Selection and genetic drift of polymorphisms within the merozoite surface protein-1 gene of Plasmodium falciparum

Intragenic recombination in the merozoite surface protein-1 gene (Msp-1) of Plasmodium falciparum is a major mechanism for allelic variation among natural parasite populations. The frequency of recombination depends on the intensity of transmission in the vector mosquito. In the present study, linkage disequilibrium between polymorphic 'loci' in the 5'- and 3'-regions of Msp-1 was examined in parasite populations from Brazilian Amazon and southern Vietnam and compared with that in a Thai population previously reported. The R2 test identified clusters of linkage disequilibria between the 5'- and 3'-regions, which are different among the three populations. However, the overall strength of linkage disequilibria was stronger in Brazil, a hypoendemic area, than in Vietnam and Thailand, mesoendemic areas, suggesting that linkage disequilibrium in Msp-1 inversely correlates with the intensity of transmission. To investigate possible mechanisms for linkage disequilibrium in Msp-1, we applied the Fst index, which measures the inter-population variance in allele frequency, to 'loci' in Msp-1 among the three populations. The Fst test identified two distinct regions with respect to inter-population allele frequency in Msp-1: one for highly divergent 'loci' in the 5'-region and the other for non-divergent 'loci' in the 3'-region. These results suggest that genetic drift is not the sole mechanism for linkage disequilibrium, but selection operates on 'loci' in the 3'-region in hypo- and mesoendemic areas of malaria.     

Allelic recombination and linkage disequilibrium within Msp-1 of Plasmodium falciparum, the malignant human malaria parasite

The C-terminal, cysteine-rich 19kDa domain of merozoite surface protein-1 (MSP-1) of Plasmodium falciparum is a target of the host's humoral immunity and thus a malaria vaccine candidate. Although variation in the 19kDa domain is limited among parasite isolates, tertiary structure-dependent intramolecular associations between the 19kDa domain and other parts of MSP-1 are suggested to be involved in immune evasion by allowing competitive binding of protective and non-protective antibodies directed to their epitopes, which are conformationally in close proximity but separated at the primary structure. Since allelic recombination can account for the major variability of the Msp-1 gene, we examined whether linkage disequilibrium occurs between polymorphic loci in the 5'- and the 3'-region, the latter encoding the 19kDa domain. From 184 Thai field isolates, we selected 69 isolates with a single allelic type in six variable blocks of Msp-1 as determined by PCR-based allelic typing. All the isolates showed no evidence of recombination in blocks 6 to 16, whereas recombination was apparent in blocks 2 to 6. Sequencing of the 3'-region revealed two potential recombination sites in block 17. Strong linkage disequilibrium was seen between polymorphic loci in the 5'- and 3'-regions. The strength of this disequilibrium did not correlate with distance between loci. We discuss the possible role of epistatic selection on particular association types (haplotypes) of Msp-1.     

Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae

Previous efforts to uncover the genetic underpinnings of ongoing ecological speciation of the M and S forms of the African malaria vector Anopheles gambiae revealed two centromere‐proximal islands of genetic divergence on X and chromosome 2. Under the assumption of considerable ongoing gene flow between M and S, these persistently divergent genomic islands were widely considered to be ‘speciation islands’. In the course of microarray‐based divergence mapping, we discovered a third centromere‐associated island of divergence on chromosome 3, which was validated by targeted re‐sequencing. To test for genetic association between the divergence islands on all three chromosomes, SNP‐based assays were applied in four natural populations of M and S spanning West, Central and East Africa. Genotyping of 517 female M and S mosquitoes revealed nearly complete linkage disequilibrium between the centromeres of the three independently assorting chromosomes. These results suggest that despite the potential for inter‐form gene flow through hybridization, actual (realized) gene flow between M and S may be substantially less than commonly assumed and may not explain most shared variation. Moreover, the possibility of very low gene flow calls into question whether diverged pericentromeric regions—characterized by reduced levels of variation and recombination—are in fact instrumental rather than merely incidental to the speciation process.     

Plasmodium falciparum: differential selection of drug resistance alleles in contiguous urban and peri-urban areas of Brazzaville, Republic of Congo

The African continent is currently experiencing rapid population growth, with rising urbanization increasing the percentage of the population living in large towns and cities. We studied the impact of the degree of urbanization on the population genetics of Plasmodium falciparum in urban and peri-urban areas in and around the city of Brazzaville, Republic of Congo. This field setting, which incorporates local health centers situated in areas of varying urbanization, is of interest as it allows the characterization of malaria parasites from areas where the human, parasite, and mosquito populations are shared, but where differences in the degree of urbanization (leading to dramatic differences in transmission intensity) cause the pattern of malaria transmission to differ greatly. We have investigated how these differences in transmission intensity affect parasite genetic diversity, including the amount of genetic polymorphism in each area, the degree of linkage disequilibrium within the populations, and the prevalence and frequency of drug resistance markers. To determine parasite population structure, heterozygosity and linkage disequilibrium, we typed eight microsatellite markers and performed haplotype analysis of the msp1 gene by PCR. Mutations known to be associated with resistance to the antimalarial drugs chloroquine and pyrimethamine were determined by sequencing the relevant portions of the crt and dhfr genes, respectively. We found that parasite genetic diversity was comparable between the two sites, with high levels of polymorphism being maintained in both areas despite dramatic differences in transmission intensity. Crucially, we found that the frequencies of genetic markers of drug resistance against pyrimethamine and chloroquine differed significantly between the sites, indicative of differing selection pressures in the two areas.     

Population genetic structure and adaptation of malaria parasites on the edge of endemic distribution

To determine whether the major human malaria parasite Plasmodium falciparum exhibits fragmented population structure or local adaptation at the northern limit of its African distribution where the dry Sahel zone meets the Sahara, samples were collected from diverse locations within Mauritania over a range of ~1000 km. Microsatellite genotypes were obtained for 203 clinical infection samples from eight locations, and Illumina paired‐end sequences were obtained to yield high coverage genomewide single nucleotide polymorphism (SNP) data for 65 clinical infection samples from four locations. Most infections contained single parasite genotypes, reflecting low rates of transmission and superinfection locally, in contrast to the situation seen in population samples from countries further south. A minority of infections shared related or identical genotypes locally, indicating some repeated transmission of parasite clones without recombination. This caused some multilocus linkage disequilibrium and local divergence, but aside from the effect of repeated genotypes there was minimal differentiation between locations. Several chromosomal regions had elevated integrated haplotype scores (|iHS|) indicating recent selection, including those containing drug resistance genes. A genomewide F_ST scan comparison with previous sequence data from an area in West Africa with higher infection endemicity indicates that regional gene flow prevents genetic isolation, but revealed allele frequency differentiation at three drug resistance loci and an erythrocyte invasion ligand gene. Contrast of extended haplotype signatures revealed none to be unique to Mauritania. Discrete foci of infection on the edge of the Sahara are genetically highly connected to the wider continental parasite population, and local elimination would be difficult to achieve without very substantial reduction in malaria throughout the region.     

Allelic diversity in the merozoite surface protein 1 gene of Plasmodium falciparum on Palawan Island, the Philippines

Allelic diversity of the Plasmodium falciparum merozoite surface protein 1 gene (msp1) is mainly generated by meiotic recombination at the mosquito stage. We investigated recombination-based allelic diversity of msp1 in a P. falciparum population from Palawan Island, the Philippines, where malaria transmission is moderate. We identified the 5' recombinant types, 3' sequence types and msp1 haplotypes (unique combinations of 5' recombinant type and 3' sequence type), and compared them with those of P. falciparum from the Solomon Islands, where malaria transmission is high. The mean number of 5' recombinant types per patient in Palawan was 1.44, which is comparable to the number for the Solomon Islands (1.41). The Palawan parasite population had 15 msp1 haplotypes, whereas the Solomon Islands population had only 8 haplotypes. The Palawan population showed strong linkage disequilibrium between polymorphic blocks/sites within msp1, which is comparable to the results for the Solomon Islands. These findings support our hypothesis that the extent of allelic diversity of msp1 is determined not only by the transmission intensity but also by the number of msp1 alleles prevalent in the local parasite population and the extent of mixed-allele infections. Contribution of a high prevalence of the chloroquine (CQ)-sensitive allele of P. falciparum CQ resistance transporter (pfcrt) to the relatively high msp1 diversity in the Palawan population is discussed.     

Polymorphism at the Apical Membrane Antigen 1 Gene (AMA1) of the Malaria Parasite Plasmodium falciparum in a Vietnamese Population

The patterns of molecular evolution of the most diverse region of the apical membrane antigen 1 (AMA1) gene in Plasmodium falciparum from a Vietnamese subpopulation (Bao Loc) were investigated. Within the Bao Loc population, the sequenced gene region showed relatively high allelic and nucleotide diversity (0.985 and 0.02694, respectively). Further, the level of population recombination was substantial, resulting in a significant decay of linkage disequilibrium along the gene region. The results suggest that AMA1 is a useful genetic marker for studying the relationships between adaptation of parasite populations (to the human host immune system) and malaria epidemiology.     

Island and taxon effects in parasitism revisited: avian malaria in the Lesser Antilles

We identify and describe the distribution of 12 genetically distinct malaria parasite lineages over islands and hosts in four common passerine birds in the Lesser Antilles. Combined parasite prevalence demonstrates strong host effects, little or no island effect, and a significant host-times-island interaction, indicating independent outcomes of host-parasite infections among island populations of the same host species. Host- and/or island-specific parasite lineages do not explain these host-parasite associations; rather, individual lineages themselves demonstrate the same type of independent interactions. Unlike overall prevalence, individual parasite lineages show considerable geographic structure (i.e., island effects) as well as species effects indicating that parasite lineages are constrained in their ability to move between hosts and locations. Together, our results suggest an upper limit to the number of host individuals that malaria parasites, as a community, can infect. Within this limit, however, the relative frequency of the different lineages varies reflecting fine scale interactions between host and parasite populations. Patterns of host-parasite associations within this system suggest both historical co-evolution and ecologically dynamic and independent host-parasite interactions.     

Plasmodium vivax and Plasmodium falciparum at the Crossroads of Exchange among Islands in Vanuatu: Implications for Malaria Elimination Strategies

Understanding the transmission and movement of Plasmodium parasites is crucial for malaria elimination and prevention of resurgence. Located at the limit of malaria transmission in the Pacific, Vanuatu is an ideal candidate for elimination programs due to low endemicity and the isolated nature of its island setting. We analyzed the variation in the merozoite surface protein 1 (msp1) and the circumsporozoite protein (csp) of P. falciparum and P. vivax populations to examine the patterns of gene flow and population structures among seven sites on five islands in Vanuatu. Genetic diversity was in general higher in P. vivax than P. falciparum from the same site. In P. vivax, high genetic diversity was likely maintained by greater extent of gene flow among sites and among islands. Consistent with the different patterns of gene flow, the proportion of genetic variance found among islands was substantially higher in P. falciparum (28.81–31.23%) than in P. vivax (-0.53–3.99%). Our data suggest that the current island-by-island malaria elimination strategy in Vanuatu, while adequate for P. falciparum elimination, might need to be complemented with more centrally integrated measures to control P. vivax movement across islands.     

Clonal reproduction shapes evolution in the lizard malaria parasite Plasmodium floridense

The preponderant clonal evolution hypothesis (PCE) predicts that frequent clonal reproduction (sex between two clones) in many pathogens capable of sexual recombination results in strong linkage disequilibrium and the presence of discrete genetic subdivisions characterized by occasional gene flow. We expand on the PCE and predict that higher rates of clonal reproduction will result in: (1) morphologically cryptic species that exhibit (2) low within‐species variation and (3) recent between‐species divergence. We tested these predictions in the Caribbean lizard malaria parasite Plasmodium floridense using 63 single‐infection samples in lizards collected from across the parasite's range, and sequenced them at two mitochondrial, one apicoplast, and five nuclear genes. We identified 11 provisionally cryptic species within P. floridense, each of which exhibits low intraspecific variation and recent divergence times between species (some diverged approximately 110,000 years ago). Our results are consistent with the hypothesis that clonal reproduction can profoundly affect diversification of species capable of sexual recombination, and suggest that clonal reproduction may have led to a large number of unrecognized pathogen species. The factors that may influence the rates of clonal reproduction among pathogens are unclear, and we discuss how prevalence and virulence may relate to clonal reproduction.     

Genetic variation and the recent worldwide expansion of Plasmodium falciparum

Plasmodium falciparum, the agent of human malignant malaria, diverged from Plasmodium reichenowi, the chimpanzee parasite, about the time the human and chimpanzee lineages diverged from each other. The absence of synonymous nucleotide variation at ten loci indicates that the world populations of P. falciparum derive most recently from one single strain, or 'cenancestor,' which lived a few thousand years ago. Antigenic genes of P. falciparum (such as Csp, Msp-1, and Msp-2) exhibit numerous polymorphisms that have been estimated to be millions of years old. We have discovered in these antigenic genes short repetitive sequences that distort the alignment of alleles and account for the apparent old age of the polymorphisms. The processes of intragenic recombination that generate the repeats occur at rates about 10(-3) to 10(-2), several orders of magnitude greater than the typical mutational process of nucleotide substitutions. We conclude that the antigenic polymorphisms of P. falciparum are consistent with a recent expansion of the world populations of the parasite from a cenancestor that lived in tropical Africa a few thousand years ago.     

Protein variation in Adh and Adh-related in Drosophila pseudoobscura. Linkage disequilibrium between single nucleotide polymorphisms and protein alleles

A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.     

Linkage disequilibrium in natural populations of Trypanosoma cruzi (flagellate), the agent of Chagas' disease

We have studied linkage disequilibrium in natural populations of Trypanosoma cruzi, the agent of Chagas' disease, by analyzing (i) a set of 524 stocks from the whole geographical range of the parasite, characterized at four gene loci coding for enzymes; (ii) a subsample of 121 stocks characterized at 12 enzyme loci; and (iii) a subset of 386 stocks from six locations in Bolivia, characterized by four enzyme loci. Our results show that the linkage disequilibrium reaches the maximum possible value, given the observed allelic frequencies, for almost all the locus pairs. This result is most consistent with the hypothesis that genetic recombination is absent or very rare in T. cruzi natural populations. Partition of the linkage disequilibrium variance for the six Bolivian populations shows that both inter- and intrapopulation components are substantial and that the relationships among the components are D2IS less than D2ST, and D'2IS less than D'2ST. These inequalities are interpreted as the result of an interplay between genetic drift, rare or absent mating, and clonal selection in generating linkage disequilibrium in T. cruzi populations.     

Nonuniform recombination within the human beta-globin gene cluster.

Population genetic analysis of 15 restriction site polymorphisms demonstrates nonuniform recombination within the human beta-globin gene cluster. These DNA polymorphisms show two clusters of high nonrandom associations, one 5' and another 3' to the beta-globin structural gene, with no significant linkage disequilibrium between the two clusters. The 5'- and 3'-association clusters are 34.6 kilobases (kb) and 19.4 kb long, respectively, and are separated by 9.1 kb of DNA immediately 5' to the beta-globin gene. For each of these three DNA regions, we have observed a relationship between nonrandom associations and physical distance between the polymorphisms. However, this relationship differed for each of these regions. On the assumption that the effective population size (Ne) is 5,000-50,000, we estimate the total recombination rate to be 0.0017%-0.0002% in the 5' cluster, 0.0931%-0.0093% in the 3' cluster, and 0.2912%-0.0219% in the 9.1-kb region between them. The beta cluster thus shows nonuniformity in recombination. Moreover, the recombination rate in the 9.1-kb DNA segment is 3-30 times greater than expected and is thus a hot spot for meiotic recombination.     

DNA polymorphic patterns and haplotype arrangements of the apo A-1, apo C-III,apo A-IV gene cluster in different ethnic groups

Summary The allelic frequency of five different restriction fragment length polymorphisms (RFLPs) in the A-1, C-III, A-IV gene region has been determined in Caucasians, Negroes, Indian Asians, and Japanese. The polymorphic sites are with Taq-1 at the 5 end of the A-1 gene, with Msp-1 in the third intron of the A-1 gene, with Pst-1 in the intergenic sequence between the A-1 and C-III genes, with Sst-1 in the 3 non-coding region of the C-III gene, and with Pvu-II in the third intron of the C-III gene. The alleles identified by three of the RFLPs showed large differences in frequency amongst the races, especially between Caucasians and non-Caucasians. Alleles of the Msp-1 polymorphism and Sst-1 polymorphism, which were rare in Caucasians (frequencies 0.03 and 0.01), were more common in Japanese (frequencies 0.37 and 0.35), Indian Asians (frequencies 0.37 and 0.26), and Negroes (frequencies 0.31 and 0.31). In contrast with a Pvu-II polymorphism one allele was rare in Japanese and in Indian Asians (frequency 0.01) but more common in Caucasians (frequency 0.11). Linkage disequilibrium was evident between some of the alleles and a total of seven haplotypes were identified among the different races.     

Patterns of polymorphism and linkage disequilibrium for cystic fibrosis

Four polymorphic markers that map within 80 kb of an HTF island which is genetically very close to the cystic fibrosis locus have been identified. We have analyzed the linkage disequilibrium between each of these markers and the cystic fibrosis mutation in 89 families from four European countries, Denmark, Finland, Spain, and Great Britain. Strong linkage disequilibrium between three polymorphic sites and cystic fibrosis was observed. The markers on the J3.11 (D7S8) side of the HTF island show stronger disequilibrium than those on the met side. Linkage disequilibrium between markers and disease alters the probability that a person of a given haplotype is a carrier in some populations and helps to identify regions of a sequence that are most likely to contain the cystic fibrosis mutation.     

Mating Patterns of Plasmodium falciparum

Recent empirical data have enabled a more informed debate over the extent of clonality in Plasmodium falciparum populations. Oocyst heterozygosity data reveal that the mating structure of malaria populations varies according to the transmission intensity. This finding provides a more detailed picture of the malaria mating structure than previous conclusions, which were based on indirect measures of population mating structure, ie. linkage disequilibrium analyses. In this article, Ric Paul and Karen Day discuss aspects of the genetic structure of malaria populations as evidenced by oocyst heterozygosity and linkage disequilibrium data. They address the difficulties of performing genetic analyses of malaria parasite population structure inherent in parasite sampling, why two identical parasites are rarely observed in the field and how features of the epidemiology determine parasite population structure.     

Linkage disequilibrium between cystic fibrosis and linked DNA polymorphisms in Italian families: A collaborative study

The locus D7S23 includes a CpG-enriched methylation-free island that maps midway between the markers J3.11 and met and is genetically very close to the mutation causing cystic fibrosis (CF). We have studied the linkage disequilibrium between four polymorphic markers from this locus (KM.19, CS.7, XV-2c, and PT-3) and the CF mutation (CF) in 127 Italian families. Strong linkage disequilibrium is found between KM.19, CS.7, and CF, and weaker but significant disequilibrium is found between XV-2c, PT-3, and CF. The disequilibrium between markers and CF for the Italian population provides additional information on the origin and homogeneity of the CF defect. This panel of probes is sufficiently informative to permit accurate prenatal diagnosis of CF in most families with an affected person, and the disequilibrium also allows indirect carrier detection/exclusion in some cases.     

Sequence Diversity and Linkage Disequilibrium within the Merozoite Surface Protein-1 (Msp-1) Locus of Plasmodium falciparum: A Longitudinal Study in Brazil

ABSTRACT. The merozoite surface protein‐1 (MSP‐1) is a major vaccine candidate for the asexual blood stage of malaria. We examined both the extent of sequence diversity in block 17, the 3′end of Msp‐1 gene coding for a 19‐kDa polypeptide (MSP‐1₁₉) putatively involved in red blood cell binding, and the patterns of linkage disequilibrium between polymorphic sites throughout the Msp‐1 locus. The parasite population sample consisted of Plasmodium falciparum isolates collected between 1985 and 1998 in Rondônia. an area of hypoendemic malaria transmission in the southwestern Brazilian Amazon. Results were summarized as follows. (I) Seven block‐17 sequence variants or haplotypes were found among 130 isolates, including two new haplotypes (novel combinations of previously reported amino acid replacements), here named Brazil‐1 (E‐TSR‐F) and Brazil‐2 (Q‐TSR‐F). (2) As previously shown for other Msp‐1 polymorphisms, frequencies of block‐17 haplotypes displayed significant temporal variation. (3) Extensive linkage disequilibrium was demonstrated between neighboring dimorphic sites within block 17, as well as between polymorphisms at the 5′and 3′ends of Msp‐1 (map distance range: 3.83–4.99 kb). (4) The overall patterns of linkage disequilibrium within Msp‐1 remained stable over a period of nearly one decade, and examples of possible ‘epidemic’ expansion of parasites carrying particular Msp‐1 alleles were found in the 1980s and 1990s. These results are discussed in relation to the population biology of P. falciparum and the development of malaria vaccines based on MSP‐1.