Biology subjects

Dallas, T. A.

Publications and source records attributed to Dallas, T. A..

5 recordsLinked to original sources

bioRxiv2021

Data proliferation, reconciliation, and synthesis in viral ecology

The fields of viral ecology and evolution have rapidly expanded in the last two decades, driven by technological improvements, and motivated by efforts to discover potentially zoonotic wildlife viruses under the rubric of pandemic prevention. One consequence has been a massive proliferation of host-virus association data, which comprise the backbone of research in viral macroecology and zoonotic risk prediction. These data remain fragmented across numerous data portals and projects, each with their own scope, structure, and reporting standards. Here, we propose that synthesis of host-virus association data is a central challenge to improve our understanding of the global virome and develop foundational theory in viral ecology. To illustrate this, we build an open reconciled mammal-virus database from four key published datasets, applying a standardized taxonomy and metadata. We show that reconciling these datasets provides a substantially richer view of the mammal virome than that offered by any one individual database. We argue for a shift in best practice towards the incremental development and use of synthetic datasets in viral ecology research, both to improve comparability and replicability across studies, and to facilitate future efforts to use machine learning to predict the structure and dynamics of the global virome.

ecology↗

bioRxiv2019

What would it take to describe the global diversity of parasites?

How many parasites are there on Earth? Here, we use helminth parasites to high-light how little is known about parasite diversity, and how insufficient our current approach will be to describe the full scope of life on Earth. Using the largest database of host-parasite associations and one of the worlds largest parasite collections, we estimate a global total of roughly 100,000 to 350,000 species of helminth endoparasites of vertebrates, of which 85% to 95% are unknown to science. The parasites of amphibians and reptiles remain the most poorly described, but the majority of undescribed species are likely parasites of birds and bony fish. Missing species are disproportionately likely to be smaller parasites of smaller hosts in undersampled countries. At current rates, it would take centuries to comprehensively sample, collect, and name vertebrate helminths. While some have suggested that macroecology can work around existing data limitations, we argue that patterns described from a small, biased sample of diversity arent necessarily reliable, especially as host-parasite networks are increasingly altered by global change. In the spirit of moon-shots like the Human Genome Project and the Global Virome Project, we consider the idea of a Global Parasite Project: a global effort to transform parasitology and inventory parasite diversity at an unprecedented pace.

ecology↗

bioRxiv2018

Leveraging pathogen community distributions to understand outbreak and emergence potential

Understanding pathogen outbreak and emergence events has important implications to the management of infectious disease. Apart from preempting infectious disease events, there is considerable interest in determining why certain pathogens are consistently found in some regions, and why others spontaneously emerge or reemerge over time. Here, we use a trait-free approach which leverages information on the global community of human infectious diseases to estimate the potential for pathogen outbreak, emergence, and re-emergence events over time. Our approach uses pairwise dissimilarities among pathogen distributions between countries and country-level pathogen composition to quantify pathogen outbreak, emergence, and re-emergence potential as a function of time (e.g., number of years between training and prediction), pathogen type (e.g., virus), and transmission mode (e.g., vector-borne). We find that while outbreak and re-emergence potential are well captured by our simple model, prediction of emergence events remains elusive, and sudden global emergences like an influenza pandemic seem beyond the predictive capacity of the model. While our approach allows for dynamic predictability of outbreak and re-emergence events, data deficiencies and the stochastic nature of emergence events may preclude accurate prediction. Together, our results make a compelling case for incorporating a community ecological perspective into existing disease forecasting efforts.

epidemiology↗

bioRxiv2018

Spatial extinction date estimation: a novel method for reconstructing spatiotemporal patterns of extinction and identifying potential zones of rediscovery

O_LIThe estimation of extinction dates from limited and incomplete sighting records is a key challenge in conservation (when experts are uncertain whether a species has gone extinct) and historical ecology (when the date and mechanism of extinction is controversial).\nC_LIO_LIWe introduce a spatially-explicit method of interpolating extinction date estimators, allowing users to estimate spatiotemporal surfaces of population persistence from georeferenced sighting data of variable quality.\nC_LIO_LIWe present the R package spatExtinct, which produces spatially-explicit extinction date surfaces from geolocated sightings, including options for custom randomization schemes to improve accuracy with limited datasets. We use simulations to illustrate the sensitivity of the method to parameterization, and apply the method to identify potential areas where Bachmans warbler (Vermivora bachmanii) might be rediscovered.\nC_LIO_LIOur method, and the spatExtinct package, has the potential to help describe and differentiate different drivers of extinction for historical datasets, and could be used to identify possible regions of population persistence for species with an uncertain extinction status, improving on non-spatial or imprecise methods that are currently in use.\nC_LI

ecology↗

bioRxiv2017

The Parasite Extinction Assessment & Red List: an open-source, online biodiversity database for neglected symbionts

Parasite conservation is a rapidly growing field at the intersection of ecology, epidemiology, parasitology, and public health. The overwhelming diversity of parasitic life on earth, and recent work showing that parasites and other symbionts face severe extinction risk, necessitates infrastructure for parasite conservation assessments. Here, we describe the release of the Parasite Extinction Assessment & Red List (PEARL) version 1.0, an open-access database of conservation assessments and distributional data for almost 500 macroparasitic invertebrates. The current approach to vulnerability assessment is based on range shifts and loss from climate change, and will be expanded as additional data (e.g., host-parasite associations and coextinction risk) is consolidated in PEARL. The web architecture is also open-source, scalable, and extensible, making PEARL a template for more eZcient red listing for other high-diversity, data-de1cient groups. Future iterations will also include new functionality, including a user-friendly open data pository and automated assessment and re-listing.

ecology↗