DOI: 10.5061/dryad.6hdr7sr5t
title: Data from: Elevational Goldilocks zone underlies the exceptional diversity of an Andean lizard radiation (Liolaemus; Liolaemidae)

description: 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 (&lt;35°S) and mid-elevations (~1000m), while
 extinction rates are highest at higher latitudes (&gt;35°S) and higher
 elevations (&gt;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.
description: 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 <em>Liolaemus </em>(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).
description: Scripts are for the R software .csv and .nex
 files can be opened with text editors or R
description: 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. 2. 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 5. 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