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 (<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_xy) between hare species.- Empirical divergence (d_xy) between hare species within each coat color association region.<br>

本仓库收录了用于复现白尾长耳大野兔（<i>Lepus townsendii</i>）季节性伪装演化相关研究分析所需的自定义代码副本及关联资源。

<b>wtjr_sdm-master.zip</b>（详见GitHub获取更多详情）
- 该压缩包内含物种分布模型（Species Distribution Model, SDM）分析所需的代码与数据，内部README文件包含完整说明。包含内容如下：
- 用于SDM建模的白尾长耳大野兔出现记录
- 用于模拟当前及未来表型的积雪停留时间数据

<b>wc0.5.zip</b>
- 用于物种分布建模的生物气候变量数据集。

<b>worldclim_projections_2080.zip</b>
- 2080年生物气候变量第2、3项的未来情景预测数据。

<b>DMNS18807_06042020_pseudohap2.1.fasta.gz 与 DMNS18807_06042020_pseudohap2.2.fasta.gz</b>
- 本研究通过Supernova软件组装的白尾长耳大野兔原始从头（de novo）基因组序列。其中主组装版本pseudohap2.1用于全部分析流程，备用组装版本pseudohap2.2仅用于BEAST分析。

<b>DMNS18807_06042020_pseudohap2.1_OryCun2.0_liftoff_annotation.gff3</b>
- 白尾长耳大野兔主参考基因组的Liftoff注释GFF3文件，该注释基于欧洲兔参考基因组（OryCun2.0）获取。

<b>OryCun2.0_repeats.bed</b>
- 来自基因组浏览器的OryCun2.0参考基因组重复区域BED格式文件。

<b>GenotypeArea_COATCOLOR_WTJR_W1_34SNPs_92INDVS.xlsx</b>
- 原始基因型数据文件。

<b>spectrophotometry_raw_files.zip</b>
- 原始反射光谱数据。

<b>wtjr_camouflage.zip</b>（详见GitHub获取更多详情）
- 包含用于BEAST分析的输入比对文件、控制文件及分化时间输出树文件，用于确定白色与棕色单倍型的分化时间；
- 包含用于GPhoCs分析的输入比对文件、控制文件及输出日志文件，用于估算野兔物种间分化的种群参数；
- 已预处理的反射光谱数据；
- 格式化后的基因型数据，以及用于关联分析与费希尔精确检验的各类输入、输出文件；
- 野兔物种间预期分化水平（d_xy）的模拟结果；
- 各毛色关联区域内野兔物种间的实测分化水平（d_xy）。