The evolution of seasonal camouflage in white-tailed jackrabbits in response to past and future climates

This repository contains copies of custom code and related resources needed to replicate analyses used to investigate the evolution of seasonal camouflage in white-tailed jackrabbits (Lepus townsendii).

wtjr_sdm-master.zip (see GitHub for more details)
- Zip archive of code and data for SDM analysis, see READMEs within for full description. Includes:- Occurrence records of WTJR used in the SDM modeling- Snow residence time data for modeling current and future phenotypes
wc0.5.zip
- Bioclim variables used for species distribution modeling.
worldclim_projections_2080.zip
- Future projections of Bioclim variables 2 and 3
DMNS18807_06042020_pseudohap2.1.fasta.gz and DMNS18807_06042020_pseudohap2.2.fasta.gz
- Original de novo genome assemblies of the white-tailed jackrabbit genome generated by Supernova. The primary assembly (used for all analyses) is pseudohap2.1 and the alternative assembly is pseudohap2.2 (used only for the BEAST analysis).
DMNS18807_06042020_pseudohap2.1_OryCun2.0_liftoff_annotation.gff3
- Liftoff gff3 annotation of the primary white-tailed jackrabbit reference genome. Annotation was obtained from the European Rabbit reference genome (OryCun2.0).
OryCun2.0_repeats.bed
-Bed file of repeat regions for OryCun2.0 from Genome Browser
GenotypeArea_COATCOLOR_WTJR_W1_34SNPs_92INDVS.xlsx
- Raw genotype data
spectrophotometry_raw_files.zip
- Raw reflectance data
wtjr_camouflage.zip (see GitHub for more details)
- Input alignments, control files and output trees with divergence times from BEAST analysis to date the divergence between white and brown haplotypes.- Input alignments, control files and output log files for GPhoCs analysis to estimate demographic parameters of divergence between hare species.- Processed reflectance data.
- Formatted genotype data, and other input and output files for association and Fisher exact test analyses .- Simulated expected divergence (dxy) between hare species.- Empirical divergence (dxy) between hare species within each coat color association region.