incomplete sweep
Garud NR & Petrov DA 2016 Elevated linkage disequilibrium and signatures of soft sweeps are common in Drosophila melanogaster. Genetics 203:863-880.
- the true demographic history of North American flies is undoubtedly much more complex than our current models can possibly capture
- Pool (2015) showed that epistatic interactions between African alleles and European alleles are abundant in the North American population
- these combinations of alleles appear to be experiencing selection against them
- this inbreeding process left behind tracts of residual heterozygosity, which were suggested by Houle and Marquez (2015) to result from epistatic interactions between inversions
- a sweep that is too weak or old cannot be distinguished from neutrality with H12 because recombination events have decayed the sweep
- a sweep that is too soft to be detected by H12 has such a high number of unique haplotypes bearing an adaptive mutation that the sweep also cannot be distinguished easily from neutrality
- virtually all sweeps in Raleigh and Zambia reach an intermediate frequency and none go to completion
- most adaptive alleles are only adaptive when rare and driven by frequency-dependent selection and then maintained at intermediate frequencies by balancing selection
- the prevalence of incomplete sweeps may have gone unnoticed until now
- previous studies often relied on shallower sample sizes in which sweeps may have looked like fixations due to sampling or could not be distinguished from neutrality
- McDonald–Kreitman estimates measure rate of adaptation by focusing on the rate of fixation over long time scales
- this will need to be tested further with forward simulations of realistic demographic and selection scenarios
