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Chapter 8 : Population Structure and Ecology of and

Authors: Anastasia P. Litvintseva1, Jianping Xu2, Thomas G. Mitchell3
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Affiliations: 1: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710; 2: Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1; 3: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
Content Type: Monograph
Publication Year: 2011

Category: Clinical Microbiology; Fungi and Fungal Pathogenesis

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Abstract:

and comprise the pathogenic species complex. This chapter focuses on the population structure and ecology of and . It summarizes the current knowledge of the population structure of and and discusses the associations of the genetically isolated subpopulations with their ecological niches. The most reliable methods developed to genotype individuals use markers that detect polymorphisms among microsatellites and similar repetitive DNA elements, restriction fragment length polymorphisms (RFLP), amplified fragment length polymorphisms (AFLP), and direct DNA sequencing, such as multilocus sequence typing (MLST). Most studies of the population genetics of the pathogenic species of use reference strains to recognize the major clades or subpopulations. These are designated as VNI through VNIV and VNB for and VGI through VGIV for . A table shows the current designation of the nine major subpopulations of the / complex and their relationships to the conventional serotypes. This method of serotyping served for years to separate (serotypes A, D, and AD) from (serotypes B and C). Analyses of the population structure presented in the chapter are concerned with (i) genetic diversity, (ii) mode of reproduction (clonality versus recombination), and (iii) population subdivision. The chapter also talks about the advances in the understanding of the intertwining effects of ecology and genetics on the lifestyle of and .

Citation: Litvintseva A, Xu J, Mitchell T. 2011. Population Structure and Ecology of and , p 97-111. In Heitman J, Kozel T, Kwon-Chung K, Perfect J, Casadevall A (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555816858.ch8

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Population Structure and Ecology of Cryptococcus neoformans and Cryptococcus gattii
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Citation: Litvintseva A, Xu J, Mitchell T. 2011. Population Structure and Ecology of and , p 97-111. In Heitman J, Kozel T, Kwon-Chung K, Perfect J, Casadevall A (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555816858.ch8
/content/10.1128/9781555816858.ch08.ch08fig01
FIGURE 1
Genetic relationships of MLST genotypes among 98 isolates of serotype A visualized by the neighbor-joining dendrogram. Numbers on each branch indicate the bootstrap values >50%, based on 500 replications. Vertical lines represent strains with identical genotypes. The clades labeled A1 to A5 and A10 correspond to AFLP genotypes ( ). VNB-A and VNB-B are two groups within the VNB subpopulation from Botswana. Isolates with the mating type are shown in bold and designated with “.” From Litvintseva et al. ( ) and used with permission.
10.1128/9781555816858/f0101-01_thmb.gif
10.1128/9781555816858/f0101-01.gif
Image of FIGURE 1
FIGURE 1

Genetic relationships of MLST genotypes among 98 isolates of serotype A visualized by the neighbor-joining dendrogram. Numbers on each branch indicate the bootstrap values >50%, based on 500 replications. Vertical lines represent strains with identical genotypes. The clades labeled A1 to A5 and A10 correspond to AFLP genotypes ( ). VNB-A and VNB-B are two groups within the VNB subpopulation from Botswana. Isolates with the mating type are shown in bold and designated with “.” From Litvintseva et al. ( ) and used with permission.

Citation: Litvintseva A, Xu J, Mitchell T. 2011. Population Structure and Ecology of and , p 97-111. In Heitman J, Kozel T, Kwon-Chung K, Perfect J, Casadevall A (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555816858.ch8
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/content/10.1128/9781555816858.ch08.ch08fig02
FIGURE 2
Genetic relationships among 58 MLST genotypes of serotype A visualized by principal component analysis. Each circle or triangle represents a genotype with a unique eight-digit allelic profile. Gray circles denote genotypes of strains that are endemic to Africa, and open triangles denote genotypes of cosmopolitan strains. Genotypes that have been isolated from African trees are marked with tree symbols, and genotypes that have been isolated from pigeon feces are marked with pigeon symbols. Genotypes without a tree or pigeon symbol are clinical strains. Note that all global strains are closely related and associated with pigeon habitats. Conversely, there is significant diversity among genotypes that are unique to Africa, and many of these African genotypes are associated with African trees ( ).
10.1128/9781555816858/f0102-01_thmb.gif
10.1128/9781555816858/f0102-01.gif
Image of FIGURE 2
FIGURE 2

Genetic relationships among 58 MLST genotypes of serotype A visualized by principal component analysis. Each circle or triangle represents a genotype with a unique eight-digit allelic profile. Gray circles denote genotypes of strains that are endemic to Africa, and open triangles denote genotypes of cosmopolitan strains. Genotypes that have been isolated from African trees are marked with tree symbols, and genotypes that have been isolated from pigeon feces are marked with pigeon symbols. Genotypes without a tree or pigeon symbol are clinical strains. Note that all global strains are closely related and associated with pigeon habitats. Conversely, there is significant diversity among genotypes that are unique to Africa, and many of these African genotypes are associated with African trees ( ).

Citation: Litvintseva A, Xu J, Mitchell T. 2011. Population Structure and Ecology of and , p 97-111. In Heitman J, Kozel T, Kwon-Chung K, Perfect J, Casadevall A (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555816858.ch8
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/content/10.1128/9781555816858.ch08.ch08fig03
FIGURE 3
Haplotype networks of eight MLST loci of serotype A. The strain haplotypes (alleles) that are unique to Africa and associated with African trees are shown in black circles. Haplotypes of cosmopolitan strains are associated with pigeon feces and shown in gray circles. Circles that are half black and half gray indicate haplotypes of strains that were isolated from both African trees and pigeon feces. Haplotypes from the VNII group are used as an outgroup and labeled. The ancestral haplotypes are internal, and derived haplotypes occupy tip or distal positions. Small dashes on lines connecting haplotypes represent mutational steps separating the alleles. Recombinant haplotypes have been excluded. For each individual gene, the ancestral haplotype is always associated with an African tree. The analyses indicate significantly greater genetic diversity among haplotypes from Africa compared to the strains with cosmopolitan haplotypes ( ).
10.1128/9781555816858/f0104-01_thmb.gif
10.1128/9781555816858/f0104-01.gif
Image of FIGURE 3
FIGURE 3

Haplotype networks of eight MLST loci of serotype A. The strain haplotypes (alleles) that are unique to Africa and associated with African trees are shown in black circles. Haplotypes of cosmopolitan strains are associated with pigeon feces and shown in gray circles. Circles that are half black and half gray indicate haplotypes of strains that were isolated from both African trees and pigeon feces. Haplotypes from the VNII group are used as an outgroup and labeled. The ancestral haplotypes are internal, and derived haplotypes occupy tip or distal positions. Small dashes on lines connecting haplotypes represent mutational steps separating the alleles. Recombinant haplotypes have been excluded. For each individual gene, the ancestral haplotype is always associated with an African tree. The analyses indicate significantly greater genetic diversity among haplotypes from Africa compared to the strains with cosmopolitan haplotypes ( ).

Citation: Litvintseva A, Xu J, Mitchell T. 2011. Population Structure and Ecology of and , p 97-111. In Heitman J, Kozel T, Kwon-Chung K, Perfect J, Casadevall A (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555816858.ch8
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Tables

Population Structure and Ecology of Cryptococcus neoformans and Cryptococcus gattii
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Citation: Litvintseva A, Xu J, Mitchell T. 2011. Population Structure and Ecology of and , p 97-111. In Heitman J, Kozel T, Kwon-Chung K, Perfect J, Casadevall A (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555816858.ch8
/content/10.1128/9781555816858.ch08.ch08table01
TABLE 1
Nomenclature of the subpopulations of and
Generic image for table
TABLE 1

Nomenclature of the subpopulations of and

Citation: Litvintseva A, Xu J, Mitchell T. 2011. Population Structure and Ecology of and , p 97-111. In Heitman J, Kozel T, Kwon-Chung K, Perfect J, Casadevall A (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555816858.ch8

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