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Zhang Z, Zhou J, García Molinos J, Mammola S, Bede-Fazekas Á, Feng X, Kitazawa D, Assis J, Qiu T, Lin Q. Incorporating physiological knowledge into correlative species distribution models minimizes bias introduced by the choice of calibration area. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:349-362. [PMID: 38827135 PMCID: PMC11136901 DOI: 10.1007/s42995-024-00226-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/20/2024] [Indexed: 06/04/2024]
Abstract
Correlative species distribution models (SDMs) are important tools to estimate species' geographic distribution across space and time, but their reliability heavily relies on the availability and quality of occurrence data. Estimations can be biased when occurrences do not fully represent the environmental requirement of a species. We tested to what extent species' physiological knowledge might influence SDM estimations. Focusing on the Japanese sea cucumber Apostichopus japonicus within the coastal ocean of East Asia, we compiled a comprehensive dataset of occurrence records. We then explored the importance of incorporating physiological knowledge into SDMs by calibrating two types of correlative SDMs: a naïve model that solely depends on environmental correlates, and a physiologically informed model that further incorporates physiological information as priors. We further tested the models' sensitivity to calibration area choices by fitting them with different buffered areas around known presences. Compared with naïve models, the physiologically informed models successfully captured the negative influence of high temperature on A. japonicus and were less sensitive to the choice of calibration area. The naïve models resulted in more optimistic prediction of the changes of potential distributions under climate change (i.e., larger range expansion and less contraction) than the physiologically informed models. Our findings highlight benefits from incorporating physiological information into correlative SDMs, namely mitigating the uncertainties associated with the choice of calibration area. Given these promising features, we encourage future SDM studies to consider species physiological information where available. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00226-0.
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Affiliation(s)
- Zhixin Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Marine Biodiversity and Ecological Evolution Research Center, South China Sea Institute of Oceanology, Guangzhou, 510301 China
- Global Ocean and Climate Research Center, South China Sea Institute of Oceanology, Guangzhou, 510301 China
| | - Jinxin Zhou
- Institute of Industrial Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8574 Japan
| | | | - Stefano Mammola
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), 28922 Verbania Pallanza, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Ákos Bede-Fazekas
- Institute of Ecology and Botany, HUN-REN Centre for Ecological Research, Vácrátót, Hungary
- Department of Environmental and Landscape Geography, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Xiao Feng
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Daisuke Kitazawa
- Institute of Industrial Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8574 Japan
| | - Jorge Assis
- Centre of Marine Sciences, University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Tianlong Qiu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Marine Biodiversity and Ecological Evolution Research Center, South China Sea Institute of Oceanology, Guangzhou, 510301 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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Brown MJM, Walker BE, Black N, Govaerts RHA, Ondo I, Turner R, Nic Lughadha E. rWCVP: a companion R package for the World Checklist of Vascular Plants. THE NEW PHYTOLOGIST 2023; 240:1355-1365. [PMID: 37289204 DOI: 10.1111/nph.18919] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/06/2023] [Indexed: 06/09/2023]
Abstract
The World Checklist of Vascular Plants (WCVP) is an extremely valuable resource that is being used to address many fundamental and applied questions in plant science, conservation, ecology and evolution. However, databases of this size require data manipulation skills that pose a barrier to many potential users. Here, we present rWCVP, an open-source R package that aims to facilitate the use of the WCVP by providing clear, intuitive functions to execute many common tasks. These functions include taxonomic name reconciliation, geospatial integration, mapping and generation of multiple different summaries of the WCVP in both data and report format. We have included extensive documentation and tutorials, providing step-by-step guides that are accessible even to users with minimal programming experience. rWCVP is available on cran and GitHub.
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Affiliation(s)
| | | | | | | | - Ian Ondo
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, UK
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Corlett RT. Achieving zero extinction for land plants. TRENDS IN PLANT SCIENCE 2023; 28:913-923. [PMID: 37142532 DOI: 10.1016/j.tplants.2023.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 05/06/2023]
Abstract
Despite the importance of plants for humans and the threats to their future, plant conservation receives far less support compared with vertebrate conservation. Plants are much cheaper and easier to conserve than are animals, but, although there are no technical reasons why any plant species should become extinct, inadequate funding and the shortage of skilled people has created barriers to their conservation. These barriers include the incomplete inventory, the low proportion of species with conservation status assessments, partial online data accessibility, varied data quality, and insufficient investment in both in and ex situ conservation. Machine learning, citizen science (CS), and new technologies could mitigate these problems, but we need to set national and global targets of zero plant extinction to attract greater support.
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Affiliation(s)
- Richard T Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan 666303, China; Center of Conservation Biology, Core Botanical Gardens, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan 666303, China.
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Xiao C, Zhang Z, Ma K, Lin Q. Mapping Asia Plants: Historical Outline and Review of Sources on Floristic Diversity in South Asia. PLANTS (BASEL, SWITZERLAND) 2023; 12:1617. [PMID: 37111841 PMCID: PMC10142850 DOI: 10.3390/plants12081617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
South Asia, which is composed of eight countries, including Afghanistan, Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan, and Sri Lanka, is an important global biodiversity hotspot. As a part of the Mapping Asia Plants (MAP) project, we reviewed the history of botanical investigations, floristic works, and publications in this region, as well as the key floras, checklists, and online databases in South Asia. The botanical survey of this region, which began during the 17th century, has two distinct phases: surveys conducted during the British India period and those conducted in the post-British period. The seven volumes of The Flora of British India are the most important contributions to flora research in South Asia because of their wider geographical coverage, which was performed by British botanists. Following on from this, different countries have launched independent floristic surveys. At the country level, Afghanistan, Bangladesh, Bhutan, India, Nepal, Pakistan, and Sri Lanka have completed, or partially completed, their flora surveys at the country level, while Maldives has not yet published its national flora survey. According to currently available information, the approximated numbers of plant taxa for each country in South Asia are as follows: Afghanistan, 5261 (vascular plants); Bangladesh, 3470 (vascular plants); Bhutan, 5985 (flowering plants); India, 21,558 (flowering plants); Maldives, 270 (common plants); Nepal, 6500 (flowering plants); Pakistan, 6000+ (vascular plants); and Sri Lanka, 4143 (flowering plants). Additionally, there are 151 books devoted to the key floras and checklists in South Asia. A total of 1.1 million digital records of specimens from this region can be found on the website of the Global Biodiversity Information Facility (GBIF). However, there are still major gaps and limitations-such as out-of-date publications, national floras that are mainly detailed only in local languages, massive non-digitized specimens, and the lack of a comprehensive online database or platform-which should be addressed in terms of their global applications.
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Affiliation(s)
- Cui Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Zhixiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Qinwen Lin
- National Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Lohonya K, Livermore L, Wajer J, Crowther R, Devenish E. Digitisation of the Natural History Museum's collection of Dalbergia, Pterocarpus and the subtribe Phaseolinae (Fabaceae, Faboideae). Biodivers Data J 2022; 10:e94939. [PMID: 36761652 PMCID: PMC9836434 DOI: 10.3897/bdj.10.e94939] [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: 09/16/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Background In 2018, the Natural History Museum (NHMUK, herbarium code: BM) undertook a pilot digitisation project together with the Royal Botanic Gardens Kew (project Lead) and the Royal Botanic Garden Edinburgh to collectively digitise non-type herbarium material of the subtribe Phaseolinae and the genera Dalbergia L.f. and Pterocarpus Jacq. (rosewoods and padauk), all from the economically important family of legumes (Leguminosae or Fabaceae).These taxonomic groups were chosen to provide specimen data for two potential use cases: 1) to support the development of dry beans as a sustainable and resilient crop; 2) to aid conservation and sustainable use of rosewoods and padauk. Collectively, these use case studies support the aims of the UK's Department for Environment Food & Rural Affairs (DEFRA)-allocated, Official Development Assistance (ODA) funding. New information We present the images and metadata for 11,222 NHMUK specimens. The metadata includes label transcription and georeferencing, along with summary data on geographic, taxonomic, collector and temporal coverage. We also provide timings and the methodology for our transcription and georeferencing protocols. Approximately 35% of specimens digitised were collected in ODA-listed countries, in tropical Africa, but also in South East Asia and South America.
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Affiliation(s)
- Krisztina Lohonya
- The Natural History Museum, London, United KingdomThe Natural History MuseumLondonUnited Kingdom
| | - Laurence Livermore
- The Natural History Museum, London, United KingdomThe Natural History MuseumLondonUnited Kingdom
| | - Jacek Wajer
- The Natural History Museum, London, United KingdomThe Natural History MuseumLondonUnited Kingdom
| | - Robyn Crowther
- The Natural History Museum, London, United KingdomThe Natural History MuseumLondonUnited Kingdom
| | - Elizabeth Devenish
- The Natural History Museum, London, United KingdomThe Natural History MuseumLondonUnited Kingdom
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Gonzáles P, Capcha-Ramos J, Niño-de-Guzmán P, Goodwin Z, Särkinen T, Valencia N, Cano A. Geographic distribution, conservation status and lectotypification of Pedersenia weberbaueri (Suess.) Holub (Amaranthaceae), an endemic and highly threatened shrub from the Marañón valley of Peru. REVISTA PERUANA DE BIOLOGÍA 2022. [DOI: 10.15381/rpb.v29i4.23214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The present study analyses the geographical distribution, conservation status, and nomenclature of Peruvian endemic Pedersenia weberbaueri. The species distribution was modelled using MaxEnt based on occurrence data and bioclimatic variables. The conservation status of the species was assessed against the categories and criteria of the IUCN Red List, and nomenclatural and typification issues were resolved. The potential distribution map of P. weberbaueri shows that the species is restricted to the seasonally dry tropical forests of the Marañón valley within a narrow latitudinal, longitudinal, and elevational range. Consequently, we propose to categorise the species as Endangered (EN) and provide the necessary information for its inclusion in the IUCN Red List. Finally, we resolve nomenclatural issues and designate a lectotype. The results contribute to the biological knowledge of P. weberbaueri and support subsequent conservation management plans.
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Marcer A, Escobar A, Garcia-Font V, Uribe F. Ali-Bey - an open collaborative georeferencing web application. Biodivers Data J 2022; 10:e81282. [PMID: 36761501 PMCID: PMC9848523 DOI: 10.3897/bdj.10.e81282] [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: 01/27/2022] [Accepted: 04/07/2022] [Indexed: 11/12/2022] Open
Abstract
Background Georeferencing preserved specimens represents a major effort at the Museu de Ciències Naturals de Barcelona (MCNB), given the available resources and limited staff that can be allocated to the task. Georeferencing is a labour-intensive and hard-to-automate task that requires software tools that can help in making it as efficient as possible. The tool we present, Ali-Bey, has been slowly developed over 15 years and its functionalities have been gradually built in a process of development, testing, use in production and refinement, rather than as a single development cycle out of a comprehensive specifications requirement document. At the start, the MCNB could not find a tool that fully satisfied the requirements listed as essential and made the decision to develop a custom tool. At the end, the initiative has proved successful since it has delivered a new georeferencing tool that meets the MCNB's needs, all in a context of yearly scarce availability of funds. The tool has been gradually matured and developed over the years, in line with the scarce financing. Only recently, after reaching a notable set of novel features, we considered to release it as an open-source project. The MCNB has supported its development up until this date and decided to open it in order to give the NHC community the opportunity to contribute to its development. New information We present the software tool Ali-Bey that provides new functionality for the georeferencing of specimens in Natural History Collections, namely the possibility of cooperation between different institutions, the traceability of georeferences and the capability of managing different versions of a same site name, namely for historical reasons. The tool is an open-source web application implemented in Python and the Django framework that leverages other commonly-used specialised geodatabase and map server tools. An API provides access to the geodatabase to externally-developed tools. In addition, for an easy installation, the tool is provided as a multi-container Docker application.
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Affiliation(s)
- Arnald Marcer
- CREAF, E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, SpainCREAFE08193 Bellaterra (Cerdanyola del Vallès), CataloniaSpain,Universitat Autònoma de Barcelona, E 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, SpainUniversitat Autònoma de BarcelonaE 08193, Bellaterra (Cerdanyola del Vallès), CataloniaSpain
| | - Agustí Escobar
- CREAF, E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, SpainCREAFE08193 Bellaterra (Cerdanyola del Vallès), CataloniaSpain
| | - Víctor Garcia-Font
- Universitat Oberta de Catalunya (UOC), Rambla del Poblenou 156. 08018 Barcelona, SpainUniversitat Oberta de Catalunya (UOC)Rambla del Poblenou 156. 08018 BarcelonaSpain,CYBERCAT-Center for Cybersecurity Research of Catalonia, Rambla del Poblenou 156. 08018 Barcelona, SpainCYBERCAT-Center for Cybersecurity Research of CataloniaRambla del Poblenou 156. 08018 BarcelonaSpain
| | - Francesc Uribe
- Museu de Ciències Naturals de Barcelona, Barcelona, SpainMuseu de Ciències Naturals de BarcelonaBarcelonaSpain
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Gomes-da-Silva J, Lanna J, Forzza RC. Distribution of endemic angiosperm species in Brazil on a municipality level. Biodivers Data J 2021; 9:e66043. [PMID: 34121849 PMCID: PMC8192407 DOI: 10.3897/bdj.9.e66043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/30/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Herbarium collections and the data they hold are the main sources of plant biodiversity information. These collections contain taxonomical and spatial data on living and extinct species; consequently, they are the fundamental basis for temporal and spatial biogeographical studies of plants. Mega projects focused on providing digital and free access to accurate biodiversity data have transformed plant science research, mainly in the past two decades. In this sense, researchers today are overwhelmed by the many different datasets in online repositories. There are also several challenges involved in using these data for biogeographical analyses. Analyses performed on the data available in the repositories show that 70-75% of the total amount of data have spatial deficiencies and a high number of records lack coordinates. This shortage of reliable primary biogeographical information creates serious impediments for biogeographical analyses and conservation assessments and taxonomic revisions consequently produces obstacles for evaluations of threats to biodiversity at global, regional and local levels. With the aim of contributing to botanical and biogeographical research, this paper provides georeferenced spatial data for angiosperm species endemic to Brazil. The information from two reliable online databases, i.e. the Flora do Brasil 2020 floristic database (BFG) and Plantas do Brasil: Resgate Histórico e Herbário Virtual para o Conhecimento e Conservação da Flora Brasileira (REFLORA), which are both based on records collected over the course of the last two centuries, is used to create this spatial dataset. NEW INFORMATION We provide three taxonomically-edited and georeferenced datasets for basal angiosperms, monocots and eudicots, covering a total of 14,992 endemic species from Brazil. Producing this consolidated dataset involved several months of detailed revision of coordinates and nomenclaturally updating of the names in these datasets. The information provided in this geo-referenced dataset, covering two centuries of specimen collections, will contribute to several botanical and mainly biogeographical studies.
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Affiliation(s)
- Janaína Gomes-da-Silva
- Instituto de Pesquisas do Jardim Botânico do Rio de Janeiro, Rio de Janeiro, BrazilInstituto de Pesquisas do Jardim Botânico do Rio de JaneiroRio de JaneiroBrazil
| | - Joâo Lanna
- Instituto de Pesquisas do Jardim Botânico do Rio de Janeiro, Rio de Janeiro, BrazilInstituto de Pesquisas do Jardim Botânico do Rio de JaneiroRio de JaneiroBrazil
| | - Rafaela Campostrini Forzza
- Instituto de Pesquisas do Jardim Botânico do Rio de Janeiro, Rio de Janeiro, BrazilInstituto de Pesquisas do Jardim Botânico do Rio de JaneiroRio de JaneiroBrazil
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