Examination of a wider array of isolates of T. gondii from different geographic regions uncovered a larger number of haplogroups than had been previously recognized. Additional sampling also established that the same haplotype of ChrIa (ChrIa*), initially known from clonal strains in North America and Europe, is widespread in lineages that predominate in South America, including haplogroups 4, 8, and 9, which propagate primarily sexually and do not display clonality. Despite the highly similar nature of ChrIa* in these regions, variation in other chromosomes is strongly partitioned geographically, as indicated by conserved SNP patterns that are associated with specific geographic regions. This contrast suggests that the ChrIa* haplotype has recently been transferred between comparatively diverse populations in South America into the founding stocks that subsequently expanded clonally in North America and Europe. The strong conservation of ChrIa* among divergent lineages from North America, Europe, and South America suggests that it confers a selective advantage under both asexual and sexual modes of propagation. Whether ChrIa* favors clonality in the north due to some other genetic element that is lacking in South America is uncertain; however, this possibility could be investigated by experimental genetic crosses.
In addition to the previously defined 12 haplogroups of T. gondii
), we have identified two new haplogroups that appear common in regions of Africa and China. Previous studies from Africa have found a mixture of canonical genotypes, including examples of types 2 and 3 that are normally found in North America and Europe (31
). These studies were based on sampling of domestic fowl from several countries (31
) and hence may have been influenced by importation of strains along with domestic animals or the relative insensitivity of RFLP markers for discovery of new polymorphisms. Studies of T. gondii
isolates from free-range animals in Gabon, Africa, have also reported strains that are highly similar to type 3 strains, as well as those that are more diverse based on MS markers (20
). Comparison of these isolates here revealed that Africa 1
is similar to haplogroup 6. Strains with similar genotypes have previously been isolated in South America and Europe, although the latter cases are thought to have originated in Africa either through travel, immigration, or importation of contaminated meat (20
). The remaining Africa 3
strains defined a new haplogroup, 14, which is distinct from those seen previously. Likewise, two Chinese strains that had previously been defined by RFLP markers (21
) defined a new haplogroup, called 13. More-complete analyses of their distribution and population structure (9
) await wider sampling of strains from these regions.
Neighbor network and STRUCTURE analyses demonstrated a strong geographic separation of T. gondii
strain types between North America-Europe and South America, similar to findings in previous reports (12
). However, there are clearly four major ancestral populations reflecting the dominant color blocks in STRUCTURE. Based on shared ancestry, haplogroup 12 is the most likely parent that led to current-day type 2, since these two lineages share large portions of their genomes. Large haploblocks of type 2 are also seen in types 1 and 3, which likely reflects their recent admixture, as suggested previously (14
). STRUCTURE also provided evidence of ancestral gene flow between north and south, as is apparent from the major color patterns that are shared across these regions at various K
values (; see also Fig. S2
in the supplemental material). Such exchanges are likely to be ancestral, because other studies have indicated that there is relatively little recent genetic exchange between these regions based on FST
analysis, phylogenic analysis, and principal-component analysis (19
). Additionally, strains types in each region are characterized by derived SNPs that differ from ancestral alleles, which are shared within specific northern or southern haplogroups (19
). These two opposing patterns of current geographic segregation versus shared ancestry are not incompatible but rather may reflect differences in genetic exchange over time.
Despite evidence for geographic separation between different continents, all of the northern lineages and a large number of southern ones share a nearly identical haplotype of ChrIa*. In particular, nearly all members of haplogroups 4, 8, and 9 from South America share this ChrIa* haplotype despite having diversified in other parts of their genomes. The abundance of ChrIa* in South American lineages was unexpected, since the ChrIa* haplotype has previously been associated primarily with the clonal lineages 1, 2, and 3 (15
). Depending on the estimate of mutational rate, the common origin of ChrIa* among these lineages is estimated to be 1,000 to 10,000 years. During this time period, extensive migration and interchange between people, livestock, rodent pests, and domestic cats may have profoundly influenced the distribution and abundance of T. gondii
, as suggested previously (34
). The apparent coincidence of the fixation of ChrIa* with the origin of the major clonal lineages led to the previous hypothesis that ChrIa* may contain genes that favor clonal transmission, driving their expansion (15
). However, based on the new finding that clonal and nonclonal strains share this same version of ChrIa*, it is now apparent that the ChrIa* haplotype is associated with highly successful (i.e., abundant) strains of T. gondii
that propagate by both sexual and asexual means.
Several possible factors could account for the paucity of diversity in ChrIa compared to the genome as a whole. It is conceivable that the ChrIa* haplotype has undergone especially strong purifying selection, enabling it to persist in an unmodified form for longer than its current diversity would otherwise indicate. Although some gene(s) found there might be subject to strong functional constraint, it is difficult to conceive how substitutions could be kept from accumulating over the entirety of the chromosome. This pattern of inheritance is unlikely to be due to drug pressure, since the majority of isolates studied here came from infected animals that were not under therapeutic treatment. Moreover, prophylactic drugs are not routinely used in humans, nor is drug resistance a common trait in T. gondii
. However, it is conceivable that ChrIa* contains some element that results in segregation distortion or meiotic drive (35
), allowing it to outcompete variant versions of ChrIa in natural crosses. Among the strains that show divergent examples of ChrIa are strains isolated from humans infected in the jungles of French Guiana (groups 5 and 10). This pattern suggests that the conservation of ChrIa* may reflect an adaptation to domestic animals or transmission by domestic cats and rodents in a cycle that is associated with human activity versus a purely sylvatic cycle. Regardless of the mechanism of its maintenance, it seems likely that the ChrIa* haplotype has recently spread via meiotic recombination between different lineages in distinct geographic regions.
Because the three northern clonal lineages (i.e., 1, 2, and 3) are thought to have arisen by genetic recombination with a progenitor of type 2 that was closely related to haplogroup 12 (9
), they share large haploblocks in common that serve as a signature for recent introgression. To test for the presence of large haploblocks of type 2-specific regions within South American strains, we examined SNP hybridization patterns for contiguous stretches of clonal alleles among southern strains. Very limited evidence was found for the presence of type 2-like haploblocks in strains isolated in South America, despite the presence of a scattering of type 2-like alleles (). When this is combined with the fact that South American strains appear to be older, there is limited support for the model that ChrIa* arrived there by introgression from northern strains. In contrast, large blocks of type 3 SNPs were shared in haplogroup 9 strains, such as P89 (TgPgUs15), and many of these showed high haplotype consistency. A similar relationship is seen between haplogroup 6 strain FOU and the type 1 lineage. Although not an exact match for the respective parental strains, these patterns are consistent with a relatively recent ancestry of haplogroup 9 leading to haplogroup 3 and, separately, haplogroup 6 leading to haplogroup 1. Such relationships have been suggested previously based on limited genetic loci (10
), and this pattern is more clearly seen in the genome-wide SNP analysis provided here. Because haplogroup 9 contains the entire monomorphic ChrIa, while haplogroup 6 is a hybrid (see Fig. S3
in the supplemental material), at present the most likely scenario is that a strain related to type 9 provided the ancestral source of ChrIa* that subsequently became widespread in North America and Europe.
Our findings reveal that a larger number of major haplotypes exist for T. gondii than previously recognized and yet many of these groups show strong geographic segregation. Although we have sampled a wider range of geographic regions, there remain large regions of the world that are still not well represented by current surveys of genetic diversity. Hence, it is likely that further sampling will discover additional major haplotypes. Remarkably, among the existing 14 haplogroups, 8 share a common haplotype of ChrIa*, which lacks significant polymorphism despite extensive divergence in the rest of the genome, and an additional 5 groups share large parts of this monomorphic ChrIa. The predominance of ChrIa* is paralleled by a relatively few meiotic events in the wild that gave rise to the major lineages defined here. Although the attributes that favor strains harboring this monomorphic ChrIa* are uncertain, it is associated with highly successful lineages that propagate by both clonal and sexual transmission, suggesting it imparts a general fitness advantage. Further defining of the dominance of this monomorphic ChrIa* will be informed by more-extensive population surveys, as well as experimental crosses to test its behavior in meiosis.