Analysis of genomic data as an approach to understanding migration in song birds

Many species of birds migrate every year thousands of kilometers, relying on sight, memory, magnetic sensors and instincts to find their way across continents. Many juvenile birds travel complicated migration routes without the guidance of more experienced adults. To successfully accomplish this they need instincts that utilizes multiple navigational senses together with a time dependent schedule. Little is known of the genetics behind migration behavior and which cellular processes are involved. Improved sequencing methods allow us to investigate migration traits from a cellular and genetic perspective. This have given us new insight of the mechanisms of migration and, in time, will let us understand the evolutionary origin of this behavior. In this thesis I focuses on the possibilities of using population genetics to discover the cellular mechanisms involved in migration.

I'm using two subspecies of the small songbird Willow warbler Phylloscopus trochilus to explore the genetics behind the migration behavior. The two subspecies Phylloscopust rochilus trochilus and Phylloscopus trochilus acredula differ significantly in their migration routes while in the same time show few genetic or phenotypic differences. Here I compare genotype and gene expression differences between this subspecies in order to find candidate genes involved in the genetics of migration.

In Paper I we sequence mRNA from brain samples of 16 birds, 8 from each subspecies, using 454-pyrosequencing. We detect three areas of recent selection pressure corresponding to regions in chromosome 1, 3 and 5 on the Zebra finch genome.

In Paper II we compare mRNA expression levels between migrating and breeding birds as well as between the two subspecies. We use a custom microarray probe design based on expressed sequence tags from the Zebra finch to measure the mRNA levels of 22,109 probesets. We find 14 probe sets with subspecies differences and 3045 that change between the breeding and migrating seasons.

In conclusion, we provide a list of genes and chromosome regions with possible importance for migration and migration behavior. Further studies needs to pair candidate genes with phenotypic differences utilizing laboratory controlled behavior or gene specific sequencing and position tracking.

List of scientific papers

I. Lundberg M, Boss J, Canbäck B, Liedvogel M, Larson KW, Grahn M, Åkesson S, Bensch S, Wright A. 2013. Characterisation of a transcriptome to find sequence differences between two differentially migrating subspecies of the willow warbler Phylloscopus trochilus. BMC Genomics 2013, 14:330.
https://doi.org/10.1186/1471-2164-14-330

II. John Boss, Miriam Liedvogel, Max Lundberg, Peter Olsson, Nils Reischke, Sara Naurin, Susanne Åkesson, Dennis Hasselquist, Anthony Wright, Mats Grahn and Staffan Bensch. Gene expression in the brain of a migratory songbird during breeding and migration. [Manuscript]