This README.txt file was generated 07.03.2023 by Alexander Skeels

GENERAL INFORMATION

1. Title of Dataset: Data from: 'Paleoenvironments shaped biotic exchange of terrestrial vertebrates across Wallace’s Line' 

2. Author Information

	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

	Co-investigator 1
		Name: Lydian M. Boschman
		Institution: Department of Earth Sciences, Utrecht University; 3584 CB Utrecht, Netherlands

	Co-investigator 2
		Name: Ian R. McFadden
		Institution: Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam; 1090 GE Amsterdam, Netherlands 
	
	Co-investigator 3
		Name: Elizabeth M. Joyce
		Institution: Systematics, Biodiversity and Evolution of Plants, Ludwig Maximilian University of Munich; Munich 80331, Germany

	Co-investigator 4
		Name: Oskar Hagen
		Institution: German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103,Germany

	Co-investigator 5
		Name: Ocatvio Jiménez Robles
		Institution: Research School of Biology, Australian National University; Canberra, 0200, Australia / Institute of Biology, École Normale Supérieure; Paris, 75005, France 

	Co-investigator 6
		Name: Wilhelmine Bach
		Institution: ETH Zürich, Zurich 8092, Switzerland / Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland

	Co-investigator 7
		Name: Victor Boussange
		Institution: ETH Zürich, Zurich 8092, Switzerland / Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland

	Co-investigator 8
		Name: Thomas Keggin
		Institution: ETH Zürich, Zurich 8092, Switzerland / Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland

	Co-investigator 9
		Name: Dr Walter Jetz
		Institution: Yale University, New Haven, CT 06520, USA.

	Co-investigator 10
		Name: Dr Loic Pellissier
		Institution: ETH Zürich, Zurich 8092, Switzerland / Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland


3. Date of data collation: 2020-2023

4. Geographic location of data collation: Global

5. Recommended citation for this dataset: Skeels et al. (2023), Data from: Paleoenvironments shaped biotic exchange of terrestrial vertebrates across Wallace’s Line 

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:

      File 1 Name: Data_S1.csv       
      File 1 Description: Distribution in seven biogeographic realms for 20433 species of terrestrial vertebrate.

      File 2 Name: Data_S2.tre  
      File 2 Description: Single phylogenetic tree randomly sampled from the posterior distribution of each classes phylogenetic analysis, for each of 227 families of tetrapod in the Indo-Australasian region. 

      File 3 Name: Data_S3.tre 
      File 3 Description: Maximum clade credibility phylogenetic tree, including only species with molecular data, for each of 227 families of tetrapod in the Indo-Australasian region. 

      File 4 Name: Data_S4.tre     
      File 4 Description: Phylogenetic relationships of tetrapod families.

      File 5 Name: Data_S5.csv    
      File 5 Description: Summary of the distribution, environmental niche breadth, rates of niche evolution, and species diversity for 227 families of terrestrial vertebrate.

      File 6 Name: Data_S6.csv                   
      File 6 Description: Summary of the distribution, environmental niche breadth, rates of niche evolution, and species diversity for 1000 simulation models generating under model M1.

      File 7 Name: Data_S7.csv  
      File 7 Description: Summary of the distribution, environmental niche breadth, rates of niche evolution, and species diversity for 5000 simulation models generating under models M2-M5.

      File 8 Name: Data_S8.csv  
      File 8 Description: Biogeographic realm connectivity matrices used in the biogeographic estimation models.
	
      File 9 Name: Data_S9.rds  
      File 9 Description: Paleoenvironmental reconstruction of paleogeography, paleotemperature, and paleoprecipitation in the Indo-Australasian region for the past 30 Ma.
	
      File 10 Name: config_generator.R  
      File 10 Description: Script to generate Gen3sis configs from config templates

      File 11 Name: config_run_file.R    
      File 11 Description: Script to run Gen3sis simulation configs.

      File 12 Name: config_template_M1_Sahul.R 
      File 12 Description: Gen3sis template for M1 model and Sahulian ancestor species.

      File 13 Name: config_template_M1_Sunda.R 
      File 13 Description: Gen3sis template for M1 model and Sundanian ancestor species.

      File 14 Name: config_template_M2_Sahul.R   
      File 14 Description: Gen3sis template for M2 model and Sahulian ancestor species.

      File 15 Name: config_template_M2_Sunda.R   
      File 15 Description: Gen3sis template for M2 model and Sundanian ancestor species.

      File 16 Name: config_template_M3_Sahul.R     
      File 16 Description: Gen3sis template for M3 model and Sahulian ancestor species.

      File 17 Name: config_template_M3_Sunda.R 
      File 17 Description: Gen3sis template for M3 model and Sundanian ancestor species.

      File 18 Name: config_template_M4_Sahul.R     
      File 18 Description: Gen3sis template for M4 model and Sahulian ancestor species.

      File 19 Name: config_template_M4_Sunda.R  
      File 19 Description: Gen3sis template for M4 model and Sundanian ancestor species.

      File 20 Name: config_template_M5_Sahul.R    
      File 20 Description: Gen3sis template for M5 model and Sahulian ancestor species.

      File 21 Name: config_template_M5_Sunda.R 
      File 21 Description: Gen3sis template for M5 model and Sundanian ancestor species.

      File 22 Name: config_template_M6_Sahul.R    
      File 22 Description: Gen3sis template for M6 model and Sahulian ancestor species.

      File 23 Name: config_template_M6_Sunda.R 
      File 23 Description: Gen3sis template for M6 model and Sundanian ancestor species.

      File 24 Name: exchange_dynamics_linear_models.R  
      File 24 Description: Script to fit phylogenetic generalised linear models of exhcange dynamics. 

      File 25 Name: landscape_generator.R 
      File 25 Description: Script to generate landscape object for Gen3sis simulations from data.
	
      File 26 Name: Table_S4.csv
      File 26 Description: Table S4.

METHODOLOGICAL INFORMATION



DATA-SPECIFIC INFORMATION FOR: Data_S1.csv   

1. Number of variables: 9

2. Number of cases/rows: 20434

3. Variable List: 
	species: species binomial
	aus: Australasian realm
	ind: Indomalayan realm
	afr: Afrotropical realm
	nea: Nearctic realm
	neo: Neotropical realm
	oce: Oceanian realm
	family: taxonomic family

4. Missing data codes: 
	None

5. Abbreviations used: 
	N/A; not applicable


6. Other relevant information: 
	

DATA-SPECIFIC INFORMATION FOR: Data_S5.csv   

1. Number of variables: 20

2. Number of cases/rows: 228

3. Variable List: 
	class: Taxonomic class
	order: Taxonomic order
	family:	Taxonomic family
	n_species: Number of species
	n_species_aus: Number of Australasian species
	n_species_indo: Number of Indomalayan species
	origin_con: Estimated biogeographic origin
	present_sunda: Present in Sunda
	present_sahul: Present in Sahul 
	present_wallacea: Present in Wallacea 
	present_australian_mainland: Present on the Australian mainland 
	exchanged: Estimated to have been exchanged between realms in biogeographic models
	n_col: Number of colonisations estimated from boigeographic models
	taxonomic_beta: Taxonomic beta diversity
	phylogenetic_beta: Phylogenetic beta diversity
	dispersal_ability: Volancy
	mean_prec_niche_breadth: mean realised precipitation niche breadth
	mean_temp_niche_breadth: mean realised temperature niche breadth
	prec_niche_evolution_sigma2: precipitation niche evolution rate
	temp_niche_evolution_sigma2: temperature niche evolution rate


4. Missing data codes: 
	None

5. Abbreviations used: 
	N/A; not applicable


6. Other relevant information: 

DATA-SPECIFIC INFORMATION FOR: Data_S6.csv   

1. Number of variables: 16

2. Number of cases/rows: 1001

3. Variable List: 
	ID: Unique simulation identifier
	temp_niche_breadth: Temperature niche breadth parameter (omega T)
	prec_niche_breadth: Temperature niche breadth parameter (omega P)
	dispersal_shape: Dispersal shape parameter (D psi)
	dispersal_scale: Dispersal scale parameter (D phi)
	niche_evolution_rate: niche evolution rate parameter (sigma)
	speciation_threshold: Speciation threshold parameter (S)
	random_seed: Random seed simulation began with (for reproducibility)
	starting_region: Sunda or Sahul origin
	final_time_step_reached: Last time step acheived in simulation
	finshed: Did the simulation finish
	n_species: Number of species generated in the simulation
	exchanged: Were species exhcanged in the simulation
	n_col: Number of colonisation events in the simulation.
	taxonomic_beta: Taxonomic beta diversity
	phylogenetic_beta: Phylogenetic beta diversity

4. Missing data codes: 
	None

5. Abbreviations used: 
	N/A; not applicable


6. Other relevant information: 


DATA-SPECIFIC INFORMATION FOR: Data_S7.csv   

1. Number of variables: 11

2. Number of cases/rows: 1001

3. Variable List: 
	ID: Unique simulation identifier
	temp_niche_breadth: Temperature niche breadth parameter (omega T)
	prec_niche_breadth: Temperature niche breadth parameter (omega P)
	dispersal_shape: Dispersal shape parameter (D psi)
	dispersal_scale: Dispersal scale parameter (D phi)
	niche_evolution_rate: niche evolution rate parameter (sigma)
	speciation_threshold: Speciation threshold parameter (S)
	random_seed: Random seed simulation began with (for reproducibility)
	starting_region: Sunda or Sahul origin
	finshed: Did the simulation finish
	region_origin: Sunda (ind) or Sahul (aus) origin
	crossed_HL_line: Crossed the Heilprin-Lydekker Line
	crossed_W_line: Crossed Wallace's Line

4. Missing data codes: 
	None

5. Abbreviations used: 
	N/A; not applicable


6. Other relevant information: 


DATA-SPECIFIC INFORMATION FOR: Data_S8.csv   

1. Number of variables: 6

2. Number of cases/rows: 6

3. Variable List: 
	aus: Australasian realm
	ind: Indomalayan realm
	afr: Afrotropical realm
	nea: Nearctic realm
	neo: Neotropical realm
	oce: Oceanian realm


4. Missing data codes: 
	None

5. Abbreviations used: 
	N/A; not applicable


6. Other relevant information: Each sheet in the .xls document corresponds to a different time period: 100-65 Ma; 65-25 Ma; 25-5 Ma; 5-0 Ma.


DATA-SPECIFIC INFORMATION FOR: Data_S10.csv   

1. Number of variables: 22

2. Number of cases/rows: 114

3. Variable List: 
	family: Taxonomic family name
	nparams0: Number of parameters of DEC
	nparams1: Number of parameters of DECTS
	nparams2: Number of parameters of DECTS+w
	LnL0: Log liklihood of DEC
	LnL1: Log liklihood of DECTS
	LnL2: Log liklihood of DECTS+w
	AIC0: AIC of DEC
	AIC1: AIC of DECTS
	AIC2: AIC of DECTS+w
	AICw0: Akaikie weight of DEC
	AICw1: Akaikie weight of DECTS
	AICw2: Akaikie weight of DECTS+w
	d0: Dispersal parameter estimate of DEC
	d1: Dispersal parameter estimate of DECTS
	d2: Dispersal parameter estimate of DECTS+w
	e0: Extinction parameter estimate of DEC
	e1: Extinction parameter estimate of DECTS
	e2: Extinction parameter estimate of DECTS+w
	w0: Dispersal weight modifier parameter estimate of DEC
	w1: Dispersal weight modifier parameter estimate of DECTS
	w2: Dispersal weight modifier parameter estimate of DECTS+w



4. Missing data codes: 
	None

5. Abbreviations used: 
	N/A; not applicable


6. Other relevant information: Each sheet in the .xls document corresponds to a different time period: 100-65 Ma; 65-25 Ma; 25-5 Ma; 5-0 Ma.