Is it a soft sweep or a hard sweep?

As the summer and my maternity leave come to an end, I am starting to think about what I will do in the fall semester. One thing that is on my to do list is to write a review paper on soft sweeps together with Joachim Hermisson, who is spending the year at UC Berkeley. Joachim and I wrote three papers on soft sweeps ten years ago (H&P 2005, P&H 2006a and 2006b) and it’ll be fun to work together again.

One of the reasons that we are planning to write such a review paper is that in the last couple of years, some controversy has arisen surrounding soft sweeps. Put very simply, some people think that soft sweeps are ubiquitous and others think that they are nonsense.

Dmitri Petrov is a strong proponent of the view that soft sweeps are very common (Garud et al 2015, Messer and Petrov 2013). Jeffrey Jensen is probably the strongest critic of the concept of soft sweeps as evidenced by his paper entitled “On the unfounded enthusiasm for soft selective sweeps.” (Jensen 2014).

I look forward to writing a paper that makes the “It’s complicated” in the flowchart I made less complicated!

References

Garud, N. R., Messer, P. W., Buzbas, E. O., Petrov, D. A., Fay, J., Wyckoff, G., … Stephan, W. (2015). Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps. PLOS Genetics, 11(2), e1005004. doi:10.1371/journal.pgen.1005004

Hermisson, J., & Pennings, P. S. (2005). Soft sweeps: Molecular population genetics of adaptation from standing genetic variation. Genetics, 169(4), 2335–2352. doi:10.1534/genetics.104.036947

Jensen, J. D., (2014). On the unfounded enthusiasm for soft selective sweeps. Nature Communications, 5, 5281. doi:10.1038/ncomms6281

Messer, P. W., & Petrov, D. A. (2013). Population genomics of rapid adaptation by soft selective sweeps. Trends in Ecology & Evolution, 28(11), 659–669.

Pennings, P. S., & Hermisson, J. (2006a). Soft sweeps II-molecular population genetics of adaptation from recurrent mutation or migration. Molecular Biology and Evolution, 23(5), 1076–1084. doi:10.1093/molbev/msj117

Pennings, P. S., & Hermisson, J. (2006b). Soft sweeps III: The signature of positive selection from recurrent mutation. Plos Genetics, 2(12), 1998–2012. doi:10.1371/journal.pgen.0020186