title: Worldwide Phylogenetic Distributions and Population Dynamics of the Genus Histoplasma.
abstract: Histoplasma capsulatum comprises a worldwide complex of saprobiotic fungi mainly found in nitrogen/phosphate (often bird guano) enriched soils. The microconidia of Histoplasma species may be inhaled by mammalian hosts, and is followed by a rapid conversion to yeast that can persist in host tissues causing histoplasmosis, a deep pulmonary/systemic mycosis. Histoplasma capsulatum sensu lato is a complex of at least eight clades geographically distributed as follows: Australia, Netherlands, Eurasia, North American classes 1 and 2 (NAm 1 and NAm 2), Latin American groups A and B (LAm A and LAm B) and Africa. With the exception of the Eurasian cluster, those clades are considered phylogenetic species.
  
  
  
  Increased Histoplasma sampling (n = 234) resulted in the revision of the phylogenetic distribution and population structure using 1,563 aligned nucleotides from four protein-coding regions. The LAm B clade appears to be divided into at least two highly supported clades, which are geographically restricted to either Colombia/Argentina or Brazil respectively. Moreover, a complex population genetic structure was identified within LAm A clade supporting multiple monophylogenetic species, which could be driven by rapid host or environmental adaptation (~0.5 MYA). We found two divergent clades, which include Latin American isolates (newly named as LAm A1 and LAm A2), harboring a cryptic cluster in association with bats.
  
  
  
  At least six new phylogenetic species are proposed in the Histoplasma species complex supported by different phylogenetic and population genetics methods, comprising LAm A1, LAm A2, LAm B1, LAm B2, RJ and BAC-1 phylogenetic species. The genetic isolation of Histoplasma could be a result of differential dispersion potential of naturally infected bats and other mammals. In addition, the present study guides isolate selection for future population genomics and genome wide association studies in this important pathogen complex.
authors.affiliation: Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, Arizona, United States of America.|Department of Cell Biology, University of Brasília, Brasilia, Brazil.
authors.forename: Marcus de M
authors.initials: Mde M
authors.lastname: Teixeira
authors.affiliation: Department of Biochemistry, University of São Paulo, São Paulo, Brazil.
authors.forename: José S L
authors.initials: JS
authors.lastname: Patané
authors.affiliation: Department of Microbiology and Parasitology, National Autonomous University of Mexico, Mexico City, Mexico.
authors.forename: Maria L
authors.initials: ML
authors.lastname: Taylor
authors.affiliation: Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia.
authors.forename: Beatriz L
authors.initials: BL
authors.lastname: Gómez
authors.affiliation: Department of Cell Biology and Genetics/ Institute of Tropical Medicine, Federal University of Rio Grande do Norte, Natal, Brazil.
authors.forename: Raquel C
authors.initials: RC
authors.lastname: Theodoro
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands.
authors.forename: Sybren
authors.initials: S
authors.lastname: de Hoog
authors.affiliation: Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, Arizona, United States of America.
authors.forename: David M
authors.initials: DM
authors.lastname: Engelthaler
authors.affiliation: Mycology Laboratory, National Institute of Infectology Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.
authors.forename: Rosely M
authors.initials: RM
authors.lastname: Zancopé-Oliveira
authors.affiliation: Department of Cell Biology, University of Brasília, Brasilia, Brazil.
authors.forename: Maria S S
authors.initials: MS
authors.lastname: Felipe
authors.affiliation: Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, Arizona, United States of America.
authors.forename: Bridget M
authors.identifier: 0000-0002-3439-4517
authors.initials: BM
authors.lastname: Barker
mesh_terms: D000818:Animals; D014644:Genetic Variation; D014943:Global Health; D006239:Haplotypes; D006658:Histoplasma / Q000235:genetics*; D006660:Histoplasmosis / Q000453:epidemiology / Q000382:microbiology*; D006801:Humans; D010802:Phylogeny; D058974:Phylogeography