_Species_environmental_data.xlsx: Contains mean, minimum, and maximum values of 11 BIO Variables across species geographic ranges.

Contains the following variables:

Variable	Explanation
binomial	Species binomial, matches Uetz and Hošek (2017)
TaxonID	Taxon ID, used to match with range shapefiles in GARD 1.5
Group	Squamate group: lizard, snake, or amphisbaenian
Family	Taxonomic family, matches Uetz and Hošek (2017)
bio1_mean	Mean value of Bio1 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio1_stddev	Standard deviation of Bio1 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio1_min	Minimum value of Bio1 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio1_max	Maximum value of Bio1 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio2_mean	Mean value of Bio2 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio2_stddev	Standard deviation of Bio2 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio2_min	Minimum value of Bio2 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio2_max	Maximum value of Bio2 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio3_mean	Mean value of Bio3 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio3_stddev	Standard deviation of Bio3 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio3_min	Minimum value of Bio3 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio3_max	Maximum value of Bio3 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio4_mean	Mean value of Bio4 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio4_stddev	Standard deviation of Bio4 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio4_min	Minimum value of Bio4 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio4_max	Maximum value of Bio4 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio5_mean	Mean value of Bio5 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio5_stddev	Standard deviation of Bio5 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio5_min	Minimum value of Bio5 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio5_max	Maximum value of Bio5 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio6_mean	Mean value of Bio6 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio6_stddev	Standard deviation of Bio6 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio6_min	Minimum value of Bio6 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio6_max	Maximum value of Bio6 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio7_mean	Mean value of Bio7 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio7_stddev	Standard deviation of Bio7 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio7_min	Minimum value of Bio7 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio7_max	Maximum value of Bio7 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio12_mean	Mean value of Bio12 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio12_stddev	Standard deviation of Bio12 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio12_min	Minimum value of Bio12 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio12_max	Maximum value of Bio12 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio13_mean	Mean value of Bio13 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio13_stddev	Standard deviation of Bio13 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio13_min	Minimum value of Bio13 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio13_max	Maximum value of Bio13 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio14_mean	Mean value of Bio14 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio14_stddev	Standard deviation of Bio14 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio14_min	Minimum value of Bio14 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio14_max	Maximum value of Bio14 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio15_mean	Mean value of Bio15 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio15_stddev	Standard deviation of Bio15 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio15_min	Minimum value of Bio15 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.
bio15_max	Maximum value of Bio15 across species range. Environmental data from CHELSA (Karger et al. 2017). See Table S2 and Karger et al. (2017) for definitions of BIO variables.

Dataset_S15_BGB_example.zip: Zip file containing sample code for BioGeoBEARS and all input data files used for reconstructions. Also includes code for calculating colonization times from BioGeoBEARS output. Contains the following files:

Squamate_realms_Nov_27.csv: list of species and realms they are assigned to by Shai Meiri in November 2024

Sample_BioGeoBEARS_analysis_Dec17.R: R code needed to conduct reconstructions and parse output.

tr_pruned_F23.tre: tree of Zheng and Wiens (2016) pruned down to species found in F23_realms_v2

F23_realms-v2.txt: input file for BioGeoBEARS

Dataset_S16_Richness_and_col_times_of_realms.xlsx: Species richness and colonization times of nine biogeographic realms sensu Falaschi et al. (2023)

Contains the following variables:

Variable	Explanation
RN	row number
Realm	Realm sensu Falaschi et al. (2023)
RA	Realm two-letter abbreviation in BioGeobears input files
maxCT	Oldest potential colonization time observed for species in realms (along the node path from a given tip to the root, age of node below oldest node in which realm with highest likelihood is the same as the one where a given tip species currently occurs)
minCT	Youngest likely colonization time (oldest node where the character state with the highest likelihood represents endemism to a given realm)
SR_all	All species from the global presence-absence matrix endemic to the realm
SR_tree	All species from the global presence-absence matrix endemic to the realm that are also found in the tree of Zheng and Wiens (2016)

Dataset_S17_Squamate_colonization_times.xlsx: Colonization time estimates for 3914 species of squamates based on DEC and DEC + J.

Contains the following variables:

Variable	Explenation
Binomial	species binomial
DEC_CL	DEC conditional likelihood estimates of colonization times (estimates with the highest likelihoods, overall best estimates given concerns with DEC +J model)
DEC_UP	DEC up pass estimates of colonization times
DEC_DP	DEC down pass estimates of colonization times (note that these ended up being the estimates with the highest CL, and so are identical to CL estimates)
DECJ_CL	DEC + J conditional likelihood estimates of colonization times (note that these are nearly identical to DEC estimates, only differ for 17 species)
DECJ_UP	DEC + J up pass estimates of colonization times
DECJ_DP	DEC +J down pass estimates of colonization times

Dataset_S18_DR_vs_SR_replicates.xlsx: Contains test statistics and P-values for 100 comparisons of species richness vs the DR statistic calculated using the trees from Dataset S4.

Contains the following variables:

Variable	Explanation
Tree	Tree used for Replicate (see Dataset S3).
DRcorr	Correlation based on Dutilleul's modified t-test for assessing bivariate correlations with spatial data
DRpvalue	P-value of correlation

Dataset_S19_additional_GIS_files.zip: Zipped archive containing shapefiles for large terrestrial water bodies and a global presence-absence for 10,213 species of squamates. See Dataset S1 for details on how these are used in our analyses and to create maps. Also contains directions for creating a "wc10" folder.

Literature Cited:

Falaschi, M., Marta, S., Lo Parrino, E., Roll, U., Meiri, S., & Ficetola, G. F. (2023). Global bioregions of reptiles confirm the consistency of bioregionalization processes across vertebrate clades. Glob. Ecol. Biogeogr., 32(8), 1272-1284.

Tonini J.F.R., Beard K.H., Ferreira R.B., Jetz W., Pyron R.A. 2016. Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status. Biol. Conserv. 204:23-31.

Zheng Y., Wiens J.J. 2016. Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Mol. Phylogenet. Evol. 94:537-547.

Data for: Global diversity patterns are explained by diversification rates and dispersal at ancient, not shallow, timescales

Data files

Abstract

README: Data for: Global diversity patterns are explained by diversification rates and dispersal at ancient, not shallow, timescales

Version change log

Works referencing this dataset