Global population genetics and evolutionary dynamics of Candida albicans

Candida albicans is a common commensal yeast and an opportunistic pathogen of global health importance. However, its global geographic and temporal patterns of genetic variation remain poorly understood. Here we analyzed sequence data on seven housekeeping loci from >5000 isolates in the C. albicans PubMLST database representing >60 countries and spanning >70 years. Diploid sequences at each locus were phased into haplotypes to provide higher-resolution insights into diversity, differentiation, and recombination. Our analyses revealed high allelic and genotypic diversities within most geographic and temporal populations. Pairwise FST estimates revealed low but statistically significant differentiation among both geographic and temporal populations, with AMOVA revealing that most genetic variation resides within rather than among subpopulations. STRUCTURE analysis identified two genetic clusters but with extensive admixture within most geographic populations, consistent with frequent gene flow. Phylogenetic and haplotype network analyses revealed evidence of clonal expansion, with globally distributed haplotypes being genetically closer to one another than among more localized haplotypes. Finally, recombination analyses revealed evidence of non-random recombination within populations, including an overall deficiency of heterozygosity, suggesting the importance of parasexuality and/or mitotic recombination in C. albicans populations. Together, these results highlight the global evolutionary dynamics and population structure of C. albicans.