Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation

# Extreme sex chromosome differentiation, likely driven by inversion, contrasts with mitochondrial paraphyly between species of crowned sparrows --- This dataset contains all the metadata, barcodes, and photos associated with the samples included in the study "Extreme sex chromosome differentiation, likely driven by inversion, contrasts with mitochondrial paraphyly between species of crowned sparrows" by Mcallum, Askelson, Fogarty, Natola, Nikelski, Huang and Irwin, as well as all scripts used in the bioinformatics pipline (Bash and perl) and data analyses (R). Associated sequences can be found on the SRA as part of the BioProject "Genotyping-by-sequencing reads from the bird genera Sphyrapicus, Zonotrichia, and Leiothlypis" ## Description of the Data and file structure barcodes_plate1.txt - Contains sample names barcodes for samples included in this study on plate 1 ("Plate 1 - Zonotrichia, and Leiothlypis GBS Library" on SRA). This is used by the demultiplex and trim perl script included in Zonotrichia-all-command-line-scripts-tidy.txt. barcodes_plate2.txt - Contains sample names barcodes for samples included in this study on plate 2 ("Plate 2 - Sphyrapicus, Zonotrichia, and Leiothlypis GBS Library" on SRA). This is used by the demultiplex and trim perl script included in Zonotrichia-all-command-line-scripts-tidy.txt. photo-archive.zip - Contains high-resolution photographs in .jpg format of all birds sampled in this study. Zonotrichia-metadata.csv - Contains metadata for all samples included in this study. Samples are organized by by sample name. Zonotrichia-metadata-README.txt - Contains detailed descriptions of the contents of each column of Zonotrichia-metadata.csv. Zonotrichia-all-command-line-scripts-tidy.txt - Contains all Bash and Perl scripts used to demulitplex, trim, and align our sequences, call and filter snps, and calculate Fst and Linkage disequilibrium. ld_heatmap_plotting__sparrows.R - Contains all R scripts used to produce figures 7B and S7B. genomics_R_functions_V2.R - Contains a variety of R functions from Irwin et al. 2016 that are used by several other R scripts used in this project. genotype-by-individual-plot.R - Contains R scipts used to produce figures 7A, S6, and S7A. GCSP_vs_WCSP_fst_nuclear_genome.R - Contains R scripts used to calculate pairwise genome-wide Fst between groups (table 1) and produce prelimiary per-snp Fst manhattan plots (Figure S5), and PCAs (figures 1B and S3) genotype_by_individual_function.R - Contains R function used by genotype-by-individual-plot.R Sparrow_slidingWindow.R - Contains R scripts that calculate Fst, Pi_between, and Pi_within accross sliding windows, perform analyses using these sliding windows, and prodce summary plots of these analyses (figures 2, 3, 4, 6, S4). Additionally, contains scripts used to compare the Z chromosome to the autosomes (table 2) and produce figure 5. ## Sharing/access Information Links to other publicly accessible locations of the data: Sequences associated with this project are uploaded to the SRA under BioProject "Genotyping-by-sequencing reads from the bird genera Sphyrapicus, Zonotrichia, and Leiothlypis" as BioSamples "Plate 1 - Zonotrichia, and Leiothlypis GBS Library" and "Plate 2 - Sphyrapicus, Zonotrichia, and Leiothlypis GBS Library". URL of BioProject: Was data derived from another source? No data was derived from another source. Some of the scripts used are derived from other sources. Please refer to the comments in the scripts and the manuscript for sources.

# 《极端性染色体分化（可能由染色体倒位驱动）与冕雀鹀（crowned sparrows）物种间的线粒体并系形成鲜明对比》
本数据集涵盖Mccallum、Askelson、Fogarty、Natola、Nikelski、Huang及Irwin开展的题为"Extreme sex chromosome differentiation, likely driven by inversion, contrasts with mitochondrial paraphyly between species of crowned sparrows"的研究中所有样本的元数据、条形码及关联照片，同时包含该研究使用的全部生物信息学流程（Bash与Perl语言）脚本与数据分析（R语言）脚本。本项目的相关序列可在序列读取档案（Sequence Read Archive, SRA）的生物项目（BioProject）"Genotyping-by-sequencing reads from the bird genera Sphyrapicus, Zonotrichia, and Leiothlypis"中获取。

## 数据与文件结构说明
1. "barcodes_plate1.txt"：包含本研究第1号板（SRA中标注为"Plate 1 - Zonotrichia, and Leiothlypis GBS Library"，即第1号板——带鹀属（Zonotrichia）与林莺属（Leiothlypis）测序分型（Genotyping-by-Sequencing, GBS）文库）的样本名称与条形码，供"Zonotrichia-all-command-line-scripts-tidy.txt"中的解多重与序列修剪Perl脚本调用。
2. "barcodes_plate2.txt"：包含本研究第2号板（SRA中标注为"Plate 2 - Sphyrapicus, Zonotrichia, and Leiothlypis GBS Library"，即第2号板——吸汁啄木鸟属（Sphyrapicus）、带鹀属（Zonotrichia）与林莺属（Leiothlypis）测序分型（Genotyping-by-Sequencing, GBS）文库）的样本名称与条形码，供"Zonotrichia-all-command-line-scripts-tidy.txt"中的解多重与序列修剪Perl脚本调用。
3. "photo-archive.zip"：包含本研究所有采样鸟类的高分辨率JPEG（.jpg）格式照片。
4. "Zonotrichia-metadata.csv"：包含本研究所有样本的元数据，按样本名称进行组织。
5. "Zonotrichia-metadata-README.txt"：详细说明"Zonotrichia-metadata.csv"各列的具体含义。
6. "Zonotrichia-all-command-line-scripts-tidy.txt"：包含用于解多重、序列修剪、序列比对，调用并过滤单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，以及计算群体分化指数（Fst）与连锁不平衡（Linkage Disequilibrium, LD）的全部Bash与Perl脚本。
7. "ld_heatmap_plotting__sparrows.R"：包含用于绘制图7B与补充图S7B的全部R脚本。
8. "genomics_R_functions_V2.R"：包含Irwin等人2016年发表的多种R函数，供本项目中其他多个R脚本调用。
9. "genotype-by-individual-plot.R"：包含用于绘制图7A、补充图S6与补充图S7A的R脚本。
10. "GCSP_vs_WCSP_fst_nuclear_genome.R"：包含用于计算组间全基因组成对Fst（表1）、绘制初步的单SNP Fst曼哈顿图（补充图S5）以及主成分分析（Principal Component Analysis, PCA，图1B与补充图S3）的R脚本。
11. "genotype_by_individual_function.R"：包含供"genotype-by-individual-plot.R"调用的R函数。
12. "Sparrow_slidingWindow.R"：包含用于计算滑动窗口内的Fst、群体间核苷酸多样性（Pi_between）与群体内核苷酸多样性（Pi_within）、基于滑动窗口开展分析，并生成对应分析结果的汇总图（图2、3、4、6与补充图S4）的R脚本；同时包含用于比较Z染色体与常染色体（表2）并生成图5的脚本。

## 共享与获取信息
本项目的相关序列已上传至SRA的BioProject"Genotyping-by-sequencing reads from the bird genera Sphyrapicus, Zonotrichia, and Leiothlypis"，对应的BioSamples为"Plate 1 - Zonotrichia, and Leiothlypis GBS Library"与"Plate 2 - Sphyrapicus, Zonotrichia, and Leiothlypis GBS Library"。
BioProject的URL：
本数据集是否源自其他数据源？本研究的核心实验数据未源自其他来源。本研究使用的部分脚本源自其他公开资源，请参阅脚本内注释及相关手稿以获取具体来源信息。