
Genotype-environment association is one of the most fundamental phenomena of landscape genomics. A species’ adaptation to its environment should mean that populations of the same species in different environments will evolve different frequencies of genetic variants that support adaptation to those different environments. So in principle, we should be able to find those locally adaptive genetic variants by “scanning” through many places in the genome to find the ones where individuals from different environments carry different variants.
There’s a catch, of course. Actually several. Isolation-by-distance and founder effects can mean that populations evolve genetic differences just as a consequence of being in different places. Even when you control for those effects, so-called genotype-environment association (GEA) is just that — an association. You can’t know for sure that a genetic locus showing a pattern of GEA has a functional relationship to traits that facilitate adaptation without independent data showing that function. A recent preprint reports a project in which plant geneticists did just that, performing experimental validation on GEA candidate loci, and they found a lot of those candidate loci don’t seem to hold up.
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