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Population genetic analyses reveal the African origin and strain variation of Cryptococcus neoformans var. grubii.

Litvintseva AP, Mitchell TG - PLoS Pathog. (2012)

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA. anastasia.litvintseva@dm.duke.edu

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Cryptococcus neoformans is a ubiquitous, saprobic yeast and the cause of life-threatening infections... The use of reproducible and robust multilocus sequence typing (MLST) has determined that the overwhelming majority of non-African strains of Cng are represented by only a few genotypes –... In comparison, five genotypes were found in Europe, and nine genotypes among isolates from central and eastern Africa, but only two different MLST genotypes were detected from South American and Australian isolates, although these were small samples... Analyses of mating indicated that 12% of these strains possess the MAT mating type, which is exceedingly rare among non-African strains, and population genetic analysis demonstrated evidence for recombination in this population... Subsequent environmental sampling confirmed that two genetically isolated subpopulations are localized in southern Africa: (i) a genetically diverse, endemic population that is restricted to southern African and associated with indigenous African trees, especially the mopane tree (Colophospermum mopane), and (ii) a cosmopolitan population of strains with molecular types that are found worldwide and frequently associated with the excreta of feral pigeons (Columba livia)... Thus, multiple features of the African strains—greatest genetic diversity, prevalence of both mating types, and association with an indigenous reservoir—suggest they represent the ancestral origin of Cng... This conclusion was supported by phylogenetic analyses of individual loci using methods of maximum likelihood and parsimony... All of these genotypes were obtained from pigeon habitats (Figure 2, brown circles), ... Furthermore, maximum likelihood analyses of three loci (TEF1, CAP59, and PLB1) indicated that the ancestral haplotypes of both the VNI and VNB populations are confined to southern Africa and associated with endemic African trees... Environmental sampling has demonstrated that African strains of VNI and VNB are associated with native African trees, whereas cosmopolitan strains of VNI are isolated from pigeon droppings... VNI strains with identical MLST genotypes have been isolated from pigeon habitats in North and South America, Europe, Asia, and Africa, ,... Although the exact origin of C. livia is unknown, historical records indicate that pigeons were probably native to the north African Mediterranean region and were spread globally over the last 400 years of European expansion, ... Thus, multiple features of the cosmopolitan population of VNI—exceptionally low genetic diversity, dominance of a single mating type, and global distribution in association with pigeon excreta—support the parsimonious conclusion that pigeons facilitated the global exportation and dispersion of African strains.

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Haplotype networks of the eight MLST loci.Haplotypes of strains of Cng that have never been found outside Africa are shown in green: filled green circles designate haplotypes of strains that were obtained from trees (most were also found in patients), and empty green circles signify haplotypes that were obtained only from patients. Cosmopolitan haplotypes are shown in brown: filled brown circles designate haplotypes of strains from pigeon excreta (most were also found in patients), and empty brown circles signify haplotypes that were obtained only from patients. Circles that are half green and half brown indicate haplotypes of strains found in trees and pigeon excreta. Haplotypes from the global VNII subpopulation of Cng are included as an outgroup; they are shown in black and lightly encircled. Red dots on the lines connecting the haplotypes represent the most parsimonious number of mutational steps required to generate the allelic polymorphisms. Recombinant haplotypes are excluded. The most common haplotype in Asia and elsewhere, M5, is shown in blue. (From reference [14] and used with permission of the publisher.)
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ppat-1002495-g002: Haplotype networks of the eight MLST loci.Haplotypes of strains of Cng that have never been found outside Africa are shown in green: filled green circles designate haplotypes of strains that were obtained from trees (most were also found in patients), and empty green circles signify haplotypes that were obtained only from patients. Cosmopolitan haplotypes are shown in brown: filled brown circles designate haplotypes of strains from pigeon excreta (most were also found in patients), and empty brown circles signify haplotypes that were obtained only from patients. Circles that are half green and half brown indicate haplotypes of strains found in trees and pigeon excreta. Haplotypes from the global VNII subpopulation of Cng are included as an outgroup; they are shown in black and lightly encircled. Red dots on the lines connecting the haplotypes represent the most parsimonious number of mutational steps required to generate the allelic polymorphisms. Recombinant haplotypes are excluded. The most common haplotype in Asia and elsewhere, M5, is shown in blue. (From reference [14] and used with permission of the publisher.)

Mentions: This conclusion was supported by phylogenetic analyses of individual loci using methods of maximum likelihood and parsimony. To illustrate, haplotype networks were analyzed by statistical parsimony to infer any phylogenetic relationships among the haplotypes. The internal nodes of these networks represent ancestral haplotypes from which the distal, derived haplotypes evolved. Numerous haplotypes from the endemic African population occupied both internal (ancestral) and distal (derived) positions on the networks (Figure 2, green circles). Conversely, haplotypes that are unique to the global population were scarce and almost always in distal positions, which suggests they originated more recently. All of these genotypes were obtained from pigeon habitats (Figure 2, brown circles) [14], [15]. Furthermore, maximum likelihood analyses of three loci (TEF1, CAP59, and PLB1) indicated that the ancestral haplotypes of both the VNI and VNB populations are confined to southern Africa and associated with endemic African trees [14].


Population genetic analyses reveal the African origin and strain variation of Cryptococcus neoformans var. grubii.

Litvintseva AP, Mitchell TG - PLoS Pathog. (2012)

Haplotype networks of the eight MLST loci.Haplotypes of strains of Cng that have never been found outside Africa are shown in green: filled green circles designate haplotypes of strains that were obtained from trees (most were also found in patients), and empty green circles signify haplotypes that were obtained only from patients. Cosmopolitan haplotypes are shown in brown: filled brown circles designate haplotypes of strains from pigeon excreta (most were also found in patients), and empty brown circles signify haplotypes that were obtained only from patients. Circles that are half green and half brown indicate haplotypes of strains found in trees and pigeon excreta. Haplotypes from the global VNII subpopulation of Cng are included as an outgroup; they are shown in black and lightly encircled. Red dots on the lines connecting the haplotypes represent the most parsimonious number of mutational steps required to generate the allelic polymorphisms. Recombinant haplotypes are excluded. The most common haplotype in Asia and elsewhere, M5, is shown in blue. (From reference [14] and used with permission of the publisher.)
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3285590&req=5

ppat-1002495-g002: Haplotype networks of the eight MLST loci.Haplotypes of strains of Cng that have never been found outside Africa are shown in green: filled green circles designate haplotypes of strains that were obtained from trees (most were also found in patients), and empty green circles signify haplotypes that were obtained only from patients. Cosmopolitan haplotypes are shown in brown: filled brown circles designate haplotypes of strains from pigeon excreta (most were also found in patients), and empty brown circles signify haplotypes that were obtained only from patients. Circles that are half green and half brown indicate haplotypes of strains found in trees and pigeon excreta. Haplotypes from the global VNII subpopulation of Cng are included as an outgroup; they are shown in black and lightly encircled. Red dots on the lines connecting the haplotypes represent the most parsimonious number of mutational steps required to generate the allelic polymorphisms. Recombinant haplotypes are excluded. The most common haplotype in Asia and elsewhere, M5, is shown in blue. (From reference [14] and used with permission of the publisher.)
Mentions: This conclusion was supported by phylogenetic analyses of individual loci using methods of maximum likelihood and parsimony. To illustrate, haplotype networks were analyzed by statistical parsimony to infer any phylogenetic relationships among the haplotypes. The internal nodes of these networks represent ancestral haplotypes from which the distal, derived haplotypes evolved. Numerous haplotypes from the endemic African population occupied both internal (ancestral) and distal (derived) positions on the networks (Figure 2, green circles). Conversely, haplotypes that are unique to the global population were scarce and almost always in distal positions, which suggests they originated more recently. All of these genotypes were obtained from pigeon habitats (Figure 2, brown circles) [14], [15]. Furthermore, maximum likelihood analyses of three loci (TEF1, CAP59, and PLB1) indicated that the ancestral haplotypes of both the VNI and VNB populations are confined to southern Africa and associated with endemic African trees [14].

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA. anastasia.litvintseva@dm.duke.edu

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Cryptococcus neoformans is a ubiquitous, saprobic yeast and the cause of life-threatening infections... The use of reproducible and robust multilocus sequence typing (MLST) has determined that the overwhelming majority of non-African strains of Cng are represented by only a few genotypes –... In comparison, five genotypes were found in Europe, and nine genotypes among isolates from central and eastern Africa, but only two different MLST genotypes were detected from South American and Australian isolates, although these were small samples... Analyses of mating indicated that 12% of these strains possess the MAT mating type, which is exceedingly rare among non-African strains, and population genetic analysis demonstrated evidence for recombination in this population... Subsequent environmental sampling confirmed that two genetically isolated subpopulations are localized in southern Africa: (i) a genetically diverse, endemic population that is restricted to southern African and associated with indigenous African trees, especially the mopane tree (Colophospermum mopane), and (ii) a cosmopolitan population of strains with molecular types that are found worldwide and frequently associated with the excreta of feral pigeons (Columba livia)... Thus, multiple features of the African strains—greatest genetic diversity, prevalence of both mating types, and association with an indigenous reservoir—suggest they represent the ancestral origin of Cng... This conclusion was supported by phylogenetic analyses of individual loci using methods of maximum likelihood and parsimony... All of these genotypes were obtained from pigeon habitats (Figure 2, brown circles), ... Furthermore, maximum likelihood analyses of three loci (TEF1, CAP59, and PLB1) indicated that the ancestral haplotypes of both the VNI and VNB populations are confined to southern Africa and associated with endemic African trees... Environmental sampling has demonstrated that African strains of VNI and VNB are associated with native African trees, whereas cosmopolitan strains of VNI are isolated from pigeon droppings... VNI strains with identical MLST genotypes have been isolated from pigeon habitats in North and South America, Europe, Asia, and Africa, ,... Although the exact origin of C. livia is unknown, historical records indicate that pigeons were probably native to the north African Mediterranean region and were spread globally over the last 400 years of European expansion, ... Thus, multiple features of the cosmopolitan population of VNI—exceptionally low genetic diversity, dominance of a single mating type, and global distribution in association with pigeon excreta—support the parsimonious conclusion that pigeons facilitated the global exportation and dispersion of African strains.

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