Spatial and temporal factors affecting parasite genotypes encountered by hosts: empirical data from American dog ticks (Dermacentor variabilis) parasitising raccoons (Procyon lotor)

Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation†

Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease-mediated extinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.

Molecular approaches reveal weak sibship aggregation and a high dispersal propensity in a non-native fish parasite

Inferring parameters related to the aggregation pattern of parasites and to their dispersal propensity are important for predicting their ecological consequences and evolutionary potential. Nonetheless, it is notoriously difficult to infer these parameters from wildlife parasites given the difficulty in tracking these organisms. Molecular-based inferences constitute a promising approach that has yet rarely been applied in the wild. Here, we combined several population genetic analyses including sibship reconstruction to document the genetic structure, patterns of sibship aggregation, and the dispersal dynamics of a non-native parasite of fish, the freshwater copepod ectoparasite Tracheliastes polycolpus. We collected parasites according to a hierarchical sampling design, with the sampling of all parasites from all host individuals captured in eight sites spread along an upstream-downstream river gradient. Individual multilocus genotypes were obtained from 14 microsatellite markers, and used to assign parasites to full-sib families and to investigate the genetic structure of T. polycolpus among both hosts and sampling sites. The distribution of full-sibs obtained among the sampling sites was used to estimate individual dispersal distances within families. Our results showed that T. polycolpus sibs tend to be aggregated within sites but not within host individuals. We detected important upstream-to-downstream dispersal events of T. polycolpus between sites (modal distance: 25.4 km; 95% CI [22.9, 27.7]), becoming scarcer as the geographic distance from their family core location increases. Such a dispersal pattern likely contributes to the strong isolation-by-distance observed at the river scale. We also detected some downstream-to-upstream dispersal events (modal distance: 2.6 km; 95% CI [2.2-23.3]) that likely result from movements of infected hosts. Within each site, the dispersal of free-living infective larvae among hosts likely contributes to increasing genetic diversity on hosts, possibly fostering the evolutionary potential of T. polycolpus.

Range-wide genetic analysis of Dermacentor variabilis and its Francisella-like endosymbionts demonstrates phylogeographic concordance between both taxa

BACKGROUND

The American dog tick, Dermacentor variabilis, is an important vector of pathogens to humans, wildlife and domestic animals in North America. Although this tick species is widely distributed in the USA and Canada, knowledge of its range-wide phylogeographic patterns remains incomplete.

METHODS

We carried out a phylogenetic analysis of D. variabilis using samples collected from 26 USA states and five Canadian provinces. Tick samples (n = 1053 in total) originated from two main sources: existing archives (2000-2011), and new collections made from 2012 to 2013. We sequenced a 691 bp fragment of the cox1 gene from a subset (n = 332) of geographically diverse D. variabilis. DNA extracted from individual ticks (n = 1053) was also screened for a Francisella-like endosymbiont, using a targeted 16S rRNA sequencing approach, and important pathogens (Rickettsia spp. and Coxiella burnetii), using species-specific quantitative PCR assays.

RESULTS

Maximum parsimony analysis of cox1 sequences revealed two major groups within D. variabilis with distinct geographical distributions: one from the eastern USA/Canada (Group 1) and one from the west coast states of the USA (California and Washington; Group 2). However, genetic subdivisions within both of these two major groups were weak to moderate and not tightly correlated with geography. We found molecular signatures consistent with Francisella-like endosymbionts in 257 of the DNA extracts from the 1053 individual ticks, as well as Rickettsia spp. and Coxiella burnetii in a small number of ticks (n = 29 and 2, respectively). Phylogenetic patterns for Francisella-like endosymbionts, constructed using sequence data from the bacterial 16S rRNA locus, were similar to those for D. variabilis, with two major groups that had a nearly perfect one-to-one correlation with the two major groups within D. variabilis.

CONCLUSIONS

Our findings reveal a distinct phylogenetic split between the two major D. variabilis populations. However, high levels of genetic mixture among widely separated geographical localities occur within each of these two major groups. Furthermore, our phylogenetic analyses provide evidence of long-term tick-symbiont co-evolution. This work has implications for understanding the dispersal and evolutionary ecology of D. variabilis and associated vector-borne diseases.

Inbreeding in stochastic subdivided mating systems: the genetic consequences of host spatial structure, aggregated transmission dynamics and life history characteristics in parasite populations

Inbreeding in parasite populations can have important epidemiological and evolutionary implications. However, theoretical models have predominantly focussed on the evolution of parasite populations under strong selection or in epidemic situations, and our understanding of neutral gene dynamics in parasite populations at equilibrium has been limited to verbal arguments or conceptual models. This study focusses on how host-parasite population dynamics affects observed levels of inbreeding in a random sample of parasites from an infinite population of hosts by bridging traditional genetic and parasitological processes utilizing a backward-forward branching Markov process embedded within a flexible statistical framework, the logarithmic-poisson mixture model. My results indicate that levels of inbreeding in parasites are impacted by demographic and/or transmission dynamics (subdivided mating, aggregated transmission dynamics and host spatial structure), and that this inbreeding is poorly estimated by 'equilibrium' levels of inbreeding calculated assuming regular systems of mating. Specifically, the model reveals that at low levels of inbreeding (F ≤ 0.1), equilibrium levels of inbreeding are lower than those observed, while at high levels of inbreeding the opposite pattern occurs. The model also indicates that inbreeding could have important epidemiological implications (e.g., the spread of recessive drug resistance genes) by directly impacting the observed frequency of rare homozygotes in parasite populations. My results indicate that frequencies of rare homozygotes are affected by aggregated transmission dynamics and host spatial structure, and also that an increase in the frequency of rare homozygotes can be caused by a decrease in effective population size solely due to the presence of a subdivided breeding system.

Heterozygote deficits in cyst plant-parasitic nematodes: possible causes and consequences

Deviations of genotypic frequencies from Hardy-Weinberg equilibrium (HWE) expectations could reveal important aspects of the biology of populations. Deviations from HWE due to heterozygote deficits have been recorded for three plant-parasitic nematode species. However, it has never been determined whether the observed deficits were due (i) to the presence of null alleles, (ii) to a high level of consanguinity and/or (iii) to a Wahlund effect. The aim of the present work was, while taking into the possible confounding effect of null alleles, to disentangle consanguinity and Wahlund effect in natural populations of those three economically important cyst nematodes using microsatellite markers: Globodera pallida, G. tabacum and Heterodera schachtii, pests of potato, tobacco and sugar beet, respectively. The results show a consistent pattern of heterozygote deficiency in the three nematode species sampled at the spatial scale of the host plant. We demonstrate that the prevalence of null alleles is weak and that heterozygote deficits do not have a single origin. Our results suggested that it is restricted dispersal that leads to heterozygote deficits through both consanguinity and substructure, which effects can be linked to soil movement, cyst density, and the number of generations per year. We discuss potential implications for the durability of plant resistances that are used to protect crops against parasites in which mating between relatives occur. While consanguineous mating leads to homozygosity at all loci, including loci governing avirulence/virulence, which favours the expression of virulence when recessive, the Wahlund effect is expected to have no particular effect on the adaptation of nematodes to resistances.

Testing local-scale panmixia provides insights into the cryptic ecology, evolution, and epidemiology of metazoan animal parasites

When every individual has an equal chance of mating with other individuals, the population is classified as panmictic. Amongst metazoan parasites of animals, local-scale panmixia can be disrupted due to not only non-random mating, but also non-random transmission among individual hosts of a single host population or non-random transmission among sympatric host species. Population genetics theory and analyses can be used to test the null hypothesis of panmixia and thus, allow one to draw inferences about parasite population dynamics that are difficult to observe directly. We provide an outline that addresses 3 tiered questions when testing parasite panmixia on local scales: is there greater than 1 parasite population/species, is there genetic subdivision amongst infrapopulations within a host population, and is there asexual reproduction or a non-random mating system? In this review, we highlight the evolutionary significance of non-panmixia on local scales and the genetic patterns that have been used to identify the different factors that may cause or explain deviations from panmixia on a local scale. We also discuss how tests of local-scale panmixia can provide a means to infer parasite population dynamics and epidemiology of medically relevant parasites.

Multiple paternity in the American dog tick, Dermacentor variabilis (Acari: Ixodidae)

The reproductive strategies and variation in reproductive success of ticks are poorly understood. We determined variation in multiple paternity in the American dog tick Dermancentor variabilis . In total, 48 blood-engorged female ticks and 22 male companion ticks were collected from 13 raccoon ( Procyon lotor ) hosts. In the laboratory, 56.3% of blood-engorged females laid eggs, of which 37.0% hatched or showed signs of development. We examined the presence of multiple paternity in the ensuing clutches by genotyping groups of eggs and larvae at 5 microsatellite loci and subtracting the known maternal alleles, thereby identifying male-contributed alleles. Seventy-five percent of the clutches presented multiple paternity, with a mode of 2 fathers siring the clutch. Males associated with the females on the host always sired some offspring. In 1 case, a male was the sire of clutches derived from 2 females, indicating both polygyny and polyandry may occur for this species. These results, combined with those of several other recent studies, suggest that multiple paternity might be frequent for ixodid ticks.

Heterozygote deficiencies in parasite populations: an evaluation of interrelated hypotheses in the raccoon tick, Ixodes texanus

Population genetics is increasingly being used to study the biology of parasites at the scales of both the host (infrapopulation, IP) and host population (component population, CP). In this study we tested three mechanistic hypotheses that could explain deviations from Hardy-Weinberg equilibrium (HWE) expectations due to heterozygote deficits (HDs) at the CP scale in raccoon ticks (Ixodes texanus; n=718) collected from raccoons (Procyon lotor; n=91) and genotyped at 11 microsatellite loci. These hypotheses were presence of technical issues (for example, null alleles), hierarchical structure (for example, host demography) and cryptic structure (for example, kin structure). Although statistical support for null alleles existed, their presence would also be expected to lead to an underestimation in levels of relatedness, and thus kin structure. However, we found the opposite pattern: significant HD at the IP scale being more likely in CPs with significant vs non-significant levels of kin structure. Our analyses revealed that pooling of kin groups could lead to highly variable levels of F(IS) among loci, a pattern usually suggestive of null alleles. We used Monte-Carlo (MC) simulations to show that the existence of subdivided breeding groups and high variance in individual reproductive success could adequately explain deviations from HWE in I. texanus. Thus, our results indicate that biological factors can lead to patterns that have usually been interpreted as technical issues (for example, null alleles), and that it is important to take such factors into consideration because loci deviating from HWE likely reflect the effects of real biological processes.