Department of Medical Biochemistry and Microbiology, Uppsala University, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Department of Veterinary Integrative Biosciences, Texas A&M University
Leif Andersson has been working on comparative genomics using domestic animals as study objects the last 30 years. In recent years the research program has been expanded to include natural populations such as the Darwin’s finches and Atlantic herring because of the new exciting opportunities opened up by the development of new sequencing technologies.
The Atlantic herring (Clupea harengus) is one of the most abundant vertebrates on earth and constitutes a huge biomass in the North Atlantic. Previous studies indicated that the Atlantic herring has an enormous current effective population size and geographically distant populations share nearly identical allele frequencies at selectively neutral loci. Minute genetic drift facilitates the detection of natural selection and we have previously shown that the Atlantic and Baltic herring show highly significant genetic differentiation at 1-2% of SNP loci. We have now generated a high-quality draft genome assembly for the herring. The genome assembly comprises 833 Mb (scaffold N50: 1.73 Mb). We have used this assembly for a population genomic study including 19 population samples of herring from the North-East Atlantic, North Sea, Skagerrak, Kattegat and Baltic Sea, and one sample of the closely related Pacific herring. Genetic adaptation has been explored by making the following contrasts: (i) populations from marine water (35 ppt salinity) vs. populations from the brackish Baltic Sea (3-12 ppt salinity) and (ii) different spawning times (spring, summer and autumn). The study has provided overwhelming evidence for genetic adaptation and we have identified hundreds of loci underlying adaptation to different ecological conditions as well as to the timing of reproduction. The study enable us to address the long standing question to which extent genetic adaptation is caused by changes in protein sequences versus changes in gene regulation. The study establishes the Atlantic herring as a novel model for evolutionary biology and biomedical research.
Host: Ulf Gyllensten
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