Population Genetic Analysis Reveals a High Genetic Diversity in the Brazilian Cryptococcus gattii VGII Population and Shifts the Global Origin from the Amazon Rainforest to the Semi-arid Desert in the Northeast of Brazil
Fig 1
Phylogenetic analysis of Brazilian Cryptococcus gattii VGII isolates inferred by maximum likelihood (ML), neighbour-joining (NJ), and maximum parsimony (MP) methods using the concatenated data set of the seven MLST genes.
All Brazilian Sequence types (81) from this study and 42 additional Sequence types representing all previously published VGII sequence types maintained in the MLST database (mlst.mycologylab.org) were included in the analysis. The tree with the highest log likelihood (-9194.7663) is shown. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories [+G, parameter = 0.0500]). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 6.6983% sites). The tree is drawn to scale, with branch lengths measuring the number of substitutions per site. Codon positions included were 1st+2nd+3rd+Noncoding. There were a total of 4,172 positions in the final dataset. Numbers at each branch indicate bootstrap values >50% based on 1,000 replicates by each of the three (ML/NJ/MP) algorithms which presented similar topologies. The taxa nomenclature includes the sequence type number (ST), Mating Type (a or alpha), country of isolation and for those isolates from Brazil the region of isolation [N = North, NE = Northeast, CW = Central-West, and SE = Southeast], and source (E = environmental; all others are clinical). All country abbreviations are designated according to the alpha-2 code of ISO 3166–1. AU: Australia, BR: Brazil, CA: Canada, CN: China, CO: Colombia, CD: Democratic Republic of the Congo, CH: Switzerland, DK: Denmark, DE: Germany, ES: Spain, FR: France, GF: French Guiana, GR: Greece, KR: Republic of Korea, SN: Senegal, TH: Thailand, US: United States of America, UY: Uruguay.
doi: https://doi.org/10.1371/journal.pntd.0004885.g001