Beyond population size: Whole-genome data reveal bottleneck legacies in the peninsular Italian wolf

Preserving genetic diversity and adaptive potential while avoiding inbreeding depression is crucial for the long-term conservation of natural populations. Despite demographic increases, traces of past bottleneck events at the genomic level should be carefully considered for population management. From this perspective, the peninsular Italian wolf is a paradigmatic case. After being on the brink of extinction in the late 1960s, peninsular Italian wolves rebounded and recolonized most of the peninsula aided by conservation measures, including habitat and legal protection. Notwithstanding their demographic recovery, a comprehensive understanding of the genomic consequences of the historical bottleneck in Italian wolves is still lacking. To fill this gap, we sequenced whole genomes of thirteen individuals sampled in the core historical range of the species in Central Italy to conduct population genomic analyses, including a comparison with wolves from two highly-inbred wolf populations (i.e..., 2.1 Sample collection & DNA extraction
Tissue samples were collected from 13 peninsular Italian wolves between 2007 and 2012 from found-death individuals in the Central Apennines, where historical strongholds of wolves in Italy are located (Zimen and Boitani, 1975). The tissue samples were stored in ethanol at -20°C and subsequently processed in the Conservation Genomics Research Unit at the Fondazione Edmund Mach (FEM). Small fragments of tissue of around 25 mg were extracted using the DNeasy Blood and Tissue Kit (Qiagen) with overnight digestion at 56°C. The elution was performed at the GLOBE Institute (University of Copenhagen) using two washes of 50 μL of AE buffer, with 10 minutes of incubation at 37°C. Until the elution, samples were stored at -20°C inside the DNeasy Mini spin columns.
2.2 Library preparation, amplification & whole genome sequencing
Extracts were fragmented in the Covaris LE220 plus Focused-ultrasonicator with the parameters set for 350-bp fragment length...., , # Beyond population size: whole-genome data reveal bottleneck legacies in the peninsular Italian wolf.

[https://doi.org/10.1093/jhered/esae041](https://doi.org/10.1093/jhered/esae041)

## Description

This dataset consists of two folders: one containing data ('Data_DRYAD') and the other one containing codes ('Codes_DRYAD').

The 'Data_DRYAD' folder includes autosome SNP genotypes in VCF format, compressed with bgzip, from newly sequenced whole genomes of Italian wolves (WIT), Scandinavian wolves (WSC), and Isle Royale wolves (WUS). After the population acronym (WIT, WSC or WUS) each file name is followed by 'CF31' or 'wolfAlign': 'CF31' means that the reads have been mapped on the dog reference genome (CanFam3.1; Lindblad-Toh et al. 2005); 'wolfAlign' means that the reads have been mapped on the wolf reference genome (Gopalakrishnan et al. 2017). The raw sequences for WSC and WUS are available on NCBI (WSC: BioProject PRJEB20635; WUS: BioProject PRJNA512209). The raw reads for WIT a...