The evolution of winter camouflage in white-tailed jackrabbits

This github contains custom code that was used to study the evolution of seasonal camouflage in white-tailed jackrabbits and supported analysis for the following publication:

Mafalda S. Ferreira et al. The evolution of white-tailed jackrabbit camouflage in response to past and future seasonal climates. Science 379, 1238-1242 (2023). DOI:10.1126/science.ade3984

Along with the custom code, I provide context code for upstream and downstream analyses so that the code can be efficiently and effectively used.

Contact: sferreira.mafalda (at) gmail.com

Analyses with low coverage short read data

1. Manhattan plots from ANGSD Association outputs

Analyses with high coverage short read data

1. Calling genotypes and creating a consensus fasta and geno files
2. Divergence between white and brown haplotypes
3. Demographic inference of divergence
4. Detecting introgression with coalescent simulations

Analyses of spectrophometry data and massarray genotype data

1. Analyses of reflectance data
2. Analyses of genotype data

Assembly of the white-tailed jackrabbit reference genome with 10X linked read data

1. Genome assembly and annotation