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Leigh DM, Vandergast AG, Hunter ME, Crandall ED, Funk WC, Garroway CJ, Hoban S, Oyler-McCance SJ, Rellstab C, Segelbacher G, Schmidt C, Vázquez-Domínguez E, Paz-Vinas I. Best practices for genetic and genomic data archiving. Nat Ecol Evol 2024:10.1038/s41559-024-02423-7. [PMID: 38789640 DOI: 10.1038/s41559-024-02423-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.
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Affiliation(s)
- Deborah M Leigh
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
| | - Amy G Vandergast
- US Geological Survey, Western Ecological Research Center, San Diego, CA, USA
| | - Margaret E Hunter
- US Geological Survey, Wetland & Aquatic Research Center, Gainesville, FL, USA
| | - Eric D Crandall
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Colin J Garroway
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean Hoban
- Center for Tree Science, The Morton Arboretum, Lisle, IL, USA
| | | | | | | | - Chloé Schmidt
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, Leipzig, Germany
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Ivan Paz-Vinas
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
- Universite Claude Bernard Lyon 1, LEHNA UMR 5023, CNRS, ENTPE, Villeurbanne, France
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2
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Sánchez-Cano A, López-Calderón C, Cardona-Cabrera T, Green AJ, Höfle U. Connectivity at the human-wildlife interface: starling movements relate to carriage of E. coli. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171899. [PMID: 38527537 DOI: 10.1016/j.scitotenv.2024.171899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
Synanthropic bird species in human, poultry or livestock environments can increase the spread of pathogens and antibiotic-resistant bacteria between wild and domestic animals. We present the first telemetry-based spatial networks for a small songbird. We quantified landscape connectivity exerted by spotless starling movements, and aimed to determine if connectivity patterns were related to carriage of potential pathogens. We captured 28 starlings on a partridge farm in 2020 and tested them for Avian influenza virus, West Nile virus WNV, Avian orthoavulavirus 1, Coronavirus, Salmonella spp. and Escherichia coli. We did not detect any viruses or Salmonella, but one individual had antibodies against WNV or cross-reacting Flaviviruses. We found E. coli in 61 % (17 of 28) of starlings, 76 % (13 of 17) of which were resistant to gentamicin, 12 % (2 of 17) to cefotaxime/enrofloxacin and 6 % (1 of 17) were phenotypic extended spectrum beta-lactamase (ESBL) carriers. We GPS-tracked 17 starlings and constructed spatial networks showing how their movements (i.e. links) connect different farms with nearby urban and natural habitats (i.e. nodes with different attributes). Using E. coli carriage as a proxy for acquisition/dispersal of bacteria, we found differences across spatial networks constructed for E. coli positive (n = 7) and E. coli negative (n = 9) starlings. We used Exponential Random Graph Models to reveal significant differences between networks. In particular, an urban roost was more connected to other sites by movements of E. coli positive than by movements of E. coli negative starlings. Furthermore, an open pine forest used mainly for roosting was more connected to other sites by movements of E. coli negative than by movements of E. coli positive starlings. Using E. coli as a proxy for a potential pathogen carried by starlings, we reveal the pathways of spread that starlings could provide between farms, urban and natural habitats.
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Affiliation(s)
- Alberto Sánchez-Cano
- SaBio Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain.
| | - Cosme López-Calderón
- Department of Conservation Biology and Global Change, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain; Grupo de Investigación en Conservación, Biodiversidad y Cambio Global, Universidad de Extremadura, Badajoz, Spain
| | - Teresa Cardona-Cabrera
- SaBio Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Andy J Green
- Department of Conservation Biology and Global Change, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Ursula Höfle
- SaBio Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain.
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3
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Wooster EIF, Nimmo DG. Functional trait databases for macrobehaviour. Trends Ecol Evol 2024:S0169-5347(24)00105-8. [PMID: 38714478 DOI: 10.1016/j.tree.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/10/2024]
Affiliation(s)
- Eamonn I F Wooster
- Gulbali Institute, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Albury, NSW, Australia.
| | - Dale G Nimmo
- Gulbali Institute, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Albury, NSW, Australia
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Hirsch BT, Kays R, Alavi S, Caillaud D, Havmoller R, Mares R, Crofoot M. Smarter foragers do not forage smarter: a test of the diet hypothesis for brain expansion. Proc Biol Sci 2024; 291:20240138. [PMID: 38808448 DOI: 10.1098/rspb.2024.0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/24/2024] [Indexed: 05/30/2024] Open
Abstract
A leading hypothesis for the evolution of large brains in humans and other species is that a feedback loop exists whereby intelligent animals forage more efficiently, which results in increased energy intake that fuels the growth and maintenance of large brains. We test this hypothesis for the first time with high-resolution tracking data from four sympatric, frugivorous rainforest mammal species (42 individuals) and drone-based maps of their predominant feeding trees. We found no evidence that larger-brained primates had more efficient foraging paths than smaller brained procyonids. This refutes a key assumption of the fruit-diet hypothesis for brain evolution, suggesting that other factors such as temporal cognition, extractive foraging or sociality have been more important for brain evolution.
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Affiliation(s)
- Ben T Hirsch
- Smithsonian Tropical Research Institute, Balboa, Republic of Panamá
- College of Science and Engineering, James Cook University, Townsville, Australia
| | - Roland Kays
- Smithsonian Tropical Research Institute, Balboa, Republic of Panamá
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Shauhin Alavi
- Department for the Ecology of Animal Societies, Max Planck Institute of Animal Behavior, Konstanz, Germany
| | - Damien Caillaud
- Department of Anthropology, University of California, Davis, One Shields Ave., Davis, CA 95616, USA
| | - Rasmus Havmoller
- Natural History Museum of Denmark, University of Copenhagen, Kobenhavn, Denmark
| | - Rafael Mares
- Smithsonian Tropical Research Institute, Balboa, Republic of Panamá
| | - Margaret Crofoot
- Smithsonian Tropical Research Institute, Balboa, Republic of Panamá
- Natural History Museum of Denmark, University of Copenhagen, Kobenhavn, Denmark
- Department of Biology, University of Konstanz, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
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5
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Hawkes LA, Davies P, Hall AE, Horton TW, Stamp T, Witt MJ, Sheehan EV. People behind the "pings"; limiting authorship threatens collaboration in telemetry. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38519854 DOI: 10.1111/jfb.15700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/09/2024] [Indexed: 03/25/2024]
Affiliation(s)
- L A Hawkes
- Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - P Davies
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - A E Hall
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - T W Horton
- Faculty of Environment, Society and Economy, University of Exeter, Penryn Campus, Penryn, UK
| | - T Stamp
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - M J Witt
- Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- Faculty of Environment, Society and Economy, University of Exeter, Penryn Campus, Penryn, UK
| | - E V Sheehan
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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Su R, Liu Y, Dodge S. ORTEGA v1.0: an open-source Python package for context-aware interaction analysis using movement data. MOVEMENT ECOLOGY 2024; 12:20. [PMID: 38461249 PMCID: PMC10925014 DOI: 10.1186/s40462-024-00460-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/17/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Interaction analysis via movement in space and time contributes to understanding social relationships among individuals and their dynamics in ecological systems. While there is an exciting growth in research in computational methods for interaction analysis using movement data, there remain challenges regarding reproducibility and replicability of the existing approaches. The current movement interaction analysis tools are often less accessible or tested for broader use in ecological research. RESULTS To address these challenges, this paper presents ORTEGA, an Object-oRiented TimE-Geographic Analytical tool, as an open-source Python package for analyzing potential interactions between pairs of moving entities based on the observation of their movement. ORTEGA is developed based on one of the newly emerged time-geographic approaches for quantifying space-time interaction patterns among animals. A case study is presented to demonstrate and evaluate the functionalities of ORTEGA in tracing dynamic interaction patterns in animal movement data. Besides making the analytical code and data freely available to the community, the developed package also offers an extension of the existing theoretical development of ORTEGA for incorporating a context-aware ability to inform interaction analysis. CONCLUSIONS ORTEGA contributes two significant capabilities: (1) the functions to identify potential interactions (e.g., encounters, concurrent interactions, delayed interactions) from movement data of two or more entities using a time-geographic-based approach; and (2) the capacity to compute attributes of potential interaction events including start time, end time, interaction duration, and difference in movement parameters such as speed and moving direction, and also contextualize the identified potential interaction events.
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Affiliation(s)
- Rongxiang Su
- Department of Geography, University of California Santa Barbara, Santa Barbara, 93106, USA.
| | - Yifei Liu
- Department of Geography, University of California Santa Barbara, Santa Barbara, 93106, USA
| | - Somayeh Dodge
- Department of Geography, University of California Santa Barbara, Santa Barbara, 93106, USA
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Fischerström K, Dryselius R, Lindblad M, Kühlmann-Berenzon S, Karamehmedovic N, Börjesson S, Hashemi N, Gunn I, Gustavsson AM, Lindroos N, Nederby-Öhd J, Widerström M, Rimhanen-Finne R, Vainio A, Rehn M. Outbreak of Salmonella Typhimurium linked to Swedish pre-washed rocket salad, Sweden, September to November 2022. Euro Surveill 2024; 29:2300299. [PMID: 38456218 PMCID: PMC10986667 DOI: 10.2807/1560-7917.es.2024.29.10.2300299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/04/2023] [Indexed: 03/09/2024] Open
Abstract
In September 2022, the Public Health Agency of Sweden observed an increase in domestic Salmonella Typhimurium cases through the Swedish electronic notification system, and an outbreak strain was identified with whole genome sequencing. Overall, 109 cases with symptom onset between 17 September and 24 November 2022 were reported from 20 of 21 Swedish regions. The median age of cases was 52 years (range 4-87 years) and 62% were female. A case-control study found cases to be associated with consumption of rocket salad (adjusted odds ratio (aOR) = 4.9; 95% confidence interval (CI): 2.4-10, p value < 0.001) and bagged mixed salad (aOR = 4.0; 95% CI: 1.9-8.1, p value < 0.001). Trace-back, supported by Finnish authorities who identified the Swedish outbreak strain in a Finnish cluster during the same time period, identified rocket salad, cultivated, pre-washed and pre-packed in Sweden as the likely source of the outbreak. No microbiological analyses of rocket salad were performed. Our investigation indicates that bagged leafy greens such as rocket salad, regardless of pre-washing procedures in the production chain, may contain Salmonella and cause outbreaks, posing a health risk to consumers. We emphasise the need for primary producers of leafy greens to identify possible contamination points to prevent outbreaks.
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Affiliation(s)
- Karolina Fischerström
- ECDC Fellowship Programme, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
- Public Health Agency of Sweden (PHAS), Solna, Sweden
| | | | | | | | | | - Stefan Börjesson
- School of Health Science, Örebro University, Örebro, Sweden
- Public Health Agency of Sweden (PHAS), Solna, Sweden
| | | | - Ingrid Gunn
- Department of Infectious Disease Prevention and Control, Region Kalmar County, Kalmar, Sweden
| | - Ann-Mari Gustavsson
- Department of Infection Prevention and Control, County of Värmland, Karlstad, Sweden
| | - Nilla Lindroos
- Department of Infectious Disease Prevention and Control, Region Halland, Halmstad, Sweden
| | - Joanna Nederby-Öhd
- Department of Infectious Disease Prevention and Control, Stockholm Region, Stockholm, Sweden
| | | | - Ruska Rimhanen-Finne
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Anni Vainio
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Moa Rehn
- Public Health Agency of Sweden (PHAS), Solna, Sweden
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Mirski P, Grosberg J, Kull T, Mellov P, Tõnisalu G, Väli V, Väli Ü. Movement of avian predators points to biodiversity hotspots in agricultural landscape. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231543. [PMID: 38204791 PMCID: PMC10776223 DOI: 10.1098/rsos.231543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/01/2023] [Indexed: 01/12/2024]
Abstract
Global agricultural landscapes are witnessing a concerning decline in biodiversity, and this trend is predicted to persist. To safeguard these biodiversity-rich areas, it is crucial to pinpoint hotspots effectively. In doing so, we used various species of avian predators as suitable sentinel animals due to their mobility and dependence on prey diversity and abundance. Between 2019 and 2021, we tracked 62 individuals from four bird of prey species using GPS loggers in Estonian farmland. Dividing the study area into 50 m grids and overlaying them with tracked individuals' locations enabled us to differentiate between hotspots of their activity and control sites. We conducted surveys on amphibian, bird, small mammal and plant abundance and diversity to determine if avian predator activity hotspots correlated with overall biodiversity. Our findings revealed significantly higher diversity and abundance in the surveyed groups within activity hotspots compared to control sites. These hotspots continued to be frequently used by raptors in the subsequent year, albeit not two years later. In conclusion, multispecies GPS telemetry of avian predators emerges as an objective, dependable and spatially accurate biodiversity indicator. With the accumulation of movement data, we anticipate increased interest and adoption of this approach in biodiversity monitoring.
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Affiliation(s)
- Paweł Mirski
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, Tartu 51006, Estonia
- Faculty of Biology, University of Białystok, Ciołkowskiego 1J, Białystok 15-245, Poland
| | - Jaan Grosberg
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, Tartu 51006, Estonia
| | - Thea Kull
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, Tartu 51006, Estonia
| | - Pelle Mellov
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, Tartu 51006, Estonia
| | - Grete Tõnisalu
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, Tartu 51006, Estonia
| | - Vivika Väli
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, Tartu 51006, Estonia
| | - Ülo Väli
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, Tartu 51006, Estonia
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9
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Albery GF, Bansal S, Silk MJ. Comparative approaches in social network ecology. Ecol Lett 2024; 27:e14345. [PMID: 38069575 DOI: 10.1111/ele.14345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 01/31/2024]
Abstract
Social systems vary enormously across the animal kingdom, with important implications for ecological and evolutionary processes such as infectious disease dynamics, anti-predator defence, and the evolution of cooperation. Comparing social network structures between species offers a promising route to help disentangle the ecological and evolutionary processes that shape this diversity. Comparative analyses of networks like these are challenging and have been used relatively little in ecology, but are becoming increasingly feasible as the number of empirical datasets expands. Here, we provide an overview of multispecies comparative social network studies in ecology and evolution. We identify a range of advancements that these studies have made and key challenges that they face, and we use these to guide methodological and empirical suggestions for future research. Overall, we hope to motivate wider publication and analysis of open social network datasets in animal ecology.
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Affiliation(s)
- Gregory F Albery
- Department of Biology, Georgetown University, Washington, District of Columbia, USA
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, District of Columbia, USA
| | - Matthew J Silk
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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10
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Urbano F, Viterbi R, Pedrotti L, Vettorazzo E, Movalli C, Corlatti L. Enhancing biodiversity conservation and monitoring in protected areas through efficient data management. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 196:12. [PMID: 38051448 PMCID: PMC10697885 DOI: 10.1007/s10661-023-11851-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 09/06/2023] [Indexed: 12/07/2023]
Abstract
A scientifically informed approach to decision-making is key to ensuring the sustainable management of ecosystems, especially in the light of increasing human pressure on habitats and species. Protected areas, with their long-term institutional mandate for biodiversity conservation, play an important role as data providers, for example, through the long-term monitoring of natural resources. However, poor data management often limits the use and reuse of this wealth of information. In this paper, we share lessons learned in managing long-term data from the Italian Alpine national parks. Our analysis and examples focus on specific issues faced by managers of protected areas, which partially differ from those faced by academic researchers, predominantly owing to different mission, governance, and temporal perspectives. Rigorous data quality control, the use of appropriate data management tools, and acquisition of the necessary skills remain the main obstacles. Common protocols for data collection offer great opportunities for the future, and complete recovery and documentation of time series is an urgent priority. Notably, before data can be shared, protected areas should improve their data management systems, a task that can be achieved only with adequate resources and a long-term vision. We suggest strategies that protected areas, funding agencies, and the scientific community can embrace to address these problems. The added value of our work lies in promoting engagement with managers of protected areas and in reporting and analysing their concrete requirements and problems, thereby contributing to the ongoing discussion on data management and sharing through a bottom-up approach.
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Affiliation(s)
| | - Ramona Viterbi
- Gran Paradiso National Park, Via Pio VII 9, 10135, Torino, Italy
| | - Luca Pedrotti
- Stelvio National Park, Via De Simoni 42, 23032, Bormio, Italy
| | - Enrico Vettorazzo
- Dolomiti Bellunesi National Park, Piazzale Zancanaro 1, 32032, Feltre, Italy
| | - Cristina Movalli
- Val Grande National Park, Piazza Pretorio 6, 28805, Vogogna, Italy
| | - Luca Corlatti
- Stelvio National Park, Via De Simoni 42, 23032, Bormio, Italy
- Chair of Wildlife Ecology and Management, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany
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Casazza ML, Lorenz AA, Overton CT, Matchett EL, Mott AL, Mackell DA, McDuie F. AIMS for wildlife: Developing an automated interactive monitoring system to integrate real-time movement and environmental data for true adaptive management. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118636. [PMID: 37574637 DOI: 10.1016/j.jenvman.2023.118636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/28/2023] [Accepted: 07/15/2023] [Indexed: 08/15/2023]
Abstract
To effectively manage species and habitats at multiple scales, population and land managers require rapid information on wildlife use of managed areas and responses to landscape conditions and management actions. GPS tracking studies of wildlife are particularly informative to species ecology, habitat use, and conservation. Combining GPS data with administrative data and a diverse suite of remotely sensed, geo-referenced environmental (e.g., climatic) data, would more comprehensively inform how animals interact with and utilize habitats and ecosystems and our goal was to create a conceptual model for a system that would accomplish this - the 'Automated Interactive Monitoring System (AIMS) for Wildlife'. Our objective for this study was to develop a Customized Wildlife Report (CWR) - the first AIMS for Wildlife deliverable product. CWRs collate and summarize our 8-year GPS tracking dataset of ∼11 million locations from 1338 individual (16 species) avifauna and make actionable, real-time data on animal movements and trends in a specific area of interest available to managers and stakeholders for rapid application in day-to-day management. The CWR exemplar presented in this paper was developed to address needs identified by habitat managers of Sacramento National Wildlife Refuge and illustrates the highly specific, information offered and how it contributes to assessing the efficacy of conservation actions while allowing for near real-time adaptive management. The report can be easily customized for any of the thousands of wildlife refuges or regional areas of interest in the United States, emphasizing the broad application of an animal movement data stream. Utilizing diverse, extensive telemetry data streams through scientific collaboration can aid managers and conservation stakeholders with short and long-term research and conservation planning and help address a cadre of issues from local-scale habitat management to improving the understanding of landscape level impacts like drought, wildfire, and climate change on wildlife populations.
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Affiliation(s)
- Michael L Casazza
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, 800 Business Park Drive, Suite D Dixon, CA, USA.
| | - Austen A Lorenz
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, 800 Business Park Drive, Suite D Dixon, CA, USA
| | - Cory T Overton
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, 800 Business Park Drive, Suite D Dixon, CA, USA
| | - Elliott L Matchett
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, 800 Business Park Drive, Suite D Dixon, CA, USA
| | - Andrea L Mott
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, 800 Business Park Drive, Suite D Dixon, CA, USA
| | - Desmond A Mackell
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, 800 Business Park Drive, Suite D Dixon, CA, USA
| | - Fiona McDuie
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, 800 Business Park Drive, Suite D Dixon, CA, USA; San Jose State University Research Foundation, Moss Landing Marine Laboratories, 8272 Moss Landing Rd. Moss Landing, CA, USA
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12
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Hurtado C, Hemming V, Burton C. Comparing wildlife habitat suitability models based on expert opinion with camera trap detections. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14113. [PMID: 37204011 DOI: 10.1111/cobi.14113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 03/21/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
Expert knowledge is used in the development of wildlife habitat suitability models (HSMs) for management and conservation decisions. However, the consistency of such models has been questioned. Focusing on 1 method for elicitation, the analytic hierarchy process, we generated expert-based HSMs for 4 felid species: 2 forest specialists (ocelot [Leopardus pardalis] and margay [Leopardus wiedii]) and 2 habitat generalist species (Pampas cat [Leopardus colocola] and puma [Puma concolor]). Using these HSMs, species detections from camera-trap surveys, and generalized linear models, we assessed the effect of study species and expert attributes on the correspondence between expert models and camera-trap detections. We also examined whether aggregation of participant responses and iterative feedback improved model performance. We ran 160 HSMs and found that models for specialist species showed higher correspondence with camera-trap detections (AUC [area under the receiver operating characteristic curve] >0.7) than those for generalists (AUC < 0.7). Model correspondence increased as participant years of experience in the study area increased, but only for the understudied generalist species, Pampas cat (β = 0.024 [SE 0.007]). No other participant attribute was associated with model correspondence. Feedback and revision of models improved model correspondence, and aggregating judgments across multiple participants improved correspondence only for specialist species. The average correspondence of aggregated judgments increased as group size increased but leveled off after 5 experts for all species. Our results suggest that correspondence between expert models and empirical surveys increases as habitat specialization increases. We encourage inclusion of participants knowledgeable of the study area and model validation for expert-based modeling of understudied and generalist species.
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Affiliation(s)
- Cindy Hurtado
- Department of Forest Resources Management, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
- Centro de Investigación Biodiversidad Sostenible-BioS, Piura, Peru
| | - Victoria Hemming
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cole Burton
- Department of Forest Resources Management, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
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Kays R, Wikelski M. The Internet of Animals: what it is, what it could be. Trends Ecol Evol 2023; 38:859-869. [PMID: 37263824 DOI: 10.1016/j.tree.2023.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 06/03/2023]
Abstract
One of the biggest trends in ecology over the past decade has been the creation of standardized databases. Recently, this has included live data, formal linkages between disparate databases, and automated analytics, a synergy that we recognize as the Internet of Animals (IoA). Early IoA systems relate animal locations to remote-sensing data to predict species distributions and detect disease outbreaks, and use live data to inform management of endangered species. However, meeting the future potential of the IoA concept will require solving challenges of taxonomy, data security, and data sharing. By linking data sets, integrating live data, and automating workflows, the IoA has the potential to enable discoveries and predictions relevant to human societies and the conservation of animals.
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Affiliation(s)
- Roland Kays
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA; North Carolina Museum of Natural Sciences, Raleigh, NC, USA; Smithsonian Tropical Research Institute, Balboa, Republic of Panama.
| | - Martin Wikelski
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama; Department of Animal Migration, Max Planck Institute of Animal Behaviour, Radolfzell, Germany; Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
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14
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Rasmussen EA, Czaja A, Cuthbert FJ, Tan GS, Lemey P, Nelson MI, Culhane MR. Influenza A viruses in gulls in landfills and freshwater habitats in Minnesota, United States. Front Genet 2023; 14:1172048. [PMID: 37229191 PMCID: PMC10203411 DOI: 10.3389/fgene.2023.1172048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/10/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction: The unpredictable evolution of avian influenza viruses (AIVs) presents an ongoing threat to agricultural production and public and wildlife health. Severe outbreaks of highly pathogenic H5N1 viruses in US poultry and wild birds since 2022 highlight the urgent need to understand the changing ecology of AIV. Surveillance of gulls in marine coastal environments has intensified in recent years to learn how their long-range pelagic movements potentially facilitate inter-hemispheric AIV movements. In contrast, little is known about inland gulls and their role in AIV spillover, maintenance, and long-range dissemination. Methods: To address this gap, we conducted active AIV surveillance in ring-billed gulls (Larus delawarensis) and Franklin's gulls (Leucophaeus pipixcan) in Minnesota's natural freshwater lakes during the summer breeding season and in landfills during fall migration (1,686 samples). Results: Whole-genome AIV sequences obtained from 40 individuals revealed three-lineage reassortants with a mix of genome segments from the avian Americas lineage, avian Eurasian lineage, and a global "Gull" lineage that diverged more than 50 years ago from the rest of the AIV global gene pool. No poultry viruses contained gull-adapted H13, NP, or NS genes, pointing to limited spillover. Geolocators traced gull migration routes across multiple North American flyways, explaining how inland gulls imported diverse AIV lineages from distant locations. Migration patterns were highly varied and deviated far from assumed "textbook" routes. Discussion: Viruses circulating in Minnesota gulls during the summer breeding season in freshwater environments reappeared in autumn landfills, evidence of AIV persistence in gulls between seasons and transmission between habitats. Going forward, wider adoption of technological advances in animal tracking devices and genetic sequencing is needed to expand AIV surveillance in understudied hosts and habitats.
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Affiliation(s)
- Elizabeth A. Rasmussen
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Agata Czaja
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Francesca J. Cuthbert
- Department of Fisheries, Wildlife and Conservation Biology, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Gene S. Tan
- J. Craig Venter Institute, La Jolla, Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Martha I. Nelson
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Marie R. Culhane
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
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15
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López-Calderón C, Martín-Vélez V, Blas J, Höfle U, Sánchez MI, Flack A, Fiedler W, Wikelski M, Green AJ. White stork movements reveal the ecological connectivity between landfills and different habitats. MOVEMENT ECOLOGY 2023; 11:18. [PMID: 36978169 PMCID: PMC10045253 DOI: 10.1186/s40462-023-00380-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Connections between habitats are key to a full understanding of anthropic impacts on ecosystems. Freshwater habitats are especially biodiverse, yet depend on exchange with terrestrial habitats. White storks (Ciconia ciconia) are widespread opportunists that often forage in landfills and then visit wetlands, among other habitats. It is well known that white storks ingest contaminants at landfills (such as plastics and antibiotic resistant bacteria), which can be then deposited in other habitats through their faeces and regurgitated pellets. METHODS We characterized the role of white storks in habitat connectivity by analyzing GPS data from populations breeding in Germany and wintering from Spain to Morocco. We overlaid GPS tracks on a land-use surface to construct a spatially-explicit network in which nodes were sites, and links were direct flights. We then calculated centrality metrics, identified spatial modules, and quantified overall connections between habitat types. For regional networks in southern Spain and northern Morocco, we built Exponential Random Graph Models (ERGMs) to explain network topologies as a response to node habitat. RESULTS For Spain and Morocco combined, we built a directed spatial network with 114 nodes and 370 valued links. Landfills were the habitat type most connected to others, as measured by direct flights. The relevance of landfills was confirmed in both ERGMs, with significant positive effects of this habitat as a source of flights. In the ERGM for southern Spain, we found significant positive effects of rice fields and salines (solar saltworks) as sinks for flights. By contrast, in the ERGM for northern Morocco, we found a significant positive effect of marshes as a sink for flights. CONCLUSIONS These results illustrate how white storks connect landfills with terrestrial and aquatic habitats, some of which are managed for food production. We identified specific interconnected habitat patches across Spain and Morocco that could be used for further studies on biovectoring of pollutants, pathogens and other propagules.
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Affiliation(s)
- Cosme López-Calderón
- Department of Wetland Ecology, Estación Biológica de Doñana CSIC, Seville, Spain.
| | - Víctor Martín-Vélez
- Department of Wetland Ecology, Estación Biológica de Doñana CSIC, Seville, Spain
| | - Julio Blas
- Department of Conservation Biology, Estación Biológica de Doñana CSIC, Seville, Spain
| | - Ursula Höfle
- SaBio Health and Biotechnology Research Group, Institute for Game and Wildlife Research (IREC), CSIC-UCLM-JCCM, Ciudad Real, Spain
| | - Marta I Sánchez
- Department of Wetland Ecology, Estación Biológica de Doñana CSIC, Seville, Spain
| | - Andrea Flack
- Collective Migration Group, Max Planck Institute of Animal Behavior, 78315, Radolfzell, Germany
- Department of Migration and Immuno-Ecology, Max Planck Institute of Animal Behaviour, Radolfzell, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78468, Constance, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Wolfgang Fiedler
- Department of Migration and Immuno-Ecology, Max Planck Institute of Animal Behaviour, Radolfzell, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78468, Constance, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Martin Wikelski
- Department of Migration and Immuno-Ecology, Max Planck Institute of Animal Behaviour, Radolfzell, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78468, Constance, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Andy J Green
- Department of Wetland Ecology, Estación Biológica de Doñana CSIC, Seville, Spain
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16
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Wild TA, van Schalkwyk L, Viljoen P, Heine G, Richter N, Vorneweg B, Koblitz JC, Dechmann DKN, Rogers W, Partecke J, Linek N, Volkmer T, Gregersen T, Havmøller RW, Morelle K, Daim A, Wiesner M, Wolter K, Fiedler W, Kays R, Ezenwa VO, Meboldt M, Wikelski M. A multi-species evaluation of digital wildlife monitoring using the Sigfox IoT network. ANIMAL BIOTELEMETRY 2023; 11:13. [PMID: 38800509 PMCID: PMC11116194 DOI: 10.1186/s40317-023-00326-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/15/2023] [Indexed: 05/29/2024]
Abstract
Bio-telemetry from small tags attached to animals is one of the principal methods for studying the ecology and behaviour of wildlife. The field has constantly evolved over the last 80 years as technological improvement enabled a diversity of sensors to be integrated into the tags (e.g., GPS, accelerometers, etc.). However, retrieving data from tags on free-ranging animals remains a challenge since satellite and GSM networks are relatively expensive and or power hungry. Recently a new class of low-power communication networks have been developed and deployed worldwide to connect the internet of things (IoT). Here, we evaluated one of these, the Sigfox IoT network, for the potential as a real-time multi-sensor data retrieval and tag commanding system for studying fauna across a diversity of species and ecosystems. We tracked 312 individuals across 30 species (from 25 g bats to 3 t elephants) with seven different device concepts, resulting in more than 177,742 successful transmissions. We found a maximum line of sight communication distance of 280 km (on a flying cape vulture [Gyps coprotheres]), which sets a new documented record for animal-borne digital data transmission using terrestrial infrastructure. The average transmission success rate amounted to 68.3% (SD 22.1) on flying species and 54.1% (SD 27.4) on terrestrial species. In addition to GPS data, we also collected and transmitted data products from accelerometers, barometers, and thermometers. Further, we assessed the performance of Sigfox Atlas Native, a low-power method for positional estimates based on radio signal strengths and found a median accuracy of 12.89 km (MAD 5.17) on animals. We found that robust real-time communication (median message delay of 1.49 s), the extremely small size of the tags (starting at 1.28 g without GPS), and the low power demands (as low as 5.8 µAh per transmitted byte) unlock new possibilities for ecological data collection and global animal observation.
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Affiliation(s)
- Timm A. Wild
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Department of Biology, University of Konstanz, 78464 Constance, Germany
- Product Development Group Zurich (pd|z), ETH Zürich, Leonhardstr. 21, 8092 Zurich, Switzerland
| | - Louis van Schalkwyk
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Department of Agriculture, Land Reform and Rural Development, P.O. Box 12, Skukuza, 1350 South Africa
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Soutpan Road, Pretoria, 0110 South Africa
| | - Pauli Viljoen
- Scientific Services, South African National Parks, Skukuza, 1350 South Africa
| | - Georg Heine
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
| | - Nina Richter
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
| | - Bernd Vorneweg
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
| | - Jens C. Koblitz
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Department of Biology, University of Konstanz, 78464 Constance, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Constance, Germany
| | - Dina K. N. Dechmann
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Department of Biology, University of Konstanz, 78464 Constance, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Constance, Germany
| | - Will Rogers
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511 USA
| | - Jesko Partecke
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Department of Biology, University of Konstanz, 78464 Constance, Germany
| | - Nils Linek
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Department of Biology, University of Konstanz, 78464 Constance, Germany
| | - Tamara Volkmer
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Department of Biology, University of Konstanz, 78464 Constance, Germany
| | - Troels Gregersen
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Section for Zoology, Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen, OE Denmark
| | - Rasmus W. Havmøller
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Section for Zoology, Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen, OE Denmark
| | - Kevin Morelle
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Department of Game Management and Wildlife Biology, Czech University of Life Science, 165 00 Prague, Czech Republic
| | - Andreas Daim
- Institute of Wildlife Biology and Game, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences (BOKU), 1180 Vienna, Austria
| | | | - Kerri Wolter
- Vulpro NpC, Vulture Programme, Plot 121 Boekenhoutkloof Road, Rietfontein, 0216 South Africa
| | - Wolfgang Fiedler
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
| | - Roland Kays
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601 USA
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27607 USA
| | - Vanessa O. Ezenwa
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511 USA
| | - Mirko Meboldt
- Product Development Group Zurich (pd|z), ETH Zürich, Leonhardstr. 21, 8092 Zurich, Switzerland
| | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Department of Biology, University of Konstanz, 78464 Constance, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Constance, Germany
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17
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Kellner A, Atwood TC, Douglas DC, Breck SW, Wittemyer G. High winds and melting sea ice trigger landward movement in a polar bear population of concern. Ecosphere 2023. [DOI: 10.1002/ecs2.4420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Annie Kellner
- Graduate Degree Program in Ecology Colorado State University Fort Collins Colorado USA
- Department of Fish, Wildlife, and Conservation Biology Colorado State University Fort Collins Colorado USA
| | - Todd C. Atwood
- U.S. Geological Survey Alaska Science Center Anchorage Alaska USA
| | | | - Stewart W. Breck
- USDA‐WS‐National Wildlife Research Center Fort Collins Colorado USA
| | - George Wittemyer
- Graduate Degree Program in Ecology Colorado State University Fort Collins Colorado USA
- Department of Fish, Wildlife, and Conservation Biology Colorado State University Fort Collins Colorado USA
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18
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Guilherme JL, Jones VR, Catry I, Beal M, Dias MP, Oppel S, Vickery JA, Hewson CM, Butchart SHM, Rodrigues ASL. Connectivity between countries established by landbirds and raptors migrating along the African-Eurasian flyway. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14002. [PMID: 36073347 PMCID: PMC10107209 DOI: 10.1111/cobi.14002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The conservation of long-distance migratory birds requires coordination between the multiple countries connected by the movements of these species. The recent expansion of tracking studies is shedding new light on these movements, but much of this information is fragmented and inaccessible to conservation practitioners and policy makers. We synthesized current knowledge on the connectivity established between countries by landbirds and raptors migrating along the African-Eurasian flyway. We reviewed tracking studies to compile migration records for 1229 individual birds, from which we derived 544 migratory links, each link corresponding to a species' connection between a breeding country in Europe and a nonbreeding country in sub-Saharan Africa. We used these migratory links to analyze trends in knowledge over time and spatial patterns of connectivity per country (across species), per species (across countries), and at the flyway scale (across all countries and all species). The number of tracking studies available increased steadily since 2010 (particularly for landbirds), but the coverage of existing tracking data was highly incomplete. An average of 7.5% of migratory landbird species and 14.6% of raptor species were tracked per country. More data existed from central and western European countries, and it was biased toward larger bodied species. We provide species- and country-level syntheses of the migratory links we identified from the reviewed studies, involving 123 populations of 43 species, migrating between 28 European and 43 African countries. Several countries (e.g., Spain, Poland, Ethiopia, Democratic Republic of Congo) are strategic priorities for future tracking studies to complement existing data, particularly on landbirds. Despite the limitations in existing tracking data, our data and results can inform discussions under 2 key policy instruments at the flyway scale: the African-Eurasian Migratory Landbirds Action Plan and the Memorandum of Understanding on the Conservation of Migratory Birds of Prey in Africa and Eurasia.
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Affiliation(s)
- João L. Guilherme
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
- BirdLife InternationalCambridgeUK
| | | | - Inês Catry
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório AssociadoUniversidade do PortoVairãoPortugal
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Laboratório AssociadoUniversidade de LisboaLisbonPortugal
- BIOPOLIS Program in GenomicsBiodiversity and Land Planning, CIBIOVairãoPortugal
| | - Martin Beal
- BirdLife InternationalCambridgeUK
- MARE – Marine and Environmental Sciences CentreISPA – Instituto UniversitárioLisbonPortugal
| | - Maria P. Dias
- BirdLife InternationalCambridgeUK
- cE3c ‐ Center for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Department of Animal BiologyFaculty of Sciences of the University of Lisbon, 1749‐016 Lisboa, Campo GrandeLisbonPortugal
| | - Steffen Oppel
- RSPB Centre for Conservation ScienceRoyal Society for the Protection of Birds, The LodgeSandyUK
| | - Juliet A. Vickery
- RSPB Centre for Conservation ScienceRoyal Society for the Protection of Birds, The LodgeSandyUK
- British Trust for Ornithology, The NunneryThetfordUK
- Department of ZoologyUniversity of CambridgeCambridgeUK
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | | | - Stuart H. M. Butchart
- BirdLife InternationalCambridgeUK
- Department of ZoologyUniversity of CambridgeCambridgeUK
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19
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Padayachee K, Reynolds C, Mateo R, Amar A. A global review of the temporal and spatial patterns of DDT and dieldrin monitoring in raptors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159734. [PMID: 36349626 DOI: 10.1016/j.scitotenv.2022.159734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/17/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Concentrations of organochlorine pesticides have been extensively monitored in birds, particularly from higher trophic guilds such as raptors. While monitoring of raptors has been ongoing for decades, patterns from monitoring activities have never been summarised on a global scale. In this study, we undertake a review to better describe the monitoring of two widespread organochlorine pesticides monitored globally in raptors, DDT and dieldrin. We provide a historical retrospective on the monitoring effort of a global environmental issue. Sampling was heavily biased geographically to the global north, with more than 90 % of studies conducted in this socio-geographic region, most from Europe and North America. Although monitoring occurred from at least 114 species, most samples came from relatively few species, with three species (Eurasian Sparrowhawk Accipiter nisus, Bald Eagle Haliaeetus leucocephalus, and Peregrine Falcon Falco peregrinus) comprising 50 % of samples. The types of raptors sampled have changed over time, with avian and mammal specialists dominating samples until the 1970s, but more diverse dietary guilds monitored in later decades, and greater proportions of samples coming from generalist species. The three most sampled tissues (egg, liver, and plasma) comprised 84 % of all samples. Eggs were the earliest tissue examined and the only tissue sampled in all decades. The geographical bias in monitoring effort and relatively narrow species focus, suggests that patterns in these pesticides are unlikely to be fully representative of all global environments occupied by raptors. While DDT has been banned throughout most of the global north, it remains in use in the global south, yet monitoring effort in the south, does not match that of the north. While monitoring remains prevalent in the global north, contemporary monitoring is limited in the global south with less than 10 % of raptors sampled in Asia, Africa, and South America, over the last 3 decades.
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Affiliation(s)
- Kailen Padayachee
- The Fitzpatrick Institute of African Ornithology, University of Cape Town, South Africa, Private Bag X3, Rondebosch 7701, Cape Town, South Africa.
| | - Chevonne Reynolds
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg South Africa, Private Bag 3 Wits, 2050 Johannesburg, South Africa.
| | - Rafael Mateo
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC, UCLM, JCCM), Ronda de Toledo, 12, 13005 Ciudad Real, Spain.
| | - Arjun Amar
- The Fitzpatrick Institute of African Ornithology, University of Cape Town, South Africa, Private Bag X3, Rondebosch 7701, Cape Town, South Africa.
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20
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Fuentes M, Van Doren BM, Fink D, Sheldon D. BirdFlow
: Learning seasonal bird movements from
eBird
data. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Miguel Fuentes
- Manning College of Information and Computer Sciences University of Massachusetts Amherst Amherst Massachusetts USA
| | | | - Daniel Fink
- Cornell Lab of Ornithology Cornell University Ithaca New York USA
| | - Daniel Sheldon
- Manning College of Information and Computer Sciences University of Massachusetts Amherst Amherst Massachusetts USA
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21
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Prakash H, Kumar RS, Lahkar B, Sukumar R, Vanak AT, Thaker M. Animal movement ecology in India: insights from 2011-2021 and prospective for the future. PeerJ 2022; 10:e14401. [PMID: 36530402 PMCID: PMC9756863 DOI: 10.7717/peerj.14401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022] Open
Abstract
The field of animal movement ecology has advanced by leaps and bounds in the past few decades with the advent of sophisticated technology, advanced analytical tools, and multiple frameworks and paradigms to address key ecological problems. Unlike the longer history and faster growth of the field in North America, Europe, and Africa, movement ecology in Asia has only recently been gaining momentum. Here, we provide a review of the field from studies based in India over the last 11 years (2011-2021) curated from the database, Scopus, and search engine, Google Scholar. We identify current directions in the research objectives, taxa studied, tracking technology and the biogeographic regions in which animals were tracked, considering the years since the last systematic review of movement ecology research in the country. As an indication of the growing interest in this field, there has been a rapid increase in the number of publications over the last decade. Class Mammalia continues to dominate the taxa tracked, with tiger and leopard being the most common species studied across publications. Invertebrates and other small and medium-sized animals, as well as aquatic animals, in comparison, are understudied and remain among the important target taxa for tracking in future studies. As in the previous three decades, researchers have focussed on characterising home ranges and habitat use of animals. There is, however, a notable shift to examine the movement decision of animals in human-modified landscapes, although efforts to use movement ecology to understand impacts of climate change remain missing. Given the biogeographic and taxonomic diversity of India, and the fact that the interface between anthropogenic activity and wildlife interactions is increasing, we suggest ways in which the field of movement ecology can be expanded to facilitate ecological insights and conservation efforts. With the advancement of affordable technologies and the availability of analytical tools, the potential to expand the field of movement ecology, shift research foci, and gain new insights is now prime.
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Affiliation(s)
- Harish Prakash
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
| | - R Suresh Kumar
- Department of Endangered Species Management, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | | | - Raman Sukumar
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Abi T Vanak
- Ashoka Trust for Research in Ecology and the Environment, Bengaluru, Karnataka, India.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Maria Thaker
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
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22
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van der Kolk HJ, Desmet P, Oosterbeek K, Allen AM, Baptist MJ, Bom RA, Davidson SC, de Jong J, de Kroon H, Dijkstra B, Dillerop R, Dokter AM, Frauendorf M, Milotić T, Rakhimberdiev E, Shamoun-Baranes J, Spanoghe G, van de Pol M, Van Ryckegem G, Vanoverbeke J, Jongejans E, Ens BJ. GPS tracking data of Eurasian oystercatchers ( Haematopusostralegus) from the Netherlands and Belgium. Zookeys 2022; 1123:31-45. [PMID: 36762038 PMCID: PMC9836607 DOI: 10.3897/zookeys.1123.90623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/05/2022] [Indexed: 11/12/2022] Open
Abstract
We describe six datasets that contain GPS and accelerometer data of 202 Eurasian oystercatchers (Haematopusostralegus) spanning the period 2008-2021. Birds were equipped with GPS trackers in breeding and wintering areas in the Netherlands and Belgium. We used GPS trackers from the University of Amsterdam Bird Tracking System (UvA-BiTS) for several study purposes, including the study of space use during the breeding season, habitat use and foraging behaviour in the winter season, and impacts of human disturbance. To enable broader usage, all data have now been made open access. Combined, the datasets contain 6.0 million GPS positions, 164 million acceleration measurements and 7.0 million classified behaviour events (i.e., flying, walking, foraging, preening, and inactive). The datasets are deposited on the research repository Zenodo, but are also accessible on Movebank and as down-sampled occurrence datasets on the Global Biodiversity Information Facility (GBIF) and Ocean Biodiversity Information System (OBIS).
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Affiliation(s)
- Henk-Jan van der Kolk
- Netherlands Institute of Ecology, Department of Animal Ecology, Wageningen, NetherlandsCentre of Avian Population Studies (CAPS)WageningenNetherlands,Dutch Bryological and Lichenological Society (BLWG), Utrecht, NetherlandsNetherlands Institute of Ecology, Department of Animal EcologyWageningenNetherlands,Radboud University, Nijmegen, NetherlandsRadboud UniversityNijmegenNetherlands,Centre of Avian Population Studies (CAPS), Wageningen, NetherlandsDutch Bryological and Lichenological Society (BLWG)UtrechtNetherlands
| | - Peter Desmet
- Research Institute for Nature and Forest (INBO), Brussels, BelgiumResearch Institute for Nature and Forest (INBO)BrusselsBelgium
| | - Kees Oosterbeek
- Sovon Dutch Centre for Field Ornithology, Nijmegen, NetherlandsSovon Dutch Centre for Field OrnithologyNijmegenNetherlands
| | - Andrew M. Allen
- Netherlands Institute of Ecology, Department of Animal Ecology, Wageningen, NetherlandsCentre of Avian Population Studies (CAPS)WageningenNetherlands,Radboud University, Nijmegen, NetherlandsRadboud UniversityNijmegenNetherlands,Centre of Avian Population Studies (CAPS), Wageningen, NetherlandsDutch Bryological and Lichenological Society (BLWG)UtrechtNetherlands
| | - Martin J. Baptist
- Wageningen Marine Research, Wageningen University and Research, Den Helder, NetherlandsWageningen University and ResearchDen HelderNetherlands
| | - Roeland A. Bom
- Royal Netherlands Institute for Sea Research, Coastal Systems, ‘t Horntje, NetherlandsRoyal Netherlands Institute for Sea Research't HorntjeNetherlands
| | - Sarah C. Davidson
- Department of Animal Migration, Max Plank Institute of Animal Behaviour, Radolfzell, GermanyDepartment of Animal Migration, Max Plank Institute of Animal BehaviourRadolfzellGermany
| | - Jan de Jong
- WetlandWacht, Vogelbescherming, Zeist, NetherlandsWetlandWacht, VogelbeschermingZeistNetherlands
| | - Hans de Kroon
- Radboud University, Nijmegen, NetherlandsRadboud UniversityNijmegenNetherlands
| | - Bert Dijkstra
- Vogelwerkgroep Assen, Assen, NetherlandsVogelwerkgroep AssenAssenNetherlands
| | - Rinus Dillerop
- Vogelwerkgroep Assen, Assen, NetherlandsVogelwerkgroep AssenAssenNetherlands
| | - Adriaan M. Dokter
- Cornell Lab of Ornithology, Cornell University, Ithaca, USACornell UniversityIthacaUnited States of America,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, NetherlandsUniversity of AmsterdamAmsterdamNetherlands
| | - Magali Frauendorf
- Netherlands Institute of Ecology, Department of Animal Ecology, Wageningen, NetherlandsCentre of Avian Population Studies (CAPS)WageningenNetherlands,Radboud University, Nijmegen, NetherlandsRadboud UniversityNijmegenNetherlands,Centre of Avian Population Studies (CAPS), Wageningen, NetherlandsDutch Bryological and Lichenological Society (BLWG)UtrechtNetherlands
| | - Tanja Milotić
- Research Institute for Nature and Forest (INBO), Brussels, BelgiumResearch Institute for Nature and Forest (INBO)BrusselsBelgium
| | - Eldar Rakhimberdiev
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, NetherlandsUniversity of AmsterdamAmsterdamNetherlands
| | - Judy Shamoun-Baranes
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, NetherlandsUniversity of AmsterdamAmsterdamNetherlands
| | - Geert Spanoghe
- Research Institute for Nature and Forest (INBO), Brussels, BelgiumResearch Institute for Nature and Forest (INBO)BrusselsBelgium
| | - Martijn van de Pol
- Netherlands Institute of Ecology, Department of Animal Ecology, Wageningen, NetherlandsCentre of Avian Population Studies (CAPS)WageningenNetherlands,Centre of Avian Population Studies (CAPS), Wageningen, NetherlandsDutch Bryological and Lichenological Society (BLWG)UtrechtNetherlands,College of Science and Engineering, James Cook University, Townsville, AustraliaJames Cook UniversityTownsvilleAustralia
| | - Gunther Van Ryckegem
- Research Institute for Nature and Forest (INBO), Brussels, BelgiumResearch Institute for Nature and Forest (INBO)BrusselsBelgium
| | - Joost Vanoverbeke
- Research Institute for Nature and Forest (INBO), Brussels, BelgiumResearch Institute for Nature and Forest (INBO)BrusselsBelgium
| | - Eelke Jongejans
- Netherlands Institute of Ecology, Department of Animal Ecology, Wageningen, NetherlandsCentre of Avian Population Studies (CAPS)WageningenNetherlands,Radboud University, Nijmegen, NetherlandsRadboud UniversityNijmegenNetherlands,Centre of Avian Population Studies (CAPS), Wageningen, NetherlandsDutch Bryological and Lichenological Society (BLWG)UtrechtNetherlands
| | - Bruno J. Ens
- Centre of Avian Population Studies (CAPS), Wageningen, NetherlandsDutch Bryological and Lichenological Society (BLWG)UtrechtNetherlands,Sovon Dutch Centre for Field Ornithology, Nijmegen, NetherlandsSovon Dutch Centre for Field OrnithologyNijmegenNetherlands
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23
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Spatial-temporal interpolation of satellite geomagnetic data to study long-distance animal migration. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Flack A, Aikens EO, Kölzsch A, Nourani E, Snell KR, Fiedler W, Linek N, Bauer HG, Thorup K, Partecke J, Wikelski M, Williams HJ. New frontiers in bird migration research. Curr Biol 2022; 32:R1187-R1199. [DOI: 10.1016/j.cub.2022.08.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Abraham A, Duvall E, Ferraro K, Webster A, Doughty C, le Roux E, Ellis‐Soto D. Understanding anthropogenic impacts on zoogeochemistry is essential for ecological restoration. Restor Ecol 2022. [DOI: 10.1111/rec.13778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew Abraham
- School of Informatics, Computing and Cyber Systems Northern Arizona University Flagstaff USA
| | - Ethan Duvall
- Department of Ecology and Evolutionary Biology Cornell University Ithaca USA
| | - Kristy Ferraro
- School of the Environment Yale University Connecticut USA
| | - Andrea Webster
- Mammal Research Institute University of Pretoria Pretoria South Africa
| | - Chris Doughty
- School of Informatics, Computing and Cyber Systems Northern Arizona University Flagstaff USA
| | - Elizabeth le Roux
- Mammal Research Institute University of Pretoria Pretoria South Africa
- Centre for Biodiversity Dynamics in a Changing World (BIOCHANGE), Section of EcoInformatics and Biodiversity, Department of Biology Aarhus University Denmark
- Environmental Change Institute, School of Geography and the Environment University of Oxford Oxford UK
| | - Diego Ellis‐Soto
- Department of Ecology and Evolutionary Biology Yale University Connecticut USA
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26
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Krondorf M, Bittner S, Plettemeier D, Knopp A, Wikelski M. ICARUS-Very Low Power Satellite-Based IoT. SENSORS (BASEL, SWITZERLAND) 2022; 22:6329. [PMID: 36080787 PMCID: PMC9460258 DOI: 10.3390/s22176329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/05/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
The ICARUS (International Cooperation for Animal Research Using Space) satellite IoT system was launched in 2020 to observe the life of animals on Earth: their migratory routes, living conditions, and causes of death. These findings will aid species conservation, protect ecosystem services by animals, measure weather and climate, and help forecast the spread of infectious zoonotic diseases and possibly natural disasters. The aim of this article is to explain the system design of ICARUS. Essential components are 'wearables for wildlife', miniature on-animal sensors, quantifying the health of animals and the surrounding environment on the move, and transmitting artificially intelligent summaries of these data globally. We introduce a new class of Internet-of-things (IoT) waveforms-the random-access, very-low-power, wide-area networks (RA-vLPWANs) which enable uncoordinated multiple access at very-low-signal power and low-signal-to-noise ratios. RA-vLPWANs used in ICARUS solve the problems hampering conventional low-power wide area network (LPWAN) IoT systems when applied to space communications. Prominent LPWANs are LoRA, SigFox, MIOTY, ESSA, NB-IoT (5G), or SCADA. Hardware and antenna aspects in the ground and the space segment are given to explain practical system constraints.
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Affiliation(s)
- Marco Krondorf
- Faculty of Engineering, HTWK Leipzig, University of Applied Sciences, 04277 Leipzig, Germany
| | | | - Dirk Plettemeier
- Photonics and Antenna Design, TU Dresden, 01062 Dresden, Germany
| | - Andreas Knopp
- Institute of Information Technology, University of the Bundeswehr Munich, 85579 Neubiberg, Germany
- Space Systems Academic Group, Naval Postgraduate School, Monterey, CA 93943, USA
| | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
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27
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Kölzsch A, Davidson SC, Gauggel D, Hahn C, Hirt J, Kays R, Lang I, Lohr A, Russell B, Scharf AK, Schneider G, Vinciguerra CM, Wikelski M, Safi K. MoveApps: a serverless no-code analysis platform for animal tracking data. MOVEMENT ECOLOGY 2022; 10:30. [PMID: 35843990 PMCID: PMC9290230 DOI: 10.1186/s40462-022-00327-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Bio-logging and animal tracking datasets continuously grow in volume and complexity, documenting animal behaviour and ecology in unprecedented extent and detail, but greatly increasing the challenge of extracting knowledge from the data obtained. A large variety of analysis methods are being developed, many of which in effect are inaccessible to potential users, because they remain unpublished, depend on proprietary software or require significant coding skills. RESULTS We developed MoveApps, an open analysis platform for animal tracking data, to make sophisticated analytical tools accessible to a global community of movement ecologists and wildlife managers. As part of the Movebank ecosystem, MoveApps allows users to design and share workflows composed of analysis modules (Apps) that access and analyse tracking data. Users browse Apps, build workflows, customise parameters, execute analyses and access results through an intuitive web-based interface. Apps, coded in R or other programming languages, have been developed by the MoveApps team and can be contributed by anyone developing analysis code. They become available to all user of the platform. To allow long-term and cross-system reproducibility, Apps have public source code and are compiled and run in Docker containers that form the basis of a serverless cloud computing system. To support reproducible science and help contributors document and benefit from their efforts, workflows of Apps can be shared, published and archived with DOIs in the Movebank Data Repository. The platform was beta launched in spring 2021 and currently contains 49 Apps that are used by 316 registered users. We illustrate its use through two workflows that (1) provide a daily report on active tag deployments and (2) segment and map migratory movements. CONCLUSIONS The MoveApps platform is meant to empower the community to supply, exchange and use analysis code in an intuitive environment that allows fast and traceable results and feedback. By bringing together analytical experts developing movement analysis methods and code with those in need of tools to explore, answer questions and inform decisions based on data they collect, we intend to increase the pace of knowledge generation and integration to match the huge growth rate in bio-logging data acquisition.
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Affiliation(s)
- Andrea Kölzsch
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315, Radolfzell, Germany.
- Department of Biology, University of Konstanz, Constance, Germany.
| | - Sarah C Davidson
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315, Radolfzell, Germany
- Department of Biology, University of Konstanz, Constance, Germany
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Constance, Germany
| | | | | | | | - Roland Kays
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Ilona Lang
- Communication, Information, Media Centre, University of Konstanz, Constance, Germany
| | - Ashley Lohr
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | | | - Anne K Scharf
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315, Radolfzell, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Gabriel Schneider
- Communication, Information, Media Centre, University of Konstanz, Constance, Germany
| | - Candace M Vinciguerra
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315, Radolfzell, Germany
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315, Radolfzell, Germany
- Department of Biology, University of Konstanz, Constance, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Constance, Germany
| | - Kamran Safi
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315, Radolfzell, Germany
- Department of Biology, University of Konstanz, Constance, Germany
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28
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Czapanskiy MF, Beltran RS. How Reproducibility Will Accelerate Discovery Through Collaboration in Physio-Logging. Front Physiol 2022; 13:917976. [PMID: 35874548 PMCID: PMC9304648 DOI: 10.3389/fphys.2022.917976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/16/2022] [Indexed: 11/22/2022] Open
Abstract
What new questions could ecophysiologists answer if physio-logging research was fully reproducible? We argue that technical debt (computational hurdles resulting from prioritizing short-term goals over long-term sustainability) stemming from insufficient cyberinfrastructure (field-wide tools, standards, and norms for analyzing and sharing data) trapped physio-logging in a scientific silo. This debt stifles comparative biological analyses and impedes interdisciplinary research. Although physio-loggers (e.g., heart rate monitors and accelerometers) opened new avenues of research, the explosion of complex datasets exceeded ecophysiology’s informatics capacity. Like many other scientific fields facing a deluge of complex data, ecophysiologists now struggle to share their data and tools. Adapting to this new era requires a change in mindset, from “data as a noun” (e.g., traits, counts) to “data as a sentence”, where measurements (nouns) are associate with transformations (verbs), parameters (adverbs), and metadata (adjectives). Computational reproducibility provides a framework for capturing the entire sentence. Though usually framed in terms of scientific integrity, reproducibility offers immediate benefits by promoting collaboration between individuals, groups, and entire fields. Rather than a tax on our productivity that benefits some nebulous greater good, reproducibility can accelerate the pace of discovery by removing obstacles and inviting a greater diversity of perspectives to advance science and society. In this article, we 1) describe the computational challenges facing physio-logging scientists and connect them to the concepts of technical debt and cyberinfrastructure, 2) demonstrate how other scientific fields overcame similar challenges by embracing computational reproducibility, and 3) present a framework to promote computational reproducibility in physio-logging, and bio-logging more generally.
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Affiliation(s)
- Max F. Czapanskiy
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States
- *Correspondence: Max F. Czapanskiy,
| | - Roxanne S. Beltran
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
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29
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Acácio M, Catry I, Soriano-Redondo A, Silva JP, Atkinson PW, Franco AMA. Timing is critical: consequences of asynchronous migration for the performance and destination of a long-distance migrant. MOVEMENT ECOLOGY 2022; 10:28. [PMID: 35725653 PMCID: PMC9901525 DOI: 10.1186/s40462-022-00328-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Migration phenology is shifting for many long-distance migrants due to global climate change, however the timing and duration of migration may influence the environmental conditions individuals encounter, with potential fitness consequences. Species with asynchronous migrations, i.e., with variability in migration timing, provide an excellent opportunity to investigate how of the conditions individuals experience during migration can vary and affect the migratory performance, route, and destination of migrants. METHODS Here, we use GPS tracking and accelerometer data to examine if timing of autumn migration influences the migratory performance (duration, distance, route straightness, energy expenditure) and migration destinations of a long-distance, asynchronous, migrant, the white stork (Ciconia ciconia). We also compare the weather conditions (wind speed, wind direction, and boundary layer height) encountered on migration and examine the influence of wind direction on storks' flight directions. RESULTS From 2016 to 2020, we tracked 172 white storks and obtained 75 complete migrations from the breeding grounds in Europe to the sub-Saharan wintering areas. Autumn migration season spanned over a 3-month period (July-October) and arrival destinations covered a broad area of the Sahel, 2450 km apart, from Senegal to Niger. We found that timing of migration influenced both the performance and conditions individuals experienced: later storks spent fewer days on migration, adopted shorter and more direct routes in the Sahara Desert and consumed more energy when flying, as they were exposed to less supportive weather conditions. In the Desert, storks' flight directions were significantly influenced by wind direction, with later individuals facing stronger easterly winds (i.e., winds blowing to the west), hence being more likely to end their migration in western areas of the Sahel region. Contrastingly, early storks encountered more supportive weather conditions, spent less energy on migration and were exposed to westerly winds, thus being more likely to end migration in eastern Sahel. CONCLUSIONS Our results show that the timing of migration influences the environmental conditions individuals face, the energetic costs of migration, and the wintering destinations, where birds may be exposed to different environmental conditions and distinct threats. These findings highlight that on-going changes in migration phenology, due to environmental change, may have critical fitness consequences for long-distance soaring migrants.
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Affiliation(s)
- Marta Acácio
- School of Environmental Sciences, University of East Anglia, Norwich, Norfolk, UK.
| | - Inês Catry
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade Do Porto, 4485-661, Vairão, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017, Lisbon, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Andrea Soriano-Redondo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade Do Porto, 4485-661, Vairão, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017, Lisbon, Portugal
- Helsinki Lab of Interdisciplinary Conservation Science (HELICS), Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Helsinki, Finland
| | - João Paulo Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade Do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | | | - Aldina M A Franco
- School of Environmental Sciences, University of East Anglia, Norwich, Norfolk, UK
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30
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Costa-Pereira R, Moll RJ, Jesmer BR, Jetz W. Animal tracking moves community ecology: Opportunities and challenges. J Anim Ecol 2022; 91:1334-1344. [PMID: 35388473 DOI: 10.1111/1365-2656.13698] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/27/2022] [Indexed: 11/28/2022]
Abstract
1. Individual decisions regarding how, why, and when organisms interact with one another and with their environment scale up to shape patterns and processes in communities. Recent evidence has firmly established the prevalence of intraspecific variation in nature and its relevance in community ecology, yet challenges associated with collecting data on large numbers of individual conspecifics and heterospecifics has hampered integration of individual variation into community ecology. 2. Nevertheless, recent technological and statistical advances in GPS-tracking, remote sensing, and behavioral ecology offer a toolbox for integrating intraspecific variation into community processes. More than simply describing where organisms go, movement data provide unique information about interactions and environmental associations from which a true individual-to-community framework can be built. 3. By linking the movement paths of both conspecifics and heterospecifics with environmental data, ecologists can now simultaneously quantify intra- and interspecific variation regarding the Eltonian (biotic interactions) and Grinnellian (environmental conditions) factors underpinning community assemblage and dynamics, yet substantial logistical and analytical challenges must be addressed for these approaches to realize their full potential. 4. Across communities, empirical integration of Eltonian and Grinnellian factors can support conservation applications and reveal metacommunity dynamics via tracking-based dispersal data. As the logistical and analytical challenges associated with multi-species tracking are surmounted, we envision a future where individual movements and their ecological and environmental signatures will bring resolution to many enduring issues in community ecology.
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Affiliation(s)
- Raul Costa-Pereira
- Departamento de Biologia Animal, Instituto de Biociências, Universidade Estadual de Campinas, Brazil
| | - Remington J Moll
- Department of Natural Resources and the Environment, University of New Hampshire, 56 College Road, Durham, NH 03824, USA
| | - Brett R Jesmer
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24061, USA.,Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St., New Haven, CT 06520, USA.,Center for Biodiversity and Global Change, Yale University, 165 Prospect St., New Haven, CT 06520, USA
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St., New Haven, CT 06520, USA.,Center for Biodiversity and Global Change, Yale University, 165 Prospect St., New Haven, CT 06520, USA
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