Genomic basis of adaptation and linkage in sticklebacks

Posted by Anna Runemark

Recently there has come out some interesting papers on the genomic basis of adaptation, linkage and recombination in sticklebacks, and I suggest that we read one of these papers and one a bit older review on linkage for this labmeeting, Jones et al. 2012 in Nature, found here and Slatkin 2008 in Nature Reviews Genetics found here, please find the abstracts posted below. Although I don’t dare to suggest more reading I would also recommend just looking at Figs. 2-3 on page 2856 in a nice paper by Roesti et al. 2012 in Molecular Ecology (found here) which shows how reduced recombination rate at centromeres result in chromosome centre biased divergence. If anyone is interested in more extra reading there is also a paper on LD in sticklebacks by Hohenlohe et al. 2012 in Phil Trans (found here) which might also be of interest for extra reading.

I’m hoping for good discussions on the implications of these findings for our expectations of adaptation in nature, and I will bring fika to hopefully stimulate such discussions.

 

The genomic basis of adaptive evolution in threespine sticklebacks

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine– freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive

evolution in nature.

Linkage disequilibrium —understanding the evolutionary past and mapping the medical future

Linkage disequilibrium — the nonrandom association of alleles at different loci — is a sensitive indicator of the population genetic forces that structure a genome. Because of the explosive growth of methods for assessing genetic variation at a fine scale, evolutionary biologists and human geneticists are increasingly exploiting linkage disequilibrium in order to understand past evolutionary and demographic events, to map genes that are associated with quantitative characters and inherited diseases, and to understand the joint evolution of linked sets of genes. This article introduces linkage disequilibrium, reviews the population genetic processes that affect it and describes some of its uses. At present, linkage disequilibrium is used much more extensively in the study of humans than in non-humans, but that is changing as technological advances make extensive genomic studies feasible in other species.