Museum occurrence data predicts genetic diversity in a species-rich clade of desert lizards

Scripts used in:

Sonal Singhal, Huateng Huang, Pascal Title, Stephen Donnellan, Iris Holmes, Daniel Rabosky

Name		Name	Last commit message	Last commit date
Latest commit History 7 Commits
R2_assemblies.py		R2_assemblies.py
README.md		README.md
TableS1_individual_data.csv		TableS1_individual_data.csv
TableS5_literature_survey.csv		TableS5_literature_survey.csv
align_reads1.py		align_reads1.py
align_reads2.py		align_reads2.py
biomes_pi.R		biomes_pi.R
calculate_pi_per_ind_by_ind.py		calculate_pi_per_ind_by_ind.py
calculate_pi_per_species.py		calculate_pi_per_species.py
date_and_plot_species_trees.R		date_and_plot_species_trees.R
evaluate_assembly.py		evaluate_assembly.py
final.R		final.R
gene_trees.py		gene_trees.py
gene_trees_polytomize.py		gene_trees_polytomize.py
get_vcf_depth.py		get_vcf_depth.py
get_vcf_depth_by_ind.py		get_vcf_depth_by_ind.py
habitat_stability.R		habitat_stability.R
heterogeneity.R		heterogeneity.R
homology_across_species.py		homology_across_species.py
make_astrid_astral.py		make_astrid_astral.py
make_nuclear_alignment.py		make_nuclear_alignment.py
prep_paleomodel_layers.R		prep_paleomodel_layers.R
pyrad_assembly.py		pyrad_assembly.py
rainbow_assemblies.py		rainbow_assemblies.py
run_admixture.py		run_admixture.py
run_admixture_chooseK.py		run_admixture_chooseK.py
simpler_homology.py		simpler_homology.py
species_counts.R		species_counts.R
trimmomatic_reads.py		trimmomatic_reads.py
vcf_to_admixture.py		vcf_to_admixture.py
vcf_to_lamarc.py		vcf_to_lamarc.py

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