Biology subjects

Becker, D.

Publications and source records attributed to Becker, D..

59 records · Page 4Linked to original sources

bioRxiv2020

Disentangling interactions between mercury, immunity, and infection in a Neotropical bat community

O_LIContaminants such as mercury are pervasive and can have immunosuppressive effects on wildlife. Impaired immunity could be important for forecasting pathogen spillover risks, as many land-use changes that generate mercury contamination also bring wildlife into close contact with humans and domestic animals. However, the interactions among contaminants, immunity, and infection are difficult to study in natural systems, and empirical tests of possible directional relationships remain rare. C_LIO_LIWe capitalized on extreme mercury variation in a diverse bat community in Belize to test association among contaminants, immunity, and infection. By comparing a previous dataset of bats sampled in 2014 with new data from 2017, representing a period of rapid agricultural land conversion, we first confirmed bat species more reliant on aquatic prey had higher fur mercury. Bats in the agricultural habitat also had higher mercury in recent years. We then tested covariation between mercury and cellular immunity and determined if such relationships mediated associations between mercury and common bacterial pathogens. As bat ecology can dictate exposure to mercury and pathogens, we also assessed species-specific patterns in mercury-infection relationships. C_LIO_LIAcross the bat community, individuals with higher mercury had fewer neutrophils but not lymphocytes, suggesting stronger associations with innate immunity. However, the odds of infection for hemoplasmas and Bartonella spp. were generally lowest in bats with high mercury, and relationships between mercury and immunity did not mediate infection patterns. Mercury also showed species- and clade-specific relationships with infection, being associated with especially low odds for hemoplasmas in Pteronotus mesoamericanus and Dermanura phaeotis. For Bartonella spp., mercury was associated with particularly low odds in the genus Pteronotus but high odds in the Stenodermatinae. C_LIO_LISynthesis and application: Lower general infection risk in bats with high mercury despite weaker innate defense suggests contaminant-driven loss of pathogen habitat (i.e., anemia) or vector mortality as possible causes. Greater attention to these potential pathways could help disentangle relationships among contaminants, immunity, and infection in anthropogenic habitats and help forecast disease risks. Our results also suggest contaminants may increase infection risk in some taxa but not others, emphasizing the importance of considering surveillance and management at different phylogenetic scales. C_LI

ecology↗

bioRxiv2020

Predicting wildlife hosts of betacoronaviruses for SARS-CoV-2 sampling prioritization

Despite global investment in One Health disease surveillance, it remains difficult--and often very costly--to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can be used to guide sampling prioritization, but predictions from any given model may be highly uncertain; moreover, systematic model validation is rare, and the drivers of model performance are consequently under-documented. Here, we use bat hosts of betacoronaviruses as a case study for the data-driven process of comparing and validating predictive models of likely reservoir hosts. In the first quarter of 2020, we generated an ensemble of eight statistical models that predict host-virus associations and developed priority sampling recommendations for potential bat reservoirs and potential bridge hosts for SARS-CoV-2. Over more than a year, we tracked the discovery of 40 new bat hosts of betacoronaviruses, validated initial predictions, and dynamically updated our analytic pipeline. We find that ecological trait-based models perform extremely well at predicting these novel hosts, whereas network methods consistently perform roughly as well or worse than expected at random. These findings illustrate the importance of ensembling as a buffer against variation in model quality and highlight the value of including host ecology in predictive models. Our revised models show improved performance and predict over 400 bat species globally that could be undetected hosts of betacoronaviruses. Although 20 species of horseshoe bats (Rhinolophus spp.) are known to be the primary reservoir of SARS-like viruses, we find at least three-fourths of plausible betacoronavirus reservoirs in this bat genus might still be undetected. Our study is the first to demonstrate through systematic validation that machine learning models can help optimize wildlife sampling for undiscovered viruses and illustrates how such approaches are best implemented through a dynamic process of prediction, data collection, validation, and updating.

ecology↗

bioRxiv2019

Ecological and evolutionary drivers of hemoplasma infection and bacterial genotype sharing in a Neotropical bat community

Most emerging pathogens can infect multiple species, underscoring the importance of understanding the ecological and evolutionary factors that allow some hosts to harbor greater infection prevalence and share pathogens with other species. However, our understanding of pathogen jumps is primarily based around viruses, despite bacteria accounting for the greatest proportion of zoonoses. Because bacterial pathogens in bats (Order: Chiroptera) can have conservation and human health consequences, studies that examine the ecological and evolutionary drivers of bacterial prevalence and barriers to pathogen sharing are crucially needed. We here studied hemotropic Mycoplasma spp. (i.e., hemoplasmas) across a species-rich bat community in Belize over two years. Across 469 bats spanning 33 species, half of individuals and two-thirds of species were hemoplasma positive. Infection prevalence was higher for males and for species with larger body mass and colony sizes. Hemoplasmas displayed high genetic diversity (21 novel genotypes) and strong host specificity. Evolutionary patterns supported co-divergence of bats and bacterial genotypes alongside phylogenetically constrained host shifts. Bat species centrality to the network of shared hemoplasma genotypes was phylogenetically clustered and unrelated to prevalence, further suggesting rare--but detectable--bacterial sharing between species. Our study highlights the importance of using fine phylogenetic scales when assessing host specificity and suggests phylogenetic similarity may play a key role in host shifts for not only viruses but also bacteria. Such work more broadly contributes to increasing efforts to understand cross-species transmission and epidemiological consequences of bacterial pathogens.

ecology↗

bioRxiv2019

Dissecting the transcriptomic basis of phenotypic evolution in an aquatic keystone grazer

Cultural eutrophication is one of the largest threats to aquatic ecosystems with devastating ecological and economic consequences. Although Daphnia, a keystone grazer crustacean, can mitigate some negative effects of eutrophication in freshwater habitats, it is itself affected by changes in nutrient composition. Previous studies have shown evolutionary adaptation of Daphnia to environmental change, including high phosphorus levels. While phosphorus is an essential macronutrient, it negatively affects Daphnia life history when present in excessive concentrations. Here, we map weighted gene co-expression networks to phosphorus-related phenotypic traits in centuries-old ancestral Daphnia and their modern descendants, contrasting pre- and post-eutrophication environments. We find that evolutionary fine-tuning of transcriptional responses is manifested at a basic (cellular) phenotypic level, and is strongly correlated to an evolved plasticity of gene expression. At a higher phenotypic level, this contributes to the maintenance of physiological homeostasis, and a robust preservation of somatic phosphorus concentration.

evolutionary biology↗

bioRxiv2017

Phylofactorization - a graph partitioning algorithm to identify phylogenetic scales of ecological data

The problem of pattern and scale is a central challenge in ecology. The problem of scale is central to community ecology, where functional ecological groups are aggregated and treated as a unit underlying an ecological pattern, such as aggregation of \"nitrogen fixing trees\" into a total abundance of a trait underlying ecosystem physiology. With the emergence of massive community ecological datasets, from microbiomes to breeding bird surveys, there is a need to objectively identify the scales of organization pertaining to well-defined patterns in community ecological data.\n\nThe phylogeny is a scaffold for identifying key phylogenetic scales associated with macroscopic patterns. Phylofactorization was developed to objectively identify phylogenetic scales underlying patterns in relative abundance data. However, many ecological data, such as presence-absences and counts, are not relative abundances, yet it is still desireable and informative to identify phylogenetic scales underlying a pattern of interest. Here, we generalize phylofactorization beyond relative abundances to a graph-partitioning algorithm for any community ecological data.\n\nGeneralizing phylofactorization connects many tools from data analysis to phylogenetically-informe analysis of community ecological data. Two-sample tests identify three phylogenetic factors of mammalian body mass which arose during the K-Pg extinction event, consistent with other analyses of mammalian body mass evolution. Projection of data onto coordinates defined by the phylogeny yield a phylogenetic principal components analysis which refines our understanding of the major sources of variation in the human gut microbiome. These same coordinates allow generalized additive modeling of microbes in Central Park soils and confirm that a large clade of Acidobacteria thrive in neutral soils. Generalized linear and additive modeling of exponential family random variables can be performed by phylogenetically-constrained reduced-rank regression or stepwise factor contrasts. We finish with a discussion of how phylofac-torization produces an ecological species concept with a phylogenetic constraint. All of these tools can be implemented with a new R package available online.

ecology↗