The evolution of seasonal camouflage in white-tailed jackrabbits in response to past and future climates
收藏Figshare2023-04-26 更新2026-04-08 收录
下载链接：
https://figshare.com/articles/dataset/The_evolution_of_seasonal_camouflage_in_white-tailed_jackrabbits_in_response_to_past_and_future_climates/14562003/1
下载链接
链接失效反馈官方服务：
资源简介：
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 (<i>Lepus townsendii</i>).<br><br><br><b>wtjr_sdm-master.zip </b>(see GitHub for more details)<br>- 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<br><b>wc0.5.zip</b><br>- Bioclim variables used for species distribution modeling.<br><b>worldclim_projections_2080.zip</b><br>- Future projections of Bioclim variables 2 and 3<br><b>DMNS18807_06042020_pseudohap2.1.fasta.gz and DMNS18807_06042020_pseudohap2.2.fasta.gz</b><br>- Original <i>de novo</i> 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).<br><b>DMNS18807_06042020_pseudohap2.1_OryCun2.0_liftoff_annotation.gff3</b><br>- Liftoff gff3 annotation of the primary white-tailed jackrabbit reference genome. Annotation was obtained from the European Rabbit reference genome (OryCun2.0).<br><b>OryCun2.0_repeats.bed</b><br>-Bed file of repeat regions for OryCun2.0 from Genome Browser <br><b>GenotypeArea_COATCOLOR_WTJR_W1_34SNPs_92INDVS.xlsx</b><br>- Raw genotype data<br><b>spectrophotometry_raw_files.zip</b><br>- Raw reflectance data<br><b>wtjr_camouflage.zip </b>(see GitHub for more details)<br>- 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.<br>- Formatted genotype data, and other input and output files for association and Fisher exact test analyses .- Simulated expected divergence (d<sub>xy</sub>) between hare species.- Empirical divergence (d<sub>xy</sub>) between hare species within each coat color association region.<br>
提供机构：
Thurman, Timothy; Farelo, Liliana; Melo-Ferreira, José; Demboski, John R.; Ferreira, Mafalda; Kumar, Alexander V.; Mills, L. Scott; Alves, Paulo C.; Good, Jeffrey; Jones, Matthew; Mortimer, Sebastian M. E.
创建时间：
2023-04-26
