Quantifying CpG variants in a pied flycatcher population

Natal dispersal is a key life-history trait determining fitness and driving population dynamics, genetic structure and species distributions. Despite existing evidence that not all phenotypes are equally likely to successfully establish in new areas, the mechanistic underpinnings of natal dispersal remain poorly understood. The propensity to disperse into a new environment can be favored by a high degree of phenotypic plasticity which facilitates local adaptation and may be achieved via epigenetic mechanisms, which modify gene expression and enable rapid phenotypic changes. Epigenetic processes occur in particular genomic regions - DNA methylation on CpG sites in vertebrates -, and thus individual genomes may differ in their capacity to be modified epigenetically. This “Epigenetic potential” (EP) may represent the range of phenotypic plasticity attainable by an individual, and be a key determinant of successful settlement in novel areas. We investigated the association between EP – quan..., Samples were collected in population of pied flycatchers (Ficedula hypoleuca) breeding in nest boxes in central Spain (La Hiruela, 41°04’ N, 3°27’ W; 1250 masl), and monitored since 1984. Total genomic DNA was extracted from blood samples using a standard ammonium acetate protocol, and diluted to a working concentration of 25 ng/μL.  Besides, on an additional set of samples from 1998 (used in one of the group comparisons), DNA had already been extracted from whole blood using Chelex resin-based extraction. Whole genome sequencing was performed by Novogene Europe in two sequencing runs, where paired-end Illumina next-generation sequencing (150bp) was carried out on an Illumina NovaSeq 6000 sequencer. Libraries were prepared using either the Novogene NGS DNA Library Prep Set (Cat No.PT004) at Novogene, or small-scale library prep (1/10th standard volumes) for Illumina DNA Prep with IDT index sets, using the Mosquito aliquoting system at the DeepSeq Facility at the University of ..., , # Quantifying CpG variants in a pied flycatcher population This repository contains all scripts, code, and data necessary to recreate the analyses presented in Jimeno et al (2025) 'Epigenetic potential and dispersal propensity in a free-living bird: a spatial and temporal approach' in Molecular Ecology. The analysis is based on called variant and invariant sites from whole genome resequencing data of *Ficedula hypoleuca*. All raw reads will be made available on the European Nucleotide Archive. Called variants can be recreated using our standardized genotyping pipeline, which is available [here](https://github.com/markravinet/genotyping_pipeline). Here, we will walk through the steps required to recreate the CpG count data and to perform the final analyses from the study. # Data and software files included cpg_counter_v0.2: Code for the count of CpG positions. cpg_totaler_v0.1: Code for the count of number of total CpG within the genome. cpg_totals_array_saga: Code for running the...,出生扩散（natal dispersal）是决定物种适合度、驱动种群动态、遗传结构与物种分布的关键生活史特征。尽管已有研究证实并非所有表型都能同等顺利地在新区域成功定植，但学界对出生扩散的机制基础仍知之甚少。向新环境扩散的倾向可通过高水平的表型可塑性（phenotypic plasticity）得到强化，而表型可塑性可助力本地适应，其实现可依赖表观遗传机制（epigenetic mechanisms）——后者可调控基因表达并介导快速表型变化。表观遗传过程常发生于特定基因组区域：例如脊椎动物中CpG位点（CpG sites）的DNA甲基化修饰，因此不同个体的基因组在表观遗传修饰的能力上存在差异。这种“表观遗传潜力（Epigenetic potential, EP）”可表征个体所能实现的表型可塑性范围，也是其能否在新区域成功定植的关键决定因素。本研究探讨了表观遗传潜力与扩散倾向之间的关联……。 研究样本采集自西班牙中部拉伊鲁埃拉（La Hiruela，北纬41°04′，西经3°27′，海拔1250米）的斑姬鹟（Ficedula hypoleuca）种群，该种群依托人工巢箱繁殖，自1984年起即被持续监测。研究团队采用标准乙酸铵提取法从血液样本中提取总基因组DNA，并将其稀释至25 ng/μL的工作浓度。此外，针对1998年采集的一组额外样本（用于其中一组组间比较），研究人员已采用基于Chelex树脂的提取法从全血中完成DNA提取。 全基因组测序（whole genome sequencing）由诺禾致源欧洲公司（Novogene Europe）通过两轮测序完成：在Illumina NovaSeq 6000测序仪上开展150bp双端Illumina下一代测序。文库制备分别采用诺禾致源的NGS DNA文库制备试剂盒（货号PT004），或采用带有IDT索引套件的Illumina DNA制备试剂盒进行小规模文库制备（体系体积为标准体系的1/10），该步骤在英国……大学深度测序中心（DeepSeq Facility）通过Mosquito移液系统完成。 # 量化斑姬鹟种群中的CpG变异 本代码仓库包含重现Jimeno等人2025年发表于《Molecular Ecology》的论文《自由生活鸟类的表观遗传潜力与扩散倾向：时空研究方法》所需的全部脚本、代码与数据。 本分析基于斑姬鹟（*Ficedula hypoleuca*）全基因组重测序数据的变异位点与不变位点调用结果。所有原始测序读段将上传至欧洲核苷酸档案馆（European Nucleotide Archive）。研究团队开发的标准化基因分型流程可用于重现已调用的变异位点，该流程已开源至[此处](https://github.com/markravinet/genotyping_pipeline)。 下文将逐步演示重现CpG计数数据并完成该研究最终分析所需的操作步骤。 # 包含的数据与软件文件 cpg_counter_v0.2：用于CpG位点计数的代码 cpg_totaler_v0.1：用于统计基因组内总CpG数量的代码 cpg_totals_array_saga：用于运行……的代码（原文未完成）