African isolates of C. neoformans var. grubii are more diverse than the global population: comparison of the diversity indices and neutrality tests at each locus.

aThe diversity of clinical and environmental strains of C. neoformans var. grubii from Botswana and South Africa was compared with that of a selection of the most genetically diverse global isolates available [10]. The “African” population included all clinical and avian isolates of C. neoformans var. grubii (85 strains) as well as 14 isolates from African trees; that is, we analyzed only one isolate per tree because multiple isolates from the same tree and surrounding soil were clonal. The “Global” sample was comprised of a larger sample of 57 previously genotyped, non-arboreal strains from 14 different countries (excluding Botswana and South Africa), and they included multiple isolates of each unique MLST or AFLP genotype [10]. Except for the CAP59 locus, this purposely enlarged and intentionally diversified global sample revealed less variation (i.e., lower h, π and d values) than the sample of African isolates.bWe excluded strains with recombinant haplotypes at a locus.cValues of Tajima's TD for which the null hypothesis of neutrality was rejected are bolded.