African isolates of <i>C. neoformans</i> var. <i>grubii</i> 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.a 本研究将来自博茨瓦纳与南非的新生隐球菌格鲁比变种（C. neoformans var. grubii）临床菌株与环境菌株的多样性，与已公开的遗传多样性最丰富的精选全球分离株集合进行了对比[10]。其中“非洲群体”涵盖所有新生隐球菌格鲁比变种的临床与禽源分离株（共85株），以及14株来自非洲树木的分离株；鉴于同一树木及其周边土壤的多株分离株均为克隆型，故每棵树仅选取一株开展分析。“全球样本”则由来自14个不同国家（不含博茨瓦纳与南非）的57株已完成基因分型的非树源分离株组成，该样本包含了每个独特多位点序列分型（Multi-Locus Sequence Typing, MLST）或扩增片段长度多态性（Amplified Fragment Length Polymorphism, AFLP）基因型的多株分离株[10]。除CAP59基因座外，这一经过刻意扩大样本量且特意增强多样性的全球样本，其遗传变异水平（即更低的h、π与d值）均低于非洲分离株样本。 b 本研究剔除了在某一基因座上存在重组单倍型的菌株。 c 拒绝中性进化零假设的塔伊马TD（Tajima's TD）统计量以粗体标注。