Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird

Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations. Across island systems, contemporary patterns of genetic diversity reflect complex population demography, including colonisation events, bottlenecks, gene flow and genetic drift. Here, we investigate whether island founder events have prolonged effects on genome-wide diversity and runs of homozygosity (ROH) distributions, using whole genome resequencing from six populations across three archipelagos of Berthelot’s pipit (Anthus berthelotii) – a passerine which has undergone island speciation relatively recently. Pairwise sequential Markovian coalescent (PSMC) analyses estimated divergence from its sister species approximately two million years ago. Results indicate that all Berthelot’s pipit populations had shared ancestry until approximately 50,000 years ago, when the Madeiran archipelago populations were founded, while the Selvagens were colonised within the last 8,000 years. We ide..., Whole genome data from six populations of Berthelot's pipit across the three archipelagos of their range in the North Atlantic. Resequencing data was generated by mapping Illumina HiSeq reads to a reference genome and calling variants using GATK HaplotypeCaller., README_datasets.txt Describes the datasets and outlines their usage to recreate and explore the findings in the current manuscript. All Pipits, Berthelots and Tawny VCF files These are the three datasets in variant call format as referred to in the manuscript. Individual level .fastq filesThese files are used to generate the input files required to run the PSMC analyses, on an individual-by-individual basis. Example files are given for EH_161 Chromosome codes Genome_chromosome_codes.txt file contains Zebra finch (Taeniopygia guttata) chromosome names and their equivalent numeric codes used in the VCF files. SCRIPTS.sh Code used to undertake analyses outlined in this paper. These scripts must be run prior to R script to produce associated outputs. R scripts to produce tables, figures and statistics ROH_analyses.R details R scripts and produces output figures and statistics detailed in the manuscript. Creating VCF datasets The first steps are detailed in example_gVCF.sh, which contains t...基因组留存着塑造种群的种群历史与演化压力的相关证据。在岛屿生态系统中，当代遗传多样性格局反映了复杂的种群动态，包括定殖事件、瓶颈效应、基因流与遗传漂变。本研究利用分布于北大西洋三个群岛共6个种群的全基因组重测序数据，探讨岛屿奠基者事件是否会对全基因组多样性及纯合性片段（runs of homozygosity, ROH）分布产生长期影响。伯氏鹨（Anthus berthelotii）是一类近期经历岛屿物种形成的雀形目鸟类。两两序列马尔可夫溯祖（Pairwise Sequential Markovian Coalescent, PSMC）分析显示，该物种与其姊妹物种的分化时间约为200万年前。分析结果表明，伯氏鹨的所有种群直至约5万年前仍共享共同祖先，此时马德拉群岛种群开始奠基；而塞尔瓦任斯群岛的种群则是在近8000年内完成定殖的。[原文此处截断] 本数据集包含分布于北大西洋三个群岛的6个伯氏鹨种群的全基因组数据。重测序数据通过将Illumina HiSeq测序reads比对至参考基因组，并使用GATK HaplotypeCaller进行变异检出生成。 README_datasets.txt：说明本数据集内容，并概述如何复现与探究本论文中的研究结果。 All Pipits、Berthelots与Tawny VCF文件：即本论文中提及的3个变异调用格式（VCF）数据集。 个体水平.fastq文件：此类文件用于逐个个体生成运行PSMC分析所需的输入文件，其中提供了EH_161的示例文件。 染色体编码文件Genome_chromosome_codes.txt：包含斑胸草雀（Taeniopygia guttata）的染色体名称，以及VCF文件中使用的对应数字编码。 SCRIPTS.sh：用于执行本论文中概述的分析流程。需先运行此类脚本，再运行R脚本以生成对应输出结果。 用于生成表格、图片与统计数据的R脚本：ROH_analyses.R详细说明了本论文中涉及的R脚本内容，并可生成对应的输出图表与统计结果。 VCF数据集构建流程：具体的第一步操作详见example_gVCF.sh，该文件包含[原文此处截断]