Candida glabrata is an opportunistic fungal pathogen that ranks as the second most common cause of systemic candidiasis. Despite its genus name, this yeast is more closely related to the model yeast Saccharomyces cerevisiae than to other Candida pathogens, and hence its ability to infect humans is thought to have emerged independently. Moreover, C. glabrata has all the necessary genes to undergo a sexual cycle but is considered an asexual organism due to the lack of direct evidence of sexual reproduction. To reconstruct the recent evolution of this pathogen and find footprints of sexual reproduction, we assessed genomic and phenotypic variation across 33 globally distributed C. glabrata isolates. We cataloged extensive copy-number variation, which particularly affects genes encoding cell-wall-associated proteins, including adhesins. The observed level of genetic variation in C. glabrata is significantly higher than that found in Candida albicans. This variation is structured into seven deeply divergent clades, which show recent geographical dispersion and large within-clade genomic and phenotypic differences. We show compelling evidence of recent admixture between differentiated lineages and of purifying selection on mating genes, which provides the first evidence for the existence of an active sexual cycle in this yeast. Altogether, our data point to a recent global spread of previously genetically isolated populations and suggest that humans are only a secondary niche for this yeast.

The T.G. group acknowledges the support of the Spanish Ministry of Economy and Competitiveness grants “Centro de Excelencia Severo Ochoa 2013–2017” SEV-2012-0208 and BFU2015-67107 cofunded by the European Regional Development Fund (ERDF); European Union and ERC Seventh Framework Programme (FP7/2007–2013) under grant agreement ERC-2012-StG-310325; Catalan Research Agency (AGAUR) SGR857; CERCA Programme/Generalitat de Catalunya; and a grant from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement H2020-MSCA-ITN-2014-642095. C.F.’s and T.G.’s groups acknowledge support from the GDRI “iGenolevures” of the French CNRS for travel and meeting funds. T.G., O.B., and E.G.-M. acknowledge funding from the European Unionunder grant agreement FP7-PEOPLE-2013-ITN-606786 “ImresFun.”