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...,