Charles D. Criscione

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.

LIFE CYCLES SHAPE PARASITE EVOLUTION: COMPARATIVE POPULATION GENETICS OF SALMON TREMATODES

Abstract Little is known about what controls effective sizes and migration rates among parasite populations. Such data are important given the medical, veterinary, and economic (e.g., fisheries) impacts of many parasites. The autogenic‐allogenic hypothesis, which describes ecological patterns of parasite distribution, provided the foundation on which we studied the effects of life cycles on the distribution of genetic variation within and among parasite populations. The hypothesis states that parasites cycling only in freshwater hosts (autogenic life cycle) will be more limited in their dispersal ability among aquatic habitats than parasites cycling through freshwater and terrestrial hosts (allogenic life cycle). By extending this hypothesis to the level of intraspecific genetic variation, we examined the effects of host dispersal on parasite gene flow. Our a priori prediction was that for a given geographic range, autogenic parasites would have lower gene flow among subpopulations. We compared intraspecific mitochondrial DNA variation for three described species of trematodes that infect salmonid fishes. As predicted, autogenic species had much more highly structured populations and much lower gene flow among subpopulations than an allogenic species sampled from the same locations. In addition, a cryptic species was identified for one of the autogenic trematodes. These results show how variation in life cycles can shape parasite evolution by predisposing them to vastly different genetic structures. Thus, we propose that knowledge of parasite life cycles will help predict important evolutionary processes such as speciation, coevolution, and the spread of drug resistance.

A comparison between mitochondrial DNA and the ribosomal internal transcribed regions in prospecting for cryptic species of platyhelminth parasites

We examined the relative merits of mitochondrial DNA loci and ribosomal DNA internal transcribed spacers for their use in prospecting for cryptic species of platyhelminth parasites. Sequence divergence at ITS1 and ITS2 was compared with divergence at 2 mtDNA loci (NADH dehydrogenase-1 and cytochrome c oxidase I) between closely related species of trematodes and cestodes. Both spacers accumulated substitutions substantially more slowly than mtDNA, which clearly shows a higher level of divergence among species relative to intra-specific variation. Besides a slow rate of substitution, other caveats that may be encountered when using ITS sequences as a prospecting marker are discussed. In particular, we note recent studies that suggest the existence of substantial levels of intra-individual variation in ITS sequences of flatworms. Because it is likely that closely related species share this phenomenon, it may confound the detection of cryptic species, especially if small sample sizes are studied. Although potential limitations of mtDNA are also recognized, the higher rate of evolution and smaller effective population size of this marker increases the probability of detecting diagnostic characters between cryptic species.

Disentangling hybridization and host colonization in parasitic roundworms of humans and pigs

Knowledge of cross-transmission and hybridization between parasites of humans and reservoir hosts is critical for understanding the evolution of the parasite and for implementing control programmes. There is now a consensus that populations of pig and human Ascaris (roundworms) show significant genetic subdivision. However, it is unclear whether this has resulted from a single or multiple host shift(s). Furthermore, previous molecular data have not been sufficient to determine whether sympatric populations of human and pig Ascaris can exchange genes. To disentangle patterns of host colonization and hybridization, we used 23 microsatellite loci to conduct Bayesian clustering analyses of individual worms collected from pigs and humans. We observed strong differentiation between populations which was primarily driven by geography, with secondary differentiation resulting from host affiliation within locations. This pattern is consistent with multiple host colonization events. However, there is low support for the short internal branches of the dendrograms. In part, the relationships among clusters may result from current hybridization among sympatric human and pig roundworms. Indeed, congruence in three Bayesian methods indicated that 4 and 7% of roundworms sampled from Guatemala and China, respectively, were hybrids. These results indicate that there is contemporary cross-transmission between populations of human and pig Ascaris.

PARASITE GENOTYPES IDENTIFY SOURCE POPULATIONS OF MIGRATORY FISH MORE ACCURATELY THAN FISH GENOTYPES

DNA-based assignment of individuals to their population of origin has many applications such as mixed-stock analysis, identifying individuals from protected populations, and elucidating migration patterns. However, low genetic differentiation among populations will cause misassignments. Thus, an alternative means of determining an individuals population of origin is needed in cases where there is little or no neutral differentiation among source populations. Here, we test the hypothesis that parasite genotypes can be used to identify the origins of hosts more accurately than host genotypes. Using microsatellite markers from steelhead trout and their trematode parasites, we show that the odds of correct assignment are four times greater with the parasites genotypes than with the hosts genotypes. Our analyses show that this result is simply explained by the greater genetic structure among populations of the trematode parasite. Recent studies on the comparative genetic structure of other host and parasite species suggest that our results are not unusual or unique to the host-parasite system we studied. Thus, our work indicates that parasites will be useful for a wide range of applied and basic research that requires the assignment of individuals to source populations.

Genomic linkage map of the human blood fluke Schistosoma mansoni

BackgroundSchistosoma mansoni is a blood fluke that infects approximately 90 million people. The complete life cycle of this parasite can be maintained in the laboratory, making this one of the few experimentally tractable human helminth infections, and a rich literature reveals heritable variation in important biomedical traits such as virulence, host-specificity, transmission and drug resistance. However, there is a current lack of tools needed to study S. mansonis molecular, quantitative, and population genetics. Our goal was to construct a genetic linkage map for S. mansoni, and thus provide a new resource that will help stimulate research on this neglected pathogen.ResultsWe genotyped grandparents, parents and 88 progeny to construct a 5.6 cM linkage map containing 243 microsatellites positioned on 203 of the largest scaffolds in the genome sequence. The map allows 70% of the estimated 300 Mb genome to be ordered on chromosomes, and highlights where scaffolds have been incorrectly assembled. The markers fall into eight main linkage groups, consistent with seven pairs of autosomes and one pair of sex chromosomes, and we were able to anchor linkage groups to chromosomes using fluorescent in situ hybridization. The genome measures 1,228.6 cM. Marker segregation reveals higher female recombination, confirms ZW inheritance patterns, and identifies recombination hotspots and regions of segregation distortion.ConclusionsThe genetic linkage map presented here is the first for S. mansoni and the first for a species in the phylum Platyhelminthes. The map provides the critical tool necessary for quantitative genetic analysis, aids genome assembly, and furnishes a framework for comparative flatworm genomics and field-based molecular epidemiological studies.

MINIMAL SELFING, FEW CLONES, AND NO AMONG-HOST GENETIC STRUCTURE IN A HERMAPHRODITIC PARASITE WITH ASEXUAL LARVAL PROPAGATION

Abstract Little is known about actual mating systems in natural populations of parasites or about what constitutes the limits of a parasite deme. These parameters are interesting because they affect levels of genetic diversity, opportunities for local adaptation, and other evolutionary processes. We expect that transmission dynamics and the distribution of parasites among hosts should have a large effect on mating systems and demic structure, but currently we have mostly speculation and very few data. For example, infrapopulations (all the parasites in a single host) should behave as demes if parasite offspring are transmitted as a clump from host to host over several generations. However, if offspring are well mixed, then the parasite component population (all the parasites among a host population) would function as the deme. Similarly, low mean intensities or a high proportion of worms in single infections should increase the selfing rate. For species having an asexual amplification stage, transmission between intermediate and definitive (final) hosts will control the variance in clonal reproductive success, which in turn could have a large influence on effective sizes and rates of inbreeding. We examined demic structure, selfing rates, and the variance in clonal reproductive success in natural populations of Plagioporus shawi, a hermaphroditic trematode that parasitizes salmon. Overall levels of genetic diversity were very high. An a posteriori inference of population structure overwhelmingly supports the component population as the deme, rather than individual infrapopulations. Only a single pair of 597 adult individuals was identified as clones. Thus, the variance in clonal reproductive success was almost zero. Despite being hermaphroditic, P. shawi appears to be almost entirely outcrossing. Genetic estimates of selfing (<5%) were in accordance with the proportion of parasites from single infections. Thus, it appears that individual flukes outcross whenever possible and only resort to selfing when alone. Finally, our data support the hypothesis that aquatic transmission and the use of several intermediate hosts promotes high genetic diversity and well‐mixed infrapopulations.

Landscape Genetics Reveals Focal Transmission of a Human Macroparasite

Macroparasite infections (e.g., helminths) remain a major human health concern. However, assessing transmission dynamics is problematic because the direct observation of macroparasite dispersal among hosts is not possible. We used a novel landscape genetics approach to examine transmission of the human roundworm Ascaris lumbricoides in a small human population in Jiri, Nepal. Unexpectedly, we found significant genetic structuring of parasites, indicating the presence of multiple transmission foci within a small sampling area (∼14 km2). We analyzed several epidemiological variables, and found that transmission is spatially autocorrelated around households and that transmission foci are stable over time despite extensive human movement. These results would not have been obtainable via a traditional epidemiological study based on worm counts alone. Our data refute the assumption that a single host population corresponds to a single parasite transmission unit, an assumption implicit in many classic models of macroparasite transmission. Newer models have shown that the metapopulation-like pattern observed in our data can adversely affect targeted control strategies aimed at community-wide impacts. Furthermore, the observed metapopulation structure and local mating patterns generate an excess of homozygotes that can accelerate the spread of recessive traits such as drug resistance. Our study illustrates how molecular analyses complement traditional epidemiological information in providing a better understanding of parasite transmission. Similar landscape genetic approaches in other macroparasite systems will be warranted if an accurate depiction of the transmission process is to be used to inform effective control strategies.

Parasite phylogeographical congruence with salmon host evolutionarily significant units: implications for salmon conservation

Comparative phylogeographical studies between parasites and their hosts or with biogeographical regions are useful to predict parasite dispersal potential over a broad geographical range. We used both microsatellite markers and mtDNA sequence data from a trematode parasite, Plagioporus shawi, to test for congruence across two evolutionarily significant unit (ESU) boundaries of its salmonid hosts (Oncorhynchus spp.). We find congruent patterns with the nuclear loci of P. shawi and the ESU boundaries of its salmonid hosts. This pattern indicates that broad‐scale phylogeographical patterns of a parasite can be predicted by the biogeographical history of their hosts. Furthermore, this pattern provides independent support for these ESU boundaries as biologically relevant barriers. The mtDNA shows some discordance with nuclear loci and a level of genetic differentiation greater than can be explained by genetic drift. Thus, the mtDNA cannot be used in isolation to infer the population history of P. shawi. The genetic differentiation at both the nuclear and mtDNA markers will be useful for salmon fisheries management by providing a tool to assign ocean‐migrating salmonids back to their freshwater population of origin.

An Infectious Topic in Reticulate Evolution: Introgression and Hybridization in Animal Parasites

Little attention has been given to the role that introgression and hybridization have played in the evolution of parasites. Most studies are host-centric and ask if the hybrid of a free-living species is more or less susceptible to parasite infection. Here we focus on what is known about how introgression and hybridization have influenced the evolution of protozoan and helminth parasites of animals. There are reports of genome or gene introgression from distantly related taxa into apicomplexans and filarial nematodes. Most common are genetic based reports of potential hybridization among congeneric taxa, but in several cases, more work is needed to definitively conclude current hybridization. In the medically important Trypanosoma it is clear that some clonal lineages are the product of past hybridization events. Similarly, strong evidence exists for current hybridization in human helminths such as Schistosoma and Ascaris. There remain topics that warrant further examination such as the potential hybrid origin of polyploid platyhelminths. Furthermore, little work has investigated the phenotype or fitness, and even less the epidemiological significance of hybrid parasites.