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I’ve searched for a definition of signature of natural selection. Unfortunately, I haven’t found any formal definition of it.

The signature of positive selection on standing genetic variation. I found this post that links to an article measuring the signature with an Fst and a Linkage Disequilibrium test.

Are we looking at only some frequency of alleles in different populations? Is the signature only a fixation of alleles in a population where this allele was positively selected?

Another article says:

A single beneficial substitution can be detected in polymorphism data, so long as it occurred recently. The fixation of a favorable allele in a population distorts patterns of variation at linked sites, thereby leaving a distinguishing signature that lasts up to about 104 generations in humans or about 106 in Drosophila melanogaster (Przeworski 2002). In principle, targets of positive selection can therefore be identified by searching polymorphism data for regions that harbor this signature (Nair et al. 2003; Wright et al. 2005).

Is it always in linkage disequilibrium?

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M. Beausoleil
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Here is how I would personally explain what a genetic signature is:

A genetic signature of a certain type of evolutionary history (type of selection or demography) refers to the effect that this specific type of evolutionary history has on genomic properties of populations today.

We are interested in understanding such signatures because knowing the association between a number of evolutionary histories and their genetic signature allows us to reconstruct the evolutionary history of a population just by looking at the genomics of this population.

For example, recent selective sweep, population expansion after a recent bottleneck and/or linkage to a swept gene are all causing negative Tajima's D. Balancing selection and/or sudden population contraction are causing positive Tajima's D. In this example Tajima's D is a statistics that is used to measure this so-called signature of the different process.

The above was NOT a citation. I am NOT aware of any publications defining rigorously what a genetic signature is. I think it is not so uncommon for authors to use a term without strictly defining it. As long as the unclarity of the definition does not yield to limit cases and misunderstanding, then it is totally fine.

Remi.b
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  • Do you have a reference to this? I mean, is this a quote? Is it like the gene signature or the genomic signature? – M. Beausoleil Jan 16 '16 at 19:43
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    Nope I don't! Feels like we already had this discussion on another post $\ddot \smile$ This is why I said I would explain... and I am not aware of any publication defining rigorously what a genetic signature is. I tried to make this point even clearer. – Remi.b Jan 16 '16 at 19:57
  • Haha! Thanks a lot for your contribution! I'm going to continue the research until I find something. This concept is, most of the time, used with selective sweep, right? For instance I found Nielsen, R. 2005. Molecular signatures of natural selection and Hohenlohe, P. A., P. C. Phillips, and W. A. Cresko. 2010. Using Population Genomics to Detect Selection in Natural Populations: Key Concepts and Methodological Considerations with nice figures (fig 1 and 4 respectively) Seems that these images could represent a "signature". – M. Beausoleil Jan 17 '16 at 23:47