Conservation genomics of the Apennine chamois

The Apennine chamois (Rupicapra pyrenaica ornata) is an endemic subspecies of the central Apennines, considered one of the rarest and most threatened chamois populations in Europe. After suffering a drastic decline in the 20th century, conservation efforts have enabled a partial recovery of the population, but the reduced numbers and geographic isolation continue to pose a threat to its long-term survival.

This project aims to:

• Analyze the genetic diversity and population structure of the Apennine chamois using the quaddRAD method.
• Compare the genome of the Apennine chamois with that of the Pyrenean and Alpine chamois through long-read analyses using Oxford Nanopore technology (ONP).
• Sequence a complete reference genome for the Apennine chamois, providing a foundation for future conservation genomics studies.

Methodology

Genetic Diversity Analysis with quaddRAD
DNA will be extracted from biological samples available at the Abruzzo, Lazio, and Molise National Park. The quaddRAD approach will allow the identification of single nucleotide polymorphisms (SNPs) and the evaluation of intra-population genetic diversity. Analyses of genetic structure and historical demography will also be conducted.

Comparative Genomics with ONP
Long-read ONP sequences will be generated for samples from the Apennine, Pyrenean, and Alpine chamois. The comparative analysis among these three taxa will help identify structural variations and genomic regions under natural selection.

Reference Genome Sequencing
A representative individual from the Apennine chamois population will be selected for complete genome sequencing. The genome will be assembled using a hybrid approach that combines long-read ONP data with high-accuracy short-read data. Genome annotation will provide information on functional regions, genes associated with adaptation, and environmental responses.