Population history inference in chickens

Background

The effective population size describes the genetic size of a population and allows predictions about how quickly it will lose diversity and increase in inbreeding. Therefore, it is a key parameter in population genetics and management of genetic diversity. The genetic history of a population can be described by its effective population size over time. Previous literature has investigated global structure and deep population history of the domestic chicken. There is less data on the recent history, which reflects breed formation and systematic breeding, and is the most relevant to conservation of genetic resources.

Goal

The project aims to infer recent population history in chickens, using SNP chip and whole-genome sequence data from different breeds and populations, and make comparisons between them.

Project description

The project will use genotype and sequence data from different chicken breeds and populations to estimate population history using the GONE software. Population genetic simulation may be used to check the performance of methods. Resulting population histories will be compared to previously published estimates.

Specifications

Suitable for: Animal Science, Bioinformatics.