This README.txt file was generated 07.03.2023 by Alexander Skeels

GENERAL INFORMATION

1. Title of Dataset: Data from: 'Elevational Goldilocks zone underlies the exceptional diversity of a large lizard radiation (Liolaemus; Liolaemidae)'
2. Author Information <br> Corresponding Investigator Name: Dr Alexander Skeels Institution: ETH Zürich, Zurich 8092, Switzerland / Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland Email: alexander.skeels@gmail.com <br> Co-investigator 2 Name: Dr. Damien Esquerre Institution: Research School of Biology, Australian National University, Canberra, 0200, Australia / University of Wollongong, Wollongong, 2522, Australia <br> Co-investigator 2 Name: Daria Lipsky Institution: ETH Zürich, Zurich 8092, Switzerland / Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland <br> Co-investigator 3 Name: Dr Loic Pellissier Institution: ETH Zürich, Zurich 8092, Switzerland / Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland <br> Co-investigator 4 Name: Dr. Lydian M. Boschman Institution: Department of Earth Sciences, Utrecht University; 3584 CB Utrecht, Netherlands
3. Date of data collation: 2020-2023
4. Geographic location of data collation: souther South America
5. Recommended citation for this dataset: Skeels et al. (2023), Data from: Elevational Goldilocks zone underlies the exceptional diversity of a large lizard radiation (Liolaemus; Liolaemidae)

DATA & FILE OVERVIEW

1. Description of dataset

These data and R scripts were generated to investigate the role of niche and dispersal traits of biotic interchange dynamics in the Indo-Australian Archipelago.

1. File List: <br> File 1 Name: SI_data_1.csvFile 1 Description: Occurence records of Liolaemus species <br> File 2 Name: SI_data_2.csvFile 2 Description: Summary of the model parameters, species diversity, and model fit for 500 simulation models <br> File 3 Name: SI_data_3.csv File 3 Description: Richnness and weighted endemism values across grid cells for simulated and empirical data <br> File 4 Name: SI_data_4.csv File 4 Description: Richness and weighted endemism values across elevation bands for empirical data <br> File 5 Name: SI_data_5.csv File 5 Description: Richness and weighted endemism values across elevation bands for simulated data <br> File 6 Name: SI_data_6.csvFile 6 Description: Lineages through time summary from best 25 simulation models <br> File 7 Name: SI_data_7.csv File 7 Description: Reconstructed tempreature data at 0.3 degrees for past 35 million years at 200 thousand year intervals <br> File 8 Name: SI_data_8.csv File 8 Description: Reconstructed elevation data at 0.2 degrees for past 35 million years at 200 thousand year intervals <br> File 9 Name: SI_data_9.csv File 9 Description: diversification rates, area, and temperature across elevational bands for past 35 million years at 1 million year intervals <br> File 10 Name: Liolaemus_MCC_tree.nex File 10 Description: Phylogenetic tree for Esquerre et al 2019a <br> File 11 Name: Simulated_phylogenies.nexFile 11 Description: Phylogenetic trees from best 25 simulation models <br> File 12 Name: Gen3sis_config_generator.RFile 12 Description: Script to genetae 500 config files to run 500 simulation models with variable parameters <br> File 13 Name: Gen3sis_config_template.R File 13 Description: Gen3sis template for simulation model <br> File 14 Name: script_1_sensitivity_analysis.RFile 14 Description: Script to explore the relationship between model parameters and goodness of fit metrics <br> File 15 Name: script_2_empirical_and_simulation_comparison.RFile 15 Description: Script to compare simulated and empirical patterns of endemism and species richness <br> File 16 Name: script_3_latitude_comparison.RFile 16 Description: Script to summarise patterns of diversity and diversification across latitudinal bands <br> File 17 Name: script_4_elevation_models.R File 17 Description: Script to explore the relationships between diversifictaion rates, area, and temperature across elevational bands

METHODOLOGICAL INFORMATION

DATA-SPECIFIC INFORMATION FOR: SI_data_1.csv

1. Number of variables: 4
2. Number of cases/rows: 7089
3. Variable List: Species: species binomial Clade: infrageneric classification Latitude: latitude Longitude: longitude
4. Missing data codes: None
5. Abbreviations used: N/A; not applicable
6. Other relevant information:

DATA-SPECIFIC INFORMATION FOR: SI_data_2.csv

1. Number of variables: 12
2. Number of cases/rows: 500
3. Variable List: TempRate: temperature niche evolution rate TempRange: temperature niche breadth S: divergence threshold WeibullShape: shape parameter of Weibull distribution of dispersal kernel WeibullScale: scale parameter of Weibull distribution of dispersal kernel ModelName: simulation ID Seed: random seed of the simulation RMSE: root mean squared error metric of simulation goodness of fit SpearmanRho: Spearman's rho metric of simulation goodness of fit n_extant_species: number of extant species n_extinct_species: number of extinct species n_total_species: number of extant and extinct species running_timestep: final timestep of simulatoin before completion or abortion
4. Missing data codes: None
5. Abbreviations used: N/A; not applicable

DATA-SPECIFIC INFORMATION FOR: SI_data_3.csv

1. Number of variables: 12
2. Number of cases/rows: 500
3. Variable List: longitude: longitude latitude: latitude empirical_richness: Liolaemus species richness empirical_WE: Liolaemus weighted endemism simulated_richness: Average simulated species richness simulated_WE: Average simulated weighted endemism
4. Missing data codes: None
5. Abbreviations used: N/A; not applicable

DATA-SPECIFIC INFORMATION FOR: SI_data_4.csv

1. Number of variables: 6
2. Number of cases/rows: 55
3. Variable List: elevation: elevational band minimum area: area. measured as number of grid cells present in each elevational band richness: Liolaemus species richness richness_std: Liolaemus species richness standardised between 0-1 we: Liolaemus weighted endemism we_std: Liolaemus weighted endemism standardised between 0-1
4. Missing data codes: None
5. Abbreviations used: N/A; not applicable

DATA-SPECIFIC INFORMATION FOR: SI_data_5.csv

1. Number of variables: 6
2. Number of cases/rows: 55
3. Variable List: elevation: elevational band minimum area: area. measured as number of grid cells present in each elevational band richness_std: Simulated species richness standardised between 0-1 richness_se: standard error of Liolaemus species richness richness_se_std: standard error of Liolaemus species richness standardised between 0-1 we: Simulated weighted endemism we_std: Simulated weighted endemism standardised between 0-1 we_se: standard error of Liolaemus weighted endemism we_se_std: standard error of Liolaemus weighted endemism standardised between 0-1
4. Missing data codes: None
5. Abbreviations used: N/A; not applicable

DATA-SPECIFIC INFORMATION FOR: SI_data_6.csv

1. Number of variables: 7
2. Number of cases/rows: 152
3. Variable List: time: time in millions of years before the present max: maximum observed species diversity across 25 simulated phylogenies min: minimum observed species diversity across 25 simulated phylogenies q_95: 95th quantile of observed species diversity across 25 simulated phylogenies q_05: 5th quantile of observed species diversity across 25 simulated phylogenies mean: mean observed species diversity across 25 simulated phylogenies type: data source
4. Missing data codes: None
5. Abbreviations used: N/A; not applicable

DATA-SPECIFIC INFORMATION FOR: SI_data_7.csv

1. Number of variables: 178
2. Number of cases/rows: 40000
3. Variable List: longitude: longitude latitude: latitude 0_Ma: reconstructed temperature value at 0 million years ago 0.2_Ma: reconstructed temperature value at 0.2 million years ago ... 35_Ma: reconstructed temperature value at 35 million years ago
4. Missing data codes: None
5. Abbreviations used: N/A; not applicable
   1. Abbreviations used: N/A; not applicable

DATA-SPECIFIC INFORMATION FOR: SI_data_8.csv

1. Number of variables: 178
2. Number of cases/rows: 90000
3. Variable List: longitude: longitude latitude: latitude 0_Ma: reconstructed elevation value at 0 million years ago 0.2_Ma: reconstructed elevation value at 0.2 million years ago ... 35_Ma: reconstructed elevation value at 35 million years ago
4. Missing data codes: None
5. Abbreviations used: N/A; not applicable

DATA-SPECIFIC INFORMATION FOR: SI_data_9.csv

1. Number of variables: 7
2. Number of cases/rows: 175
3. Variable List: er: extinction rate sr: speciation rate dr: net diversification rate a: area t: temperature band: elevational band time: time in million of years before present
4. Missing data codes: None
5. Abbreviations used: N/A; not applicable