Published February 20, 2022 | Version v1.0
Dataset Open

Data for article: A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils

Creators

  • 1. Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
  • 2. Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, 13083-862, Brazil
  • 3. Departamento de Ecologia, Universidade de São Paulo, São Paulo 05508-900, Brazil
  • 4. Department of Animal Ecology and Systematics, Justus Liebig University, Giessen, Germany

Description

Supplementary information for:

A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils

Torsten Hauffe, Mathias M. Pires, Tiago B. Quental, Thomas Wilke, and Daniele Silvestro

 

  •  Simulations
    • Scripts
      • Scenario1_SamplingHeterogeneity.R: Script to simulate biogeographic histories with sampling heterogeneity
      • Scenario3_SealevelInvasion.R: Script to simulate biogeographic histories where sea level facilitates dispersal and invasion induces extinction
      • Scenario3_DiversityDependence.R: Script to simulate diversity-dependent biogeographic histories
      • Scenario4_TraitDependence.R: Script to simulate trait-dependent biogeographic histories
      • Scenario5_CategoricalTraitDependence.R: Script to simulate trait-dependent biogeographic histories
    • Results
      • Scenario1_SamplingHeterogenetiy_alpha05.txt: Results of simulations scenario 1 with a sampling heterogeneity of alpha = 0.5
      • Scenario1_SamplingHeterogenetiy_alpha1.txt: Results of simulations scenario 1 with a sampling heterogeneity of alpha = 1
      • Scenario1_SamplingHeterogenetiy_alpha2.txt: Results of simulations scenario 1 with a sampling heterogeneity of alpha = 2
      • Scenario1_SamplingHeterogenetiy_alpha10.txt: Results of simulations scenario 1 with a sampling heterogeneity of alpha = 10
      • Scenario2_Independent_dispersal_and_extinction.txt: Results of simulation scenario 2 with sea-level independent dispersal and no invasion induced extinction
      • Scenario2_Sealevel_dependent_dispersal_and_independent_extinction.txt: Results of simulation scenario 2 with sea-level dependent dispersal and no invasion induced extinction
      • Scenario2_Sealevel_independent_dispersal_and_invasion_induced_extinction.txt: Results of simulation scenario 2 with sea-level independent dispersal and invasion induced extinction
      • Scenario2_Sealevel_dependent_dispersal_and_invasion_induced_extinction.txt: Results of simulation scenario 2 with sea-level dependent dispersal and invasion induced extinction
      • Scenario3_Independent_dispersal_and_extinction.txt: Results of simulations scenario 3 with diversity-independent dispersal and extinction
      • Scenario3_Diversity_dependent_dispersal_and_independent_extinction.txt: Results of simulations scenario 3 with diversity-dependent dispersal and diversity-independent extinction
      • Scenario3_Independent_dispersal_and_Diversity_dependent_extinction.txt: Results of simulations scenario 3 with diversity-dependent dispersal and diversity-independent extinction
      • Scenario3_Diversity_dependent_dispersal_and_extinction.txt: Results of simulations scenario 3 with diversity-dependent dispersal and extinction
      • Scenario4_Independent_dispersal_and_extinction.txt: Results of scenario 4 with trait-independent dispersal and extinction
      • Scenario4_Trait_dependent_dispersal_and_independent_extinction.txt: Results of scenario 4 with trait-dependent dispersal and independent extinction
      • Scenario4_Independent_dispersal_and_trait_dependent_extinction.txt: Results of scenario 4 with independent dispersal and trait-dependent extinction
      • Scenario4_trait_dependent_dispersal_and_extinction.txt: Results of scenario 4 with trait-dependent dispersal and extinction
      • Scenario5_CatTrait_dependent_dispersal_and_independent_extinction.txt: Results of model 2 with categorical traits (e.g family) influence dispersal but no influence of a category-specific continuous traits
  • Carnivora
    • BinnedOccurrence: Folder with 100 replicates of binned occurrences of max. 330 carnivoran genera throughout the Neogene
    • BodyMass: Folder with 100 replicates of body mass for 330 carnivoran genera
    • Sealevel: Folder with sea level through the Neogene
    • Temperature: Folder with the temperature record of the Neogene
    • Families: Folder with families as taxonomic proxy for phylogeny. FamilyGeneraNumeric.txt is the numeric coding used for the Bayesian analyses of carnivoran biogeography

Files

Hauffe_et_al.zip

Files (1.8 MB)

Name Size Download all
md5:56accef6090f740b0fc73b4932e2869f
1.8 MB Preview Download

Additional details

Funding

New methods to infer population dynamics from the fossil record PCEFP3_187012
Swiss National Science Foundation