Data from: Soft selective sweeps in fungicide resistance evolution: recurrent mutations without fitness costs in grapevine downy mildew

Adaptation produces hard or soft selective sweeps depending on the supply
of adaptive genetic polymorphism. The evolution of pesticide resistance in
parasites is a striking example of rapid adaptation that can shed light on
selection processes. Plasmopara viticola, which causes grapevine downy
mildew, forms large populations, in which resistance has rapidly evolved
due to excessive fungicide use. We investigated the pathways by which
fungicide resistance has evolved in this plant pathogen, to determine
whether hard or soft selective sweeps were involved. An analysis of
nucleotide polymorphism in 108 field isolates from the Bordeaux region
revealed recurrent mutations of cytb and CesA3 conferring resistance to
quinone outside inhibiting (QoI) and carboxylic acid amide (CAA)
fungicides, respectively. Higher levels of genetic differentiation were
observed for nucleotide positions involved in resistance than for neutral
microsatellites, consistent with local adaptation of the pathogen to
fungicide treatments. No hitchhiking was found between selected sites and
neighbouring polymorphisms in cytb and CesA3, confirming multiple origins
of resistance alleles. We assessed resistance costs, by evaluating the
fitness of the 108 isolates through measurements of multiple quantitative
pathogenicity traits under controlled conditions. No significant
differences were found between sensitive and resistant isolates,
suggesting that fitness costs may be absent or negligible. Our results
indicate that the rapid evolution of fungicide resistance in P. viticola
has involved a soft sweep.