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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: matthew.moreira@ua.pt

B. Name: John J. Wiens
Institution: University of Arizona
Address: Tucson, AR USA
Email: wiensj@arizona.edu

C. Name: Carlos Fonseca
Institution: ForestWISE
Address: Vila Real, Portugal
Email: cfonseca@ua.pt

D. Name: Danny Rojas
Institution: Pontificia Universidad Javeriana Cali
Address: Cali, Colombia
Email: rojasmartin.cu@gmail.com

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. https://doi.org/10.1111/jbi.14802

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. https://doi.org/10.5061/dryad.f4qrfj72v

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