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Ridley FA, Rushton SP, Hickinbotham EJ, Suggitt AJ, McGowan PJK, Mair L. Global mismatches between threat mapping research effort and the potential of threat abatement actions to reduce extinction risk. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14271. [PMID: 38623873 DOI: 10.1111/cobi.14271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/23/2024] [Accepted: 01/31/2024] [Indexed: 04/17/2024]
Abstract
Threat mapping is a necessary tool for identifying and abating direct threats to species in the ongoing extinction crisis. There are known gaps in the threat mapping literature for particular threats and geographic locations, and it remains unclear if the distribution of research effort is appropriately targeted relative to conservation need. We aimed to determine the drivers of threat mapping research effort and to quantify gaps that, if filled, could inform actions with the highest potential to reduce species' extinction risk. We used a negative binomial generalized linear model to analyze research effort as a function of threat abatement potential (quantified as the potential reduction in species extinction risk from abating threats), species richness, land area, and human pressure. The model showed that threat mapping research effort increased by 1.1 to 1.2 times per standardized unit change in threat abatement potential. However, species richness and land area were stronger predictors of research effort overall. The greatest areas of mismatch between research effort and threat abatement potential, receiving disproportionately low research effort, were related to the threats to species of agriculture, aquaculture, and biological resource use across the tropical regions of the Americas, Asia, and Madagascar. Conversely, the threat of linear infrastructure (e.g., roads and rails) across regions, the threat of biological resource use (e.g., hunting or collection) in sub-Saharan Africa, and overall threats in North America and Europe all received disproportionately high research effort. We discuss the range of methodological and sociopolitical factors that may be behind the overall trends and specific areas of mismatch we found. We urge a stronger emphasis on targeting research effort toward those threats and geographic locations where threat abatement activities could make the greatest contribution to reducing global species extinction risk.
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Affiliation(s)
- Francesca A Ridley
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Stephen P Rushton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Emily J Hickinbotham
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew J Suggitt
- Department of Geography and Environmental Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Philip J K McGowan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Louise Mair
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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2
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Parker EJ, Weiskopf SR, Oliver RY, Rubenstein MA, Jetz W. Insufficient and biased representation of species geographic responses to climate change. GLOBAL CHANGE BIOLOGY 2024; 30:e17408. [PMID: 38984769 DOI: 10.1111/gcb.17408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
The geographic redistributions of species due to a rapidly changing climate are poised to perturb ecological communities and significantly impact ecosystems and human livelihoods. Effectively managing these biological impacts requires a thorough understanding of the patterns and processes of species geographic range shifts. While substantial recent redistributions have been identified and recognized to vary by taxon, region, and range geometry, there are large gaps and biases in the available evidence. Here, we use the largest compilation of geographic range change observations to date, comprised of 33,016 potential redistributions across 12,009 species, to formally assess within- and cross-species coverage and biases and to motivate future data collection. We find that species coverage varies strongly by taxon and underrepresents species at high and low latitudes. Within species, assessments of potential redistributions came from parts of their geographic range that were highly uneven and non-representative. For most species and taxa, studies were strongly biased toward the colder parts of species' distributions and thus significantly underrepresented populations that might get pushed beyond their maximum temperature limits. Coverage of potential leading and trailing geographic range edges under a changing climate was similarly uneven. Only 8% of studied species were assessed at both high and low latitude and elevation range edges, with most only covered at one edge. This suggests that substantial within-species biases exacerbate the considerable geographic and taxonomic among-species unevenness in evidence. Our results open the door for a more quantitative accounting for existing knowledge biases in climate change ecology and a more informed management and conservation. Our findings offer guidance for future data collection that better addresses information gaps and provides a more effective foundation for managing the biological impacts of climate change.
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Affiliation(s)
- Evan J Parker
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
| | - Sarah R Weiskopf
- U.S. Geological Survey National Climate Adaptation Science Center, Reston, Virginia, USA
| | - Ruth Y Oliver
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
- Bren School of Environmental Science & Management, UC Santa Barbara, Santa Barbara, California, USA
| | - Madeleine A Rubenstein
- U.S. Geological Survey National Climate Adaptation Science Center, Reston, Virginia, USA
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
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3
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Wang Z, Chen T, Yang L, Chapman CA, Fan P. Effects of protected area coverage and research on conservation status of primates globally. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024:e14311. [PMID: 38853694 DOI: 10.1111/cobi.14311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/10/2024] [Accepted: 04/22/2024] [Indexed: 06/11/2024]
Abstract
Conducting conservation research and establishing protected areas (PAs) based on research results are critical to biodiversity conservation. However, the effect of research and PAs on conservation of threatened species has rarely been evaluated simultaneously. We collected data on PAs from 2000 for 2021 and determined the number of publications on global primates (published from 1950 to 2021) to assess the effect of PAs, research, and biological and socioeconomic factors on the current International Union for Conservation of Nature endangered status and change in status. We used the MCMCglmm package to conduct a phylogenetic comparative analysis to control the phylogenetic relationship of primate species. The status of 24.6% (82 of 333) of species assessed at least twice declined. Only the black lion tamarin (Leontopithecus chrysopygus) had an improved status. Species with status declines mostly occurred on the south coast of West Africa and in Madagascar. PAs covered 22.1% of each species' range. Forest loss in PAs (5.5%) was significantly lower than forest loss within 5 km outside PAs (13.8%), suggesting PAs effectively mitigated forest loss. Both the median number of total publications and conservation publications on critically endangered species were higher than those of other categories. Models showed that PA coverage and number of publications or conservation-focused publications were not related to current status or change in status over time. A decline in status was not related to creation of PAs or increase of research since the last assessment. Our results suggest that current PAs and research are not reversing the extinction crisis of global primates. Doing more conservation-oriented research, strengthening management of current PAs, and expanding PAs will be needed to protect primates globally.
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Affiliation(s)
- Zhining Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Li Yang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Colin A Chapman
- Woodrow Wilson International Center for Scholars, Washington, District of Columbia, USA
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
- School of Life Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
- The College of Life Sciences, Northwest University, Xi'an, China
| | - Pengfei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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4
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Ricci L, Di Musciano M, Sabatini FM, Chiarucci A, Zannini P, Gatti RC, Beierkuhnlein C, Walentowitz A, Lawrence A, Frattaroli AR, Hoffmann S. A multitaxonomic assessment of Natura 2000 effectiveness across European biogeographic regions. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14212. [PMID: 37904665 DOI: 10.1111/cobi.14212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 11/01/2023]
Abstract
The Natura 2000 (N2K) protected area (PA) network is a crucial tool to limit biodiversity loss in Europe. Despite covering 18% of the European Union's (EU) land area, its effectiveness at conserving biodiversity across taxa and biogeographic regions remains uncertain. Testing this effectiveness is, however, difficult because it requires considering the nonrandom location of PAs, and many possible confounding factors. We used propensity score matching and accounted for the confounding effects of biogeographic regions, terrain ruggedness, and land cover to assess the effectiveness of N2K PAs on the distribution of 1769 species of conservation priority in the EU's Birds and Habitats Directives, including mammals, birds, amphibians, reptiles, arthropods, fishes, mollusks, and vascular and nonvascular plants. We compared alpha, beta, and gamma diversity between matched selections of protected and unprotected areas across EU's biogeographic regions with generalized linear models, generalized mixed models, and nonparametric tests for paired samples, respectively, for each taxonomic group and for the entire set of species. PAs in N2K hosted significantly more priority species than unprotected land, but this difference was not consistent across biogeographic regions or taxa. Total alpha diversity and alpha diversity of amphibians, arthropods, birds, mammals, and vascular plants were significantly higher inside PAs than outside, except in the Boreal biogeographical region. Beta diversity was in general significantly higher inside N2K PAs than outside. Similarly, gamma diversity had the highest values inside PAs, with some exceptions in Boreal and Atlantic regions. The planned expansion of the N2K network, as dictated by the European Biodiversity Strategy for 2030, should therefore target areas in the southern part of the Boreal region where species diversity of amphibians, arthropods, birds, mammals, and vascular plants is high and species are currently underrepresented in N2K.
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Affiliation(s)
- Lorenzo Ricci
- Department of Life, Health & Environmental Science, University of L'Aquila, L'Aquila, Italy
| | - Michele Di Musciano
- Department of Life, Health & Environmental Science, University of L'Aquila, L'Aquila, Italy
- BIOME Lab, BiGeA Department, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Francesco Maria Sabatini
- BIOME Lab, BiGeA Department, Alma Mater Studiorum - University of Bologna, Bologna, Italy
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Praha, Czech Republic
| | - Alessandro Chiarucci
- BIOME Lab, BiGeA Department, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Piero Zannini
- BIOME Lab, BiGeA Department, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Roberto Cazzolla Gatti
- BIOME Lab, BiGeA Department, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Carl Beierkuhnlein
- Department of Biogeography, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center of Ecology and Environmental Research, BayCEER, University of Bayreuth, Bayreuth, Germany
- Geographical Institute of the University of Bayreuth, GIB, Bayreuth, Germany
| | - Anna Walentowitz
- Department of Biogeography, University of Bayreuth, Bayreuth, Germany
| | | | - Anna Rita Frattaroli
- Department of Life, Health & Environmental Science, University of L'Aquila, L'Aquila, Italy
| | - Samuel Hoffmann
- Department of Biogeography, University of Bayreuth, Bayreuth, Germany
- Bayerisches Landesamt für Umwelt, Augsburg, Germany
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5
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Huijsmans TERG, Courtiol A, Van Soom A, Smits K, Rousset F, Wauters J, Hildebrandt TB. Quantifying maternal investment in mammals using allometry. Commun Biol 2024; 7:475. [PMID: 38637653 PMCID: PMC11026411 DOI: 10.1038/s42003-024-06165-x] [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: 10/18/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Maternal investment influences the survival and reproduction of both mothers and their progeny and plays a crucial role in understanding individuals' life-history and population ecology. To reveal the complex mechanisms associated with reproduction and investment, it is necessary to examine variations in maternal investment across species. Comparisons across species call for a standardised method to quantify maternal investment, which remained to be developed. This paper addresses this limitation by introducing the maternal investment metric - MI - for mammalian species, established through the allometric scaling of the litter mass at weaning age by the adult mass and investment duration (i.e. gestation + lactation duration) of a species. Using a database encompassing hundreds of mammalian species, we show that the metric is not highly sensitive to the regression method used to fit the allometric relationship or to the proxy used for adult body mass. The comparison of the maternal investment metric between mammalian subclasses and orders reveals strong differences across taxa. For example, our metric confirms that Eutheria have a higher maternal investment than Metatheria. We discuss how further research could use the maternal investment metric as a valuable tool to understand variation in reproductive strategies.
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Affiliation(s)
- Tim E R G Huijsmans
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
| | - Alexandre Courtiol
- Department of Evolutionary Genetics, Leibniz Institute for Zoo & Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
| | - Ann Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Katrien Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - François Rousset
- Institute of Evolutionary Science of Montpellier, University of Montpellier, CNRS, IRD, campus Triolet, 34095, Montpellier cedex 05, France
| | - Jella Wauters
- Department of Reproduction Biology, Leibniz Institute for Zoo & Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Thomas B Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo & Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
- Freie Universität Berlin, Kaiserswerther Str. 16-18, 14195, Berlin, Germany
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6
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Mammola S, Adamo M, Antić D, Calevo J, Cancellario T, Cardoso P, Chamberlain D, Chialva M, Durucan F, Fontaneto D, Goncalves D, Martínez A, Santini L, Rubio-Lopez I, Sousa R, Villegas-Rios D, Verdes A, Correia RA. Drivers of species knowledge across the tree of life. eLife 2023; 12:RP88251. [PMID: 37846960 PMCID: PMC10581686 DOI: 10.7554/elife.88251] [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] [Indexed: 10/18/2023] Open
Abstract
Knowledge of biodiversity is unevenly distributed across the Tree of Life. In the long run, such disparity in awareness unbalances our understanding of life on Earth, influencing policy decisions and the allocation of research and conservation funding. We investigated how humans accumulate knowledge of biodiversity by searching for consistent relationships between scientific (number of publications) and societal (number of views in Wikipedia) interest, and species-level morphological, ecological, and sociocultural factors. Across a random selection of 3019 species spanning 29 Phyla/Divisions, we show that sociocultural factors are the most important correlates of scientific and societal interest in biodiversity, including the fact that a species is useful or harmful to humans, has a common name, and is listed in the International Union for Conservation of Nature Red List. Furthermore, large-bodied, broadly distributed, and taxonomically unique species receive more scientific and societal attention, whereas colorfulness and phylogenetic proximity to humans correlate exclusively with societal attention. These results highlight a favoritism toward limited branches of the Tree of Life, and that scientific and societal priorities in biodiversity research broadly align. This suggests that we may be missing out on key species in our research and conservation agenda simply because they are not on our cultural radar.
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Affiliation(s)
- Stefano Mammola
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of HelsinkiHelsinkiFinland
- National Biodiversity Future CenterPalermoItaly
| | - Martino Adamo
- National Biodiversity Future CenterPalermoItaly
- Department of Life Sciences and Systems Biology, University of TurinTorinoItaly
| | - Dragan Antić
- University of Belgrade - Faculty of BiologyBelgradeSerbia
| | - Jacopo Calevo
- Royal Botanic GardensLondonUnited Kingdom
- School of Molecular and Life Sciences, Curtin UniversityPerthAustralia
| | - Tommaso Cancellario
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of HelsinkiHelsinkiFinland
| | - Dan Chamberlain
- Department of Life Sciences and Systems Biology, University of TurinTorinoItaly
| | - Matteo Chialva
- National Biodiversity Future CenterPalermoItaly
- Department of Life Sciences and Systems Biology, University of TurinTorinoItaly
| | - Furkan Durucan
- Department of Aquaculture, Isparta University of Applied SciencesIspartaTurkey
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
- National Biodiversity Future CenterPalermoItaly
| | - Duarte Goncalves
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of PortoMatosinhosPortugal
| | - Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
| | - Luca Santini
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Iñigo Rubio-Lopez
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
| | - Ronaldo Sousa
- CBMA – Centre of Molecular and Environmental Biology, Department of Biology, University of MinhoMinhoPortugal
| | | | - Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias NaturalesMadridSpain
| | - Ricardo A Correia
- Helsinki Lab of Interdisciplinary Conservation Science (HELICS), Department of Geosciences and Geography, University of HelsinkiHelsinkiFinland
- Helsinki Institute of Sustainability Science (HELSUS), University of HelsinkiHelsinkiFinland
- CESAM – Centre for Environmental and Marine Studies, University of AveiroAveiroPortugal
- Biodiversity Unit, University of TurkuTurkuFinland
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7
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Poulin R, Presswell B, Bennett J, de Angeli Dutra D, Salloum PM. Biases in parasite biodiversity research: why some helminth species attract more research than others. Int J Parasitol Parasites Wildl 2023; 21:89-98. [PMID: 37182112 PMCID: PMC10172627 DOI: 10.1016/j.ijppaw.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/16/2023]
Abstract
As the number of known and described parasite species grows every year, one might ask: how much do we actually know about these species beyond the fact they exist? For free-living taxa, research effort is biased toward a small subset of species based on their properties or human-centric factors. Here, using a large data set on over 2500 helminth parasite species described in the past two decades, we test the importance of several predictors on two measures of research effort: the number of times a species description is cited following its publication, and the number of times a species' name is mentioned in the scientific literature. Our analysis highlights some taxonomic biases: for instance, descriptions of acanthocephalans and nematodes tend to receive more citations than those of other helminths, and species of cestodes are less frequently mentioned in the literature than other helminths. We also found that helminths infecting host species of conservation concern receive less research attention, perhaps because of the constraints associated with research on threatened animals, while those infecting host species of human use receive greater research effort. Intriguingly, we found that species originally described by many co-authors subsequently attract more research effort than those described by one or few authors, and that research effort correlates negatively with the human population size of the country where a species was discovered, but not with its economic strength, measured by its gross domestic product. Overall, our findings reveal that we have conducted very little research, or none at all, on the majority of helminth parasite species following their discovery. The biases in study effort we identify have serious implications for future research into parasite biodiversity and conservation.
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8
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Rafiq K, Appleby RG, Davies A, Abrahms B. SensorDrop: A system to remotely detach individual sensors from wildlife tracking collars. Ecol Evol 2023; 13:e10220. [PMID: 37408628 PMCID: PMC10318577 DOI: 10.1002/ece3.10220] [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: 01/06/2023] [Revised: 05/12/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
The growing diversity of animal-borne sensor types is revolutionizing our understanding of wildlife biology. For example, researcher-developed sensors, such as audio and video loggers, are being increasingly attached to wildlife tracking collars to provide insights into a range of topics from species interactions to physiology. However, such devices are often prohibitively power-intensive, relative to conventional wildlife collar sensors, and their retrieval without compromising long-term data collection and animal welfare remains a challenge. We present an open-source system (SensorDrop) for remotely detaching individual sensors from wildlife collars. SensorDrop facilitates the retrieval of power-intensive sensors while leaving non-resource-intensive sensors intact on animals. SensorDrop systems can be made using commercially available components and are a fraction of the cost of other timed drop-off devices that detach full wildlife tracking collars. From 2021 to 2022, eight SensorDrop units were successfully deployed on free-ranging African wild dog packs in the Okavango Delta as part of audio-accelerometer sensor bundles attached to wildlife collars. All SensorDrop units detached after 2-3 weeks and facilitated the collection of audio and accelerometer data while leaving wildlife GPS collars intact to continue collecting locational data (>1 year), critical for long-term conservation population monitoring in the region. SensorDrop offers a low-cost method to remotely detach and retrieve individual sensors from wildlife collars. By selectively detaching battery-depleted sensors, SensorDrop maximizes the amount of data collected per wildlife collar deployment and mitigates ethical concerns on animal rehandling. SensorDrop adds to the growing body of open-source animal-borne technologies being utilized by wildlife researchers to innovate and expand upon data collection practices and supports the continued ethical use of novel technologies within wildlife studies.
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Affiliation(s)
- K. Rafiq
- Department of Biology, Center for Ecosystem SentinelsUniversity of WashingtonSeattleWashingtonUSA
- Botswana Predator ConservationMaunBotswana
| | - R. G. Appleby
- Centre for Planetary Health and Food SecurityGriffith UniversityBrisbaneQueenslandAustralia
- Wild Spy Pty LtdBrisbaneQueenslandAustralia
| | | | - B. Abrahms
- Department of Biology, Center for Ecosystem SentinelsUniversity of WashingtonSeattleWashingtonUSA
- Botswana Predator ConservationMaunBotswana
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9
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Froidevaux JSP, Toshkova N, Barbaro L, Benítez-López A, Kerbiriou C, Le Viol I, Pacifici M, Santini L, Stawski C, Russo D, Dekker J, Alberdi A, Amorim F, Ancillotto L, Barré K, Bas Y, Cantú-Salazar L, Dechmann DKN, Devaux T, Eldegard K, Fereidouni S, Furmankiewicz J, Hamidovic D, Hill DL, Ibáñez C, Julien JF, Juste J, Kaňuch P, Korine C, Laforge A, Legras G, Leroux C, Lesiński G, Mariton L, Marmet J, Mata VA, Mifsud CM, Nistreanu V, Novella-Fernandez R, Rebelo H, Roche N, Roemer C, Ruczyński I, Sørås R, Uhrin M, Vella A, Voigt CC, Razgour O. A species-level trait dataset of bats in Europe and beyond. Sci Data 2023; 10:253. [PMID: 37137926 PMCID: PMC10156679 DOI: 10.1038/s41597-023-02157-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Knowledge of species' functional traits is essential for understanding biodiversity patterns, predicting the impacts of global environmental changes, and assessing the efficiency of conservation measures. Bats are major components of mammalian diversity and occupy a variety of ecological niches and geographic distributions. However, an extensive compilation of their functional traits and ecological attributes is still missing. Here we present EuroBaTrait 1.0, the most comprehensive and up-to-date trait dataset covering 47 European bat species. The dataset includes data on 118 traits including genetic composition, physiology, morphology, acoustic signature, climatic associations, foraging habitat, roost type, diet, spatial behaviour, life history, pathogens, phenology, and distribution. We compiled the bat trait data obtained from three main sources: (i) a systematic literature and dataset search, (ii) unpublished data from European bat experts, and (iii) observations from large-scale monitoring programs. EuroBaTrait is designed to provide an important data source for comparative and trait-based analyses at the species or community level. The dataset also exposes knowledge gaps in species, geographic and trait coverage, highlighting priorities for future data collection.
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Affiliation(s)
- Jérémy S P Froidevaux
- University of Stirling, Biological and Environmental Sciences, Faculty of Natural Sciences, FK9 4LJ, Stirling, UK.
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France.
- School of Biological Sciences, University of Bristol, Life Sciences Building, BS8 1TQ, Bristol, UK.
| | - Nia Toshkova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000, Sofia, Bulgaria
- National Museum of Natural History at the Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luc Barbaro
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- DYNAFOR, INRAE-INPT, University of Toulouse, Castanet-Tolosan, France
| | - Ana Benítez-López
- Integrative Ecology Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
- Department of Zoology, University of Granada, Granada, Spain
| | - Christian Kerbiriou
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Isabelle Le Viol
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Michela Pacifici
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Luca Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Clare Stawski
- Department of Biology, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Danilo Russo
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università, 100, 80055, Portici (Napoli), Italy.
| | - Jasja Dekker
- Jasja Dekker Dierecologie BV, Arnhem, the Netherlands
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Francisco Amorim
- 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
| | - Leonardo Ancillotto
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università, 100, 80055, Portici (Napoli), Italy
| | - Kévin Barré
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Yves Bas
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Lisette Cantú-Salazar
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation, 41 rue du Brill, L-4422, Belvaux, Luxemburg
| | - Dina K N Dechmann
- Max Planck Institute of Animal Behavior, Department of Migration, Am Obstberg 1, 78315, Radolfzell, Germany
- University of Konstanz, Department of Biology, Universitätsstr. 10, 78464, Konstanz, Germany
| | - Tiphaine Devaux
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Katrine Eldegard
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Sasan Fereidouni
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Joanna Furmankiewicz
- Department of Behavioural Ecology, Faculty of Biological Sciences, University of Wroclaw, Sienkiewicza 21, 50-335, Wroclaw, Poland
| | - Daniela Hamidovic
- Ministry of Economy and Sustainable Development, Institute for Environment and Nature, Radnička cesta 80, HR-10000, Zagreb, Croatia
- Croatian Biospeleological Society, Rooseveltov trg 6, HR-10000, Zagreb, Croatia
| | - Davina L Hill
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Carlos Ibáñez
- Department Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Jean-François Julien
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Javier Juste
- Department Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
- CIBER de Epidemiología y Salud Pública, CIBERESP, 28220, Madrid, Spain
| | - Peter Kaňuch
- Institute of Forest Ecology, Slovak Academy of Sciences, Zvolen, Slovakia
| | - Carmi Korine
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 8499000, Midreshet Ben-Gurion, Israel
| | - Alexis Laforge
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Gaëlle Legras
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Camille Leroux
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- Auddicé Biodiversité- ZAC du Chevalement, 5 rue des Molettes, 59286, Roost-Warendin, France
| | - Grzegorz Lesiński
- Institute of Animal Science, Warsaw University of Life Sciences (SGGW), Ciszewskiego 8, 02-787, Warsaw, Poland
| | - Léa Mariton
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, CNRS, MNHN, IRD, 61 Rue Buffon, 75005, Paris, France
| | - Julie Marmet
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Vanessa A Mata
- 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
| | - Clare M Mifsud
- Conservation Biology Research Group, Biology Department, University of Malta, MSD2080, Msida, Malta
| | | | - Roberto Novella-Fernandez
- Technical University of Munich, Terrestrial Ecology Research Group, Department for Life Science Systems, School of Life Sciences, Freising, Germany
| | - Hugo Rebelo
- 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
- ESS, Polytechnic Institute of Setúbal, Campus do IPS - Estefanilha, 2910-761, Setúbal, Portugal
| | - Niamh Roche
- Bat Conservation Ireland, Carmichael House, 4-7, North Brunswick Street, Dublin, D07 RHA8, Ireland
| | - Charlotte Roemer
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Ireneusz Ruczyński
- Mammal Research Institute Polish Academy of Sciences, Stoczek 1, 17-230, Białowieża, Poland
| | - Rune Sørås
- Department of Biology, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Marcel Uhrin
- Institute of Biology and Ecology, Faculty of Science, P. J, Šafárik University in Košice, Košice, Slovakia
| | - Adriana Vella
- Conservation Biology Research Group, Biology Department, University of Malta, MSD2080, Msida, Malta
| | - Christian C Voigt
- Department Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
| | - Orly Razgour
- Biosciences, University of Exeter, Streatham Campus, Hatherly Laboratories, Prince of Wales Road, Exeter, EX4 4PS, UK.
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10
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Reintroduction biology and the IUCN Red List: The dominance of species of Least Concern in the peer-reviewed literature. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02242] [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] Open
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11
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Tam J, Lagisz M, Cornwell W, Nakagawa S. Quantifying research interests in 7,521 mammalian species with h-index: a case study. Gigascience 2022; 11:6665406. [PMID: 35962776 PMCID: PMC9375528 DOI: 10.1093/gigascience/giac074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/11/2022] [Accepted: 06/27/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Taxonomic bias is a known issue within the field of biology, causing scientific knowledge to be unevenly distributed across species. However, a systematic quantification of the research interest that the scientific community has allocated to individual species remains a big data problem. Scalable approaches are needed to integrate biodiversity data sets and bibliometric methods across large numbers of species. The outputs of these analyses are important for identifying understudied species and directing future research to fill these gaps. FINDINGS In this study, we used the species h-index to quantity the research interest in 7,521 species of mammals. We tested factors potentially driving species h-index, by using a Bayesian phylogenetic generalized linear mixed model (GLMM). We found that a third of the mammals had a species h-index of zero, while a select few had inflated research interest. Further, mammals with higher species h-index had larger body masses; were found in temperate latitudes; had their humans uses documented, including domestication; and were in lower-risk International Union for Conservation of Nature Red List categories. These results surprisingly suggested that critically endangered mammals are understudied. A higher interest in domesticated species suggested that human use is a major driver and focus in mammalian scientific literature. CONCLUSIONS Our study has demonstrated a scalable workflow and systematically identified understudied species of mammals, as well as identified the likely drivers of this taxonomic bias in the literature. This case study can become a benchmark for future research that asks similar biological and meta-research questions for other taxa.
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Affiliation(s)
- Jessica Tam
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Malgorzata Lagisz
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Will Cornwell
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
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12
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Broekman MJE, Hilbers JP, Huijbregts MAJ, Mueller T, Ali AH, Andrén H, Altmann J, Aronsson M, Attias N, Bartlam‐Brooks HLA, van Beest FM, Belant JL, Beyer DE, Bidner L, Blaum N, Boone RB, Boyce MS, Brown MB, Cagnacci F, Černe R, Chamaillé‐Jammes S, Dejid N, Dekker J, L. J. Desbiez A, Díaz‐Muñoz SL, Fennessy J, Fichtel C, Fischer C, Fisher JT, Fischhoff I, Ford AT, Fryxell JM, Gehr B, Goheen JR, Hauptfleisch M, Hewison AJM, Hering R, Heurich M, Isbell LA, Janssen R, Jeltsch F, Kaczensky P, Kappeler PM, Krofel M, LaPoint S, Latham ADM, Linnell JDC, Markham AC, Mattisson J, Medici EP, de Miranda Mourão G, Van Moorter B, Morato RG, Morellet N, Mysterud A, Mwiu S, Odden J, Olson KA, Ornicāns A, Pagon N, Panzacchi M, Persson J, Petroelje T, Rolandsen CM, Roshier D, Rubenstein DI, Saïd S, Salemgareyev AR, Sawyer H, Schmidt NM, Selva N, Sergiel A, Stabach J, Stacy‐Dawes J, Stewart FEC, Stiegler J, Strand O, Sundaresan S, Svoboda NJ, Ullmann W, Voigt U, Wall J, Wikelski M, Wilmers CC, Zięba F, Zwijacz‐Kozica T, Schipper AM, Tucker MA. Evaluating expert-based habitat suitability information of terrestrial mammals with GPS-tracking data. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2022; 31:1526-1541. [PMID: 36247232 PMCID: PMC9544534 DOI: 10.1111/geb.13523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 06/16/2023]
Abstract
AIM Macroecological studies that require habitat suitability data for many species often derive this information from expert opinion. However, expert-based information is inherently subjective and thus prone to errors. The increasing availability of GPS tracking data offers opportunities to evaluate and supplement expert-based information with detailed empirical evidence. Here, we compared expert-based habitat suitability information from the International Union for Conservation of Nature (IUCN) with habitat suitability information derived from GPS-tracking data of 1,498 individuals from 49 mammal species. LOCATION Worldwide. TIME PERIOD 1998-2021. MAJOR TAXA STUDIED Forty-nine terrestrial mammal species. METHODS Using GPS data, we estimated two measures of habitat suitability for each individual animal: proportional habitat use (proportion of GPS locations within a habitat type), and selection ratio (habitat use relative to its availability). For each individual we then evaluated whether the GPS-based habitat suitability measures were in agreement with the IUCN data. To that end, we calculated the probability that the ranking of empirical habitat suitability measures was in agreement with IUCN's classification into suitable, marginal and unsuitable habitat types. RESULTS IUCN habitat suitability data were in accordance with the GPS data (> 95% probability of agreement) for 33 out of 49 species based on proportional habitat use estimates and for 25 out of 49 species based on selection ratios. In addition, 37 and 34 species had a > 50% probability of agreement based on proportional habitat use and selection ratios, respectively. MAIN CONCLUSIONS We show how GPS-tracking data can be used to evaluate IUCN habitat suitability data. Our findings indicate that for the majority of species included in this study, it is appropriate to use IUCN habitat suitability data in macroecological studies. Furthermore, we show that GPS-tracking data can be used to identify and prioritize species and habitat types for re-evaluation of IUCN habitat suitability data.
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Affiliation(s)
- Maarten J. E. Broekman
- Department of Environmental ScienceInstitute for Wetland and Water Research, Faculty of Science, Radboud UniversityNijmegenThe Netherlands
| | - Jelle P. Hilbers
- Department of Environmental ScienceInstitute for Wetland and Water Research, Faculty of Science, Radboud UniversityNijmegenThe Netherlands
| | - Mark A. J. Huijbregts
- Department of Environmental ScienceInstitute for Wetland and Water Research, Faculty of Science, Radboud UniversityNijmegenThe Netherlands
| | - Thomas Mueller
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für NaturforschungFrankfurt (Main)Germany
- Department of Biological SciencesGoethe UniversityFrankfurt (Main)Germany
| | | | - Henrik Andrén
- Grimsö Wildlife Research Station, Department of EcologySwedish University of Agricultural SciencesRiddarhyttanSweden
| | - Jeanne Altmann
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Malin Aronsson
- Grimsö Wildlife Research Station, Department of EcologySwedish University of Agricultural SciencesRiddarhyttanSweden
- Department of ZoologyStockholm UniversityStockholmSweden
| | - Nina Attias
- Ecology and Conservation Graduate ProgramFederal University of Mato Grosso do SulCampo GrandeMato Grosso do SulBrazil
- Instituto de Conservação de Animais Silvestres (ICAS)Campo GrandeMato Grosso do SulBrazil
| | | | | | - Jerrold L. Belant
- Global Wildlife Conservation CenterState University of New York College of Environmental Science and ForestrySyracuseNew YorkUSA
| | - Dean E. Beyer
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
| | - Laura Bidner
- Department of AnthropologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Niels Blaum
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
| | - Randall B. Boone
- Department of Ecosystem Science and SustainabilityColorado State UniversityFort CollinsColoradoUSA
| | - Mark S. Boyce
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Michael B. Brown
- Giraffe Conservation FoundationErosNamibia
- Conservation Ecology CenterSmithsonian National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Francesca Cagnacci
- Department of Biodiversity and Molecular EcologyResearch and Innovation Centre, Fondazione Edmund MachTrentoItaly
| | - Rok Černe
- Slovenia Forest ServiceLjubljanaSlovenia
| | - Simon Chamaillé‐Jammes
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Nandintsetseg Dejid
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für NaturforschungFrankfurt (Main)Germany
| | | | - Arnaud L. J. Desbiez
- Instituto de Conservação de Animais Silvestres (ICAS)Campo GrandeMato Grosso do SulBrazil
- IPÊ (Instituto de Pesquisas Ecológicas; Institute for Ecological Research)São PauloBrazil
- Royal Zoological Society of Scotland (RZSS)EdinburghUK
| | - Samuel L. Díaz‐Muñoz
- Department of Microbiology and Molecular GeneticsUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Claudia Fichtel
- German Primate Center, Behavioral Ecology and Sociobiology UnitGöttingenGermany
| | - Christina Fischer
- Faunistics and Wildlife Conservation, Department of Agriculture, Ecotrophology, and Landscape DevelopmentAnhalt University of Applied SciencesBernburgGermany
| | - Jason T. Fisher
- School of Environmental StudiesUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | | | - Adam T. Ford
- Department of Biology, Faculty of ScienceUniversity of British ColumbiaKelownaBritish ColumbiaCanada
| | - John M. Fryxell
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
| | - Benedikt Gehr
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Jacob R. Goheen
- Department of Zoology and PhysiologyUniversity of WyomingLaramieWyomingUSA
| | - Morgan Hauptfleisch
- Department of Agriculture And Natural Resources Sciences, Biodiversity Research CentreNamibia University of Science and TechnologyWindhoekNamibia
| | - A. J. Mark Hewison
- Université de Toulouse, INRAE, CEFSCastanet‐TolosanFrance
- LTSER ZA Pyrénées GaronneAuzeville‐TolosaneFrance
| | - Robert Hering
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
| | - Marco Heurich
- Department of Conservation and ResearchBavarian Forest National ParkGrafenauGermany
- Chair of Wildlife Ecology and ManagementAlbert Ludwigs University of FreiburgFreiburgGermany
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesKoppangNorway
| | - Lynne A. Isbell
- Department of AnthropologyUniversity of CaliforniaDavisCaliforniaUSA
- Animal Behavior Graduate GroupUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Florian Jeltsch
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
| | - Petra Kaczensky
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesKoppangNorway
- Norwegian Institute for Nature ResearchTrondheimNorway
- Research Institute of Wildlife EcologyUniversity of Veterinary Medicine ViennaViennaAustria
| | - Peter M. Kappeler
- German Primate Center, Behavioral Ecology and Sociobiology UnitGöttingenGermany
| | - Miha Krofel
- Department of Forestry and Renewable Forest Resources, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Scott LaPoint
- Black Rock ForestCornwallNew YorkUSA
- Lamont‐Doherty Earth ObservatoryColumbia UniversityPalisadesNew YorkUSA
| | - A. David M. Latham
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Wildlife Ecology and ManagementManaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - John D. C. Linnell
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesKoppangNorway
- Norwegian Institute for Nature ResearchTrondheimNorway
| | | | | | - Emilia Patricia Medici
- IPÊ (Instituto de Pesquisas Ecológicas; Institute for Ecological Research)São PauloBrazil
- International Union for Conservation of Nature (IUCN) Species Survival Commission (SSC) Tapir Specialist Group (TSG)Campo GrandeMato Grosso do SulBrazil
| | | | | | - Ronaldo G. Morato
- National Research Center for Carnivores ConservationChico Mendes Institute for the Conservation of BiodiversityAtibaiaBrazil
| | - Nicolas Morellet
- Université de Toulouse, INRAE, CEFSCastanet‐TolosanFrance
- LTSER ZA Pyrénées GaronneAuzeville‐TolosaneFrance
| | - Atle Mysterud
- Centre for Ecological and Evolutionary Synthesis, Department of BiosciencesUniversity of OsloOsloNorway
| | - Stephen Mwiu
- Wildlife Research and Training InstituteNaivashaKenya
| | - John Odden
- Norwegian Institute for Nature ResearchOsloNorway
| | - Kirk A. Olson
- Wildlife Conservation Society, Mongolia ProgramUlaanbaatarMongolia
| | - Aivars Ornicāns
- Latvian State Forest Research Institute “Silava”SalaspilsLatvia
| | | | | | - Jens Persson
- Grimsö Wildlife Research Station, Department of EcologySwedish University of Agricultural SciencesRiddarhyttanSweden
| | - Tyler Petroelje
- Global Wildlife Conservation CenterState University of New York College of Environmental Science and ForestrySyracuseNew YorkUSA
| | | | - David Roshier
- Australian Wildlife ConservancySubiacoWestern AustraliaAustralia
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Sonia Saïd
- Direction de la Recherche et de l'Appui ScientifiqueOffice Français de la BiodiversitéBirieuxFrance
| | - Albert R. Salemgareyev
- Association for the Conservation of Biodiversity of Kazakhstan (ACBK)Nur‐SultanKazakhstan
| | - Hall Sawyer
- Western Ecosystems Technology Inc.LaramieWyomingUSA
| | - Niels Martin Schmidt
- Department of BioscienceAarhus UniversityRoskildeDenmark
- Arctic Research CentreAarhus UniversityAarhusDenmark
| | - Nuria Selva
- Institute of Nature Conservation Polish Academy of SciencesKrakowPoland
| | - Agnieszka Sergiel
- Institute of Nature Conservation Polish Academy of SciencesKrakowPoland
| | - Jared Stabach
- Conservation Ecology CenterSmithsonian National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Jenna Stacy‐Dawes
- Conservation Science and Wildlife HealthSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
| | - Frances E. C. Stewart
- School of Environmental StudiesUniversity of VictoriaVictoriaBritish ColumbiaCanada
- Department of BiologyWilfrid Laurier UniversityWaterlooOntarioCanada
| | - Jonas Stiegler
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
| | - Olav Strand
- Norwegian Institute for Nature ResearchTrondheimNorway
| | | | - Nathan J. Svoboda
- Carnivore Ecology Laboratory, Forest and Wildlife Research CenterMississippi State UniversityMississippi StateMississippiUSA
- Alaska Department of Fish and GameKodiakAlaskaUSA
| | - Wiebke Ullmann
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
| | - Ulrich Voigt
- Institute for Terrestrial and Aquatic Wildlife ResearchUniversity of Veterinary Medicine Hannover FoundationHannoverGermany
| | | | - Martin Wikelski
- Department of MigrationMax Planck Institute of Animal BehaviorRadolfzellGermany
- Centre for the Advanced Study of Collective BehaviourUniversity of KonstanzConstanceGermany
| | - Christopher C. Wilmers
- Center for Integrated Spatial Research, Environmental Studies DepartmentUniversity of CaliforniaSanta CruzCaliforniaUSA
| | | | | | - Aafke M. Schipper
- Department of Environmental ScienceInstitute for Wetland and Water Research, Faculty of Science, Radboud UniversityNijmegenThe Netherlands
- PBL Netherlands Environmental Assessment AgencyThe HagueThe Netherlands
| | - Marlee A. Tucker
- Department of Environmental ScienceInstitute for Wetland and Water Research, Faculty of Science, Radboud UniversityNijmegenThe Netherlands
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13
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Berba CMP, Matias AMA. State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data. PeerJ 2022; 10:e13146. [PMID: 35341040 PMCID: PMC8944339 DOI: 10.7717/peerj.13146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/01/2022] [Indexed: 01/12/2023] Open
Abstract
Anthropogenic changes in the natural environment have led to alarming rates of biodiversity loss, resulting in a more urgent need for conservation. Although there is an increasing cognizance of the importance of incorporating biodiversity data into conservation, the accuracy of the inferences generated from these records can be highly impacted by gaps and biases in the data. Because of the Philippines' status as a biodiversity hotspot, the assessment of potential gaps and biases in biodiversity documentation in the country can be a critical step in the identification of priority research areas for conservation applications. In this study, we systematically assessed biodiversity data on animal and plant taxa found in the Philippines by examining the extent of metadata gaps, taxonomic biases, and spatial biases in DNA barcode data while using species occurrence data as a backdrop of the 'Philippines' biodiversity. These barcode and species occurrence datasets were obtained from public databases, namely: GenBank, Barcode of Life Data System and Global Biodiversity Information Facility. We found that much of the barcode data had missing information on either records and publishing, geolocation, or taxonomic metadata, which consequently, can limit the usability of barcode data for further analyses. We also observed that the amount of barcode data can be directly associated with the amount of species occurrence data available for a particular taxonomic group and location-highlighting the potential sampling biases in the barcode data. While the majority of barcode data came from foreign institutions, there has been an increase in local efforts in recent decades. However, much of the contribution to biodiversity documentation only come from institutions based in Luzon.
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14
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Wright PGR, Croose E, Macpherson JL. A global review of the conservation threats and status of mustelids. Mamm Rev 2022. [DOI: 10.1111/mam.12288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Patrick G. R. Wright
- Vincent Wildlife Trust Eastnor LedburyHR8 1EPUK
- University of Sussex Falmer BrightonBN1 9QGUK
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15
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Abstract
Abstract
Carnivore population declines are a time-sensitive global challenge in which mitigating decreasing populations requires alignment of applied practice and research priorities. However, large carnivore conservation is hindered by gaps among research, conservation practice and policy formation. One potential driver of this research–implementation gap is research bias towards charismatic species. Using depredation of livestock by large carnivores in sub-Saharan Africa as a case study, we examined whether taxonomic bias could be detected and explored the potential effects of such a bias on the research–implementation gap. Via a literature review, we compared the central large carnivore species in research to the species identified as the primary livestock depredator. We detected a substantial misalignment between these factors for two species. Spotted hyaenas Crocuta crocuta were the most common depredator of livestock (58.5% of studies), but were described as a central species among only 20.7% of the studies. In comparison, African lions Panthera leo were the most common central species (45% of studies) but were the primary depredator in just 24.4% of studies. Such patterns suggest that taxonomic bias is prevalent within this research. Although spotted hyaenas may depredate livestock most often, their low charisma in comparison to sympatric species such as the African lion and leopard Panthera pardus may be limiting research-informed conservation efforts for them. Efforts to mitigate human-carnivore conflict designed for one species may not be applicable to another co-occurring species, and thus, taxonomic bias could undermine the efficacy of interventions built to reduce livestock depredation by carnivores.
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16
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Brereton J, Rose P. An evaluation of the role of 'biological evidence' in zoo and aquarium enrichment practices. Anim Welf 2022. [DOI: 10.7120/09627286.31.1.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Evidence-based approaches are key to advancing all areas of zoo and aquarium practice. Output from empirical study must be disseminated to those within the industry so that results can support changes to husbandry and management for individual species. Information on enrichment techniques
is published in a range of sources, including papers in the peer-reviewed and 'grey literature' (ie professional but non-reviewed publications). To investigate how evidence is implemented into enrichment practices, we sampled all enrichment studies identified in one online repository of peer-reviewed
papers and two grey literature publications across an elevenyear period. We recorded whether the enrichment was supported with biological evidence (whether it was developed using published enrichment-focused research for that species and/or with the species' ecology and behaviour information)
alongside analysis of the type of enrichment used and the chosen study species. Enrichment articles were more likely to be supported by biological evidence in peer-reviewed than grey literature. Taxonomic differences in the use of evidence were noted; for example, enrichment provided to carnivores
and parrots was more likely to be supported with biological evidence compared to that used for penguins. Of the five enrichment types, nutritional enrichment was most often based on biological evidence. Multi-category and physical enrichment types were more common across all literature sources
whereas social enrichment was less common, suggesting barriers to implementation of all enrichment types in zoological facilities. Our research suggests that zoo and aquarium professionals are considering species-specific welfare needs by ensuring that enrichment protocols are supported by
biological evidence. However, opportunities to diversify the enrichment types being offered and species being researched are identified.
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Affiliation(s)
- J Brereton
- University Centre Sparsholt, Westley Lane, Sparsholt, Winchester SO21 2NF, UK
| | - P Rose
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4SB, UK
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17
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LaBarge LR, Evans MJ, Miller JRB, Cannataro G, Hunt C, Elbroch LM. Pumas
Puma concolor
as ecological brokers: a review of their biotic relationships. Mamm Rev 2022. [DOI: 10.1111/mam.12281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Laura R. LaBarge
- Program in Evolution, Ecology and Behavior, Department of Environment and Sustainability, The State University of New York University at Buffalo Amherst NY14260USA
- Center for Conservation Innovation Defenders of Wildlife Washington DC20036USA
- Max Planck Institute of Animal Behavior Bücklestraße 5 Konstanz DE78467Germany
| | - Michael J. Evans
- Center for Conservation Innovation Defenders of Wildlife Washington DC20036USA
- Department of Environmental Science and Policy George Mason University 4400 University Dr Fairfax VA22030USA
| | - Jennifer R. B. Miller
- Center for Conservation Innovation Defenders of Wildlife Washington DC20036USA
- Department of Environmental Science and Policy George Mason University 4400 University Dr Fairfax VA22030USA
| | - Gillian Cannataro
- Center for Conservation Innovation Defenders of Wildlife Washington DC20036USA
- Conservation, Management and Welfare Sciences Association of Zoos and Aquariums 8403 Colesville Rd., Suite 710 Silver Spring MD20910‐3314USA
| | - Christian Hunt
- Field Conservation Defenders of Wildlife Washington DC20036USA
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18
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Becker FK, Shabangu FW, Gridley T, Wittmer HU, Marsland S. Sounding out a continent: seven decades of bioacoustics research in Africa. BIOACOUSTICS 2022. [DOI: 10.1080/09524622.2021.2021987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Frowin K. Becker
- School of Biological Sciences, Victoria University of Wellington/Te Herenga Waka, Wellington, New Zealand
- National Geographic Okavango Wilderness Project, Maun, Botswana
| | - Fannie W. Shabangu
- Fisheries Management Branch, Department of Forestry, Fisheries and the Environment, Cape Town, South Africa
- Mammal Research Institute Whale Unit, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Tess Gridley
- Sea Search Research and Conservation Npc, Cape Town, South Africa
- Department of Botany and Zoology, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Heiko U. Wittmer
- School of Biological Sciences, Victoria University of Wellington/Te Herenga Waka, Wellington, New Zealand
| | - Stephen Marsland
- School of Mathematics and Statistics, Victoria University of Wellington/Te Herenga Waka, Wellington, New Zealand
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19
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Tourani M. A review of spatial capture-recapture: Ecological insights, limitations, and prospects. Ecol Evol 2022; 12:e8468. [PMID: 35127014 PMCID: PMC8794757 DOI: 10.1002/ece3.8468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 11/14/2021] [Accepted: 11/29/2021] [Indexed: 11/28/2022] Open
Abstract
First described by Efford (2004), spatial capture-recapture (SCR) has become a popular tool in ecology. Like traditional capture-recapture, SCR methods account for imperfect detection when estimating ecological parameters. In addition, SCR methods use the information inherent in the spatial configuration of individual detections, thereby allowing spatially explicit estimation of population parameters, such as abundance, survival, and recruitment. Paired with advances in noninvasive survey methods, SCR has been applied to a wide range of species across different habitats, allowing for population- and landscape-level inferences with direct consequences for conservation and management. I conduct a literature review of SCR studies published since the first description of the method and provide an overview of their scope in terms of the ecological questions answered with this tool, taxonomic groups targeted, geography, spatio-temporal extent of analyses, and data collection methods. In addition, I review approaches for analytical implementation and provide an overview of parameters targeted by SCR studies and conclude with current limitations and future directions in SCR methods.
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Affiliation(s)
- Mahdieh Tourani
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
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20
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Ellison G, Jones M, Cain B, Bettridge CM. Taxonomic and geographic bias in 50 years of research on the behaviour and ecology of galagids. PLoS One 2021; 16:e0261379. [PMID: 34910792 PMCID: PMC8673608 DOI: 10.1371/journal.pone.0261379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/29/2021] [Indexed: 11/18/2022] Open
Abstract
Identifying knowledge gaps and taxonomic and geographic bias in the literature is invaluable for guiding research towards a more representative understanding of animal groups. Galagids are nocturnal African primates and, for many species, detailed information on their behaviour and ecology is unavailable. To identify gaps and bias in the literature we reviewed published peer-reviewed research articles on galagid behaviour and ecology over a 50-year period from January 1971 to December 2020. Using the Web of Science and Google Scholar databases, we identified 758 articles, assessed 339 full texts for eligibility and included 211 in the review. Species of Otolemur have been extensively researched in comparison to other genera (78.2% of studies; Euoticus: 13.3% of studies; Galago: 66.4% of studies; Galagoides: 20.9% of studies; Paragalago: 22.3% of studies; Sciurocheirus: 15.2% of studies). The most common category of research was physiology (55.0% of studies), followed by behavioural ecology (47.4% of studies), and fewer studies were on genetics and taxonomy (16.1% of studies) and habitat and distribution (14.2% of studies). Text mining revealed that the word 'behaviour' was the most common word used in abstracts and keywords, and few words were related to ecology. Negative binomial regression revealed that mean body mass and geographic range size were significant positive predictors of the total number of scientific outputs on each species. Research on wild populations was carried out in only 24 (60%) of the 40 countries galagids are thought to inhabit. Studies were undertaken in locations with lower mean annual temperatures and higher human population densities over warmer and less populated areas. We encourage a more equal sampling effort both taxonomically and geographically that in particular addresses the paucity of research on smaller species and those with restricted ranges. Research on in situ populations, especially in warmer and remote areas, is urgently needed, particularly in West, Central and some Southern African countries.
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Affiliation(s)
- Grace Ellison
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Martin Jones
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Bradley Cain
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Caroline M. Bettridge
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
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21
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García-Macía J, Pérez I, Rodríguez-Caro RC. Biases in conservation: A regional analysis of Spanish vertebrates. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Investigating the Effect of Enrichment on the Behavior of Zoo-Housed Southern Ground Hornbills. JOURNAL OF ZOOLOGICAL AND BOTANICAL GARDENS 2021. [DOI: 10.3390/jzbg2040043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Enrichment is essential for the welfare of many zoo-housed animals, yet the value of enrichment is not well understood for all taxa. As an intelligent, long-lived species, the southern ground hornbill (Bucorvus leadbeateri) is a good model for enrichment research. A pair of southern ground hornbills, housed at Beale Wildlife Park and Gardens, were observed during study periods in 2014, 2018, and 2019. Three types of enrichment were provided for the birds; these enrichment types were developed based on information on the habits of the species as found in natural history papers. The enrichment types consisted of a pile of twigs, small animal carcasses, and plastic mirrors. Overall, the carcass feeds and the mirrors resulted in the greatest changes in behavior, with hornbills engaging in long periods of food manipulation with carcasses. For the mirror condition, hornbills spent time stalking around and pecking at mirrors, similar to the ‘window smashing’ behavior seen in wild hornbills. Overall, the research suggests that not only can enrichment modify the behavior of southern ground hornbills, but non-nutritional enrichment may be equally valuable to the animals. Natural history papers may have some value in inspiring novel enrichment items for zoo-housed animals.
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23
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Meineke EK, Daru BH. Bias assessments to expand research harnessing biological collections. Trends Ecol Evol 2021; 36:1071-1082. [PMID: 34489117 DOI: 10.1016/j.tree.2021.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/22/2022]
Abstract
Biological collections are arguably the most important resources for investigations into the impacts of human activities on biodiversity. However, the apparent opportunities presented by museum-derived datasets have not resulted in consistent or widespread use of specimens in ecology outside phenological research and species distribution modeling. We attribute this gap between opportunity and application to biases introduced by collectors, curators, and preservation practices and an imperfect understanding of these biases and how to mitigate them. To facilitate broader use of specimen-based data, we characterize collection biases across key axes and explore interactions among them. We then present a framework for determining the bias assessments needed when extracting data from biological collections. We show that bias assessments required by particular ecological studies will depend on the response variables being measured and the predictor axes of interest. We argue that quantification of biases in specimen-derived datasets is needed to facilitate the widespread application of these data.
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Affiliation(s)
- Emily K Meineke
- Department of Entomology and Nematology, University of California, Davis 95616, CA, USA.
| | - Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA.
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24
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Abstract
The order Psittaciformes is one of the most prevalent groups in the illegal wildlife trade. Efforts to understand this threat have focused on describing the elements of the trade itself: actors, extraction rates, and routes. However, the development of policy-oriented interventions also requires an understanding of how research aims and actions are distributed across the trade chain, regions, and species. We used an action-based approach to review documents published on illegal Psittaciformes trade at a global scale to analyze patterns in research aims and actions. Research increased exponentially in recent decades, recording 165 species from 46 genera, with an over representation of American and Australasian genera. Most of the research provided basic knowledge for the intermediary side of the trade chain. Aims such as the identification of network actors, zoonosis control, and aiding physical detection had numerous but scarcely cited documents (low growth rate), while behavior change had the highest growth rate. The Americas had the highest diversity of research aims, contributing with basic knowledge, implementation, and monitoring across the whole trade chain. Better understanding of the supply side dynamics in local markets, actor typology, and actor interactions are needed. Protecting areas, livelihood incentives, and legal substitutes are actions under-explored in parrots, while behavior change is emerging.
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25
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Vickers CJ, Fraga D, Patrick WM. Quantifying the taxonomic bias in enzymology. Protein Sci 2021; 30:914-921. [PMID: 33583070 PMCID: PMC7980516 DOI: 10.1002/pro.4041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/31/2022]
Abstract
The ongoing biotechnological revolution is rooted in our knowledge of enzymes. However, metagenomics is showing how little we know about Earth's enzyme repertoire. Deep sequencing has revolutionized our view of the tree of life. The genomes of newly‐discovered organisms are replete with novel sequences, emphasizing the trove of enzyme structures and functions waiting to be explored by biochemists. Here, we sought to draw attention to the vastness of the “enzymatic dark matter” within the tree of life by placing enzymological knowledge in the context of phylogeny. We used kinetic parameters from the BRaunschweig ENzyme DAtabase (BRENDA) as our proxy for enzymological knowledge. Mapping 12,677 BRENDA entries onto the phylogenetic tree revealed that 55% of these data were from eukaryotes, even though they are the least diverse part of the tree. At the next taxonomic level, only four of 18 archaeal phyla and 24 of 111 bacterial phyla are represented in the BRENDA dataset. One phylum, the Proteobacteria, accounts for over half of all bacterial entries. Similarly, the supergroup Amorphea, which includes animals and fungi, contains over half the data on eukaryotes. Many major taxonomic groups are notable for their complete absence from BRENDA, including the ultra‐diverse bacterial Candidate Phyla Radiation. At the species level, five mammals (including human) contribute 15% of BRENDA entries. The taxonomic bias in enzymology is strong, but in the era of gene synthesis we now have the tools to address it. Doing so promises to enrich our biochemical understanding of life and uncover powerful new biocatalysts.
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Affiliation(s)
- Chelsea J Vickers
- Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Dean Fraga
- Department of Biology, The College of Wooster, Wooster, Ohio, USA
| | - Wayne M Patrick
- Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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26
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Buxton RT, Nyboer EA, Pigeon KE, Raby GD, Rytwinski T, Gallagher AJ, Schuster R, Lin H, Fahrig L, Bennett JR, Cooke SJ, Roche DG. Avoiding wasted research resources in conservation science. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.329] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
| | | | | | - Graham D. Raby
- Department of Biology Trent University Peterborough Ontario Canada
| | - Trina Rytwinski
- Department of Biology Carleton University Ottawa Ontario Canada
- Institute of Environmental and Interdisciplinary Science, Carleton University Ottawa Ontario Canada
| | | | | | - Hsien‐Yung Lin
- Department of Biology Carleton University Ottawa Ontario Canada
| | - Lenore Fahrig
- Department of Biology Carleton University Ottawa Ontario Canada
| | - Joseph R. Bennett
- Department of Biology Carleton University Ottawa Ontario Canada
- Institute of Environmental and Interdisciplinary Science, Carleton University Ottawa Ontario Canada
| | - Steven J. Cooke
- Department of Biology Carleton University Ottawa Ontario Canada
- Institute of Environmental and Interdisciplinary Science, Carleton University Ottawa Ontario Canada
| | - Dominique G. Roche
- Department of Biology Carleton University Ottawa Ontario Canada
- Institut de Biologie, Université de Neuchâtel Neuchâtel Switzerland
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27
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Guerisoli MDLM, Luengos Vidal E, Caruso N, Giordano AJ, Lucherini M. Puma–livestock conflicts in the Americas: a review of the evidence. Mamm Rev 2020. [DOI: 10.1111/mam.12224] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Maria de las Mercedes Guerisoli
- GECOBI (Grupo de Genética y Ecología en Conservación y Biodiversidad) División Mastozoología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” Angel Gallardo 490 Buenos Aires1405Argentina
- Departamento de Biología, Bioquímica y Farmacia e Instituto de Ciencias Biológicas y Biomédicas del Sur Universidad Nacional del Sur ‐ CONICET San Juan 670 Bahía Blanca8000Argentina
- S.P.E.C.I.E.S P.O. Box 7403 Ventura California USA
| | - Estela Luengos Vidal
- Departamento de Biología, Bioquímica y Farmacia e Instituto de Ciencias Biológicas y Biomédicas del Sur Universidad Nacional del Sur ‐ CONICET San Juan 670 Bahía Blanca8000Argentina
| | - Nicolás Caruso
- Departamento de Biología, Bioquímica y Farmacia e Instituto de Ciencias Biológicas y Biomédicas del Sur Universidad Nacional del Sur ‐ CONICET San Juan 670 Bahía Blanca8000Argentina
| | | | - Mauro Lucherini
- Departamento de Biología, Bioquímica y Farmacia e Instituto de Ciencias Biológicas y Biomédicas del Sur Universidad Nacional del Sur ‐ CONICET San Juan 670 Bahía Blanca8000Argentina
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28
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Silva AFD, Malhado AC, Correia RA, Ladle RJ, Vital MV, Mott T. Taxonomic bias in amphibian research: Are researchers responding to conservation need? J Nat Conserv 2020. [DOI: 10.1016/j.jnc.2020.125829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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