Climate predicts wMel Wolbachia frequency variation in Drosophila melanogaster, but genomic variation reflects a recent incomplete cytoplasmic sweep

Maternally transmitted Wolbachia occupy roughly half of terrestrial arthropod species, but the factors maintaining their variable population frequencies are poorly understood. In Drosophila melanogaster, the wMel Wolbachia variant occurs at intermediate and variable frequencies globally. We document rapid wMel frequency shifts up to 0.33 between consecutive weeks in experimental and natural orchards in the eastern United States, with frequencies peaking at intermediate temperatures and declining at thermal extremes. Seven years of seasonal sampling at a Pennsylvania orchard showed wMel frequencies consistently higher in summer than fall, consistent with temperature-dependent maternal transmission. Bayesian models applied to 248 locations across five continents and 42 years of sampling corroborated the previously described wMel frequency cline in eastern Australia but found no latitudinal pattern on any other continent. Precipitation seasonality and driest-quarter precipitation were the strongest global predictors, absorbing the among-continent wMel frequency variation that latitude left unexplained. Wet-season temperature predicted wMel frequency in Australia, where the wettest quarter coincides with summer and peak host reproduction. Analysis of 339 individually sequenced wMel genomes identified 38 wMel SNPs associated with latitude, but these associations did not persist after accounting for cytoplasmic lineage structure, and 35 of the 38 were private to a remnant southwestern European lineage. Our results establish that local climatic conditions shape wMel frequencies globally, plausibly through effects on maternal transmission fidelity that depend on the seasonal alignment of warm temperatures with host reproduction. wMel genomic variation, in contrast, reflects the incomplete replacement of ancestral wMelCS by wMel, rather than local adaptation.