From chickens to wild birds

Background

SNP arrays can genotype thousands of genetic markers simultaneously and they are regularly used to investigate genetic diversity, population structure and evolutionary history. A problem with using them on non-model species with commercial arrays is that they are developed for domestic animals or model species. For non-model organisms, the usefulness depends on conserved targeted sequences, accurate genotyping and how many informative markers remain.

Compared to many other organism groups, birds have a relatively conserved genome, and most birds have the same chromosome count. Nevertheless, markers selected in other species can have a biased representation of genetic variation. Assessing both performance and robustness of the underlying biology is therefore needed, especially since using arrays for cross-species genotyping can expand the genetic tools available for small studies of wild birds and other animals, where other tools are too expensive.

This project will investigate if a chicken SNP array can be used for population-genomic analyses of boreal bird Siberian jay (Persioreus infaustus).

Aims

The aim is to evaluate cross-species usability of a chicken SNP array and to determine if the data can be used to give new insight into the genetic variation and evolutionary history of Siberian jay populations.

Available material

Genotype data is available from 12 Siberian jays from five populations, two in Sweden and three in the eastern part of Russia. From the 60k chicken SNP array, the call rate was between 38 and 68%. Analysis on how well the chicken-based SNP markers perform on Siberian jays is a part of the project.

Methods and analysis approach

The project will start with a quality assessment of the Siberian jay genotypes where marker completeness, polymorphism and heterozygosity will be estimated. After that, exploratory population-genetic analyses will be evaluated with principal component analysis. Since the data contains individuals from several populations, populations differentiation will be explored. The evolutionary and population histories of the bird population will be investigated using SNAPP with BEAST2. In this software, both main population histories and alternative histories can be explored. Further analyses will examine population divergence and SNAPP will be used to estimate historical population sizes.

Expected outcomes and significance

This project will identify informative markers and investigate their usefulness for population-genomic analyses in Siberian jays. It will show if the data from chicken SNP arrays can be used to estimate population relationships and past demography. It will also reveal which analyses can be performed with this data.

In this project you will gain experience in genetic data handling, population genetics, Bayesian evolutionary analysis and critical evaluation of genomic methods for non-model species.

Field work

Depending on availability, a shorter field work period may be offered in northern Sweden.

Prerequisites

This project is suitable for a student with an interest in evolutionary biology, bioinformatics and data analysis.