Pinworm & host BUCKy trees and pinworm COI BEAST tree

H_cucullatum_COI_quadrivittatus_cytb_BUCKy.tre: BUCKy tree with concordance values for H. cucullatum COI MrBayes trees and quadrivittatus group cytb MrBayes trees H_cucullatum_R_eutamii_COI_BUCKy.tre: BUCKy tree with concordance values for H. cucullatum and R. eutamii COI MrBayes trees H_cucullatum_and_R_eutamii_COI_beast_rate_estimates_only.tre: BEAST tree of COI sequences for H. cucullatum and R. eutamii, used only to estimate relative rates H_cucullatum_COI_T_minimus_cytb_BUCKy.tre: BUCKy tree with concordance values for H. cucullatum COI MrBayes trees and T. minimus cytb MrBayes trees R_eutamii_COI_T_minimus_cytb_BUCKy.tre: BUCKy tree with concordance values for R. eutamii COI MrBayes trees and T. minimus cytb MrBayes trees R_eutamii_COI_quadrivittatus_cytb_BUCKy.tre: BUCKy tree with concordance values for R. eutamii COI MrBayes trees and quadrivittatus group cytb MrBayes tree

Heteroxynema cucullatum DNA sequence alignments and phylogenies

H_cucullatum_3loci_concatenated_MrBayes.tre: MrBayes tree of Heteroxynema cucullatum concatenated loci COI, ITS+, 28S H_cucullatum_3loci_starbeast.tre: Starbeast species tree of Heteroxynema cucullatum loci COI, ITS+, 28S H_cucullatum_COI_quadrivittatus_hosts_MrBayes.tre: MrBayes gene tree of COI for Heteroxynema cucullatum individuals that corespond to quadrivittatus group hosts (used in tanglegram) H_cucullatum_COI_T_minimus_hosts_MrBayes.tre: MrBayes gene tree of COI for Heteroxynema cucullatum individuals that corespond to Tamias minimus hosts (used in tanglegram) Heteroxynema_cucullatum_28S_MrBayes.tre: MrBayes gene tree of Heteroxynema cucullatum 28S Heteroxynema_cucullatum_28S_alignment.nex: DNA sequence alignment of Heteroxynema cucullatum 28S Heteroxynema_cucullatum_COI_MrBayes.tre: MrBayes gene tree of Heteroxynema cucullatum COI Heteroxynema_cucullatum_COI_RAxML.tre: RAxML gene tree of Heteroxynema cucullatum COI Heteroxynema_cucullatum_COI_alignment.nex: DNA sequence alignment of Heteroxynema cucullatum COI Heteroxynema_cucullatum_ITS_MrBayes.tre: MrBayes gene tree of Heteroxynema cucullatum ITS+ Heteroxynema_cucullatum_ITS_alignment.nex: DNA sequence alignment of Heteroxynema cucullatum ITS

Rauschtineria eutamii DNA sequence alignments and phylogenies

R_eutamii_4loci_concatenated_MrBayes.tre: MrBayes tree of Rauschtineria eutamii concatenated loci COI, 12S, 18S, 28S R_eutamii_4loci_starbeast.tre: Starbeast species tree of Rauschtineria eutamii loci COI, 12S, 18S, 28S R_eutamii_COI_minimus_hosts_MrBayes.tre: MrBayes gene tree of COI for Rauschtineria eutamii individuals that corespond to Tamias minimus hosts (used in tanglegram) R_eutamii_COI_quadrivittatus_hosts_MrBayes.tre: MrBayes gene tree of COI for Rauschtineria eutamii individuals that corespond to quadrivittatus group hosts (used in tanglegram) Rauschtineria_eutamii_12S_MrBayes.tre: MrBayes gene tree of Rauschtineria eutamii 12S Rauschtineria_eutamii_12S_alignment.nex: DNA sequence alignment of Rauschtineria eutamii 12S Rauschtineria_eutamii_18S_MrBayes.tre: MrBayes gene tree of Rauschtineria eutamii 18S Rauschtineria_eutamii_18S_alignment.nex: DNA sequence alignment of Rauschtineria eutamii 18S Rauschtineria_eutamii_28S_MrBayes.tre: MrBayes gene tree of Rauschtineria eutamii 28S Rauschtineria_eutamii_28S_alignment.nex: DNA sequence alignment of Rauschtineria eutamii 28S Rauschtineria_eutamii_COI_MrBayes.tre: MrBayes gene tree of Rauschtineria eutamii COI Rauschtineria_eutamii_COI_RAxML.tre: RAxML gene tree of Rauschtineria eutamii COI Rauschtineria_eutamii_COI_alignment.nex: DNA sequence alignment of Rauschtineria eutamii CO

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 phenotypeswc0.5.zip- Bioclim variables used for species distribution modeling.worldclim_projections_2080.zip- Future projections of Bioclim variables 2 and 3DMNS18807_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 dataspectrophotometry_raw_files.zip- Raw reflectance datawtjr_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.</div