Yersinia pestis Survival and Replication in Potential Ameba Reservoir.

Plague ecology is characterized by sporadic epizootics, then periods of dormancy. Building evidence suggests environmentally ubiquitous amebae act as feral macrophages and hosts to many intracellular pathogens. We conducted environmental genetic surveys and laboratory co-culture infection experiments to assess whether plague bacteria were resistant to digestion by 5 environmental ameba species. First, we demonstrated that Yersinia pestis is resistant or transiently resistant to various ameba species. Second, we showed that Y. pestis survives and replicates intracellularly within Dictyostelium discoideum amebae for ˃48 hours postinfection, whereas control bacteria were destroyed in <1 hour. Finally, we found that Y. pestis resides within ameba structures synonymous with those found in infected human macrophages, for which Y. pestis is a competent pathogen. Evidence supporting amebae as potential plague reservoirs stresses the importance of recognizing pathogen-harboring amebae as threats to public health, agriculture, conservation, and biodefense.

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions.

Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.

Ecological Traits Driving the Outbreaks and Emergence of Zoonotic Pathogens.

Infectious diseases that are transmitted from wildlife hosts to humans, such as the Ebola virus and MERS virus, can be difficult to understand because the pathogens emerge from complex multifaceted ecological interactions. We use a wildlife-pathogen system-prairie dogs (Cynomys ludovicianus) and the plague bacterium (Yersinia pestis)-to describe aspects of disease ecology that apply to many cases of emerging infectious disease. We show that the monitoring and surveillance of hosts and vectors during the buildup to disease outbreaks are crucial for understanding pathogen-transmission dynamics and that a community-ecology framework is important to identify reservoir hosts. Incorporating multidisciplinary approaches and frameworks may improve wildlife-pathogen surveillance and our understanding of seemingly sporadic and rare pathogen outbreaks.

Genetic basis of differences in myxospore count between whirling disease-resistant and susceptible strains of rainbow trout.

We used a quantitative genetics approach and estimated broad sense heritability (h2b) of myxospore count and the number of genes involved in myxospore formation to gain a better understanding of how resistance to Myxobolus cerebralis, the parasite responsible for whirling disease, is inherited in rainbow trout Oncorhynchus mykiss. An M. cerebralis-resistant strain of rainbow trout, the German Rainbow (GR), and a wild, susceptible strain of rainbow trout, the Colorado River Rainbow (CRR), were spawned to create 3 intermediate crossed populations (an F1 cross, F2 intercross, and a B2 backcross between the F1 and the CRR). Within each strain or cross, h2b was estimated from the between-family variance of myxospore counts using full-sibling families. Estimates of h2b and average myxospore counts were lowest in the GR strain, F1 cross, and F2 intercross (h2b = 0.34, 0.42, and 0.34; myxospores fish-1 = 275, 9566, and 45780, respectively), and highest in the B2 backcross and CRR strain (h2b = 0.93 and 0.89; myxospores fish-1 = 97865 and 187595, respectively). Comparison of means and a joint-scaling test suggest that resistance alleles arising from the GR strain are dominant to susceptible alleles from the CRR strain. Resistance was retained in the intermediate crosses but decreased as filial generation number increased (F2) or backcrossing occurred (B2). The estimated number of segregating loci responsible for differences in myxospore count in the parental strains was 9 ± 5. Our results indicate that resistance to M. cerebralis is a heritable trait within these populations and would respond to either artificial selection in hatcheries or natural selection in the wild.

From outbreaks to endemic disease.

Relief from the effects of epidemics may signal the start of low-level disease persistence.

Phylogeny and biogeography of the eastern Asian-North American disjunct wild-rice genus (Zizania L., Poaceae).

The wild-rice genus Zizania includes four species disjunctly distributed in eastern Asia and North America, with three species (Z. aquatica, Z. palustris, and Z. texana) in North America and one (Z. latifolia) in eastern Asia. The phylogeny of Zizania was constructed using sequences of seven DNA fragments (atpB-rbcL, matK, rps16, trnL-F, trnH-psbA, nad1, and Adh1a) from chloroplast, mitochondrial, and nuclear genomes. Zizania is shown to be monophyletic with the North American species forming a clade and the eastern Asian Z. latifolia sister to the North American clade. The divergence between the eastern Asian Z. latifolia and the North American clade was dated to be 3.74 (95% HPD: 1.04-7.23) million years ago (mya) using the Bayesian dating method with the combined atpB-rbcL, matK, rps16, trnL-F, and nad1 data. Biogeographic analyses using a likelihood method suggest the North American origin of Zizania and its migration into eastern Asia via the Bering land bridge. Among the three North American species, the organellar data and the haplotype network of the nuclear Adh1a gene show a close relationship between Z. palustris and the narrowly distributed endangered species Z. texana. Bayesian dating estimated the divergence of North American Zizania to be 0.71 (95% HPD: 0.12-1.54) mya in the Pleistocene. The non-monophyly of Z. palustris and Z. aquatica in the organellar and nuclear data is most likely caused by incomplete lineage sorting, yet low-frequency unidirectional introgression of Z. palustris into Z. aquatica is present in the nuclear data as well.

Ecological Fallacy and Aggregated Data: A Case Study of Fried Chicken Restaurants, Obesity and Lyme Disease.

Interdisciplinary approaches are merited when attempting to understand the complex and idiosyncratic processes driving the spillover of pathogens from wildlife and vector species to human populations. Public health data are often available for zoonotic pathogens but can lead to erroneous conclusions if the data have been spatially or temporally aggregated. As an illustration, we use human Lyme disease incidence data as a case study to examine correlations between mammalian biodiversity, fried chicken restaurants and obesity rates on human disease incidence. We demonstrate that Lyme disease incidence is negatively correlated with mammalian biodiversity, the abundance of fried chicken restaurants and obesity rates. We argue, however, that these correlations are spurious, representing both an 'ecologic fallacy' and Simpson's paradox, and are generated by the use of aggregated data. We argue that correlations based on aggregated data across large spatial scales must be rigorously examined before being invoked as proof of disease ecology theory or as a rationale for public health policy.

Estimating abundance using mark-resight when sampling is with replacement or the number of marked individuals is unknown.

Although mark-resight methods can often be a less expensive and less invasive means for estimating abundance in long-term population monitoring programs, two major limitations of the estimators are that they typically require sampling without replacement and/or the number of marked individuals available for resighting to be known exactly. These requirements can often be difficult to achieve. Here we address these limitations by introducing the Poisson log and zero-truncated Poisson log-normal mixed effects models (PNE and ZPNE, respectively). The generalized framework of the models allow the efficient use of covariates in modeling resighting rate and individual heterogeneity parameters, information-theoretic model selection and multimodel inference, and the incorporation of individually unidentified marks. Both models may be implemented using standard statistical computing software, but they have also been added to the mark-recapture freeware package Program MARK. We demonstrate the use and advantages of (Z)PNE using black-tailed prairie dog data recently collected in Colorado. We also investigate the expected relative performance of the models in simulation experiments. Compared to other available estimators, we generally found (Z)PNE to be more precise with little or no loss in confidence interval coverage. With the recent introduction of the logit-normal mixed effects model and (Z)PNE, a more flexible and efficient framework for mark-resight abundance estimation is now available for the sampling conditions most commonly encountered in these studies.

Evidence for the involvement of an alternate rodent host in the dynamics of introduced plague in prairie dogs.

1. The introduction of plague to North America is a significant threat to colonies of prairie dogs (Cynomys ludovicianus), a species of conservation concern in the Great Plains. Other small rodents are exposed to the causative agent, Yersinia pestis, during or after epizootics; yet, its effect on these rodents is not known, and their role in transmitting and maintaining plague in the absence of prairie dogs remains unclear. 2. We live-trapped small rodents and collected their fleas on 11 colonies before, during and after plague epizootics in Colorado, USA, from 2004 to 2006. Molecular genetic (polymerase chain reaction) assays were used to identify Y. pestis in fleas. 3. Abundance of northern grasshopper mice (Onychomys leucogaster) was low on sites following epizootics in 2004, and declined markedly following plague onset on other colonies in 2005. These changes coincided with exposure of grasshopper mice to plague, and with periods when mice became infested with large numbers of prairie dog fleas (Oropsylla hirsuta), including some that were infected with Y. pestis. Additionally, several Pleochaetis exilis, fleas restricted to grasshopper mice and never found on prairie dogs on our site, were polymerase chain reaction-positive for Y. pestis, indicating that grasshopper mice can infect their own fleas. No changes in abundance of other rodent species could be attributed to plague, and no other rodents hosted O. hirsuta during epizootics, or harboured Y. pestis-infected fleas. 4. In spring 2004, grasshopper mice were most numerous in colonies that suffered plague the following year, and the pattern of colony extinctions over a 12-year period mirrored patterns of grasshopper mouse abundance in our study area, suggesting that colonies with high densities of grasshopper mice may be more susceptible to outbreaks. We speculate that grasshopper mice help spread Y. pestis during epizootics through their ability to survive infection, harbour prairie dog fleas and, during their wide-ranging movements, transport infected fleas among burrows, which functionally connects prairie dog coteries that would otherwise be socially distinct.

Oropsylla hirsuta (Siphonaptera: Ceratophyllidae) can support plague epizootics in black-tailed prairie dogs (Cynomys ludovicianus) by early-phase transmission of Yersinia pestis.

Plague, caused by the bacterium Yersinia pestis, often leads to rapid decimation of black-tailed prairie dog colonies. Flea-borne transmission of Y. pestis has been thought to occur primarily via blocked fleas, and therefore studies of vector efficiency have focused on the period when blockage is expected to occur (> or =5 days post-infection [p.i.]). Oropsylla hirsuta, a prairie dog flea, rarely blocks and transmission is inefficient > or =5 days p.i.; thus, this flea has been considered incapable of explaining rapid dissemination of Y. pestis among prairie dogs. By infecting wild-caught fleas with Y. pestis and exposing naïve mice to groups of fleas at 24, 48, 72, and 96 h p.i., we examined the early-phase (1-4 days p.i.) efficiency of O. hirsuta to transmit Y. pestis to hosts and showed that O. hirsuta is a considerably more efficient vector at this largely overlooked stage (5.19% of fleas transmit Y. pestis at 24 h p.i.) than at later stages. Using a model of vectorial capacity, we suggest that this level of transmission can support plague at an enzootic level in a population when flea loads are within the average observed for black-tailed prairie dogs in nature. Shared burrows and sociality of prairie dogs could lead to accumulation of fleas when host population is reduced as a result of the disease, enabling epizootic spread of plague among prairie dogs.

Analysis of the sensitivity properties of a model of vector-borne bubonic plague.

Model sensitivity is a key to evaluation of mathematical models in ecology and evolution, especially in complex models with numerous parameters. In this paper, we use some recently developed methods for sensitivity analysis to study the parameter sensitivity of a model of vector-borne bubonic plague in a rodent population proposed by Keeling & Gilligan. The new sensitivity tools are based on a variational analysis involving the adjoint equation. The new approach provides a relatively inexpensive way to obtain derivative information about model output with respect to parameters. We use this approach to determine the sensitivity of a quantity of interest (the force of infection from rats and their fleas to humans) to various model parameters, determine a region over which linearization at a specific parameter reference point is valid, develop a global picture of the output surface, and search for maxima and minima in a given region in the parameter space.

Exposure of small rodents to plague during epizootics in black-tailed prairie dogs.

Plague, caused by the bacterium Yersinia pestis, causes die-offs of colonies of prairie dogs (Cynomys ludovicianus). It has been argued that other small rodents are reservoirs for plague, spreading disease during epizootics and maintaining the pathogen in the absence of prairie dogs; yet there is little empirical support for distinct enzootic and epizootic cycles. Between 2004 and 2006, we collected blood from small rodents captured in colonies in northern Colorado before, during, and for up to 2 yr after prairie dog epizootics. We screened 1,603 blood samples for antibodies to Y. pestis, using passive hemagglutination and inhibition tests, and for a subset of samples we cultured blood for the bacterium itself. Of the four species of rodents that were common in colonies, the northern grasshopper mouse (Onychomys leucogaster) was the only species with consistent evidence of plague infection during epizootics, with 11.1-23.1% of mice seropositive for antibody to Y. pestis during these events. Seropositive grasshopper mice, thirteen-lined ground squirrels (Spermophilus tridecemlineatus), and deer mice (Peromyscus maniculatus) were captured the year following epizootics. The appearance of antibodies to Y. pestis in grasshopper mice coincided with periods of high prairie dog mortality; subsequently, antibody prevalence rates declined, with no seropositive individuals captured 2 yr after epizootics. We did not detect plague in any rodents off of colonies, or on colonies prior to epizootics, and found no evidence of persistent Y. pestis infection in blood cultures. Our results suggest that grasshopper mice could be involved in epizootic spread of Y. pestis, and possibly, serve as a short-term reservoir for plague, but provide no evidence that the grasshopper mouse or any small rodent acts as a long-term, enzootic host for Y. pestis in prairie dog colonies.

Transmission pathways and spillover of an erythrocytic bacterial pathogen from domestic cats to wild felids.

Many pathogens infect multiple hosts, and spillover from domestic to wild species poses a significant risk of spread of diseases that threaten wildlife and humans. Documentation of cross-species transmission, and unraveling the mechanisms that drive it, remains a challenge. Focusing on co-occurring domestic and wild felids, we evaluate possible transmission mechanisms and evidence of spillover of "Candidatus Mycoplasma haemominutum" (CMhm), an erythrocytic bacterial parasite of cats. We examine transmission and possibility of spillover by analyzing CMhm prevalence, modeling possible transmission pathways, deducing genotypes of CMhm pathogens infecting felid hosts based on sequences of the bacterial 16S rRNA gene, and conducting phylogenetic analyses with ancestral state reconstruction to identify likely cross-species transmission events. Model selection analyses suggest both indirect (i.e., spread via vectors) and direct (i.e., via interspecific predation) pathways may play a role in CMhm transmission. Phylogenetic analyses indicate that transmission of CMhm appears to predominate within host species, with occasional spillover, at unknown frequency, between species. These analyses are consistent with transmission by predation of smaller cats by larger species, with subsequent within-species persistence after spillover. Our results implicate domestic cats as a source of global dispersal and spillover to wild felids via predation. We contribute to the emerging documentation of predation as a common means of pathogen spillover from domestic to wild cats, including pathogens of global conservation significance. These findings suggest risks for top predators as bioaccumulators of pathogens from subordinate species.

The potential role of swift foxes (Vulpes velox) and their fleas in plague outbreaks in prairie dogs.

Swift foxes (Vulpes velox) have been proposed as potential carriers of fleas infected with the bacterium Yersinia pestis between areas of epizootics in black-tailed prairie dogs (Cynomys ludovicianus). We examined antibody prevalence rates of a population of swift foxes in Colorado, USA, and used polymerase chain reaction (PCR) assays to examine their flea biota for evidence of Y. pestis. Fifteen of 61 (24%) captured foxes were seropositive, and antibody prevalence was spatially correlated with epizootic plague activity in prairie dog colonies in the year of, and previous to, the study. Foxes commonly harbored the flea Pulex simulans, though none of the fleas was positive for Y. pestis.

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation.

Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RADseq studies, we developed a simple model using different numbers of RAD-tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best-case modelling scenario, we found that RADseq using six- or eight-base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RADseq for genome scans and found that the median density of markers across these studies was 4.08 RAD-tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RADseq study. Thus, we conclude that genome scans based on RADseq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.

Responsible RAD: Striving for best practices in population genomic studies of adaptation.

Two recent articles were written in response to our paper "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing scans of adaptation." While we agree with some of the comments made by the authors of these two response papers, we still believe caution should be employed in RADseq studies that aim to detect loci that contribute to adaptation. In this rebuttal, we evaluate the key points made in these papers, attempt to identify a middle ground and make suggestions for responsibly conducting future studies to understand the genomewide mechanisms of adaptation.

Extreme plasticity in thermoregulatory behaviors of free-ranging black-tailed prairie dogs.

In the natural environment, hibernating sciurids generally remain dormant during winter and enter numerous deep torpor bouts from the time of first immergence in fall until emergence in spring. In contrast, black-tailed prairie dogs (Cynomys ludovicianus) remain active throughout winter but periodically enter short and shallow bouts of torpor. While investigating body temperature (T(b)) patterns of black-tailed prairie dogs from six separate colonies in northern Colorado, we observed one population that displayed torpor patterns resembling those commonly seen in hibernators. Five individuals in this population experienced multiple torpor bouts in immediate succession that increased in length and depth as winter progressed, whereas 16 prairie dogs in five neighboring colonies remained euthermic for the majority of winter and entered shallow bouts of torpor infrequently. Our results suggest that these differences in torpor patterns did not result from differences in the physiological indicators that we measured because the prairie dogs monitored had similar body masses and concentrations of stored lipids across seasons. Likewise, our results did not support the idea that differences in overwinter T(b) patterns between prairie dogs in colonies with differing torpor patterns resulted from genetic differences between populations; genetic analyses of prairie dog colonies revealed high genetic similarity between the populations and implied that individuals regularly disperse between colonies. Local environmental conditions probably played a role in the unusual T(b) patterns experienced by prairie dogs in the colony where hibernation-like patterns were observed; this population received significantly less rainfall than neighboring colonies during the summer growing seasons before, during, and after the year of the winter in which they hibernated. Our study provides a rare example of extreme plasticity in thermoregulatory behaviors of free-ranging prairie dogs and provides evidence contrary to models that propose a clear delineation between homeothermy, facultative torpor, and hibernation.

Host usage and seasonal activity patterns of Ixodes kingi and I. sculptus (Acari: Ixodidae) nymphs in a Colorado prairie landscape, with a summary of published North American host records for all life stages.

We examined host usage and seasonal activity patterns of the nymphal stage of the ticks Ixodes kingi and I. sculptus within a prairie rodent community in north-central Colorado. Ixodes kingi was commonly encountered on both northern grasshopper mice (Onychomys leucogaster) and thirteen-lined ground squirrels (Spermophilus tridecemlineatus), whereas I. sculptus frequently infested S. tridecemlineatus but was absent from O. leucogaster. Low numbers of ticks of both species were collected from deer mice (Peromyscus maniculatus) and Ord's kangaroo rats (Dipodomys ordii). Nymphal loads of I. kingi and I. sculptus increased dramatically on commonly infested rodent species from spring (May-June) to summer (July-August). Further, rodents trapped on prairie-dog towns tended to experience increased nymphal loads of I. kingi (O. leucogaster, S. tridecemlineatus) but decreased loads of I. sculptus (S. tridecemlineatus) following plague epizootics among prairie dog populations. A summary of published North American host records revealed that I. kingi has been recorded from humans, domestic animals (cat, dog), 17 species of carnivores, 40 species of rodents, and four species of lagomorphs, and that I. sculptus has been recorded from humans, domestic animals (cat, dog, goat), 13 species of carnivores, 34 species of rodents, and three species of lagomorphs. In accordance with our observations from Colorado, I. kingi commonly has been found to infest heteromyid and murid rodents (such as grasshopper mice), whereas I. sculptus most frequently has been collected from ground-dwelling sciurid rodents, especially Spermophilus ground squirrels. The potential roles of I. kingi and I. sculptus as enzootic vectors of human pathogens, particularly the agents of tularemia (Francisella tularensis), Q fever (Coxiella burnetii), and Colorado tick fever (CTF virus), are discussed.

Intra-host mathematical model of chronic wasting disease dynamics in deer (Odocoileus).

Bioassays of native cervid hosts have established the presence of infectious chronic wasting disease (CWD) prions in saliva, blood, urine, and feces of clinically diseased and pre-clinical infected deer. The intra-host trafficking of prions from the time of initial infection to shedding has been less well defined. We created a discrete-time compartmentalized model to simulate the misfolding catalysis, trafficking, and shedding of infectious prions throughout the organ systems of CWD-infected cervids. Using parameter values derived from experimental infections of North American deer (Odocoileus spp.), the exponential-based model predicts prion deposition over time with: 1) nervous tissues containing the highest deposition of prions at 20 months post-infection and 2) excreted fluids containing low levels of prions throughout infection with the highest numbers of prions predicted to be shed in saliva and feces (as high as 10 lethal doses (1.34 × 1029 prions) in 11-15 months). These findings are comparable to prion deposition described in literature as assayed by conventional and ultrasensitive amplification assays. The comparison of our model to published data suggests that highly sensitive assays (sPMCA, RT-QuIC, and bioassay) are appropriate for early prion detection in bodily fluids and secretions. The model provides a view of intra-host prion catalysis leading to pre-clinical shedding and provides a framework for continued development of antemortem diagnostic methods.