Dynamic Population Models with Temporal Preferential Sampling to Infer Phenology

To study population dynamics, ecologists and wildlife biologists use relative abundance data, which are often subject to temporal preferential sampling. Temporal preferential sampling occurs when sampling effort varies across time. To account for preferential sampling, we specify a Bayesian hierarchical abundance model that considers the dependence between observation times and the ecological process of interest. The proposed model improves abundance estimates during periods of infrequent observation and accounts for temporal preferential sampling in discrete time. Additionally, our model facilitates posterior inference for population growth rates and mechanistic phenometrics. We apply our model to analyze both simulated data and mosquito count data collected by the National Ecological Observatory Network. In the second case study, we characterize the population growth rate and abundance of several mosquito species in the Aedes genus.Comment: 29 pages, 5 figures, 1 tabl

Data from: Community disassembly and disease: realistic – but not randomized – biodiversity losses enhance parasite transmission

Debates over the relationship between biodiversity and disease dynamics underscore the need for a more mechanistic understanding of how changes in host community composition influence parasite transmission. Focusing on interactions between larval amphibians and trematode parasites, we experimentally contrasted the effects of host richness and species composition to identify the individual and joint contributions of both parameters on the infection levels of three trematode species. By combining experimental approaches with field surveys from 147 ponds, we further evaluated how richness effects differed between randomized and realistic patterns of species loss (i.e., community disassembly). Our results indicated that community-level changes in infection levels were due to host species composition, rather than richness. However, when composition patterns mirrored empirical observations along a natural assembly gradient, each added host species reduced infection success by 12 to 55%. No such effects occurred when assemblages were randomized. Mechanistically, these patterns were due to non-random host species assembly/disassembly: while highly competent species predominated in low diversity systems, less susceptible hosts became progressively more common as richness increased. These findings highlight the potential for combining information on host traits and assembly patterns to forecast diversity-mediated changes in multi-host disease systems

experiment_infection_totals_UPLOAD

experiment_infection_totals_UPLOA

The Influence of Landscape and Environmental Factors on Ranavirus Epidemiology in a California Amphibian Assemblage

A fundamental goal of disease ecology is to determine the landscape and environmental processes that drive disease dynamics at different biological levels to guide management and conservation. Although ranaviruses (family Iridoviridae) are emerging amphibian pathogens, few studies have conducted comprehensive field surveys to assess potential drivers of ranavirus disease dynamics. We examined the factors underlying patterns in site‐level ranavirus presence and individual‐level ranavirus infection in 76 ponds and 1,088 individuals representing five amphibian species within the East Bay region of California. Based on a competing‐model approach followed by variance partitioning, landscape and biotic variables explained the most variation in site‐level presence. However, biotic and individual‐level variables explained the most variation in individual‐level infection. Distance to nearest ranavirus‐infected pond (the landscape factor) was more important than biotic factors at the site level; however, biotic factors were most influential at the individual level. At the site level, the probability of ranavirus presence correlated negatively with distance to nearest ranavirus‐positive pond, suggesting that the movement of water or mobile taxa (e.g., adult amphibians, birds, reptiles) may facilitate the movement of ranavirus between ponds and across the landscape. Taxonomic richness associated positively with ranavirus presence at the site level, but vertebrate richness associated negatively with infection prevalence in the host population. This might reflect the contrasting influences of diversity on pathogen colonisation versus transmission among hosts. Amphibian host species differed in their likelihood of ranavirus infection: American bullfrogs (Rana catesbeiana) had the weakest association with infection while rough‐skinned newts (Taricha granulosa) had the strongest. After accounting for host species effects, hosts with greater snout–vent length had a lower probability of infection. Our study demonstrates the array of landscape, environmental, and individual‐level factors associated with ranavirus epidemiology. Moreover, our study helps illustrate that the importance of these factors varies with biological level

Landscape and environmental factors and ranavirus epidemiology in an amphibian assemblage, East Bay, California

Aim To quantify the influence of a suite of landscape, abiotic, biotic, and host-level variables on ranavirus disease dynamics in amphibian assemblages at two biological levels (site and host-level). Location Wetlands within the East Bay region of California, USA. Methods We used competing models, multimodel inference, and variance partitioning to examine the influence of 16 landscape and environmental factors on patterns in site-level ranavirus presence and host-level ranavirus infection in 76 wetlands and 1,377 amphibian hosts representing five species. Results The landscape factor explained more variation than any other factors in site-level ranavirus presence, but biotic and host-level factors explained more variation in host-level ranavirus infection. At both the site- and host-level, the probability of ranavirus presence correlated negatively with distance to nearest ranavirus-positive wetland. At the site-level, ranavirus presence was associated positively with taxonomic richness. However, infection prevalence within the amphibian population correlated negatively with vertebrate richness. Finally, amphibian host species differed in their likelihood of ranavirus infection: American Bullfrogs had the weakest association with infection while Western Toads had the strongest. After accounting for host species effects, hosts with greater snout-vent length had a lower probability of infection. Main conclusions Strong spatial influences at both biological levels suggest that mobile taxa (e.g., adult amphibians, birds, reptiles) may facilitate the movement of ranavirus among hosts and across the landscape. Higher taxonomic richness at sites may provide more opportunities for colonization or the presence of reservoir hosts that may influence ranavirus presence. Higher host richness correlating with higher ranavirus infection is suggestive of a dilution effect that has been observed for other amphibian disease systems and warrants further investigation. Our study demonstrates that an array of landscape, environmental, and host-level factors were associated with ranavirus epidemiology and illustrates that their importance varies with biological level

The Influence of Landscape and Environmental Factors on Ranavirus Epidemiology in a California Amphibian Assemblage

A fundamental goal of disease ecology is to determine the landscape and environmental processes that drive disease dynamics at different biological levels to guide management and conservation. Although ranaviruses (family Iridoviridae) are emerging amphibian pathogens, few studies have conducted comprehensive field surveys to assess potential drivers of ranavirus disease dynamics. We examined the factors underlying patterns in site‐level ranavirus presence and individual‐level ranavirus infection in 76 ponds and 1,088 individuals representing five amphibian species within the East Bay region of California. Based on a competing‐model approach followed by variance partitioning, landscape and biotic variables explained the most variation in site‐level presence. However, biotic and individual‐level variables explained the most variation in individual‐level infection. Distance to nearest ranavirus‐infected pond (the landscape factor) was more important than biotic factors at the site level; however, biotic factors were most influential at the individual level. At the site level, the probability of ranavirus presence correlated negatively with distance to nearest ranavirus‐positive pond, suggesting that the movement of water or mobile taxa (e.g., adult amphibians, birds, reptiles) may facilitate the movement of ranavirus between ponds and across the landscape. Taxonomic richness associated positively with ranavirus presence at the site level, but vertebrate richness associated negatively with infection prevalence in the host population. This might reflect the contrasting influences of diversity on pathogen colonisation versus transmission among hosts. Amphibian host species differed in their likelihood of ranavirus infection: American bullfrogs (Rana catesbeiana) had the weakest association with infection while rough‐skinned newts (Taricha granulosa) had the strongest. After accounting for host species effects, hosts with greater snout–vent length had a lower probability of infection. Our study demonstrates the array of landscape, environmental, and individual‐level factors associated with ranavirus epidemiology. Moreover, our study helps illustrate that the importance of these factors varies with biological level

Johnson et al RAW DATA

This CVS file individual dissection dat