Molecular ecology of Schistosoma mansoni transmission inferred from the genetic composition of larval and adult infrapopulations within intermediate and definitive hosts

Accumulation of diverse parasite genotypes within the bivalve second intermediate host of the digenean Gymnophallus sp

The complex life cycle of digenean trematodes with alternating stages of asexual multiplication and sexual reproduction can generate interesting within-host population genetic patterns. Metacercarial stages found in the second intermediate host are generally accumulated from the environment. Highly mobile second intermediate hosts can sample a broad range of cercarial genotypes and accumulate genetically diverse packets of metacercariae, but it is unclear whether the same would occur in systems where the second intermediate host is relatively immobile and cercarial dispersal is the sole mechanism that can maintain genetic homogeneity at the population level. Here, using polymorphic microsatellite markers, we addressed this issue by genotyping metacercariae of the trematode Gymnophallus sp. from the New Zealand cockle Austrovenus stutchburyi. Despite the relatively sessile nature of the second intermediate host of Gymnophallus, very high genotypic diversity of metacercariae was found within cockles, with only two cockles harbouring multiple copies of a single clonal lineage. There was no evidence of population structuring at the scale of our study, suggesting the existence of a well-mixed population. Our results indicate that (i) even relatively sessile second intermediate hosts can accumulate a high diversity of genotypes and (ii) the dispersal ability of cercariae, whether passive or not, is much greater than expected for such small and short-lived organisms. The results also support the role of the second intermediate host as an accumulator of genetic diversity in the trematode life cycle.

Multiple near-identical genotypes of Schistosoma japonicum can occur in snails and have implications for population-genetic analyses

We genotyped (using 16 or 17 microsatellite loci) numerous adult Schistosoma japonicum raised in rabbits exposed to pooled cercariae from small numbers of naturally infected snails from several localities in China. As expected, duplicate multi-locus genotypes (MLGs) were found among these worms. Additionally, many more MLGs, often near-identical, were found than snails used as sources of cercariae. Explanations for these results include (i) genotyping errors, (ii) development within each infected snail of multiple sibling miracidia and (iii) somatic mutation producing genetically varied cercariae from a single miracidium. To control for genotyping errors we re-analysed samples from many individual worms, including repeating the initial PCR. Explanations invoking the development of multiple sibling miracidia within a single snail are not likely to be correct because almost all duplicate MLGs fell within same-sex clusters in a principal coordinates analysis. We would expect both sexes to be represented in a multi-miracidium infection. In addition, we exposed several snails to infection by a single miracidium. One such snail, via an experimentally infected mouse, yielded 48 adult worms. The presence of at least nine near-identical MLGs among these worms was confirmed by re-genotyping. We regard somatic mutation as the most likely explanation for our results. The implications of multiple MLGs for population-genetic studies in S. japonicum are discussed.

An analysis of genetic diversity and inbreeding in Wuchereria bancrofti: implications for the spread and detection of drug resistance

Estimates of genetic diversity in helminth infections of humans often have to rely on genotyping (immature) parasite transmission stages instead of adult worms. Here we analyse the results of one such study investigating a single polymorphic locus (a change at position 200 of the beta-tubulin gene) in microfilariae of the lymphatic filarial parasite Wuchereria bancrofti. The presence of this genetic change has been implicated in benzimidazole resistance in parasitic nematodes of farmed ruminants. Microfilariae were obtained from patients of three West African villages, two of which were sampled prior to the introduction of mass drug administration. An individual-based stochastic model was developed showing that a wide range of allele frequencies in the adult worm populations could have generated the observed microfilarial genetic diversity. This suggests that appropriate theoretical null models are required in order to interpret studies that genotype transmission stages. Wright's hierarchical F-statistic was used to investigate the population structure in W. bancrofti microfilariae and showed significant deficiency of heterozygotes compared to the Hardy-Weinberg equilibrium; this may be partially caused by a high degree of parasite genetic differentiation between hosts. Studies seeking to quantify accurately the genetic diversity of helminth populations by analysing transmission stages should increase their sample size to account for the variability in allele frequency between different parasite life-stages. Helminth genetic differentiation between hosts and non-random mating will also increase the number of hosts (and the number of samples per host) that need to be genotyped, and could enhance the rate of spread of anthelmintic resistance.

Multiple infections by the anther smut pathogen are frequent and involve related strains

Population models of host-parasite interactions predict that when different parasite genotypes compete within a host for limited resources, those that exploit the host faster will be selected, leading to an increase in parasite virulence. When parasites sharing a host are related, however, kin selection should lead to more cooperative host exploitation that may involve slower rates of parasite reproduction. Despite their potential importance, studies that assess the prevalence of multiple genotype infections in natural populations remain rare, and studies quantifying the relatedness of parasites occurring together as natural multiple infections are particularly scarce. We investigated multiple infections in natural populations of the systemic fungal plant parasite Microbotryum violaceum, the anther smut of Caryophyllaceae, on its host, Silene latifolia. We found that multiple infections can be extremely frequent, with different fungal genotypes found in different stems of single plants. Multiple infections involved parasite genotypes more closely related than would be expected based upon their genetic diversity or due to spatial substructuring within the parasite populations. Together with previous sequential inoculation experiments, our results suggest that M. violaceum actively excludes divergent competitors while tolerating closely related genotypes. Such an exclusion mechanism might explain why multiple infections were less frequent in populations with the highest genetic diversity, which is at odds with intuitive expectations. Thus, these results demonstrate that genetic diversity can influence the prevalence of multiple infections in nature, which will have important consequences for their optimal levels of virulence. Measuring the occurrence of multiple infections and the relatedness among parasites within hosts in natural populations may be important for understanding the evolutionary dynamics of disease, the consequences of vaccine use, and forces driving the population genetic structure of parasites.

Genetic diversity and population structuring of Schistosoma mansoni in a Brazilian village

The digenean trematode Schistosoma mansoni is responsible for chronic schistosomiasis worldwide, and in Brazil alone an estimated 35 million people are at risk. To evaluate epidemiological patterns among human definitive hosts, we assessed genetic diversity and population subdivision of S. mansoni infrapopulations in human hosts from the highly endemic village of Virgem das Graças in the state of Minas Gerais, Brazil. We believe this is the largest such survey to date. Genetic diversity of parasites, measured over eight polymorphic microsatellite loci, was relatively high and standard measures of inbreeding indicated that the population was panmictic. Furthermore, there was no significant isolation-by-distance of parasite infrapopulations, and measures of population subdivision indicated significant but low to moderate levels of population differentiation. We conclude that patients within this village sample from a broad range of schistosome genetic diversity and effectively act as "genetic mixing bowls" for the parasites. These results contrast with those previously observed in the Brazilian village of Melqui ades and thus provide the opportunity for comparisons of environmental and epidemiological differences that are likely to influence host-parasite coevolution and parasite transmission.

Making the most of mitochondrial genomes--markers for phylogeny, molecular ecology and barcodes in Schistosoma (Platyhelminthes: Digenea)

An increasing number of complete sequences of mitochondrial (mt) genomes provides the opportunity to optimise the choice of molecular markers for phylogenetic and ecological studies. This is particularly the case where mt genomes from closely related taxa have been sequenced; e.g., within Schistosoma. These blood flukes include species that are the causative agents of schistosomiasis, where there has been a need to optimise markers for species and strain recognition. For many phylogenetic and population genetic studies, the choice of nucleotide sequences depends primarily on suitable PCR primers. Complete mt genomes allow individual gene or other mt markers to be assessed relative to one another for potential information content, prior to broad-scale sampling. We assess the phylogenetic utility of individual genes and identify regions that contain the greatest interspecific variation for molecular ecological and diagnostic markers. We show that variable characters are not randomly distributed along the genome and there is a positive correlation between polymorphism and divergence. The mt genomes of African and Asian schistosomes were compared with the available intraspecific dataset of Schistosoma mansoni through sliding window analyses, in order to assess whether the observed polymorphism was at a level predicted from interspecific comparisons. We found a positive correlation except for the two genes (cox1 and nad1) adjoining the putative control region in S. mansoni. The genes nad1, nad4, nad5, cox1 and cox3 resolved phylogenies that were consistent with a benchmark phylogeny and in general, longer genes performed better in phylogenetic reconstruction. Considering the information content of entire mt genome sequences, partial cox1 would not be the ideal marker for either species identification (barcoding) or population studies with Schistosoma species. Instead, we suggest the use of cox3 and nad5 for both phylogenetic and population studies. Five primer pairs designed against Schistosoma mekongi and Schistosoma malayensis were tested successfully against Schistosoma japonicum. In combination, these fragments encompass 20-27% of the variation amongst the genomes (average total length approximately 14,000bp), thus providing an efficient means of encapsulating the greatest amount of variation within the shortest sequence. Comparative mitogenomics provides the basis of a rational approach to molecular marker selection and optimisation.

Clonal diversity of the marine trematode Maritrema novaezealandensis within intermediate hosts: the molecular ecology of parasite life cycles

We quantified the clonal diversity of the New Zealand marine trematode Maritrema novaezealandensis (n = 1250) within Zeacumantus subcarinatus snail (n = 25) and Macrophthalmus hirtipes crab (n = 25) intermediate hosts using four to six microsatellite loci, and investigated the potential biological and physical factors responsible for the observed genetic patterns. Individual snails harboured one to five trematode genotypes and 48% of snails were infected by multiple parasite genotypes. Overall, the number of parasite genotypes did not increase with snail size, but was highest in intermediate-sized snails. Significantly larger numbers of parasite genotypes were detected in crabs (relative to snails; P < 0.001), with 16-25 genotypes recovered from individual crabs. Although crabs are typically infected by small numbers of cercariae sourced from many snails, they are occasionally infected by large numbers of cercariae sourced from single snails. The latter cases explain the significant genetic differentiation of trematode populations detected among their crab hosts (F(ST) = 0.009, P < 0.001). Our results suggest that the timing of infection and/or intraspecific competition among parasite clones within snails determine(s) the diversity of parasite clones that snails harbour. The presence of a large number of infected snails and tidal mixing of cercariae prior to infection results in crabs potentially harbouring hundreds of parasite genotypes despite the crabs' territorial behaviour.

Genetic filtering and optimal sampling of Schistosoma mansoni populations

Allelic variation in 6 microsatellite markers was compared between frozen Schistosoma mansoni eggs and laboratory-passaged worms originating from the same 5 fecal samples obtained from Brazilian residents. Based on allelic richness values, the number of alleles detected per locus did not differ between egg and worm DNA templates. However, our ability to score loci differed between these DNA templates, with worms providing more scored loci per individual than eggs. Differences also existed between the worms and eggs in the identity of the specific alleles that were detected. Additionally, we observed a reduction in homozygous genotypes among laboratory-passaged worms relative to the eggs. Allelic diversity curves were calculated by genotyping all worms from a representative host sample to determine the relationship between the number of alleles detected at a locus and the number of worms genotyped. Curves for the 5 residents' worm infrapopulations for each of the loci were very similar. The equation y=19.55 x ln(x) + 9.992 explained the association between sampling effort (x) and number of alleles detected (y) with an R(2) of 0.775. In conclusion, egg DNA templates and allelic diversity curves can benefit efforts to discern the sociological, ecological and evolutionary forces impacting the genetic diversity and disease epidemiology of human schistosomes.

Speciation in parasites: a population genetics approach

Parasite speciation and host-parasite coevolution should be studied at both macroevolutionary and microevolutionary levels. Studies on a macroevolutionary scale provide an essential framework for understanding the origins of parasite lineages and the patterns of diversification. However, because coevolutionary interactions can be highly divergent across time and space, it is important to quantify and compare the phylogeographic variation in both the host and the parasite throughout their geographical range. Furthermore, to evaluate demographic parameters that are relevant to population genetics structure, such as effective population size and parasite transmission, parasite populations must be studied using neutral genetic markers. Previous emphasis on larger-scale studies means that the connection between microevolutionary and macroevolutionary events is poorly explored. In this article, we focus on the spatial fragmentation of parasites and the population genetics processes behind their diversification in an effort to bridge the micro- and macro-scales.

Snail odour-clouds: spreading and contribution to the transmission success of Trichobilharzia ocellata (Trematoda, Digenea) miracidia

Chemical communication among freshwater organisms is an adaptation to improve their coexistence. Here,we focus on the chemical cues secreted by the freshwater gastropod Lymnaea stagnalis, which are known to stimulate behavioural responses of Trichobilharzia ocellata (Plathelminthes, Digenea, Trematoda) miracidia. Such responses are commonly claimed to influence transmission positively, but in response to chemical cues miracidia randomly change their swimming direction. This kind of response does not necessarily increase transmission, because miracidia may be trapped at the periphery of very large snail odour-clouds, which may prevent them from approaching the snail. On the other hand, the odour clouds may be too small to improve host-localisation. To shed light on these scenarios, the spreading of molecules released around L. stagnalis (active space) was visualised by recording host-finding responses of T. ocellata miracidia when they approached snails. Behavioural responses of miracidia indicated the spreading of compounds forming an attractive active space only around the host-snail L. stagnalis, but not around sympatric non-host-snail species. The active space increased approximately linearly with the time the snail rested at the same spot and within 5 min it reached a volume of more than 30 times that of the snail. We also demonstrated in a large-scale experiment, that the active space of L. stagnalis significantly increases the transmission success of T. ocellata miracidia. Additionally, the microhabitat selection of T. ocellata miracidia was studied, demonstrating that peripheral locations near the water surface were preferred, which are also preferred sites of L. stagnalis. Improved chemoperception and microhabitat selection may have been a consequence of coevolution with snails and benefited miracidia, which became efficient transmissive stages.

How a complex life cycle can improve a parasite's sex life

How complex life cycles of parasites are maintained is still a fascinating and unresolved topic. Complex life cycles using three host species, free-living stages, asexual and sexual reproduction are widespread in parasitic helminths. For such life cycles, we propose here that maintaining a second intermediate host in the life cycle can be advantageous for the individual parasite to increase the intermixture of different clones and therefore decrease the risk of matings between genetically identical individuals in the definitive host. Using microsatellite markers, we show that clone mixing occurs from the first to the second intermediate host in natural populations of the eye-fluke Diplostomum pseudospathaceum. Most individuals released by the first intermediate host belonged to one clone. In contrast, the second intermediate host was infected with a diverse array of mostly unique parasite genotypes. The proposed advantage of increased parasite clone intermixture may be a novel selection pressure favouring the maintenance of complex life cycles.

Population genetics of multi-host parasites – the case for molecular epidemiological studies of Schistosoma japonicum using larval stages from naturally infected hosts

Population genetics of multi-host pathogens offers great potential for the understanding of their complex epidemiology but care must be taken to ensure that the sampling procedure does not bias estimates of population indices. The transfer of material to laboratory passage, in particular, runs the risk of bottlenecking and imposing non-random host-induced selection pressures according to the hosts used in passage. We present a novel technique allowing single-locus microsatellite genotyping of the naturally sampled larval stages, enabling unbiased population genetic studies of the multi-host zoonotic parasite Schistosoma japonicum. The utility of these larval genotyping methods for molecular epidemiological studies are illustrated in results from 3 separate data sets. In the first data set, potential loss of alleles based on the definitive host species used for laboratory maintenance was identified by comparing adult worm populations derived from mice and rabbits infected with cercarial populations originating from the same set of snails. In the second data set, bottlenecking was demonstrated by the loss of alleles in adult worms derived within a single generation of laboratory maintenance compared to their parent field-collected cercarial samples. In the final data set, comparison of miracidia and adult worms recovered from naturally infected animals demonstrated that larval analyses can provide stage-specific epidemiological information and that population genetics of schistosomes can be well described by analysis of larval stages. Our results thus advocate the use of natural life-cycle stages to obtain an accurate and ethical representation of the population genetic structure of S. japonicum and other multi-host pathogens.

Molecular ecology of parasites: elucidating ecological and microevolutionary processes

We review studies that have used molecular markers to address ecological and microevolutionary processes in parasites. Our goal is to highlight areas of research that may be of particular interest in relation to the parasitic lifestyle, and to draw attention to areas that require additional study. Topics include species identification, phylogeography, host specificity and speciation, population genetic structure, modes of reproduction and transmission patterns, and searching for loci under selection.

F-statistics under alternation of sexual and asexual reproduction: a model and data from schistosomes (platyhelminth parasites)

Accurate inferences on population genetics data require a sound underlying theoretical null model. Nearly nothing is known about the gene dynamics of organisms with complex life cycles precluding any biological interpretation of population genetics parameters. In this article, we used an infinite island model to derive the expectations of those parameters for the life cycle of a dioecious organism obligatorily alternating sexual and asexual reproductions as it is the case for schistosomes (plathyhelminth parasites). This model allowed us to investigate the effects of the degree of mixing among individuals coming from different subpopulations at each new generation (represented in the model by the migration rates before and after clonal reproductions) and the variance in the reproductive success of individuals during the clonal phase. We also consider the effects of different migration rates and degrees of clonal reproductive skew between male and female individuals. Results show that the variance in the reproductive success of clones is very important in shaping the distribution of the genetic variability both within and among subpopulations. Thus, higher variance in the reproductive success of clones generates heterozygous excesses within subpopulations and also increases genetic differentiation between them. Migration occurring before and after asexual reproduction has different effects on the patterns of F(IS) and F(ST). When males and females display different degrees of reproductive skew or migration rates, we observe differences in their respective population genetic structure. While results of the model apply to any organism alternating sexual and clonal reproductions (e.g. all parasitic trematodes, many plants, and all aphididae), we finally confront some of these theoretical expectations to empirical data from Schistosoma mansoni infecting Rattus rattus in Guadeloupe.

Population genetics of complex life-cycle parasites: an illustration with trematodes

Accurate inferences on population genetics data require a sound underlying theoretical null model. Organisms alternating sexual and asexual reproduction during their life-cycle have been largely neglected in theoretical population genetic models, thus limiting the biological interpretation of population genetics parameters measured in natural populations. In this article, we derive the expectations of those parameters for the life-cycle of monoecious trematodes, a group comprising several important human and livestock parasites that obligatorily alternate sexual and asexual reproduction during their life-cycle. We model how migration rates between hosts, sexual and asexual mutation rates, adult selfing rate and the variance in reproductive success of parasites during the clonal phase affect the amount of neutral genetic diversity of the parasite (effective population size) and its apportionment within and between definitive hosts (using F-statistics). We demonstrate, in particular, that variance in reproductive success of clones, a parameter that has been completely overlooked in previous population genetics models, is very important in shaping the distribution of the genetic variability both within and among definitive hosts. Within definitive hosts, the parameter F(IS) (a measure of the deviation from random mating) is decreased by high variance in clonal reproductive success of larvae but increased by high adult self-fertilisation rates. Both clonal multiplication and selfing have similar effects on between-host genetic differentiation (F(ST)). Migration occurring before and after asexual reproduction can have different effects on the patterns of F(IS), depending on values of the other parameters such as the mutation rate. While the model applies to any hermaphroditic organism alternating sexual and clonal reproduction (e.g. many plants), the results are specifically discussed in the light of the limited population genetic data on monoecious trematodes available to date and their previous interpretation. We hope that our model will encourage more empirical population genetics studies on monoecious trematodes and other organisms with similar life-cycles.