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Journal Article

Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks

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http://pubman.mpdl.mpg.de/cone/persons/resource/persons56628

Chain,  Frédéric J. J.
Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons56854

Panchal,  Mahesh
Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons56659

Eizaguirre,  Christophe
Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons56756

Kalbe,  Martin
Research Group Parasitology, Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons56796

Lenz,  Tobias L.
Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons56896

Samonte,  Irene E.
Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons56825

Milinski,  Manfred
Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons56884

Reusch,  Thorsten B. H.
Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

Feulner, P. G. D., Chain, F. J. J., Panchal, M., Eizaguirre, C., Kalbe, M., Lenz, T. L., et al. (2013). Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks. Molecular Ecology, 22(3), 635-649. doi:10.1111/j.1365-294X.2012.05680.x.


Cite as: http://hdl.handle.net/11858/00-001M-0000-000F-EA78-0
Abstract
Since the end of the Pleistocene, the three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to various freshwater habitats probably originating from ancestral marine populations. Standing genetic variation and the underlying genomic architecture both have been speculated to contribute to recent adaptive radiations of sticklebacks. Here, we expand on the current genomic resources of this fish by providing extensive genome-wide variation data from six individuals from a marine (North Sea) stickleback population. Using next-generation sequencing and a combination of pairedend and mate-pair libraries, we detected a wide size range of genetic variation. Among the six individuals, we found more than 7% of the genome is polymorphic, consisting of 2 599 111 SNPs, 233 464 indels and structural variation (SV) (>50 bp) such as 1054 copynumber variable regions (deletions and duplications) and 48 inversions. Many of these polymorphisms affect gene and coding sequences. Based on SNP diversity, we determined outlier regions concordant with signatures expected under adaptive evolution. As some of these outliers overlap with pronounced regions of copy-number variation, we propose the consideration of such SV when analysing SNP data from re-sequencing approaches. We further discuss the value of this resource on genome-wide variation for further investigation upon the relative contribution of standing variation on the parallel evolution of sticklebacks and the importance of the genomic architecture in adaptive radiation.