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Speciation genomics in a wild bird populations

Final Report Summary - SPECIATIONGENOMICS (Speciation genomics in a wild bird populations)

Maintenance of biodiversity requires that species are able to adapt to changes in the environment they live in. This ability depends to a large extent on the genetic basis of traits subject to natural selection. Understanding the genetic basis of quantitative traits in natural populations is therefore one of the ultimate goals of evolutionary biology. The aim of this research was to contribute to this goal by examining the genetic architecture of traits that are targets of natural and sexual selection. To do this we used a long-term study of collared flycatchers (Ficedula albicollis) that breed on the Swedish islands of Öland and Gotland. This species breed readily in nest boxes, which, along with their high site fidelity make it possible to collect data on morphology, behaviour and reproductive performance from all breeding individuals and their offspring and to build pedigrees for quantitative genetic studies.
Most quantitative genetic studies assume an autosomal basis to traits, however, it has been shown in several cases that genes linked to the sex chromosomes can play a particularly important role in evolution. We wanted to extend standard quantitative genetic models to fit Z-effects and examine to what degree genes coding for relevant traits are located on the autosomes or sex chromosomes (the Z chromosome in particular as W chromosome contain very few genes in birds). Separating autosomal and sex linked genetic variance provides additional insight into the genetic architecture of quantitative traits in natural populations in general and is particularly important for understanding the rate of change in a phenotypic character under selection. This is because, if variation in a trait is due to genes on the Z chromosome then this trait is expected to diverge faster between populations because the Z chromosome has low patterns of introgression and a smaller effective population size, resulting in increased strength of selection.
By using long-term pedigree data on two systems of birds (the collared flycatcher and the zebra finch) we were able to significantly increase our knowledge about the importance of sex linked genetic variance in quantitative traits (Husby et al. 2013). In particular we found that in most cases Z-linked genetic variance was minor compared to the autosomal genetic variance although one interesting exception is the wing patch size in collared flycatchers. Our work has already stimulated further interest in separating different sources of genetic variance in other systems to gain a better understanding of sources of genetic variance in natural populations and how this can influence the speed of evolutionary change.
A substantial aim of the proposed research was to examine the molecular genetic basis of trait variation using association mapping to detect QTLs for fitness related traits. Initially, the plan was to genotype many individuals (~960) for a relatively small number of markers (~768 SNPs) using the latest ‘next-generation’ genotyping technology (Ilumina Golden Gate Assay). Because we have information on the phenotype of the individuals as well as pedigree information this allow us to do a QTL mapping analysis to detect genomic regions influencing the traits we are interested in (ecological and sexually selected traits. Finding such candidate ‘speciation genes’ will greatly improve our understanding of how reproductive isolation and speciation in natural populations take place. Given the recent sequencing of the genome of the collared flycatcher (Ellegren et al. 2012) this opened the possibility to substantially increase the number of markers from the planned ~800 to 50,000. We therefore genotyped 1100 individuals on this SNP chip and are currently in the progress of mapping QTLs for fitness related traits. This will be an important advancement compared to quantitative genetic studies as it allows us to examine the number of genes underlying traits, their genomic location and their effect on the phenotype. Such research is needed for a better mechanistic understanding of how evolutionary change proceeds. Thus, the production of papers was delayed by the need to first have access to the assembled flycatcher genome but the quality of the QTL mapping effort has been substantially improved and many exciting papers are in the pipeline to become published.