Use of hidden Markov capture–recapture models to estimate abundance in the presence of uncertainty: Application to the estimation of prevalence of hybrids in animal populations

Estimating the relative abundance (prevalence) of different population segments is a key step in addressing fundamental research questions in ecology, evolution, and conservation. The raw percentage of individuals in the sample (naive prevalence) is generally used for this purpose, but it is likely to be subject to two main sources of bias. First, the detectability of individuals is ignored; second, classification errors may occur due to some inherent limits of the diagnostic methods. We developed a hidden Markov (also known as multievent) capture–recapture model to estimate prevalence in free‐ranging populations accounting for imperfect detectability and uncertainty in individual's classification. We carried out a simulation study to compare naive and model‐based estimates of prevalence and assess the performance of our model under different sampling scenarios. We then illustrate our method with a real‐world case study of estimating the prevalence of wolf (Canis lupus) and dog (Canis lupus familiaris) hybrids in a wolf population in northern Italy. We showed that the prevalence of hybrids could be estimated while accounting for both detectability and classification uncertainty. Model‐based prevalence consistently had better performance than naive prevalence in the presence of differential detectability and assignment probability and was unbiased for sampling scenarios with high detectability. We also showed that ignoring detectability and uncertainty in the wolf case study would lead to underestimating the prevalence of hybrids. Our results underline the importance of a model‐based approach to obtain unbiased estimates of prevalence of different population segments. Our model can be adapted to any taxa, and it can be used to estimate absolute abundance and prevalence in a variety of cases involving imperfect detection and uncertainty in classification of individuals (e.g., sex ratio, proportion of breeders, and prevalence of infected individuals).     

Tuberculosis (Mycobacterium microti) in wild field vole populations

Vole tuberculosis (TB; Mycobacterium microti) is an understudied endemic infection. Despite progressing slowly, it causes severe clinical pathology and overt symptoms in its rodent host. TB was monitored for 2 years in wild field voles in Kielder Forest, UK. The prevalence of characteristic cutaneous TB lesions was monitored longitudinally at 4 sites, with individuals live-trapped and repeatedly monitored. A prevalence of 5.2% of individuals with lesions was recorded (n=2791). In a cross-sectional study, 27 sites were monitored bi-annually, with TB assessed by post-mortem examination for macroscopic lesions, and by culture and histopathology. Seventy-nine voles (10.78%; n=733) were positive for mycobacteria, with the highest prevalence in spring (13.15%; n=327). TB prevalence varied, with between 0% and 50% of voles infected per site. Prevalence increased with age (mass), and apparent seasonality was due to a higher proportion of older animals in spring. Survival analysis supported this result, with cutaneous lesions only manifesting in the advanced stages of infection, and therefore only being found on older voles. The body condition of individuals with lesions declined at the time when the lesion was first recorded, when compared to individuals without lesions, suggesting there may be an acute phase of infection during its advanced stage. Although predicted survival following the appearance of a cutaneous lesion was lower than for uninfected individuals, this was not significant.     

The epidemiological consequences of leprosy-tuberculosis co-infection

While in antiquity both leprosy and tuberculosis were prevalent in Europe, leprosy declined thereafter and, simultaneously, tuberculosis prevalence increased. Since both diseases are caused by mycobacterial infections, it has been suggested that there might be a causal relationship between both epidemics.Chaussinand observed the inverse prevalence of leprosy and tuberculosis and suggested that individuals with a latent tuberculosis infection are protected from acquiring leprosy. His cross-immunity hypothesis has been countered more recently by a co-infection hypothesis. The latter suggestion, proposed by Donoghue, states that people being infected with multi-bacillary leprosy are more susceptible to tuberculosis, which leads to increased mortality from the disease.This study utilizes mathematical modeling to explore the epidemiological consequences of the co-infection hypothesis for realistically confined parameter values. While the co-infection hypothesis appears plausible at first glance, a second thought reveals that it comprises also substantial consequences for tuberculosis epidemics: if co-infection raises the mortality rate above that of purely tuberculosis infected persons, then tuberculosis might as well be eradicated by leprosy. It is the specific interplay of both increased susceptibility towards tuberculosis and increased death rate when co-infected that determines the epidemiological fate.As a result of this analysis, it is shown that there is a large parameter region where the eventual disappearance of leprosy could indeed be explained by co-infection. This parameter region is considerably larger than that predicted by the cross-immunity hypothesis. This shows that the co-infection hypothesis should be considered a significant alternative to the cross-immunity hypothesis. The time scales at which the effects of co-infection are observed depend critically on the spatial distribution of the individuals but reach epidemiologically realistic values for rather immobile individuals with local interaction.     

Variable exposure and immunological response to Lyme disease Borrelia among North Atlantic seabird species

Colonial seabirds often breed in large aggregations. These individuals can be exposed to parasitism by the tick Ixodes uriae, but little is known about the circulation of pathogens carried by this ectoparasite, including Lyme disease Borrelia. Here we investigated the prevalence of antibodies (Ab) against Borrelia burgdorferi sensu lato in seabird species sampled at eight locations across the North Atlantic. Using enzyme-linked immunosorbent assay tests, we found that the prevalence of anti-Borrelia Ab in adult seabirds was 39.6% on average (over 444 individuals), but that it varied among colonies and species. Common guillemots showed higher seroprevalence (77.1%+/-5.9) than black-legged kittiwakes (18.6%+/-6.7) and Atlantic puffins (22.6%+/-6.3). Immunoblot-banding patterns of positive individuals, reflecting the variability of Borrelia antigens against which Ab were produced, also differed among locations and species, and did not tightly match the prevalence of Borrelia phylogroups previously identified in ticks collected from the same host individuals. These results represent the first report of the widespread prevalence of Ab against Borrelia within an assemblage of seabird species and demonstrate that Borrelia is an integrated aspect in the interaction between seabirds and ticks. More detailed studies on the dynamics of Borrelia within and among seabird species at different spatial scales will now be required to better understand the implications of this interaction for seabird ecology and the epidemiology of Lyme disease.     

Estimating infection prevalence: Best practices and their theoretical underpinnings

Accurately estimating infection prevalence is fundamental to the study of population health, disease dynamics, and infection risk factors. Prevalence is estimated as the proportion of infected individuals (“individual‐based estimation”), but is also estimated as the proportion of samples in which evidence of infection is detected (“anonymous estimation”). The latter method is often used when researchers lack information on individual host identity, which can occur during noninvasive sampling of wild populations or when the individual that produced a fecal sample is unknown. The goal of this study was to investigate biases in individual‐based versus anonymous prevalence estimation theoretically and to test whether mathematically derived predictions are evident in a comparative dataset of gastrointestinal helminth infections in nonhuman primates. Using a mathematical model, we predict that anonymous estimates of prevalence will be lower than individual‐based estimates when (a) samples from infected individuals do not always contain evidence of infection and/or (b) when false negatives occur. The mathematical model further predicts that no difference in bias should exist between anonymous estimation and individual‐based estimation when one sample is collected from each individual. Using data on helminth parasites of primates, we find that anonymous estimates of prevalence are significantly and substantially (12.17%) lower than individual‐based estimates of prevalence. We also observed that individual‐based estimates of prevalence from studies employing single sampling are on average 6.4% higher than anonymous estimates, suggesting a bias toward sampling infected individuals. We recommend that researchers use individual‐based study designs with repeated sampling of individuals to obtain the most accurate estimate of infection prevalence. Moreover, to ensure accurate interpretation of their results and to allow for prevalence estimates to be compared among studies, it is essential that authors explicitly describe their sampling designs and prevalence calculations in publications.     

Investigation of 15q11-q13, 16p11.2 and 22q13 CNVs in Autism Spectrum Disorder Brazilian Individuals with and without Epilepsy

Copy number variations (CNVs) are an important cause of ASD and those located at 15q11-q13, 16p11.2 and 22q13 have been reported as the most frequent. These CNVs exhibit variable clinical expressivity and those at 15q11-q13 and 16p11.2 also show incomplete penetrance. In the present work, through multiplex ligation-dependent probe amplification (MLPA) analysis of 531 ethnically admixed ASD-affected Brazilian individuals, we found that the combined prevalence of the 15q11-q13, 16p11.2 and 22q13 CNVs is 2.1% (11/531). Parental origin could be determined in 8 of the affected individuals, and revealed that 4 of the CNVs represent de novo events. Based on CNV prediction analysis from genome-wide SNP arrays, the size of those CNVs ranged from 206 kb to 2.27 Mb and those at 15q11-q13 were limited to the 15q13.3 region. In addition, this analysis also revealed 6 additional CNVs in 5 out of 11 affected individuals. Finally, we observed that the combined prevalence of CNVs at 15q13.3 and 22q13 in ASD-affected individuals with epilepsy (6.4%) was higher than that in ASD-affected individuals without epilepsy (1.3%; p<0.014). Therefore, our data show that the prevalence of CNVs at 15q13.3, 16p11.2 and 22q13 in Brazilian ASD-affected individuals is comparable to that estimated for ASD-affected individuals of pure or predominant European ancestry. Also, it suggests that the likelihood of a greater number of positive MLPA results might be found for the 15q13.3 and 22q13 regions by prioritizing ASD-affected individuals with epilepsy.     

Distribution of the disease pathogen Batrachochytrium dendrobatidis in non‐epidemic amphibian communities of western Canada

Chytridiomycosis is an emerging infectious disease of amphibians caused by the waterborne pathogen Batrachochytrium dendrobatidis (Bd) and is responsible for the recent decline of species worldwide. Elucidating patterns in disease prevalence has proved challenging, as small‐scale studies to date have provided conflicting results. We present data on the prevalence of Bd (the proportion of individuals with Bd) collected from amphibians sampled throughout British Columbia. We had two different datasets: our original dataset includes 1129 individuals sampled in 103 sites representing 14 species. A second dataset has 839 individuals sampled in 19 sites representing 10 species. We use a Bayesian state‐space occupancy modelling approach to estimate the probability that an individual is Bd+ as a function of individual and site characteristics. Cross‐validation techniques and the original dataset were used to find the best model: this model includes species, life stage, and geographic location. Our results suggest that Bd prevalence is not strongly related to seasonality, latitude or site type. Within a species, Bd prevalence depended on life stage; the watershed in which a site occurs may also usefully predict prevalence. Overall observed infection prevalence was ～16%. Our best model accurately assigns Bd status to an individual ～ 42% of the time. Taking advantage of the Bayesian framework, we ran an analysis with the second dataset using estimates from the original model as prior values. We present posterior density distributions for those sites and species with narrow credible intervals, and show that sites tend to be either highly likely or highly unlikely to have individuals with Bd, while individuals of some stages of some species have an intermediate likelihood of being Bd‐positive. The Bayesian model using informed priors had increased accuracy rates in assigning Bd status to both individuals and groups of individuals.     

Modeling the effect of information quality on risk behavior change and the transmission of infectious diseases

How the quality of information about the prevalence of an infectious disease affects individuals’ incentives to adopt self-protective actions to reduce the risk of infection is studied using an economic/game-theoretic model of epidemics. In the model, agents make inferences regarding the current prevalence of a disease by observing the health status of a subset of the population. Therefore, the higher the number of agents whose infection status can be observed, the better one’s information about the current prevalence is. In particular, it is assumed that an agent’s estimate of the current prevalence depends on observations of the current health status of other agents and on the agent’s estimate of past prevalence, and that the agent places more weight on the current observations in forming an estimate of the prevailing prevalence when the number of observations increases. It is shown that the likelihood of eradicating an infectious disease through behavioral changes depends critically on the amount of information that individuals have access to, which also determines whether prevalence will be relatively stable or will exhibit cyclical patterns over time. Increasing the amount of information that individuals possess may lower the likelihood of eradication.     

Dispersal to predator‐free space counterweighs fecundity costs in alate aphid morphs

1. Specialisation in dispersal by alate aphids often imposes constraints on other functions, particularly a reduction in fecundity due to wing development. Short‐distance flight from patches of high population density to uninfested plants may provide temporary predator‐free space, compensating for low fecundity. However, this theoretical prediction has not been explored experimentally. 2. To test this hypothesis, a field cage experiment was conducted in which Aphis glycines populations initiated with controlled proportions of apterous and alate individuals were exposed to predation, while predator‐free space was accessible only through flight. It was predicted that an investment in alate individuals would benefit a population under predation, regardless of associated costs to fecundity. 3. As expected, a strong trade‐off was observed between fecundity and wing development. However, populations initiated with a fixed proportion of alate and apterous individuals showed no reductions in final population size compared with populations initiated with apterous individuals exclusively. Moreover, the initial presence of alate individuals in the populations increased aphid prevalence (i.e. proportion of plants colonised). Similarly, both increased population size and prevalence were observed when predator‐free space was accessible through flight, as opposed to when it was inaccessible. 4. These results show that despite high costs to fecundity, an investment in alate individuals is neither beneficial nor detrimental to population size when predator‐free space is accessible, but increases aphid prevalence. It is concluded that prevalence might provide an ecological advantage important enough to warrant the production of alate morphs under intense predation.     

Masochistic Dreams: A Gender-Related Diathesis for Depression Revisited

Masochistic dreams, as defined by Beck (1967), are reportedly more prevalent among women and individuals with past or present depression. However, it is unclear whether these prevalence differences are a function of depressogenic personality traits or fluctuating mood symptoms. In the present study, 30 men and 30 women without histories of major depression slept two consecutive nights in a sleep laboratory and reported their dreams from each REM period on the second night. Dream content from this sample was compared to that of 60 depressed participants who were studied previously under the same protocol. Analyses did not support a heightened prevalence of masochistic dreams among women or depressed individuals. Interestingly, the masochistic dreams of the non-depressed sample were equally distributed across the night, whereas depressed individuals tend to report masochistic dreams closer to morning. This hypothesized pattern suggests that masochistic dreams may be pathognomic of depression in that their occurrence near the end of the night affects morning mood with negative dream residue.     

Detection of human herpesvirus 6 and 7 DNA in saliva from healthy adults from Rio de Janeiro, Brazil

In this study, we aimed to evaluate virus shedding in the saliva of healthy adults from the metropolitan region of the city of Rio de Janeiro, Brazil, in order to verify the prevalence of both human herpesviruses 6 and 7 (HHV-6, HHV-7). The studied group comprised 182 healthy individuals at Pedro Ernesto University Hospital, who were being seen for annual odontologic revisions. Saliva specimens were subjected to a multiplex polymerase chain reaction (PCR) to detect the presence of HHV-6A, HHV-6B and HHV-7. The total Roseolovirus DNA prevalence was 22.4%. The PCR detected a HHV-6 prevalence of 9.8%, with HHV-6A detected in 7.1% of the samples and HHV-6B in 2.7%. HHV-7 DNA was revealed in 12.6% of the studied cases. Multiple infections caused by HHV-6A and 7 were found in 2.1% of the samples. No statistical differences were observed regarding age, but for HHV-7 infection, an upward trend was observed in female patients. Compared to studies from other countries, low prevalence rates of herpesvirus DNA were detected in saliva from the healthy individuals in our sample. PCR methodology thus proved to be a useful tool for Roseolovirus detection and it is important to consider possible geographic and populations differences that could explain the comparatively low prevalence rates described here.     

Sperm velocity in an Alpine whitefish: effects of age, size, condition, fluctuating asymmetry and gonad abnormalities

The relationship between sperm velocity and individual age, size, body condition and fluctuating asymmetry was investigated in Alpine whitefish Coregonus fatioi . The fish analysed belonged to one among several sympatric whitefish populations of Lake Thun, Switzerland, which are characterized by a high prevalence of gonad alterations. Therefore, sperm velocity data were also tested for a link between gonad deformation and sperm swimming speed. Sperm velocity was significantly lower in larger-grown individuals and in individuals of higher body condition. As expected, sperm velocity was higher in males with higher levels of fluctuating asymmetry, but it did not significantly vary with male age. Moreover, variation in sperm velocity was found to be significantly higher in individuals showing some types of gonad alterations but it did not significantly correlate with the presence of other types of alterations.     

The prevalence of factor V Leiden,prothrombin G20210A and methylenetetrahydrofolate reductase polymorphism C677T among G6PD deficient individuals from Western Iran

It has been suggested that the allele frequency of thrombophilic mutations is affected by glucose-6-phosphate dehydrogenase (G6PD) deficiency. The prevalence of thrombophilic mutations were studied in sixty G6PD deficient individuals including 57 males and three females with the mean age of 15 ± 3.08 and 110 age and sex matched healthy individuals consisted of 95 males and 15 females with the mean age of 16.19 ± 2.17 from the Kermanshah Province of Iran. Using a combination of PCR-RFLP technique, single strand conformation polymorphism (SSCP) analysis and DNA sequencing polymorphic G6PD mutations were identified. The factor V Leiden, prothrombin G20210A and methylenetetrahydrofolate reductase (MTHFR) C677T were detected by PCR-RFLP method using MnlI, HindIII and HinfI restriction enzymes, respectively. Three mutations, G6PD Mediterranean, G6PD Chatham and G6PD Cosenza were identified in 60 G6PD deficient individuals with highest prevalence of G6PD Mediterranean (91.6%). In G6PD deficient individuals the prevalence of factor V Leiden tended to be higher (5%) compared to healthy individuals (2.7%). The prevalence of prothrombin G20210A mutation in G6PD deficient individuals was 1.7%. However, in normal subjects the prevalence of this mutation was 2.7%. The frequency of T allele in G6PD deficient individuals were insignificantly higher (29.16%) than those in healthy individuals (26.8%). Our finding indicates that the prevalence of factor V Leiden, prothrombin G20210A and MTHFR C677T in G6PD deficient individuals is not statistically different compared to normal subjects and G6PD deficiency is not associated with these thrombophilic mutations in Western Iran.     

Auricular exostoses in the prehistoric population of Gran Canaria

Auditory exostoses are bone anomalies located in the external auditory canal. The bulk of clinical observations and some experimental data support the idea that their development depends on prolonged exposure to cold water. This study was performed in order to analyze the prevalence of auditory exostoses among the prehispanic population of Gran Canaria, comparing it between men and women and between individuals buried in coastal regions and central highlands. We analyzed 323 crania, 41 of which showed auditory exostoses. Marked differences in prevalence were observed between the individuals buried in the central highlands (0.88%) and those buried in coastal regions (40.21%). Among the latter, the prevalence was similar in men (41.67%) and in women (38.89%). These data support the hypothesis that individuals buried in coastal regions performed economic activities related to exploitation of marine resources, whereas those living in the central highlands did not; however, diachronic variation cannot be excluded.     

Neurocysticercosis as a Cause of Epilepsy and Seizures in Two Community-Based Studies in a Cysticercosis-Endemic Region in Peru

Background

The prevalence of epilepsy added to inadequate treatment results in chronic morbidity and considerable mortality in poor populations. Neurocysticercosis (NCC), a helminthic disease of the central nervous system, is a leading cause of seizures and epilepsy in most of the world.

Methods

Taking advantage of a cysticercosis elimination program, we performed two community-based cross-sectional studies between 2006 and 2007 in 58 rural communities (population 20,610) to assess the prevalence and characteristics of epilepsy and epileptic seizures in this endemic region. Serological and computed tomography (CT) data in individuals with epilepsy were compared to previous surveys in general population from the same region.

Principal findings

In two surveys, 17,450 individuals were evaluated. Lifetime prevalence of epilepsy was 17.25/1000, and prevalence of active epilepsy was 10.8/1000 inhabitants. The prevalence of epilepsy increased after age 25 years and dropped after age 45. Only 24% (45/188) of patients with active epilepsy were taking antiepileptic drugs, all at sub-therapeutic doses. Antibodies to cysticercosis were found in approximately 40% of individuals with epilepsy in both studies. In one survey only individuals presenting strong antibody reactions were significantly associated with having epilepsy (OR 5.74; p<0.001). In the second, the seroprevalence as well as the proportion presenting strong antibody reactions were both significantly higher in individuals with epilepsy (OR 2.2 and 4.33, respectively). Brain CT showed NCC-compatible images in 109/282 individuals with epilepsy (39%). All individuals with viable parasites on CT were seropositive.

Conclusion

The prevalence of epilepsy in this cysticercosis endemic region is high and NCC is an important contributor to it.     

Maxillary sinusitis in Medieval Chichester,England

Maxillary sinusitis is a common medical complaint, affecting more than 30 million people per year in the United States alone. Very little palaeopathological work on this disease has been carried out, probably because of the enclosed nature of the sinuses in intact skulls and the lack of a suitable method for examination. This study tested the hypothesis that maxillary sinusitis was more common in people with leprosy than in people without it in Medieval England. The prevalence of maxillary sinusitis by age and sex was recorded in 133 individuals, some diagnosed as being leprous, derived from a later Medieval (12th to 17th centuries AD) urban hospital population at Chichester, Sussex, England using both macroscopic and endoscopic methods of examination. Of the 133 individuals with one or both sinuses available for examination, 54.9% (73) had evidence of bone change within the sinuses. There was no difference in prevalence between those with leprosy and those without, although clinical studies suggest that over 50% of lepromatous leprous individuals may develop sinusitis. Comparison with another study on Medieval British sites with a 3.6% prevalence (3 of 83) indicates that the prevalence at Chichester is much greater. The problems with diagnosing sinusitis are addressed and reasons behind the high frequency in this study are discussed. Aetiological factors predisposing to maxillary sinusitis are considered with reference to possible environmental conditions prevailing in the later Medieval period in Britain. © 1995 Wiley-Liss, Inc.     

Molecular genetics of usher syndrome

Usher syndrome (USH) is inherited in an autosomal recessive mode. The disease is characterized by hearing loss, progressing vision loss, and vestibular dysfunction. In most cases, it is the reason for deafness and blindness in school-age children. The prevalence of USH in the main population is estimated as 4.4 per 100000 individuals, approximately. The prevalence of heterozygous carriers can reach 1 per 70 normally hearing individuals. There is currently no effective treatment of USH. The patients are provided with hearing aids, but, in case of severe hearing impairement these aids give no effect. In view of this, developing diagnostic methods is important. It is believed that molecular genetic investigations will enable early diagnostics of the syndrome.     

Helminths and allergy: the example of tropomyosin

Parasitic worms contain potent allergens, but epidemiological and experimental studies suggest that infections with certain helminths are negatively associated with the prevalence of allergic diseases. This seeming contradiction can be addressed by using filarial tropomyosin as an example. This protein shares structural features and crossreacting B-cell epitopes with other highly allergenic invertebrate tropomyosins. Nevertheless, it usually does not provoke allergic disease in infected individuals. In addition, it is one of the most prominent candidates for an anti-nematode vaccine. Recent data suggest mechanisms that might prevent hosts from developing allergic reactions against allergens of their parasites, such as filarial tropomyosin.     

Improving the Modeling of Disease Data from the Government Surveillance System: A Case Study on Malaria in the Brazilian Amazon

The study of the effect of large-scale drivers (e.g., climate) of human diseases typically relies on aggregate disease data collected by the government surveillance network. The usual approach to analyze these data, however, often ignores a) changes in the total number of individuals examined, b) the bias towards symptomatic individuals in routine government surveillance, and; c) the influence that observations can have on disease dynamics. Here, we highlight the consequences of ignoring the problems listed above and develop a novel modeling framework to circumvent them, which is illustrated using simulations and real malaria data. Our simulations reveal that trends in the number of disease cases do not necessarily imply similar trends in infection prevalence or incidence, due to the strong influence of concurrent changes in sampling effort. We also show that ignoring decreases in the pool of infected individuals due to the treatment of part of these individuals can hamper reliable inference on infection incidence. We propose a model that avoids these problems, being a compromise between phenomenological statistical models and mechanistic disease dynamics models; in particular, a cross-validation exercise reveals that it has better out-of-sample predictive performance than both of these alternative models. Our case study in the Brazilian Amazon reveals that infection prevalence was high in 2004–2008 (prevalence of 4% with 95% CI of 3–5%), with outbreaks (prevalence up to 18%) occurring during the dry season of the year. After this period, infection prevalence decreased substantially (0.9% with 95% CI of 0.8–1.1%), which is due to a large reduction in infection incidence (i.e., incidence in 2008–2010 was approximately one fifth of the incidence in 2004–2008).We believe that our approach to modeling government surveillance disease data will be useful to advance current understanding of large-scale drivers of several diseases.