Dataset Information

Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units.

ABSTRACT: Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae.

SUBMITTER: Schurch AC

PROVIDER: S-EPMC4139337 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units.

Schürch Anita C AC Schipper Debby D Bijl Maarten A MA Dau Jim J Beckmen Kimberlee B KB Schapendonk Claudia M E CM Raj V Stalin VS Osterhaus Albert D M E AD Haagmans Bart L BL Tryland Morten M Smits Saskia L SL

PloS one 20140820 8

Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample c ...[more]

PMID: 25140520

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Project description:BackgroundCaribou and reindeer across the Arctic spend more than two thirds of their lives moving in snow. Yet snow-specific mechanisms driving their winter ecology and potentially influencing herd health and movement patterns are not well known. Integrative research coupling snow and wildlife sciences using observations, models, and wildlife tracking technologies can help fill this knowledge void.MethodsHere, we quantified the effects of snow depth on caribou winter range selection and movement. We used location data of Central Arctic Herd (CAH) caribou in Arctic Alaska collected from 2014 to 2020 and spatially distributed and temporally evolving snow depth data produced by SnowModel. These landscape-scale (90 m), daily snow depth data reproduced the observed spatial snow-depth variability across typical areal extents occupied by a wintering caribou during a 24-h period.ResultsWe found that fall snow depths encountered by the herd north of the Brooks Range exerted a strong influence on selection of two distinct winter range locations. In winters with relatively shallow fall snow depth (2016/17, 2018/19, and 2019/20), the majority of the CAH wintered on the tundra north of the Brooks Range mountains. In contrast, during the winters with relatively deep fall snow depth (2014/15, 2015/16, and 2017/18), the majority of the CAH caribou wintered in the mountainous boreal forest south of the Brooks Range. Long-term (19 winters; 2001-2020) monitoring of CAH caribou winter distributions confirmed this relationship. Additionally, snow depth affected movement and selection differently within these two habitats: in the mountainous boreal forest, caribou avoided areas with deeper snow, but when on the tundra, snow depth did not trigger significant deep-snow avoidance. In both wintering habitats, CAH caribou selected areas with higher lichen abundance, and they moved significantly slower when encountering deeper snow.ConclusionsIn general, our findings indicate that regional-scale selection of winter range is influenced by snow depth at or prior to fall migration. During winter, daily decision-making within the winter range is driven largely by snow depth. This integrative approach of coupling snow and wildlife observations with snow-evolution and caribou-movement modeling to quantify the multi-facetted effects of snow on wildlife ecology is applicable to caribou and reindeer herds throughout the Arctic.

Project description:BackgroundMigrations in temperate systems typically have two migratory phases, spring and autumn, and many migratory ungulates track the pulse of spring vegetation growth during a synchronized spring migration. In contrast, autumn migrations are generally less synchronous and the cues driving them remain understudied. Our goal was to identify the cues that migrants use in deciding when to initiate migration and how this is updated while en route.MethodsWe analyzed autumn migrations of Arctic barren-ground caribou (Rangifer tarandus) as a series of persistent and directional movements and assessed the influence of a suite of environmental factors. We fitted a dynamic-parameter movement model at the individual-level and estimated annual population-level parameters for weather covariates on 389 individual-seasons across 9 years.ResultsOur results revealed strong, consistent effects of decreasing temperature and increasing snow depth on migratory movements, indicating that caribou continuously update their migratory decision based on dynamic environmental conditions. This suggests that individuals pace migration along gradients of these environmental variables. Whereas temperature and snow appeared to be the most consistent cues for migration, we also found interannual variability in the effect of wind, NDVI, and barometric pressure. The dispersed distribution of individuals in autumn resulted in diverse environmental conditions experienced by individual caribou and thus pronounced variability in migratory patterns.ConclusionsBy analyzing autumn migration as a continuous process across the entire migration period, we found that caribou migration was largely related to temperature and snow conditions experienced throughout the journey. This mechanism of pacing autumn migration based on indicators of the approaching winter is analogous to the more widely researched mechanism of spring migration, when many migrants pace migration with a resource wave. Such a similarity in mechanisms highlights the different environmental stimuli to which migrants have adapted their movements throughout their annual cycle. These insights have implications for how long-distance migratory patterns may change as the Arctic climate continues to warm.

Dataset Information

Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units.

Publications

Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units.

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