Elucidating population structure and levels of genetic diversity and recombination is necessary to understand the evolution and adaptation of species. Candida albicans is the second most frequent agent of human fungal infections worldwide, causing high-mortality rates. Here we present the genomic sequences of 182 C. albicans isolates collected worldwide, including commensal isolates, as well as ones responsible for superficial and invasive infections, constituting the largest dataset to date for this major fungal pathogen. Although, C. albicans shows a predominantly clonal population structure, we find evidence of gene flow between previously known and newly identified genetic clusters, supporting the occurrence of (para)sexuality in nature. A highly clonal lineage, which experimentally shows reduced fitness, has undergone pseudogenization in genes required for virulence and morphogenesis, which may explain its niche restriction. Candida albicans thus takes advantage of both clonality and gene flow to diversify.

This work was supported by grants from the Agence Nationale de Recherche (ANR-10-LABX-62-IBEID), the Genoscope (projet #15 AP2008/2009 SNP C. albicans) and the Swiss National Science Foundation (Sinergia CRSII5_173863/1) to C.E., J.R. was supported by a Pasteur-Roux fellowship from Institut Pasteur. D.D. was the recipient of a PhD fellowship from Institut National de la Recherche Agronomique. E.P. was the recipient of a post-doctoral fellowship from the Wellcome Trust (WT088858MA). M.M.-H. and T.G. were supported by a grant from the Spanish Ministry of Economy and Competitiveness, BFU2015–67107 cofunded by the European Regional Development Fund (ERDF). C.E., M.-E.B., S.H.K., and J.H.S. were supported by a grant from the French and Korean Ministries for Foreign Affairs (PHC STAR 2011 25841YA). R.C.M. was supported by project MitoFun, funded by the European Research Council under the European Union’s Seventh Framework Programme (FP/2007–2013)/ERC Grant Agreement No. 614562 and by a Wolfson Research Merit Award from the Royal Society. R.C.M. and K.V. were funded by the Surgical Reconstruction and Microbiology Research Centre, which is supported by the National Institute of Health Research, UK. G.S. was supported by the NIH grants R01-HG003468 and RO1-DE015873. C.E. and T.G. are members of the CNRS GDRI 0814 iGenolevures consortium. High-throughput sequencing has been performed on the Genomics Platform, member of France Génomique consortium (ANR10-INBS-09-08). We thank Bernard Dujon and Tatiana Giraud for providing insights on an earlier version of this manuscript.