DOI: 10.5061/dryad.f4qrfj72v
title: Data for: Climatic-niche breadth, niche position, and speciation in lizards and snakes

description: Aim: The climatic niche is associated with diversification in many groups
 of animals and plants. However, the relationships between climatic-niche
 breadth evolution, climatic-niche position evolution, and speciation
 remain underexplored. It is particularly unclear whether changes in
 climatic-niche breadth are related to diversification. We tested two
 hypotheses relating niche breadth, niche position, and speciation using
 climatic data in Squamata (lizards and snakes), one of the largest
 radiations of tetrapods. These hypotheses were: (1) the oscillation
 hypothesis (niche breadth changes along with niche position and
 speciation); and (2) the musical chairs hypothesis (niche breadth remains
 relatively constant when niche position changes during speciation).
 Location: Global. Taxon: Squamata (lizards and snakes). Methods: We
 estimated rates of speciation and evolutionary rates for both
 climatic-niche position and climatic-niche breadth for 5,320 squamate
 species. We tested relationships among these rates using Bayesian
 phylogenetic generalized linear-mixed models. Results: Higher speciation
 rates were associated with higher rates of evolution in niche position and
 in niche breadth. Faster rates of change in niche breadth were related to
 narrower niches and faster rates of change in niche position. Main
 Conclusions: Our results support the oscillation hypothesis to explain the
 relationships between speciation and changes in climatic niche position
 and climatic niche breadth. We found that species that changed
 climatic-niche breadths more rapidly: (1) speciated faster; (2) evolved
 towards narrower niche breadths; and (3) changed climatic-niche positions
 more rapidly. These results suggest that the oscillation between wider and
 narrower niches is coupled with climatic-niche divergence and speciation.
 These conclusions may apply to many other groups of plants and animals in
 which speciation is often related to climatic-niche divergence.
description: <strong>Climatic-niche data</strong>
 We obtained historic climatic data and distribution maps for
 5,320 squamate species. We calculated two characteristics of the realized
 climatic niche for each species: niche position and niche breadth. For
 niche position, we performed a phylogenetic principal component analysis
 (pPCA) and focused on the first two axes: PC1 and PC2. For niche breadth
 we calculated two distinct but complementary metrics: species niche
 breadth for temperature (SNBT) and species niche breadth for precipitation
 (SNBP). <strong>Speciation
 rates</strong> We estimated species-specific
 speciation rates (and rates of climatic-niche evolution) for all 5,320
 species of Squamata included in the tree. We estimated speciation rates
 (λ) using the ClaDS approach. <strong>Rates of
 climatic-niche evolution</strong> We used BAMM to
 infer the evolutionary rates (<em>r</em>) for changes in
 species’ climatic-niche position (PC1 and PC2) and climatic-niche breadth
 (SNBT and SNBP) on the final tree. We then calculated pathwise rates of
 evolution (∑<em>r</em>) for each climatic-niche variable using
 the mean trait rates per-branch obtained from BAMM. The pathwise rate for
 a given species is the sum of the mean rates per branch from the root of
 the tree to that species’ terminal branch, and quantifies the amount of
 changes in rates that a trait has experienced along the evolutionary path
 leading from the root to each individual species.
 <strong>Statistical analyses</strong>
 We tested the oscillation and musical chairs hypotheses using
 Phylogenetic Generalized Linear Mixed Models (PGLMM). Specifically, we
 used PGLMM to estimate regression coefficients for the relationships
 between speciation rates and rates of climatic-niche evolution. First, we
 tested for a relationship between speciation rates and rates of
 climatic-niche change. Second, we tested whether species evolved towards
 narrower niches (oscillation hypothesis) or maintained relatively constant
 niche breadths (musical chairs hypothesis). Finally, we tested if rates of
 change in climatic-niche breadth were correlated with rates of change in
 climatic-niche position.
description: # Data for: Climatic-niche breadth, niche position, and speciation in
 lizards and snakes [Access this dataset on
 Dryad](https://doi.org/10.5061/dryad.f4qrfj72v) ## Description of the data
 and file structure This README file was generated on 29-01-2024 by Matthew
 Moreira. ### GENERAL INFORMATION 1\. Title of Dataset Data for:
 Climatic-niche breadth, niche position, and speciation in lizards and
 snakes 2\. Author Information A. Name: Matthew Owen Moreira Institution:
 University of Aveiro Address: Aveiro, Portugal Email:
 B. Name: John J. Wiens Institution:
 University of Arizona Address: Tucson, AR USA Email:
 C. Name: Carlos Fonseca Institution: ForestWISE
 Address: Vila Real, Portugal Email: D. Name: Danny
 Rojas Institution: Pontificia Universidad Javeriana Cali Address: Cali,
 Colombia Email: 3\. Date of data
 collection (single date, range, approximate date): 2021-2023 4\.
 Geographic location of data collection: None 5\. Information about funding
 sources that supported the collection of the data PD/BD/135554/2018;
 UIDP/50017/2020+UIDB/50017/2020+LA/P/0094/2020; 1053; 1251-866-75985;
 NSF-DEB-1655690; NORTE-06-3559-FSE-000045 ### SHARING/ACCESS INFORMATION
 1\. Licenses/restrictions placed on the data CC0 1.0 Universal (CC0 1.0)
 Public Domain Dedication 2\. Links to publications that cite or use the
 data Moreira, MO, JJ Wiens, C Fonseca, D Rojas (2024). Climatic-niche
 breadth, niche position, and speciation in lizards and snakes. Journal of
 Biogeography. 3\. Links to other
 publicly accessible locations of the data: None 4\. Links/relationships to
 ancillary data sets: None 5\. Was data derived from another source? No 6\.
 Recommended citation for this dataset: Moreira, MO, JJ Wiens, C Fonseca, D
 Rojas (2024). Data for: Climatic-niche breadth, niche position, and
 speciation in lizards and snakes [Dataset]. Dryad.
 ### DATA & FILE
 OVERVIEW 1\. File List: A) Dataset S1.xlsx B) Dataset S2.xlsx C) Dataset
 S3.trees D) Dataset S4.xlsx E) Dataset S5.xlsx F) Dataset S6.tre G)
 Dataset S7.xlsx H) Dataset S8.xlsx I) Dataset S9.xlsx 2\. Relationship
 between files, if important: None 3\. Additional related data collected
 that was not included in the current data package: None 4\. Are there
 multiple versions of the dataset? No #### DATA-SPECIFIC INFORMATION FOR:
 Dataset S1.xlsx pPCA scores and decomposition of eigenvalues, and pPCA
 loadings. Results from the phylogenetic principal components analysis
 (pPCA) for climatic-niche position, including the pPCA scores on the first
 sheet, and pPCA loadings on the second sheet. 1\. Number of sheets: 2
 Sheet 1: pPCA scores 1.1. Number of variables: 7 1.2. Number of
 cases/rows: 8 1.3. Variable List: * pPCA scores | var: explained variance
 from each PC axis for the non-phylogenetic PCA * pPCA scores | cum:
 cumulative explained variance * pPCA scores | ratio: ratio of explained
 variance * pPCA scores | moran: autocorrelation metric * pPCA eigenvalues
 decomposition | eig: eigenvalues for each PC axis * pPCA eigenvalues
 decomposition | var: explained variance from each PC axis for the
 phylogenetic PCA * pPCA eigenvalues decomposition | moran: phylogenetic
 autocorrelation metric, reflecting life histories that are
 phylogenetically structured Sheet 2: pPCA loadings 2.1. Number of
 variables: 8 2.2. Number of cases/rows: 8 2.3. Variable List: PC:
 coordinates onto each phylogenetic principal component (PC1 to PC8) 2\.
 Missing data codes: None 3\. Specialized formats or other abbreviations
 used: None #### DATA-SPECIFIC INFORMATION FOR: Dataset S2.xlsx Climatic
 data for 5,320 species in the study. Climatic data extracted from species
 ranges. 1\. Number of variables: 62 2\. Number of cases/rows: 5320 3\.
 Variable List: * Clade: one of the seven major clades (Dibamia, Gekkota,
 Scincoidea, Lacertoidea, Anguimorpha, Iguania, Serpentes) * Family:
 taxonomic rank * Genus: taxonomic rank * Binomial: species name * Bio1_:
 annual mean temperature * Bio4_: temperature seasonality * Bio5_: maximum
 temperature of the warmest month * Bio6_: minimum temperature of the
 coldest month * Bio12_: annual precipitation * Bio15_: precipitation
 seasonality * Bio16_: precipitation of wettest quarter * Bio17_:
 precipitation of driest quarter * \_mean: mean value across all grid cells
 of the species range * \_min: minimum value across all grid cells of the
 species range * \_max: maximum value across all grid cells of the species
 range * \_median: median value across all grid cells of the species range
 * \_sd: standard deviation across all grid cells of the species range *
 \_n: number of grid cells across the species range at approximately 1km
 resolution * PC: coordinates onto each phylogenetic principal component
 (PC1 to PC8) * SNBT: species niche breadth for temperature * SNBP: species
 niche breadth for precipitation 4\. Missing data codes: None 5\.
 Specialized formats or other abbreviations used: None #### DATA-SPECIFIC
 INFORMATION FOR: Dataset S3.trees Phylogeny from Tonini et al. (2016).
 Phylogeny used in the main text in NEXUS format. 1\. Number of species:
 5,320 #### DATA-SPECIFIC INFORMATION FOR: Dataset S4.xlsx Speciation rates
 for 5,320 species in the study. Estimated speciation rates for each
 species in the phylogeny using ClaDS. 1\. Number of variables: 5 2\.
 Number of cases/rows: 5320 3\. Variable List: * Clade: one of the seven
 major clades (Dibamia, Gekkota, Scincoidea, Lacertoidea, Anguimorpha,
 Iguania, Serpentes) * Family: taxonomic rank * Genus: taxonomic rank *
 Binomial: species name * ClaDS: speciation rates [species per Myr]
 obtained from the augmented version of the cladogenetic diversification
 rate shift. 4\. Missing data codes: None 5\. Specialized formats or other
 abbreviations used: None #### DATA-SPECIFIC INFORMATION FOR: Dataset
 S5.xlsx Rates of climatic-niche evolution for 5,320 species in the study.
 Path-wise rates of climatic-niche evolution calculated for each species in
 the phylogeny for both climatic-niche position and climatic-niche breadth,
 using the mean trait rates per-branch obtained from BAMM. 1\. Number of
 variables: 10 2\. Number of cases/rows: 5320 3\. Variable List: * Clade:
 one of the seven major clades (Dibamia, Gekkota, Scincoidea, Lacertoidea,
 Anguimorpha, Iguania, Serpentes) * Family: taxonomic rank * Genus:
 taxonomic rank * Binomial: species name * ∑r: pathwise rates * PC:
 phylogenetic principal component (PC1 to PC4) * SNBT: species niche
 breadth for temperature * SNBP: species niche breadth for precipitation
 4\. Missing data codes: None 5\. Specialized formats or other
 abbreviations used: None #### DATA-SPECIFIC INFORMATION FOR: Dataset
 S6.tre Subsampled phylogeny. Subsampled phylogeny including approximately
 half of the species that were present in the main analyses (n=2,658). We
 ensure that all seven major clades (Dibamia, Gekkota, Scincoidea,
 Lacertoidea, Anguimorpha, Iguania, Serpentes) were represented with
 similar proportions from the phylogeny used in the main text. See Appendix
 S2 for details. 1\. Number of species: 2,658 #### DATA-SPECIFIC
 INFORMATION FOR: Dataset S7.xlsx pPCA scores and decomposition of
 eigenvalues, and pPCA loadings for the sampling analyses Results for the
 phylogenetic principal components analysis (pPCA) for climatic-niche
 position, including the pPCA scores on the first sheet, and pPCA loadings
 on the second sheet. 1\. Number of sheets: 2 Sheet 1: pPCA scores 1.1.
 Number of variables: 7 1.2. Number of cases/rows: 8 1.3. Variable List: *
 pPCA scores | var: explained variance from each PC axis for the
 non-phylogenetic PCA * pPCA scores | cum: cumulative explained variance *
 pPCA scores | ratio: ratio of explained variance * pPCA scores | moran:
 autocorrelation metric * pPCA eigenvalues decomposition | eig: eigenvalues
 for each PC axis * pPCA eigenvalues decomposition | var: explained
 variance from each PC axis for the phylogenetic PCA * pPCA eigenvalues
 decomposition | moran: phylogenetic autocorrelation metric, reflecting
 life histories that are phylogenetically structured Sheet 2: pPCA loadings
 2.1. Number of variables: 8 2.2. Number of cases/rows: 8 2.3. Variable
 List: PC: coordinates onto each phylogenetic principal component (PC1 to
 PC8) 2\. Missing data codes: None 3\. Specialized formats or other
 abbreviations used: None #### DATA-SPECIFIC INFORMATION FOR: Dataset
 S8.xlsx Climatic data for 2,658 species in the sampling analyses. Climatic
 data extracted from species ranges. 1\. Number of variables: 12 2\. Number
 of cases/rows: 2658 3\. Variable List: * Clade: one of the seven major
 clades (Dibamia, Gekkota, Scincoidea, Lacertoidea, Anguimorpha, Iguania,
 Serpentes) * Binomial: species name * PC: coordinates onto each
 phylogenetic principal component (PC1 to PC8) * SNBT: species niche
 breadth for temperature * SNBP: species niche breadth for precipitation
 4\. Missing data codes: None 5\. Specialized formats or other
 abbreviations used: None #### DATA-SPECIFIC INFORMATION FOR: Dataset
 S9.xlsx Speciation rates and rates of climatic-niche evolution for 2,658
 species in the sampling analyses. Estimated speciation rates for each
 species in the phylogeny using ClaDS, as well as the path-wise rates of
 climatic-niche evolution calculated for each species in the phylogeny for
 both climatic-niche position and climatic-niche breadth, using the mean
 trait rates per-branch obtained from BAMM. 1\. Number of variables: 7 2\.
 Number of cases/rows: 2658 3\. Variable List: * Clade: one of the seven
 major clades (Dibamia, Gekkota, Scincoidea, Lacertoidea, Anguimorpha,
 Iguania, Serpentes) * Binomial: species name * ClaDS: speciation rates
 [species per Myr] obtained from the augmented version of the cladogenetic
 diversification rate shift. * ∑r: pathwise rates * PC: phylogenetic
 principal component (PC1 to PC2) * SNBT: species niche breadth for
 temperature * SNBP: species niche breadth for precipitation 4\. Missing
 data codes: None 5\. Specialized formats or other abbreviations used: None