A monomorphic haplotype of chromosome Ia is associated with widespread success in clonal and nonclonal populations of Toxoplasma gondii

Abstract

Toxoplasma gondii is a common parasite of animals that also causes a zoonotic infection in humans. Previous studies have revealed a strongly clonal population structure that is shared between North America and Europe, while South American strains show greater genetic diversity and evidence of sexual recombination. The common inheritance of a monomorphic version of chromosome Ia (referred to as ChrIa*) among three clonal lineages from North America and Europe suggests that inheritance of this chromosome might underlie their recent clonal expansion. To further examine the diversity and distribution of ChrIa, we have analyzed additional strains with greater geographic diversity. Our findings reveal that the same haplotype of ChrIa* is found in the clonal lineages from North America and Europe and in older lineages in South America, where sexual recombination is more common. Although lineages from all three continents harbor the same conserved ChrIa* haplotype, strains from North America and Europe are genetically separate from those in South America, and these respective geographic regions show limited evidence of recent mixing. Genome-wide, array-based profiling of polymorphisms provided evidence for an ancestral flow from particular older southern lineages that gave rise to the clonal lineages now dominant in the north. Collectively, these data indicate that ChrIa* is widespread among nonclonal strains in South America and has more recently been associated with clonal expansion of specific lineages in North America and Europe. These findings have significant implications for the spread of genetic loci influencing transmission and virulence in pathogen populations.

Importance: Understanding parasite population structure is important for evaluating the potential spread of pathogenicity determinants between different geographic regions. Examining the genetic makeup of different isolates of Toxoplasma gondii from around the world revealed that chromosome Ia is highly homogeneous among lineages that predominate on different continents and within genomes that were otherwise quite divergent. This pattern of recent shared ancestry is highly unusual and suggests that some gene(s) found on this chromosome imparts an unusual fitness advantage that has resulted in its recent spread. Although the basis for the conservation of this particularly homogeneous chromosome is unknown, it may have implications for the transmission of infection and spread of human disease.

FIG 1

Population structure analysis of T. gondii. (A) Neighbor net developed from analysis of 5 intron sequences from 74 T. gondii strains. Strong geographic separation was evident between North American-European (blue lettering) and South American (red lettering) T. gondii strains. The major branches were classified into 14 haplogroups (numbers in circles). Circles indicate monomorphic ChrIa* (yellow) and divergent ChrIa (blue). Further details on strains are provided in Table S1 in the supplemental material. (B) STRUCTURE analysis of 74 T. gondii isolates, conducted using concatenated intron sequences. An ancestral population size of K = 6, based on a linkage model, was chosen. See Fig. S2 for additional K values. Haplogroups (HG) are listed at the top. Ch, China; Af, Africa.

FIG 2

Network analysis of sequenced regions from ChrIa reveals four major clusters. Green indicates 3′ chimeric, red indicates 5′ chimeric, yellow indicates the monomorphic ChrIa* haplotype, and blue represents divergent ChrIa. Haplogroup numbers are indicated in brackets. Sizes of spheres are proportional to the numbers of strains. Strains included are listed in Table S1 in the supplemental material. See Fig. S3 for a diagram of regions included in the analysis.

FIG 3

Neighbor network analyses of the genome as a whole based on intron sequences versus regions of ChrIa. (A) Overall genetic relatedness based on introns shows a strong split between North America-Europe and South America that is based on moderately deep branches. (B) In contrast, ChrIa* contains very low diversity among these same strains. Note that the scale differs 10-fold from that in panel A. Color coding indicates the continent of origin: North America and Europe (blue), South America (red), or Chinese (maroon). Strains included contain monomorphic ChrIa* (yellow cluster in Fig. 2; see also Table S1 in the supplemental material).

FIG 4

Model of evolutionary history of T. gondii lineages. The separation of T. gondii populations from North America and South America was estimated to have occurred 10⁶ years ago. The monomorphic ChrIa* haplotype was found in the nonclonal South American haplogroups 4, 8, and 9, which have diverged over the past 10⁵ years, and within the North American-European clonal lineages, which have a more recent common origin within the last 10⁴ years. Age estimates are from Table S2 in the supplemental material and reference .

FIG 5

Genome-wide SNP typing of T. gondii strains based on microarray hybridization. (A) Chromosomes are indicated by alternating gray and white bars, starting with Ia on the left. For each strain, SNPs represented on the array are shown as dots, segregated into three rows representing SNPs unique to type 1, type 2, or type 3. Color indicates hybridization to the defining allele (red, type 1; green, type 2; blue, type 3), while gray indicates hybridization to the alternative allele (or failure to hybridize). Strain names at left are colored blue/red to indicate North America-European versus South American origin and shaded yellow to indicate the presence of monomorphic ChrIa*. Haplogroups are indicated in parentheses. (B) Microarray-based genotyping of T. gondii strains. Allelic patterns for representative type 1 (GT1), 2 (ME49), and 3 (CTG) strains. Results for P89 (C) or FOU (D) are shown based on similarity to type 1 (red), type 2 (green), or type 3 (blue). Dots above and below each graph represent strain-dependent match (top) or mismatch (bottom) hybridizations. Line graphs indicate concordance with type 1, 2, or 3 over an 11-SNP sliding window, shown as % identity on the y axis.