Gene flow contributes to diversification of the major fungal pathogen $Candida\ albicans$

Abstract : 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.