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Crane M, Silva I, Grainger MJ, Gale GA. Limitations and gaps in global bat wing morphology trait data. Mamm Rev 2021. [DOI: 10.1111/mam.12270] [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)
- Matt Crane
- Conservation Ecology Program King Mongkut’s University of Technology Thonburi 49 Thakham, Bangkhuntien Bangkok10150Thailand
| | - Inês Silva
- Center for Advanced Systems Understanding (CASUS) Am Untermarkt 20 Görlitz02826Germany
- Helmholtz‐Zentrum Dresden‐Rossendorf (HZDR) Bautzner Landstraße 400 Dresden01328Germany
| | - Matthew J. Grainger
- Norwegian Institute for Nature Research Postbox 5685 Torgarden Trondheim7485Norway
| | - George A. Gale
- Conservation Ecology Program King Mongkut’s University of Technology Thonburi 49 Thakham, Bangkhuntien Bangkok10150Thailand
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Iversen CM, McCormack ML. Filling gaps in our understanding of belowground plant traits across the world: an introduction to a Virtual Issue. THE NEW PHYTOLOGIST 2021; 231:2097-2103. [PMID: 34405907 DOI: 10.1111/nph.17326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Colleen M Iversen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6301, USA
| | - M Luke McCormack
- Center for Tree Science, The Morton Arboretum, Liesle, IL, 60515, USA
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Stringham OC, Toomes A, Kanishka AM, Mitchell L, Heinrich S, Ross JV, Cassey P. A guide to using the internet to monitor and quantify the wildlife trade. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:1130-1139. [PMID: 33277940 DOI: 10.1111/cobi.13675] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/18/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
The unrivaled growth in e-commerce of animals and plants presents an unprecedented opportunity to monitor wildlife trade to inform conservation, biosecurity, and law enforcement. Using the internet to quantify the scale of the wildlife trade (volume and frequency) is a relatively recent and rapidly developing approach that lacks an accessible framework for locating relevant websites and collecting data. We produced an accessible guide for internet-based wildlife trade surveillance. We detailed a repeatable method involving a systematic internet search, with search engines, to locate relevant websites and content. For data collection, we highlight web-scraping technology as an efficient way to collect data in an automated fashion at regularly timed intervals. Our guide is applicable to the multitude of trade-based contexts because researchers can tailor search keywords for specific taxa or derived products and locations of interest. We provide information for working with the diversity of websites used in wildlife trade. For example, to locate relevant content on social media (e.g., posts or groups), each social media platform should be examined individually via the site's internal search engine. A key advantage of using the internet to study wildlife trade is the relative ease of access to an increasing amount of trade-related data. However, not all wildlife trade occurs online and it may occur on unobservable sections of the internet.
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Affiliation(s)
- Oliver C Stringham
- Invasion Science & Wildlife Ecology Lab, University of Adelaide, Adelaide, SA, 5005, Australia
- School of Mathematical Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Adam Toomes
- Invasion Science & Wildlife Ecology Lab, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Aurelie M Kanishka
- Invasion Science & Wildlife Ecology Lab, University of Adelaide, Adelaide, SA, 5005, Australia
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, 2601, Australia
| | - Lewis Mitchell
- School of Mathematical Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sarah Heinrich
- Invasion Science & Wildlife Ecology Lab, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Joshua V Ross
- School of Mathematical Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Phillip Cassey
- Invasion Science & Wildlife Ecology Lab, University of Adelaide, Adelaide, SA, 5005, Australia
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Abstract
Background Many traditional biological concepts continue to be debated by biologists, scientists and philosophers of science. The specific objective of this brief reflection is to offer an alternative vision to the definition of life taking as a starting point the traits common to all living beings. Results and Conclusions Thus, I define life as a process that takes place in highly organized organic structures and is characterized by being preprogrammed, interactive, adaptative and evolutionary. If life is the process, living beings are the system in which this process takes place. I also wonder whether viruses can be considered living things or not. Taking as a starting point my definition of life and, of course, on what others have thought about it, I am in favor of considering viruses as living beings. I base this conclusion on the fact that viruses satisfy all the vital characteristics common to all living things and on the role they have played in the evolution of species. Finally, I argue that if there were life elsewhere in the universe, it would be very similar to what we know on this planet because the laws of physics and the composition of matter are universal and because of the principle of the inexorability of life.
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Kearney MR, Jusup M, McGeoch MA, Kooijman SALM, Chown SL. Where do functional traits come from? The role of theory and models. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13829] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Michael R. Kearney
- School of BioSciences Faculty of Science The University of Melbourne Melbourne Vic. Australia
| | - Marko Jusup
- Tokyo Tech World Hub Research Initiative Institute of Innovative Research Tokyo Institute of Technology Tokyo Japan
| | - Melodie A. McGeoch
- Department of Ecology Environment and Evolution School of Life Sciences La Trobe University Melbourne Vic. Australia
| | | | - Steven L. Chown
- Securing Antarctica's Environmental Future School of Biological Sciences Monash University Melbourne Vic. Australia
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Arlé E, Zizka A, Keil P, Winter M, Essl F, Knight T, Weigelt P, Jiménez‐Muñoz M, Meyer C. bRacatus
: A method to estimate the accuracy and biogeographical status of georeferenced biological data. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eduardo Arlé
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Faculty of Biosciences, Pharmacy and Psychology University of Leipzig Leipzig Germany
| | - Alexander Zizka
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Naturalis Biodiversity Center Leiden The Netherlands
| | - Petr Keil
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute of Computer Science Martin Luther University Halle‐Wittenberg Halle (Saale) Germany
- Faculty of Environmental Sciences Czech University of Life Sciences Prague Praha Czech Republic
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| | - Franz Essl
- Division of Conservation, Vegetation and Landscape Ecology Department of Botany and Biodiversity Research University Vienna Vienna Austria
| | - Tiffany Knight
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute of Biology Martin Luther University Halle‐Wittenberg Halle (Saale) Germany
- Department of Community Ecology Helmholtz Centre for Environmental Research ‐ UFZ Halle (Saale) Germany
| | - Patrick Weigelt
- Biodiversity, Macroecology & Biogeography University of Goettingen Göttingen Germany
| | - Marina Jiménez‐Muñoz
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| | - Carsten Meyer
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Faculty of Biosciences, Pharmacy and Psychology University of Leipzig Leipzig Germany
- Institute of Geosciences and Geography Martin Luther University Halle‐Wittenberg Halle Germany
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Abstract
Quantifying the abundance of species is essential to ecology, evolution, and conservation. The distribution of species abundances is fundamental to numerous longstanding questions in ecology, yet the empirical pattern at the global scale remains unresolved, with a few species' abundance well known but most poorly characterized. In large part because of heterogeneous data, few methods exist that can scale up to all species across the globe. Here, we integrate data from a suite of well-studied species with a global dataset of bird occurrences throughout the world-for 9,700 species (∼92% of all extant species)-and use missing data theory to estimate species-specific abundances with associated uncertainty. We find strong evidence that the distribution of species abundances is log left skewed: there are many rare species and comparatively few common species. By aggregating the species-level estimates, we find that there are ∼50 billion individual birds in the world at present. The global-scale abundance estimates that we provide will allow for a line of inquiry into the structure of abundance across biogeographic realms and feeding guilds as well as the consequences of life history (e.g., body size, range size) on population dynamics. Importantly, our method is repeatable and scalable: as data quantity and quality increase, our accuracy in tracking temporal changes in global biodiversity will increase. Moreover, we provide the methodological blueprint for quantifying species-specific abundance, along with uncertainty, for any organism in the world.
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Affiliation(s)
- Corey T Callaghan
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW 2052, Australia;
- Ecology & Evolution Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Shinichi Nakagawa
- Ecology & Evolution Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - William K Cornwell
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
- Ecology & Evolution Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
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Westoby M, Gillings MR, Madin JS, Nielsen DA, Paulsen IT, Tetu SG. Trait dimensions in bacteria and archaea compared to vascular plants. Ecol Lett 2021; 24:1487-1504. [PMID: 33896087 DOI: 10.1111/ele.13742] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 01/04/2023]
Abstract
Bacteria and archaea have very different ecology compared to plants. One similarity, though, is that much discussion of their ecological strategies has invoked concepts such as oligotrophy or stress tolerance. For plants, so-called 'trait ecology'-strategy description reframed along measurable trait dimensions-has made global syntheses possible. Among widely measured trait dimensions for bacteria and archaea three main axes are evident. Maximum growth rate in association with rRNA operon copy number expresses a rate-yield trade-off that is analogous to the acquisitive-conservative spectrum in plants, though underpinned by different trade-offs. Genome size in association with signal transduction expresses versatility. Cell size has influence on diffusive uptake and on relative wall costs. These trait dimensions, and potentially others, offer promise for interpreting ecology. At the same time, there are very substantial differences from plant trait ecology. Traits and their underpinning trade-offs are different. Also, bacteria and archaea use a variety of different substrates. Bacterial strategies can be viewed both through the facet of substrate-use pathways, and also through the facet of quantitative traits such as maximum growth rate. Preliminary evidence shows the quantitative traits vary widely within substrate-use pathways. This indicates they convey information complementary to substrate use.
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Affiliation(s)
- Mark Westoby
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Joshua S Madin
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI, USA
| | - Daniel A Nielsen
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Dept of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- Dept of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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Geange SR, von Oppen J, Strydom T, Boakye M, Gauthier TJ, Gya R, Halbritter AH, Jessup LH, Middleton SL, Navarro J, Pierfederici ME, Chacón‐Labella J, Cotner S, Farfan‐Rios W, Maitner BS, Michaletz ST, Telford RJ, Enquist BJ, Vandvik V. Next-generation field courses: Integrating Open Science and online learning. Ecol Evol 2021; 11:3577-3587. [PMID: 33898010 PMCID: PMC8057340 DOI: 10.1002/ece3.7009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/12/2020] [Accepted: 10/16/2020] [Indexed: 11/17/2022] Open
Abstract
As Open Science practices become more commonplace, there is a need for the next generation of scientists to be well versed in these aspects of scientific research. Yet, many training opportunities for early career researchers (ECRs) could better emphasize or integrate Open Science elements. Field courses provide opportunities for ECRs to apply theoretical knowledge, practice new methodological approaches, and gain an appreciation for the challenges of real-life research, and could provide an excellent platform for integrating training in Open Science practices. Our recent experience, as primarily ECRs engaged in a field course interrupted by COVID-19, led us to reflect on the potential to enhance learning outcomes in field courses by integrating Open Science practices and online learning components. Specifically, we highlight the opportunity for field courses to align teaching activities with the recent developments and trends in how we conduct research, including training in: publishing registered reports, collecting data using standardized methods, adopting high-quality data documentation, managing data through reproducible workflows, and sharing and publishing data through appropriate channels. We also discuss how field courses can use online tools to optimize time in the field, develop open access resources, and cultivate collaborations. By integrating these elements, we suggest that the next generation of field courses will offer excellent arenas for participants to adopt Open Science practices.
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Affiliation(s)
- Sonya R. Geange
- Department of Biological SciencesUniversity of BergenBergenNorway
- Bjerknes Center for Climate ResearchBergenNorway
| | - Jonathan von Oppen
- Section for Ecoinformatics & BiodiversityDepartment of BiologyAarhus UniversityAarhus CDenmark
- Center for Biodiversity Dynamics in a Changing WorldDepartment of BiologyAarhus UniversityAarhus CDenmark
| | - Tanya Strydom
- Department of EcologyEnvironment and Plant SciencesStockholm UniversityStockholmSweden
| | - Mickey Boakye
- Department of Environmental Science Policy and ManagementUniversity of CaliforniaBerkeleyCAUSA
| | | | - Ragnhild Gya
- Department of Biological SciencesUniversity of BergenBergenNorway
- Bjerknes Center for Climate ResearchBergenNorway
| | - Aud H. Halbritter
- Department of Biological SciencesUniversity of BergenBergenNorway
- Bjerknes Center for Climate ResearchBergenNorway
| | - Laura H. Jessup
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteINUSA
- Department of Ecological Science and EngineeringPurdue UniversityWest LafayetteINUSA
| | | | - Jocelyn Navarro
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - Maria Elisa Pierfederici
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
| | | | - Sehoya Cotner
- Department of Biological SciencesUniversity of BergenBergenNorway
- Department of Biology Teaching and LearningUniversity of MinnesotaMinneapolisMNUSA
| | - William Farfan‐Rios
- Living Earth CollaborativeWashington UniversitySt LouisMOUSA
- Center for Conservation and Sustainable DevelopmentMissouri Botanical GardenSt LouisMOUSA
| | - Brian S. Maitner
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - Sean T. Michaletz
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCCanada
| | - Richard J. Telford
- Department of Biological SciencesUniversity of BergenBergenNorway
- Bjerknes Center for Climate ResearchBergenNorway
| | - Brian J. Enquist
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - Vigdis Vandvik
- Department of Biological SciencesUniversity of BergenBergenNorway
- Bjerknes Center for Climate ResearchBergenNorway
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Sterner BW, Gilbert EE, Franz NM. Decentralized but Globally Coordinated Biodiversity Data. Front Big Data 2021; 3:519133. [PMID: 33693407 PMCID: PMC7931950 DOI: 10.3389/fdata.2020.519133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 08/31/2020] [Indexed: 11/22/2022] Open
Abstract
Centralized biodiversity data aggregation is too often failing societal needs due to pervasive and systemic data quality deficiencies. We argue for a novel approach that embodies the spirit of the Web (“small pieces loosely joined”) through the decentralized coordination of data across scientific languages and communities. The upfront cost of decentralization can be offset by the long-term benefit of achieving sustained expert engagement, higher-quality data products, and ultimately more societal impact for biodiversity data. Our decentralized approach encourages the emergence and evolution of multiple self-identifying communities of practice that are regionally, taxonomically, or institutionally localized. Each community is empowered to control the social and informational design and versioning of their local data infrastructures and signals. With no single aggregator to exert centralized control over biodiversity data, decentralization generates loosely connected networks of mid-level aggregators. Global coordination is nevertheless feasible through automatable data sharing agreements that enable efficient propagation and translation of biodiversity data across communities. The decentralized model also poses novel integration challenges, among which the explicit and continuous articulation of conflicting systematic classifications and phylogenies remain the most challenging. We discuss the development of available solutions, challenges, and outline next steps: the global effort of coordination should focus on developing shared languages for data signal translation, as opposed to homogenizing the data signal itself.
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Affiliation(s)
- Beckett W Sterner
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Edward E Gilbert
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Nico M Franz
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
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Westoby M, Falster DS, Schrader J. Motivating data contributions via a distinct career currency. Proc Biol Sci 2021; 288:20202830. [PMID: 33653143 PMCID: PMC7935020 DOI: 10.1098/rspb.2020.2830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/02/2021] [Indexed: 01/18/2023] Open
Abstract
If collecting research data is perceived as poorly rewarded compared to data synthesis and analysis, this can slow overall research progress via two effects. People who have already collected data may be slow to make it openly accessible. Also, researchers may reallocate effort from collecting fresh data to synthesizing and analysing data already accessible. Here, we advocate for a second career currency in the form of data contributions statements embedded within applications for jobs, promotions and research grants. This workable step forward would provide for peer opinion to operate across thousands of selection and promotion committees and granting panels. In this way, fair valuation of data contributions relative to publications could emerge.
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Affiliation(s)
- Mark Westoby
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Daniel S. Falster
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 1466, Australia
| | - Julian Schrader
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Department of Biodiversity, Macroecology and Biogeography, University of Goettingen, Goettingen, Germany
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63
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Stewart PS, Hill RA, Stephens PA, Whittingham MJ, Dawson W. Impacts of invasive plants on animal behaviour. Ecol Lett 2021; 24:891-907. [PMID: 33524221 DOI: 10.1111/ele.13687] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 01/08/2023]
Abstract
The spread of invasive species is a threat to ecosystems worldwide. However, we know relatively little about how invasive species affect the behaviour of native animals, even though behaviour plays a vital role in the biotic interactions which are key to understanding the causes and impacts of biological invasions. Here, we explore how invasive plants - one of the most pervasive invasive taxa - impact the behaviour of native animals. To promote a mechanistic understanding of these behavioural impacts, we begin by introducing a mechanistic framework which explicitly considers the drivers and ecological consequences of behavioural change, as well as the moderating role of environmental context. We then synthesise the existing literature within this framework. We find that while some behavioural impacts of invasive plants are relatively well-covered in the literature, others are supported by only a handful of studies and should be explored further in the future. We conclude by identifying priority topics for future research, which will benefit from an interdisciplinary approach uniting invasion ecology with the study of animal behaviour and cognition.
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Affiliation(s)
- Peter S Stewart
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Russell A Hill
- Department of Anthropology, Durham University, Durham, DH1 3LE, UK
| | | | - Mark J Whittingham
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-Upon-Tyne, NE1 7RU, UK
| | - Wayne Dawson
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
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Marx HE, Jorgensen SA, Wisely E, Li Z, Dlugosch KM, Barker MS. Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11409. [PMID: 33680580 PMCID: PMC7910807 DOI: 10.1002/aps3.11409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Large-scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from diverse plant communities. METHODS We generated >650 Gbp of RNA-seq for 24 vascular plant species representing 12 genera and nine families at the Harvard Forest NEON site. Each species was sampled twice in 2016 (July and August). We assessed transcriptome quality and content with TransRate, BUSCO, and Gene Ontology annotations. RESULTS Only modest differences in assembly quality were observed across multiple k-mers. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated transcripts between diploid and polyploid transcriptomes. DISCUSSION We provide new RNA-seq data sets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high-quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers opportunities for large-scale studies at the intersection of ecology and genomics.
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Affiliation(s)
- Hannah E. Marx
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichigan48109‐1048USA
| | - Stacy A. Jorgensen
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
| | - Eldridge Wisely
- Genetics Graduate Interdisciplinary ProgramUniversity of ArizonaTucsonArizona85721USA
| | - Zheng Li
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
| | - Katrina M. Dlugosch
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
| | - Michael S. Barker
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
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A. Maureaud A, Frelat R, Pécuchet L, Shackell N, Mérigot B, Pinsky ML, Amador K, Anderson SC, Arkhipkin A, Auber A, Barri I, Bell RJ, Belmaker J, Beukhof E, Camara ML, Guevara‐Carrasco R, Choi J, Christensen HT, Conner J, Cubillos LA, Diadhiou HD, Edelist D, Emblemsvåg M, Ernst B, Fairweather TP, Fock HO, Friedland KD, Garcia CB, Gascuel D, Gislason H, Goren M, Guitton J, Jouffre D, Hattab T, Hidalgo M, Kathena JN, Knuckey I, Kidé SO, Koen‐Alonso M, Koopman M, Kulik V, León JP, Levitt‐Barmats Y, Lindegren M, Llope M, Massiot‐Granier F, Masski H, McLean M, Meissa B, Mérillet L, Mihneva V, Nunoo FKE, O'Driscoll R, O'Leary CA, Petrova E, Ramos JE, Refes W, Román‐Marcote E, Siegstad H, Sobrino I, Sólmundsson J, Sonin O, Spies I, Steingrund P, Stephenson F, Stern N, Tserkova F, Tserpes G, Tzanatos E, van Rijn I, van Zwieten PAM, Vasilakopoulos P, Yepsen DV, Ziegler P, T. Thorson J. Are we ready to track climate-driven shifts in marine species across international boundaries? - A global survey of scientific bottom trawl data. GLOBAL CHANGE BIOLOGY 2021; 27:220-236. [PMID: 33067925 PMCID: PMC7756400 DOI: 10.1111/gcb.15404] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 05/09/2023]
Abstract
Marine biota are redistributing at a rapid pace in response to climate change and shifting seascapes. While changes in fish populations and community structure threaten the sustainability of fisheries, our capacity to adapt by tracking and projecting marine species remains a challenge due to data discontinuities in biological observations, lack of data availability, and mismatch between data and real species distributions. To assess the extent of this challenge, we review the global status and accessibility of ongoing scientific bottom trawl surveys. In total, we gathered metadata for 283,925 samples from 95 surveys conducted regularly from 2001 to 2019. We identified that 59% of the metadata collected are not publicly available, highlighting that the availability of data is the most important challenge to assess species redistributions under global climate change. Given that the primary purpose of surveys is to provide independent data to inform stock assessment of commercially important populations, we further highlight that single surveys do not cover the full range of the main commercial demersal fish species. An average of 18 surveys is needed to cover at least 50% of species ranges, demonstrating the importance of combining multiple surveys to evaluate species range shifts. We assess the potential for combining surveys to track transboundary species redistributions and show that differences in sampling schemes and inconsistency in sampling can be overcome with spatio-temporal modeling to follow species density redistributions. In light of our global assessment, we establish a framework for improving the management and conservation of transboundary and migrating marine demersal species. We provide directions to improve data availability and encourage countries to share survey data, to assess species vulnerabilities, and to support management adaptation in a time of climate-driven ocean changes.
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Affiliation(s)
- Aurore A. Maureaud
- Centre for Ocean LifeNational Institute of Aquatic Resources (DTU Aqua)Technical University of DenmarkKgs. LyngbyDenmark
- Section for Ecosystem based Marine ManagementNational Institute of Aquatic Resources (DTU Aqua)Technical University of DenmarkKgs. LyngbyDenmark
| | - Romain Frelat
- Aquaculture and Fisheries GroupWageningen University & ResearchWageningenThe Netherlands
| | - Laurène Pécuchet
- Norwegian College of Fishery ScienceUiT The Arctic University of NorwayTromsøNorway
| | - Nancy Shackell
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | | | - Malin L. Pinsky
- Department of Ecology, Evolution, and Natural ResourcesRutgers, The State University of New JerseyNew BrunswickNJUSA
| | - Kofi Amador
- Fisheries Scientific Survey DivisionFisheries CommissionTemaGhana
| | - Sean C. Anderson
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - Alexander Arkhipkin
- Falkland Islands Fisheries DepartmentDirectorate of Natural ResourcesStanleyFalkland Islands
| | - Arnaud Auber
- Halieutique Manche Mer du Nord unitFrench Research Institute for the Exploitation of the Sea (IFREMER)Boulogne‐sur‐MerFrance
| | - Iça Barri
- Centro de Investigaçao Pesqueira Aplicada (CIPA)BissauGuinea‐Bissau
| | | | - Jonathan Belmaker
- School of Zoology and The Steinhardt Museum of Natural HistoryTel AvivIsrael
| | | | - Mohamed L. Camara
- HalieuteNational Center of Fisheries Sciences of BoussouraConakryRepublic of Guinea
| | - Renato Guevara‐Carrasco
- General Directorate of Demersal and Coastal Resources ResearchInstituto del Mar Perú (IMARPE)CallaoPerú
| | - Junghwa Choi
- Fisheries Resources Research CenterNational Institute of Fisheries ScienceTongyeong‐siKorea
| | | | - Jason Conner
- Resource Assessment and Conservation Engineering, Alaska Fisheries Science Center, National Marine Fisheries ServiceNOAASeattleWAUSA
| | - Luis A. Cubillos
- COPAS Sur‐AustralDepartamento de OceanografíaUniversity of ConcepcionConcepciónChile
| | | | - Dori Edelist
- Recanati Institute for Maritime Studies and Department of Maritime CivilizationsCharney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | | | - Billy Ernst
- Millennium Nucleus of Ecology and Sustainable Management of Oceanic Islands (ESMOI)Departamento de OceanografíaFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
| | | | - Heino O. Fock
- Thuenen Institute of Sea FisheriesBremerhavenGermany
| | - Kevin D. Friedland
- Narragansett LaboratoryNational Marine Fisheries ServiceNarragansettRIUSA
| | - Camilo B. Garcia
- Departamento de BiologiaUniversidad Nacional de ColombiaBogotáColombia
| | - Didier Gascuel
- ESE, Ecology and Ecosystem HealthInstitut AgroRennesFrance
| | - Henrik Gislason
- Section for Ecosystem based Marine ManagementNational Institute of Aquatic Resources (DTU Aqua)Technical University of DenmarkKgs. LyngbyDenmark
| | - Menachem Goren
- School of Zoology and The Steinhardt Museum of Natural HistoryTel AvivIsrael
| | - Jérôme Guitton
- ESE, Ecology and Ecosystem HealthInstitut AgroRennesFrance
| | | | | | - Manuel Hidalgo
- Ecosystem Oceanography Group (GRECO)Instituto Español de OceanografíaCentre Oceanogràfic de les BalearsPalma de MallorcaSpain
| | - Johannes N. Kathena
- National Marine Information and Research CentreMinistry of Fisheries and Marine Resources (MFMR)SwakopmundNamibia
| | - Ian Knuckey
- Fishwell Consulting Pty LtdQueenscliffVic.Australia
| | - Saïkou O. Kidé
- Institut Mauritanien de Recherches Océanographiques et des PêchesNouadhibouMauritania
| | - Mariano Koen‐Alonso
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNLCanada
| | - Matt Koopman
- Fishwell Consulting Pty LtdQueenscliffVic.Australia
| | - Vladimir Kulik
- Pacific Branch (TINRO) of Russian Federal Research Institute Of Fisheries and Oceanography (VNIRO)VladivostokRussia
| | - Jacqueline Palacios León
- General Directorate of Demersal and Coastal Resources ResearchInstituto del Mar Perú (IMARPE)CallaoPerú
| | | | - Martin Lindegren
- Centre for Ocean LifeNational Institute of Aquatic Resources (DTU Aqua)Technical University of DenmarkKgs. LyngbyDenmark
| | - Marcos Llope
- Instituto Español de OceanografíaCádizAndalucíaSpain
| | - Félix Massiot‐Granier
- Département Adaptations du vivantUMR BOREAMuseum National d’Histoire NaturelleParisFrance
| | - Hicham Masski
- Institut National de Recherche HalieutiqueCasablancaMorocco
| | - Matthew McLean
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | - Beyah Meissa
- Institut Mauritanien de Recherches Océanographiques et des PêchesNouadhibouMauritania
| | - Laurène Mérillet
- National Museum of Natural HistoryParisFrance
- IfremerLorientFrance
| | | | | | - Richard O'Driscoll
- National Institute of Water and Atmospheric Research LimitedWellingtonNew Zealand
| | - Cecilia A. O'Leary
- Resource Assessment and Conservation Engineering Division, Alaska Fisheries Science CenterNOAASeattleWAUSA
| | | | - Jorge E. Ramos
- Falkland Islands Fisheries DepartmentDirectorate of Natural ResourcesStanleyFalkland Islands
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobartTas.Australia
| | - Wahid Refes
- National Higher School of Marine Sciences and Coastal ManagementDély IbrahimAlgeria
| | | | | | | | | | - Oren Sonin
- Israeli Fisheries Division, Fisheries and Aquaculture DepartmentMinistry of AgricultureKiryat HaimIsrael
| | - Ingrid Spies
- Resource Ecology and Fisheries Management, Alaska Fisheries Science Center, National Marine Fisheries ServiceNOAASeattleWAUSA
| | | | - Fabrice Stephenson
- National Institute of Water and Atmospheric Research LimitedWellingtonNew Zealand
| | - Nir Stern
- Israel Oceanographic and Limnological Research InstituteHaifaIsrael
| | | | | | | | | | - Paul A. M. van Zwieten
- Aquaculture and Fisheries GroupWageningen University & ResearchWageningenThe Netherlands
| | | | - Daniela V. Yepsen
- Programa de Doctorado en Ciencias con Mención en Manejo de Recursos Acuáticos Renovables (MaReA)Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
| | - Philippe Ziegler
- Antarctic Conservation and Management ProgramAustralian Antarctic DivisionDepartment of Agriculture, Water, and the EnvironmentKingstonTas.Australia
| | - James T. Thorson
- Habitat and Ecological Processes Research ProgramAlaska Fisheries Science Center, National Marine Fisheries ServiceNOAASeattleWAUSA
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Raes N, Casino A, Goodson H, Islam S, Koureas D, Schiller E, Schulman L, Tilley L, Robertson T. White paper on the alignment and interoperability between the Distributed System of Scientific Collections (DiSSCo) and EU infrastructures - The case of the European Environment Agency (EEA). RESEARCH IDEAS AND OUTCOMES 2020. [DOI: 10.3897/rio.6.e62361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Distributed System of Scientific Collections (DiSSCo) Research Infrastructure (RI) is presently in its preparatory phase. DiSSCo is developing a new distributed RI to operate as a one-stop-shop for the envisaged European Natural Science Collection (NSC) and all its derived information. Through mass digitisation, DiSSCo will transform the fragmented landscape of NSCs, including an estimated 1.5 billion specimens, into an integrated knowledge base that will provide interconnected evidence of the natural world. Data derived from European NSCs underpin countless discoveries and innovations, including tens of thousands of scholarly publications and official reports annually (supporting legislative and regulatory processes on sustainability, environmental change, land use, societal infrastructure, health, food, security, etc.); base-line biodiversity data; inventions and products essential to bio-economy; databases, maps and descriptions of scientific observations; educational material for students; and instructive and informative resources for the public. To expand the user community, DiSSCo will strengthen capacity building across Europe for maximum engagement of stakeholders in the biodiversity-related field and beyond, including industry and the private sector, but also policy-driving entities. Hence, it is opportune to reach out to relevant stakeholders in the European environmental policy domain represented by the European Environment Agency (EEA). The EEA aims to support sustainable development by helping to achieve significant and measurable improvement in Europe's environment, through the provision of timely, targeted, relevant and reliable information to policy-making agents and the public. The EEA provides information through the European Environment Information and Observation System (Eionet). The aim of this white paper is to open the discussion between DiSSCo and the EEA and identify the common service interests that are relevant for the European environmental policy domain. The first section describes the significance of (digital) Natural Science Collections (NHCs). Section two describes the DiSSCo programme with all DiSSCo aligned projects. Section three provides background information on the EEA and the biodiversity infrastructures that are developed and maintained by the EEA. The fourth section illustrates a number of use cases where the DiSSCo consortium sees opportunities for interaction between the DiSSCo RI and the Eionet portal of the EEA. Opening the discussion with the EEA in this phase of maturity of DiSSCo will ensure that the infrastructural design of DiSSCo and the development of e-Services accommodate the present and future needs of the EEA and assure data interoperability between the two infrastructures.
The aim of this white paper is to present benefits from identifying the common service interests of DiSSCo and the EEA. A brief introduction to natural science collections as well as the two actors is given to facilitate the understanding of the needs and possibilities in the alignment of DiSSCo with the EEA.
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Teletchea S, Teletchea F. STOREFISH 2.0: a database on the reproductive strategies of teleost fishes. Database (Oxford) 2020; 2020:baaa095. [PMID: 33216894 PMCID: PMC7678788 DOI: 10.1093/database/baaa095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/04/2020] [Accepted: 10/14/2020] [Indexed: 01/08/2023]
Abstract
Teleost fishes show the most outstanding reproductive diversity of all vertebrates. Yet to date, no one has been able to decisively explain this striking variability nor to perform large-scale phylogenetic analyses of reproductive modes. Here, we describe STrategies Of REproduction in FISH (STOREFISH) 2.0, an online database easing the sharing of an original data set on reproduction published in 2007, enriched with automated data extraction and presentation to display the knowledge acquired on temperate freshwater fish species. STOREFISH 2.0 contains the information for 80 freshwater fish species and 50 traits from the analysis of 1219 references. It is anticipated that this new database could be useful for freshwater biodiversity research, conservation, assessment and management. Database URL: www.storefish.org.
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Affiliation(s)
- Stéphane Teletchea
- UFIP, Université de Nantes, UMR CRNS 6286, 2 rue de la Houssinière, 44322 Nantes cedex 3, France
| | - Fabrice Teletchea
- University of Lorraine, INRAE, UR AFPA, 2 avenue de la Forêt de Haye - BP 20163
, F-54000, Vandoeuvre-lès-Nancy Cedex, France
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68
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Webb TJ, Vanhoorne B. Linking dimensions of data on global marine animal diversity. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190445. [PMID: 33131434 DOI: 10.1098/rstb.2019.0445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recent decades have seen an explosion in the amount of data available on all aspects of biodiversity, which has led to data-driven approaches to understand how and why diversity varies in time and space. Global repositories facilitate access to various classes of species-level data including biogeography, genetics and conservation status, which are in turn required to study different dimensions of diversity. Ensuring that these different data sources are interoperable is a challenge as we aim to create synthetic data products to monitor the state of the world's biodiversity. One way to approach this is to link data of different classes, and to inventory the availability of data across multiple sources. Here, we use a comprehensive list of more than 200 000 marine animal species, and quantify the availability of data on geographical occurrences, genetic sequences, conservation assessments and DNA barcodes across all phyla and broad functional groups. This reveals a very uneven picture: 44% of species are represented by no record other than their taxonomy, but some species are rich in data. Although these data-rich species are concentrated into a few taxonomic and functional groups, especially vertebrates, data are spread widely across marine animals, with members of all 32 phyla represented in at least one database. By highlighting gaps in current knowledge, our census of marine diversity data helps to prioritize future data collection activities, as well as emphasizing the importance of ongoing sustained observations and archiving of existing data into global repositories. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.
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Affiliation(s)
- Thomas J Webb
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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Thessen AE, Walls RL, Vogt L, Singer J, Warren R, Buttigieg PL, Balhoff JP, Mungall CJ, McGuinness DL, Stucky BJ, Yoder MJ, Haendel MA. Transforming the study of organisms: Phenomic data models and knowledge bases. PLoS Comput Biol 2020; 16:e1008376. [PMID: 33232313 PMCID: PMC7685442 DOI: 10.1371/journal.pcbi.1008376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.
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Affiliation(s)
- Anne E. Thessen
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America
- Ronin Institute for Independent Scholarship, Monclair, New Jersey, United States of America
| | - Ramona L. Walls
- Bio5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Lars Vogt
- TIB Leibniz Information Centre for Science and Technology, Hannover, Germany
| | | | | | - Pier Luigi Buttigieg
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - James P. Balhoff
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christopher J. Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | | | - Brian J. Stucky
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Matthew J. Yoder
- Illinois Natural History Survey, Champaign, Illinois, United States of America
| | - Melissa A. Haendel
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America
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Perez TM, Rodriguez J, Mason Heberling J. Herbarium-based measurements reliably estimate three functional traits. AMERICAN JOURNAL OF BOTANY 2020; 107:1457-1464. [PMID: 32945535 DOI: 10.1002/ajb2.1535] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
PREMISE The use of functional traits has surged in recent decades, providing new insights ranging from individual plant fitness to ecosystem processes. Global plant trait databases have advanced our understanding of plant functional diversity, but they remain incomplete because of geographic and taxonomic biases. Herbarium specimens may help fill these gaps by providing trait information across space and time. We tested whether herbarium specimen-derived measurements are reliable estimates of three important, commonly measured functional traits-specific leaf area (SLA), branch wood specific gravity, and leaf thickness. METHODS Leaves and branches were collected from species cultivated at Fairchild Tropical Botanic Garden and Florida International University in Miami, FL, USA. Fresh components of SLA (area), branch wood specific gravity (volume), and leaf thickness were measured following standard trait measurement protocols. We compared these trait values to corresponding measurements using plant tissues dried in a plant press following standard herbarium plant collecting protocols. RESULTS Herbarium-derived trait measurements (dried tissues) were highly correlated with those measured using fresh tissues following standard protocols (SLA: R2 = 0.72-0.97, p < 0.01; wood specific gravity: R2 = 0.74-0.75, p < 0.01; leaf thickness: R2 = 0.96, p < 0.01). However, except for leaf thickness, linear model slope or intercept coefficients differed from 1, indicating herbarium-derived trait measurements may provide biased estimates of fresh traits without the use of correction factors. CONCLUSIONS Herbarium-derived traits cannot always be used interchangeably with those measured from fresh tissues because of tissue shrinkage. However, herbarium-derived trait data still have the potential to drastically expand the temporal, geographic, and taxonomic scope of global trait databases.
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Affiliation(s)
- Timothy M Perez
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
- Fairchild Tropical Botanic Garden, Coral Gables, FL, 33156, USA
| | - Jessica Rodriguez
- Department of Earth and Environment, Florida International University, Miami, FL, 33199, USA
| | - J Mason Heberling
- Section of Botany, Carnegie Museum of Natural History, Pittsburgh, PA, 15213, USA
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Mussmann SM, Douglas MR, Oakey DD, Douglas ME. Defining relictual biodiversity: Conservation units in speckled dace (Leuciscidae: Rhinichthys osculus) of the Greater Death Valley ecosystem. Ecol Evol 2020; 10:10798-10817. [PMID: 33072297 PMCID: PMC7548178 DOI: 10.1002/ece3.6736] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/19/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species-population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units-Canada); MUs (management units); SSP (subspecies); ESUs (Evolutionarily Significant Units); and UIEUs (uniquely identified evolutionary units)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates this approach in speckled dace (Leuciscidae: Rhinichthys osculus) endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem. These fish persist in the Mojave Desert as isolated Plio-Pleistocene relicts and are of conservation concern, but lack formal taxonomic descriptions/designations. Double digest RAD (ddRAD) methods identified 14,355 SNP loci across 10 populations (N = 140). Species delimitation analyses [multispecies coalescent (MSC) and unsupervised machine learning (UML)] delineated four putative ESUs. F ST outlier loci (N = 106) were juxtaposed to uncover the potential for localized adaptations. We detected one hybrid population that resulted from upstream reconnection of habitat following contemporary pluvial periods, whereas remaining populations represent relics of ancient tectonism within geographically isolated springs and groundwater-fed streams. Our study offers three salient conclusions: a blueprint for a multifaceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically endangered Death Valley ecosystem fishes.
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Affiliation(s)
- Steven M. Mussmann
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - David D. Oakey
- School of Life SciencesArizona State UniversityTempeAZUSA
- Present address:
Arizona State Veteran HomePhoenixAZUSA
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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Culina A, van den Berg I, Evans S, Sánchez-Tójar A. Low availability of code in ecology: A call for urgent action. PLoS Biol 2020; 18:e3000763. [PMID: 32722681 PMCID: PMC7386629 DOI: 10.1371/journal.pbio.3000763] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Access to analytical code is essential for transparent and reproducible research. We review the state of code availability in ecology using a random sample of 346 nonmolecular articles published between 2015 and 2019 under mandatory or encouraged code-sharing policies. Our results call for urgent action to increase code availability: only 27% of eligible articles were accompanied by code. In contrast, data were available for 79% of eligible articles, highlighting that code availability is an important limiting factor for computational reproducibility in ecology. Although the percentage of ecological journals with mandatory or encouraged code-sharing policies has increased considerably, from 15% in 2015 to 75% in 2020, our results show that code-sharing policies are not adhered to by most authors. We hope these results will encourage journals, institutions, funding agencies, and researchers to address this alarming situation. Publication of the analytical code underlying a scientific study is increasingly expected or even mandated by journals, allowing others to reproduce the results. However, a survey of more than 300 recently published ecology papers finds the majority have no code publicly available, handicapping efforts to improve scientific transparency.
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Affiliation(s)
- Antica Culina
- Department of Animal Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, the Netherlands
- * E-mail: (AC); (AST)
| | - Ilona van den Berg
- Department of Animal Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, the Netherlands
- Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Simon Evans
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Alfredo Sánchez-Tójar
- Department of Evolutionary Biology, Bielefeld University, Bielefeld, Germany
- * E-mail: (AC); (AST)
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Sparrow BD, Foulkes JN, Wardle GM, Leitch EJ, Caddy-Retalic S, van Leeuwen SJ, Tokmakoff A, Thurgate NY, Guerin GR, Lowe AJ. A Vegetation and Soil Survey Method for Surveillance Monitoring of Rangeland Environments. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00157] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Valbuena R, O'Connor B, Zellweger F, Simonson W, Vihervaara P, Maltamo M, Silva CA, Almeida DRA, Danks F, Morsdorf F, Chirici G, Lucas R, Coomes DA, Coops NC. Standardizing Ecosystem Morphological Traits from 3D Information Sources. Trends Ecol Evol 2020; 35:656-667. [PMID: 32423635 DOI: 10.1016/j.tree.2020.03.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 12/31/2022]
Abstract
3D-imaging technologies provide measurements of terrestrial and aquatic ecosystems' structure, key for biodiversity studies. However, the practical use of these observations globally faces practical challenges. First, available 3D data are geographically biased, with significant gaps in the tropics. Second, no data source provides, by itself, global coverage at a suitable temporal recurrence. Thus, global monitoring initiatives, such as assessment of essential biodiversity variables (EBVs), will necessarily have to involve the combination of disparate data sets. We propose a standardized framework of ecosystem morphological traits - height, cover, and structural complexity - that could enable monitoring of globally consistent EBVs at regional scales, by flexibly integrating different information sources - satellites, aircrafts, drones, or ground data - allowing global biodiversity targets relating to ecosystem structure to be monitored and regularly reported.
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Affiliation(s)
- R Valbuena
- United Nations Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntington Road, CB3 0DL Cambridge, UK; Department of Plant Sciences in the Conservation Research Institute, University of Cambridge, Downing Street, CB2 3EA Cambridge, UK; School of Natural Sciences, Bangor University, Thoday Building, Bangor LL57 2UW, UK.
| | - B O'Connor
- United Nations Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntington Road, CB3 0DL Cambridge, UK
| | - F Zellweger
- Department of Plant Sciences in the Conservation Research Institute, University of Cambridge, Downing Street, CB2 3EA Cambridge, UK; Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - W Simonson
- United Nations Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntington Road, CB3 0DL Cambridge, UK
| | - P Vihervaara
- Biodiversity Centre, Finnish Environment Institute (SYKE), Latokartanonkaari 11, 00790 Helsinki, Finland
| | - M Maltamo
- Faculty of Forest Sciences, University of Eastern Finland, PO Box 111, Joensuu, Finland
| | - C A Silva
- Department of Geographical Sciences, University of Maryland, College Park, MD, USA; School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - D R A Almeida
- Department of Forest Sciences, 'Luiz de Queiroz' College of Agriculture (USP/ESALQ), University of São Paulo, Piracicaba, SP, Brazil
| | - F Danks
- United Nations Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntington Road, CB3 0DL Cambridge, UK
| | - F Morsdorf
- Remote Sensing Laboratories, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - G Chirici
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università degli Studi di Firenze, via San Bonaventura 13, 50145 Florence, Italy
| | - R Lucas
- Earth Observation and Ecosystem Dynamics Research Group, Aberystwyth University, Aberystwyth SY23 3DB, UK
| | - D A Coomes
- Department of Plant Sciences in the Conservation Research Institute, University of Cambridge, Downing Street, CB2 3EA Cambridge, UK
| | - N C Coops
- Department of Forest Resource Management, University of British Columbia, 2424 Main Mall, Vancouver V6T 1Z4, Canada
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How phantom databases could contribute to conservation assessments. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2020; 107:21. [DOI: 10.1007/s00114-020-01679-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/06/2020] [Accepted: 04/27/2020] [Indexed: 10/24/2022]
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