Biology subjects

Carlson, C. J.

Publications and source records attributed to Carlson, C. J..

40 records · Page 3Linked to original sources

bioRxiv2017

A cross-validation-based approach for delimiting reliable home range estimates

BackgroundWith decreasing costs of GPS telemetry devices, data repositories of animal movement paths are increasing almost exponentially in size. A series of complex statistical tools have been developed in conjunction with this increase in data. Each of these methods offers certain improvements over previously proposed methods, but each has certain assumptions or shortcomings that make its general application difficult. In the case of the recently developed Time Local Convex Hull (T-LoCoH) method, the subjectivity in parameter selection serves as one of the primary impediments to its more widespread use. While there are certain advantages to the flexibility it offers for question-driven research, the lack of an objective approach for parameter selection may prevent some users from exploring the benefits of the method.\n\nResultsHere we present a cross-validation-based approach for selecting parameter values to optimize the T-LoCoH algorithm. We demonstrate the utility of the approach using a case study from the Etosha National Park anthrax system. Utilizing the proposed algorithm, rather than the guidelines in the T-LoCoH documentation, results in significantly different values for derived site fidelity metrics.\n\nConclusionsDue to its basis in principles of cross-validation, the application of this method offers a more objective approach than the relatively subjective guidelines set forth in the T-LoCoH documentation and enables a more accurate basis for the comparison of home ranges among individuals and species, as well as among studies.

ecology↗

bioRxiv2017

Spores and soil from six sides: interdisciplinarity and the environmental biology of anthrax (Bacillus anthracis)

Environmentally Transmitted Diseases Are Comparatively Poorly Understood And Managed, And Their Ecology Is Particularly Understudied. Here We Identify Challenges Of Studying Environmental Transmission And Persistence With A Six-Sided Interdisciplinary Review Of The Biology Of Anthrax (Bacillus Anthracis). Anthrax Is A Zoonotic Disease Capable Of Maintaining Infectious Spore Banks In Soil For Decades (Or Even Potentially Centuries), And The Mechanisms Of Its Environmental Persistence Have Been The Topic Of Significant Research And Controversy. Where Anthrax Is Endemic, It Plays An Important Ecological Role, Shaping The Dynamics Of Entire Herbivore Communities. The Complex Eco-Epidemiology Of Anthrax, And The Mysterious Biology Of Bacillus Anthracis During Its Environmental Stage, Have Necessitated An Interdisciplinary Approach To Pathogen Research. Here, We Illustrate Different Disciplinary Perspectives Through Key Advances Made By Researchers Working In Etosha National Park, A Long-Term Ecological Research Site In Namibia That Has Exemplified The Complexities Of AnthraxS Enzootic Process Over Decades Of Surveillance. In Etosha, The Role Of Scavengers And Alternate Routes (Waterborne Transmission And Flies) Has Proved Unimportant, Relative To The Long-Term Persistence Of Anthrax Spores In Soil And Their Infection Of Herbivore Hosts. Carcass Deposition Facilitates Green-Ups Of Vegetation To Attract Herbivores, Potentially Facilitated By Anthrax Spores Role In The Rhizosphere. The Underlying Seasonal Pattern Of Vegetation, And Herbivores Immune And Behavioral Responses To Anthrax Risk, Interact To Produce Regular \"Anthrax Seasons\" That Appear To Be A Stable Feature Of The Etosha Ecosystem. Through The Lens Of Microbiologists, Geneticists, Immunologists, Ecologists, Epidemiologists, And Clinicians, We Discuss How Anthrax Dynamics Are Shaped At The Smallest Scale By Population Genetics And Interactions Within The Bacterial Communities Up To The Broadest Scales Of Ecosystem Structure. We Illustrate The Benefits And Challenges Of This Interdisciplinary Approach To Disease Ecology, And Suggest Ways Anthrax Might Offer Insights Into The Biology Of Other Important Pathogens. Bacillus Anthracis, And The More Recently Emerged Bacillus Cereus Biovar Anthracis, Share Key Features With Other Environmentally-Transmitted Pathogens, Including Several Zoonoses And Panzootics Of Special Interest For Global Health And Conservation Efforts. Understanding The Dynamics Of Anthrax, And Developing Interdisciplinary Research Programs That Explore Environmental Persistence, Is A Critical Step Forward For Understanding These Emerging Threats.

ecology↗

bioRxiv2017

Consensus and conflict among ecological forecasts of Zika virus outbreaks in the United States

Ecologists are increasingly involved in the pandemic prediction process. In the course of the Zika outbreak in the Americas, several ecological models were developed to forecast the potential global distribution of the disease. Conflicting results produced by alternative methods are unresolved, hindering the development of appropriate public health forecasts. We compare ecological niche models and experimentally-driven mechanistic forecasts for Zika transmission in the continental United States, a region of high model conflict. We use generic and uninformed stochastic county-level simulations to demonstrate the downstream epidemiological consequences of conflict among ecological models, and show how assumptions and parameterization in the ecological and epidemiological models propagate uncertainty and produce downstream model conflict. We conclude by proposing a basic consensus method that could resolve conflicting models of potential outbreak geography and seasonality. Our results illustrate the unacceptable and often undocumented margin of uncertainty that could emerge from using any one of these predictions without reservation or qualification. In the short term, ecologists face the task of developing better post hoc consensus that accurately forecasts spatial patterns of Zika virus outbreaks. Ultimately, methods are needed that bridge the gap between ecological and epidemiological approaches to predicting transmission and realistically capture both outbreak size and geography.

ecology↗

bioRxiv2017

Estimating The Extinction Date Of The Thylacine Accounting For Unconfirmed Sightings

The thylacine (Thylacinus cynocephalus), one of Australias most characteristic megafauna, was the largest marsupial carnivore until hunting, and potentially disease, drove them to extinction in 1936. Current knowledge suggests that thylacines became extinct on mainland Australia two millennia prior to their extirpation on Tasmania, but recent \"plausible\" sightings on the Cape York Peninsula have emerged, leading some to speculate the species may persist, undetected. Here we show that the continued survival of the thylacine is entirely implausible based on most current mathematical theories of extinction. We present a dataset including physical evidence, expert-validated sightings, and unconfirmed sightings leading up to the present day, and use a Bayesian framework that takes all three types of data into account by modelling them as independent processes, to evaluate the likelihood of the thylacines persistence. Although the last captive thylacine died in 1936, our model suggests the most likely extinction date would be 1940, or at the latest the 1950s. We validated this result by using other extinction estimator methods, all of which confirmed that the thylacines extinction likely fell between 1936 and 1943; even the most optimistic scenario suggests the species did not persist beyond 1956. The search for the thylacine, much like similar efforts to \"rediscover\" other recently extinct charismatic species, is likely to be fruitless, especially given that persistence on Tasmania would have been no guarantee the species could reappear in regions that had been unoccupied for millennia. The search for the thylacine may become a rallying point for conservation and wildlife biology, and could indirectly help fund and support critical research in understudied areas like Cape York. However, our results suggest that attempts to rediscover the thylacine will likely be unsuccessful.

ecology↗