Data from: Elevational Goldilocks zone underlies the exceptional diversity of an Andean lizard radiation (Liolaemus; Liolaemidae)
Data files
Sep 19, 2023 version files 100.42 MB
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Liolaemus_MCC_tree.nex
9.20 KB
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README.md
9.50 KB
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SI_data_1.csv
363.42 KB
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SI_data_2.csv
49.34 KB
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SI_data_3.csv
662.63 KB
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SI_data_4.csv
2.53 KB
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SI_data_5.csv
4.84 KB
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SI_data_6.csv
5.41 KB
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SI_data_7.csv
33.63 MB
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SI_data_8.csv
65.55 MB
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SI_data_9.csv
8.63 KB
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simulated_phylogenies.nex
129.97 KB
Abstract
Mountains are among the most biodiverse regions on the planet, and how these landforms shape diversification through the interaction of biological traits and geo-climatic dynamics is integral to understanding global biodiversity. In this study we investigate the dual roles of climate change and mountain uplift on the evolution of a hyper diverse radiation, Liolaemus lizards, with a spatially explicit model of diversification using a reconstruction of uplift and paleotemperature in central and southern South America. The diversification model captures a hotspot for Liolaemus around 40°S in lineages with low dispersal ability and narrow niche breadths. Under the model, speciation rates are highest in low latitudes (<35°S) and mid-elevations (~1000m), while extinction rates are highest at higher latitudes (>35°S) and higher elevations (>2000m). Temperature change through the Cenozoic explained variation in speciation and extinction rates through time and across different elevational bands. Our results point to the conditions of mid-elevations being optimal for diversification (i.e., Goldilocks Zone), driven by the combination of (1) a complex topography which facilitates speciation during periods of climatic change, and (2) a relatively moderate climate which enables the persistence of ectothermic lineages and buffers species from extinction.
This README.txt file was generated 07.03.2023 by Alexander Skeels
GENERAL INFORMATION
- Title of Dataset: Data from: 'Elevational Goldilocks zone underlies the exceptional diversity of a large lizard radiation (Liolaemus; Liolaemidae)'
- 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
- Date of data collation: 2020-2023
- Geographic location of data collation: souther South America
- 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
- 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.
- 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
- Number of variables: 4
- Number of cases/rows: 7089
- Variable List: Species: species binomial Clade: infrageneric classification Latitude: latitude Longitude: longitude
- Missing data codes: None
- Abbreviations used: N/A; not applicable
- Other relevant information:
DATA-SPECIFIC INFORMATION FOR: SI_data_2.csv
- Number of variables: 12
- Number of cases/rows: 500
- 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
- Missing data codes: None
- Abbreviations used: N/A; not applicable
DATA-SPECIFIC INFORMATION FOR: SI_data_3.csv
- Number of variables: 12
- Number of cases/rows: 500
- 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
- Missing data codes: None
- Abbreviations used: N/A; not applicable
DATA-SPECIFIC INFORMATION FOR: SI_data_4.csv
- Number of variables: 6
- Number of cases/rows: 55
- 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
- Missing data codes: None
- Abbreviations used: N/A; not applicable
DATA-SPECIFIC INFORMATION FOR: SI_data_5.csv
- Number of variables: 6
- Number of cases/rows: 55
- 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
- Missing data codes: None
- Abbreviations used: N/A; not applicable
DATA-SPECIFIC INFORMATION FOR: SI_data_6.csv
- Number of variables: 7
- Number of cases/rows: 152
- 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
- Missing data codes: None
- Abbreviations used: N/A; not applicable
DATA-SPECIFIC INFORMATION FOR: SI_data_7.csv
- Number of variables: 178
- Number of cases/rows: 40000
- 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
- Missing data codes: None
- Abbreviations used:
N/A; not applicable
- Abbreviations used: N/A; not applicable
DATA-SPECIFIC INFORMATION FOR: SI_data_8.csv
- Number of variables: 178
- Number of cases/rows: 90000
- 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
- Missing data codes: None
- Abbreviations used: N/A; not applicable
DATA-SPECIFIC INFORMATION FOR: SI_data_9.csv
- Number of variables: 7
- Number of cases/rows: 175
- 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
- Missing data codes: None
- Abbreviations used: N/A; not applicable
We collated occurrence records for 7220 locations of 297 described and candidate species. These records were obtained from the Global Biodiversity Information Facility (GBIF), the scientific literature and museum records, and were carefully curated for errors, inaccuracies and taxonomic updates. We followed the taxonomy and distributions provided by Abdala et al. (2021) as a reference to clean the dataset.
We simulated 500 clades under a range of model parameters using the Gen3sis engine.
We provide raw occurence record data for Liolaemus (SI_data_1), the raw paleoenvironmental reconstructions of tempreature and elevation (SI_data_7, SI_data_8), as well as summary of simulated data (SI_data_2), summarised spatial patterns of emprical and simulated data across grid cells (SI_data_3) and elevational bands (SI_data_4, SI_data_5, SI_data_9), and summarised phylogenetic data (SI_data_6).
Scripts are for the R software
.csv and .nex files can be opened with text editors or R