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
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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
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Co-investigator 2
Name: Dr. Damien Esquerre
Institution: Research School of Biology, Australian National University, Canberra, 0200, Australia / University of Wollongong, Wollongong, 2522, Australia
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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
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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
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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:
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File 1 Name: SI_data_1.csvFile 1 Description: Occurence records of Liolaemus species
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File 2 Name: SI_data_2.csvFile 2 Description: Summary of the model parameters, species diversity, and model fit for 500 simulation models
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File 3 Name: SI_data_3.csv
File 3 Description: Richnness and weighted endemism values across grid cells for simulated and empirical data
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File 4 Name: SI_data_4.csv
File 4 Description: Richness and weighted endemism values across elevation bands for empirical data
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File 5 Name: SI_data_5.csv
File 5 Description: Richness and weighted endemism values across elevation bands for simulated data
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File 6 Name: SI_data_6.csvFile 6 Description: Lineages through time summary from best 25 simulation models
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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
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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
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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
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File 10 Name: Liolaemus_MCC_tree.nex
File 10 Description: Phylogenetic tree for Esquerre et al 2019a
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File 11 Name: Simulated_phylogenies.nexFile 11 Description: Phylogenetic trees from best 25 simulation models
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File 12 Name: Gen3sis_config_generator.RFile 12 Description: Script to genetae 500 config files to run 500 simulation models with variable parameters
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File 13 Name: Gen3sis_config_template.R
File 13 Description: Gen3sis template for simulation model
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File 14 Name: script_1_sensitivity_analysis.RFile 14 Description: Script to explore the relationship between model parameters and goodness of fit metrics
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File 15 Name: script_2_empirical_and_simulation_comparison.RFile 15 Description: Script to compare simulated and empirical patterns of endemism and species richness
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File 16 Name: script_3_latitude_comparison.RFile 16 Description: Script to summarise patterns of diversity and diversification across latitudinal bands
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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
- Abbreviations used:
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