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1. Estimating species relative abundances from museum records

   https://doi.org/10.1111/2041-210X.13705  

   Gotelli, Nicholas J.; Booher, Douglas B.; Urban, Mark C.; Ulrich, Werner; Suarez, Andrew V.; Skelly, David K.; Russell, David J.; Rowe, Rebecca J.; Rothendler, Matthew; Rios, Nelson; et al (September 2021, Methods in Ecology and Evolution)

   Abstract Dated, geo‐referenced museum specimens are a rich data source for reconstructing species' distribution and abundance patterns. However, museum records are potentially biased towards over‐representation of rare species, and it is unclear whether museum records can be used to estimate relative abundance in the field.We assembled 17 coupled field and museum datasets to quantitatively compare relative abundance estimates with the Dirichlet distribution. Collectively, these datasets comprise 73,039 museum records and 1,405,316 field observations of 2,240 species.Although museum records of rare species overestimated relative abundance by 1‐fold to over 100‐fold (median study = 9.0), the relative abundance of species estimated from museum occurrence records was strongly correlated with relative abundance estimated from standardized field surveys (r²range of 0.10–0.91, median study = 0.43).These analyses provide a justification for estimating species relative abundance with carefully curated museum occurrence records, which may allow for the detection of temporal or spatial shifts in the rank ordering of common and rare species. 

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2. Environmental DNA ‐based detection of pathogens in trade and captive settings: Best practices and validation for Batrachochytrium salamandrivorans

   https://doi.org/10.1111/2041-210X.14217  

   Brunner, Jesse L.; Yarber, Christian M.; Pearhill, Robert A. I.; Goldberg, Caren S. (September 2023, Methods in Ecology and Evolution)

   Abstract Detecting pathogens in the live animal trade is critical for tracking and preventing their movement, introduction and spillover into susceptible fauna. However, the scale of the live animal trade makes individually testing animals infeasible for all but the most economically important taxa. For instance, while the fungal pathogen,Batrachochytrium salamandrivorans(Bsal), threatens amphibian, particularly caudate diversity, in Europe and the Americas, screening even a fraction of the millions of live amphibians imported into the United States, alone, is impractically laborious and expensive. A promising alternative to individual‐level sampling (e.g. swabbing the skin of salamanders) is to instead collect DNA from the animals' environment (e.g. housing container or water) which allows us to screen a whole group of animals at a time.We used a series of experiments withBsal‐spiked water and substrates and experimentally infected rough‐skinned newts (Taricha granulosa) to determine which methods yield the mostBsalenvironmental DNA (eDNA) and evaluate the capacity of these methods to detectBsal‐infected animals in conditions found in captive settings and trade.We found that filtering water housing infected animals for even an hour can consistently recover detectable levels ofBsaleDNA, that there is little evidence ofBsaleDNA being clumped in housing containers or swamped or inhibited by dirty housing containers, and that eDNA‐based methods achieves an equivalent or higher chance of detectingBsalinfections in a (virtual) population of co‐housed newts with fewer samples than individual swabs.By sampling the genetic materials accumulated from a whole group of animals, eDNA‐based methods are a powerful means of detecting pathogens, such asBsal, in shipments and captive populations. These methods bring routine pathogen surveillance into reach in many more contexts and can thus be an important tool in conservation and disease control. 

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3. The Movebank system for studying global animal movement and demography

   https://doi.org/10.1111/2041-210X.13767  

   Kays, Roland; Davidson, Sarah C.; Berger, Matthias; Bohrer, Gil; Fiedler, Wolfgang; Flack, Andrea; Hirt, Julian; Hahn, Clemens; Gauggel, Dominik; Russell, Benedict; et al (December 2021, Methods in Ecology and Evolution)

   Abstract Quantifying movement and demographic events of free‐ranging animals is fundamental to studying their ecology, evolution and conservation. Technological advances have led to an explosion in sensor‐based methods for remotely observing these phenomena. This transition to big data creates new challenges for data management, analysis and collaboration.We present the Movebank ecosystem of tools used by thousands of researchers to collect, manage, share, visualize, analyse and archive their animal tracking and other animal‐borne sensor data. Users add sensor data through file uploads or live data streams and further organize and complete quality control within the Movebank system. All data are harmonized to a data model and vocabulary. The public can discover, view and download data for which they have been given access to through the website, the Animal Tracker mobile app or by API. Advanced analysis tools are available through the EnvDATA System, the MoveApps platform and a variety of user‐developed applications. Data owners can share studies with select users or the public, with options for embargos, licenses and formal archiving in a data repository.Movebank is used by over 3,100 data owners globally, who manage over 6 billion animal location and sensor measurements across more than 6,500 studies, with thousands of active tags sending over 3 million new data records daily. These data underlie >700 published papers and reports. We present a case study demonstrating the use of Movebank to assess life‐history events and demography, and engage with citizen scientists to identify mortalities and causes of death for a migratory bird.A growing number of researchers, government agencies and conservation organizations use Movebank to manage research and conservation projects and to meet legislative requirements. The combination of historic and new data with collaboration tools enables broad comparative analyses and data acquisition and mapping efforts. Movebank offers an integrated system for real‐time monitoring of animals at a global scale and represents a digital museum of animal movement and behaviour. Resources and coordination across countries and organizations are needed to ensure that these data, including those that cannot be made public, remain accessible to future generations. 

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4. Plant conservation assessment at scale: Rapid triage of extinction risks

   https://doi.org/10.1002/ppp3.10355  

   AuBuchon‐Elder, Taylor; Minx, Patrick; Bookout, Bess; Kellogg, Elizabeth A. (January 2023, PLANTS, PEOPLE, PLANET)

   Societal Impact StatementThe current rate of global biodiversity loss creates a pressing need to increase efficiency and throughput of extinction risk assessments in plants. We must assess as many plant species as possible, working with imperfect knowledge, to address the habitat loss and extinction threats of the Anthropocene. Using the biodiversity database, Botanical Information and Ecology Network (BIEN), and the Andropogoneae grass tribe as a case study, we demonstrate that large‐scale, preliminary conservation assessments can play a fundamental role in accelerating plant conservation pipelines and setting priorities for more in‐depth investigations. SummaryThe International Union for the Conservation of Nature (IUCN) Red List criteria are widely used to determine extinction risks of plant and animal life. Here, we used The Red List's criterion B, Geographic Range Size, to provide preliminary conservation assessments of the members of a large tribe of grasses, the Andropogoneae, with ~1100 species, including maize, sorghum, and sugarcane and their wild relatives.We used georeferenced occurrence data from the Botanical Information and Ecology Network (BIEN) and automated individual species assessments using ConR to demonstrate efficacy and accuracy in using time‐saving tools for conservation research. We validated our results with those from the IUCN‐recommended assessment tool, GeoCAT.We discovered a remarkably large gap in digitized information, with slightly more than 50% of the Andropogoneae lacking sufficient information for assessment. ConR and GeoCAT largely agree on which taxa are of least concern (>90%) or possibly threatened (<10%), highlighting that automating assessments with ConR is a viable strategy for preliminary conservation assessments of large plant groups. Results for crop wild relatives are similar to those for the entire dataset.Increasing digitization and collection needs to be a high priority. Available rapid assessment tools can then be used to identify species that warrant more comprehensive investigation. 

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5. Decoupling the effects of food and density on life‐history plasticity of wild animals using field experiments: Insights from the steward who sits in the shadow of its tail, the North American red squirrel

   https://doi.org/10.1111/1365-2656.13341  

   Dantzer, Ben; McAdam, Andrew_G; Humphries, Murray_M; Lane, Jeffrey_E; Boutin, Stan; Pelletier, ed., Fanie (October 2020, Journal of Animal Ecology)

   Abstract Long‐term studies of wild animals provide the opportunity to investigate how phenotypic plasticity is used to cope with environmental fluctuations and how the relationships between phenotypes and fitness can be dependent upon the ecological context.Many previous studies have only investigated life‐history plasticity in response to changes in temperature, yet wild animals often experience multiple environmental fluctuations simultaneously. This requires field experiments to decouple which ecological factor induces plasticity in fitness‐relevant traits to better understand their population‐level responses to those environmental fluctuations.For the past 32 years, we have conducted a long‐term integrative study of individually marked North American red squirrelsTamiasciurus hudsonicusErxleben in the Yukon, Canada. We have used multi‐year field experiments to examine the physiological and life‐history responses of individual red squirrels to fluctuations in food abundance and conspecific density.Our long‐term observational study and field experiments show that squirrels can anticipate increases in food availability and density, thereby decoupling the usual pattern where animals respond to, rather than anticipate, an ecological change.As in many other study systems, ecological factors that can induce plasticity (such as food and density) covary. However, our field experiments that manipulate food availability and social cues of density (frequency of territorial vocalizations) indicate that increases in social (acoustic) cues of density in the absence of additional food can induce similar life‐history plasticity, as does experimental food supplementation.Changes in the levels of metabolic hormones (glucocorticoids) in response to variation in food and density are one mechanism that seems to induce this adaptive life‐history plasticity.Although we have not yet investigated the energetic response of squirrels to elevated density or its association with life‐history plasticity, energetics research in red squirrels has overturned several standard pillars of knowledge in physiological ecology.We show how a tractable model species combined with integrative studies can reveal how animals cope with resource fluctuations through life‐history plasticity. 

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