Biodiversity Informatics最新文献

{"title":"Interpreting and Georeferencing the Concept of “Near” in Biodiversity Records","authors":"P. Campbell","doi":"10.17161/qe3d5373","DOIUrl":"https://doi.org/10.17161/qe3d5373","url":null,"abstract":"Georeferencing historical biodiversity specimens is a difficult but necessary task to bring data accumulated in the course of past scientific efforts into full currency for modern use. Textual locality descriptions vary widely, and are prone to error involved in interpretation of brief descriptions and often-unclear terms. Each type of locality description requires particular georeferencing methods to maximize precision and accuracy of resulting coordinates and uncertainty. Current “best practice” methods concerning textual descriptions referring to proximity to a locality (i.e., “near” a locality) are arbitrary, restrictive, or undefined. In this paper, I explore these challenges, and provide new methods for assigning geographic coordinates and uncertainty (with appropriate metadata) to such locality descriptions using point, line, or polygon shapes as the basis for Voronoi diagrams. Voronoi diagrams define the geographic space nearer to a given point than to any other point in a collection, making them ideally suited for determining the shape of such locality descriptions.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"107 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141016015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The IBdata Web System for Biological Collections: Design Focused on Usability","authors":"Miguel Murguía-Romero, Bernardo Serrano-Estrada, Gerardo A. Salazar, Gerardo E. Sánchez-González, Ubaldo Melo Samper Palacios, D. Gernandt, Susana Magallón, Víctor Sánchez-Cordero","doi":"10.17161/bi.v18i.20516","DOIUrl":"https://doi.org/10.17161/bi.v18i.20516","url":null,"abstract":"The software design process must put users at the core of the process to enable them to meet their specific objectives effectively, efficiently, and successfully. Thus, a software design for a computing system to consult biological collections guided by the concept of usability will result in an effective and efficient biodiversity informatics tool. Here, we introduce IBdata, a web system to consult biological collections, developed using a design approach based on the architecture of three layers: database, business rules, and user interface. The user interface design was guided by the concept of usability focused on four core concepts: simplicity, adaptability, guide the user through the journey, and feedback. The IBdata web system that we developed is composed of three modules (query, capture and editing, and administration), permitting it to query a database with about 1.7 million specimen records. Biodiversity data query systems must be effective and efficient and should meet the user’s expectations. Software design methodologies play a central role in achieving these goals, and, in this context, interface design techniques that put the user at the core of development are valuable, as in the development of the IBdata web system.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"15 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139686624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Guide francophone pour la modélisation de niches écologiques","authors":"Anaïs Vignoles","doi":"10.17161/bi.v17i.17593","DOIUrl":"https://doi.org/10.17161/bi.v17i.17593","url":null,"abstract":"(english) \u0000Correlational ecological niche modeling (ENM) is a popular group of methods in the field of distributional ecology and is employed for a variety of applications. Although the conceptual and methodological framework of ENM has been widely described in the literature, there is still no exhaustive synthesis of it in the French language. In this article, theoretical bases of ENM are exposed through a history of the concept of ecological niche as well as its implications for the study of species macroscale distributions. Then, the different steps of ENM are described, emphasizing on the importance of controlling the quality of input data. Various recommendations concerning algorithm choice, model calibration and evaluation as well post-modeling analyses, such as niche comparison and transfer to other periods/regions, are presented. Particular emphasis is placed on 1/ the operation of Maxent and the need for parameter tuning prior modeling, 2/ the importance of the choice of the M calibration area, 3/ the need to take into account accessible environments (M) for model transfer and comparison, and 4/ the importance of evaluating and presenting the variability of models resulting from methodological choices at different stages (occurrence data partitioning, choice of a climate model, choice of algorithm, choice of the calibration area, etc.). To conclude, contextualizing any ENM study in a clear and explicit theoretical and methodological framework is paramount to ensure the pertinence of subsequent interpretations. \u0000Key-words: ecological niche modeling ; good practices ; conceptual framework ; model calibration and evaluation ; model transfer ; model comparison \u0000(french) \u0000La modélisation corrélationnelle de niches écologiques (ENM) est un ensemble de méthodes populaire dans le champ de l’écologie de la distribution d’espèces et est employée pour une multitude d’applications. Si le cadre conceptuel et méthodologique de l’ENM a été largement décrit dans la littérature, il n’existe pas de synthèse exhaustive en langue française. Dans cet article, nous exposons les bases théoriques de l’ENM à travers un historique du concept de niche écologique et ses implications pour l’étude de la distribution macro-géographique des espèces. Nous décrivons ensuite les différentes étapes d’une étude ENM, en insistant tout d’abord sur l’importance de contrôler la qualité des données d’entrées. Différentes préconisations concernant le choix des algorithmes, la calibration et l’évaluation des modèles ainsi que les analyses postérieures, telles que les comparaisons de niches ou le transfert à d’autres périodes/régions, sont présentées. Nous insistons en particulier sur 1/ le fonctionnement de l’algorithme Maxent et la nécessité d’un processus de réglage de ses paramètres, 2/ l’importance du choix de l’aire de calibration M, 3/ la nécessité de prendre en compte les environnements accessibles (M) dans le transfert et la comparaison des modèles, et 4/ l’importance d’év","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131279830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Best Practices for Data Management in Citizen Science - An Indian Outlook","authors":"Thomas Vattakaven, V. Barve, G. Ramaswami, Priya Singh, Suneha Jagannathan, B. Dhandapani","doi":"10.17161/bi.v17i.16441","DOIUrl":"https://doi.org/10.17161/bi.v17i.16441","url":null,"abstract":"Citizen science has been in practice since the 1800s and is an important source of data for scientists and other applied users. It plays a vital role in democratizing science, providing equitable access to scientific participation and data, helps build the capacity of its participants, inculcates the spirit of scientific endeavor and discovery and sensitizes participants towards species and habitat conservation, creating a sense of stewardship towards nature. In recent years, citizen science, especially in biodiversity, has rapidly developed with the rising popularity of smartphones, and widespread access to the internet, leading to wider adoption globally. India has also witnessed a surge in the number of new citizen science projects being initiated and increased participation in these projects. With more proponents looking at initiating such projects, there is little documentation from an Indian perspective on setting up, collecting, managing, and maintaining biodiversity-focused citizen science projects, especially in a data-management context. We have attempted to fill this void by examining the best practices across the data life cycle of citizen science projects while keeping in mind sensitivities and scenarios in India. We hope this will prove to be an important reference for citizen science practitioners looking to better manage their data in their projects.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127455715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ENM2020: A Free Online Course and Set of Resources on Modeling Species' Niches and Distributions","authors":"A. Peterson, Matthew E. Aiello‐Lammens, G. Amatulli, R. Anderson, M. Cobos, J. Diniz‐Filho, LE Escobar, Xiao Feng, J. Franklin, Luiz M. R. Gadelha, D. Georges, M. Guéguen, Tomer Gueta, K. Ingenloff, S. Jarvie, L. Jiménez, D. Karger, J. Kass, M. Kearney, R. Loyola, Fernando Machado-Stredel, E. Martínez‐Meyer, C. Merow, Maria Luiza Mondelli, S. Mortara, Robert Muscarella, C. Myers, B. Naimi, Daniel Noesgaard, I. Ondo, L. Osorio-Olvera, H. Owens, Richard Pearson, G. Pinilla‐Buitrago, A. Sánchez-Tapia, E. Saupe, W. Thuiller, Sara Varela, D. Warren, John Wieczorek, K. Yates, G. Zhu, G. Zuquim, D. Zurell","doi":"10.17161/bi.v17i.15016","DOIUrl":"https://doi.org/10.17161/bi.v17i.15016","url":null,"abstract":"The field of distributional ecology has seen considerable recent attention, particularly surrounding the theory, protocols, and tools for Ecological Niche Modeling (ENM) or Species Distribution Modeling (SDM). Such analyses have grown steadily over the past two decades—including a maturation of relevant theory and key concepts—but methodological consensus has yet to be reached. In response, and following an online course taught in Spanish in 2018, we designed a comprehensive English-language course covering much of the underlying theory and methods currently applied in this broad field. Here, we summarize that course, ENM2020, and provide links by which resources produced for it can be accessed into the future. ENM2020 lasted 43 weeks, with presentations from 52 instructors, who engaged with >2500 participants globally through >14,000 hours of viewing and >90,000 views of instructional video and question-and-answer sessions. Each major topic was introduced by an “Overview” talk, followed by more detailed lectures on subtopics. The hierarchical and modular format of the course permits updates, corrections, or alternative viewpoints, and generally facilitates revision and reuse, including the use of only the Overview lectures for introductory courses. All course materials are free and openly accessible (CC-BY license) to ensure these resources remain available to all interested in distributional ecology.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"64 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131011890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biodiversity and distribution of Isopoda and Polychaeta along the Northwestern Pacific and the Arctic Ocean","authors":"H. Saeedi, Nils L. Jacobsen, A. Brandt","doi":"10.17161/bi.v17i.15581","DOIUrl":"https://doi.org/10.17161/bi.v17i.15581","url":null,"abstract":" \u0000The northwestern Pacific Ocean is one of the hotspots of species richness and one of the high endemicity areas of the World Ocean. However, large-scale biodiversity patterns of major deep‑sea taxa such as Isopoda and Polychaeta are still poorly studied. The goal of this research is to study the distribution, biodiversity, and community composition of Isopoda and Polychaeta (including Siboglinidae and Echiura) across the northwestern Pacific Ocean and the adjacent Arctic Ocean. The study area was divided into equal-sized hexagonal cells (c. 700,000 km²), ecoregions, 5° latitudinal bands, and 200 m depth intervals as unit of analysis. Our results revealed that the area around the Philippines and the Laptev Sea had the highest isopod and polychaete’s species richness compared to the other geographic regions of our study, with a latitudinal decline of species richness in shallow waters in both taxa. In the deep sea, maximum species richness increased towards the temperate latitudes. Gamma species richness (number of species per 200 m depth interval) also declined with depth. Rarefied species richness of isopods peaked around 5000 m depth. Rarefaction curves demonstrated a great potential for undiscovered richness across 5° latitudinal bands and depth intervals. In shallow waters, polychaetes with a pelagic larval phase had a wider distribution range compared to brooding isopods, but, in the deep sea, isopods had slightly wider distribution ranges compared to polychaetes. These results thus demonstrated that shallow water taxa with pelagic larvae and polychaete species with a wide vertical distribution range could potentially invade higher latitudes, such as species from the Northwest Pacific invading the Arctic Ocean under the rapid climate change and catastrophic reduction of sea ice cover. These changes might dramatically change the benthic communities of the Arctic Ocean and management of such should take an adaptive approach and apply measures that take potential extension and invasion of species into account.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"113959530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global land-use and land-cover data for ecologists: Historical, current, and future scenarios","authors":"Tainá Rocha, Mariana M. Vale, Matheus S. Lima-Ribeiro","doi":"10.17161/bi.v16i1.15483","DOIUrl":"https://doi.org/10.17161/bi.v16i1.15483","url":null,"abstract":"Land-use land-cover (LULC) data are important predictors of species occurrence and biodiversity threat. Although there are LULC datasets available for ecologists under current conditions, there is a lack of such data under historical and future climatic conditions. This hinders, for example, projecting niche and distribution models under global change scenarios at different times. The Land Use Harmonization Project (LUH2) is a global terrestrial dataset at 0.25o spatial resolution that provides LULC data from 850 to 2300 for 12 LULC state classes. The dataset, however, is compressed in a file format (NetCDF) that is incompatible with most ecological analysis and intractable for most ecologists. Here we selected and transformed the LUH2 data in order to make it more useful for ecological studies. We provide LULC for every year from 850 to 2100, with data from 2015 on provided under two Shared Socioeconomic Pathways (SSP2 and SSP5). We provide two types of file for each year: separate files with continuous values for each of the 12 LULC state classes, and a single categorical file with all state classes combined. To create the categorical layer, we assigned the state with the highest value in a given pixel among the 12 continuous data. The final dataset provides LULC data for 1251 years that will be of interest for macroecology, ecological niche modeling, global change analysis, and other applications in ecology and conservation. We also provide a description of LUH2 prediction of future LULC change through time.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"88 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114042441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicting multi-species bark beetle (Coleoptera: Curculionidae: Scolytinae) occurrence in Alaska: First use of open access big data mining and open source GIS to provide robust inference and a role model for progress in forest conservation","authors":"Khodabakhsh Zabihi, F. Huettmann, Brian D. Young","doi":"10.17161/bi.v16i1.14758","DOIUrl":"https://doi.org/10.17161/bi.v16i1.14758","url":null,"abstract":"Native bark beetles (Coleoptera: Curculionidae: Scolytinae) are a multi-species complex that rank among the key disturbances of coniferous forests of western North America. Many landscape-level variables are known to influence beetle outbreaks, such as suitable climatic conditions, spatial arrangement of incipient populations, topography, abundance of mature host trees, and disturbance history that include former outbreaks and fire. We assembled the first open access data, which can be used in open source GIS platforms, for understanding the ecology of the bark beetle organism in Alaska. We used boosted classification and regression tree as a machine learning data mining algorithm to model-predict the relationship between 14 environmental variables, as model predictors, and 838 occurrence records of 68 bark beetle species compared to pseudo-absence locations across the state of Alaska. The model predictors include topography- and climate-related predictors as well as feature proximities and anthropogenic factors. We were able to model, predict, and map the multi-species bark beetle occurrences across the state of Alaska on a 1-km spatial resolution in addition to providing a good quality environmental dataset freely accessible for the public. About 16% of the mixed forest and 59% of evergreen forest are expected to be occupied by the bark beetles based on current climatic conditions and biophysical attributes of the landscape. The open access dataset that we prepared, and the machine learning modeling approach that we used, can provide a foundation for future research not only on scolytines but for other multi-species questions of concern, such as forest defoliators, and small and big game wildlife species worldwide.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125386340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Weighing the Evidence for the Abundant-Center Hypothesis","authors":"T. Dallas, L. Santini, R. Decker, A. Hastings","doi":"10.17161/bi.v15i3.11989","DOIUrl":"https://doi.org/10.17161/bi.v15i3.11989","url":null,"abstract":"The abundant-center hypothesis posits that species density should be highest in the center of the geographic range or climatic niche of a species, based on the idea that the center of either will be the area with the highest demographic performance (e.g., greater fecundity, survival, or carrying capacity). While intuitive, current support for the hypothesis is quite mixed. Here, we discuss the current state of the abundant-center hypothesis, highlighting the relatively low level of support for the relationship. We then discuss the potential reasons for this lack of empirical support, emphasizing the inherent ecological complexity which may prevent the observation of the abundant-center in natural systems. This includes the role of non-equilibrial population dynamics, species interactions, landscape structure, and dispersal processes, as well as variable data quality and inconsistent methodology. The incorporation of this complexity into studies of the distribution of species densities in geographic or niche space may underlie the limited empirical support for the abundant-center hypothesis. We end by discussing potentially fruitful research avenues. Most notably, we highlight the need for theoretical development and controlled experimental testing of the abundant-center hypothesis.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125206036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Abundant Niche-centroid Hypothesis: Key Points About Unfilled Niches and the Potential Use of Supraspecfic Modeling Units","authors":"Carlos Yañez, Gerardo Martin, L. Osorio-Olvera, Jazmín Escobar-Luján, S. Castaño-Quintero, X. Chiappa-Carrara, E. Martínez‐Meyer","doi":"10.17161/bi.v15i2.13218","DOIUrl":"https://doi.org/10.17161/bi.v15i2.13218","url":null,"abstract":"Correlative estimates of fundamental niches are gaining momentum as an alternative to predict species’ abundances, particularly via the abundant niche-centroid hypothesis (an expected inverse relationship between species’ abundance variation across its range and the distance to the geometric centroid of its multidimensional ecological niche). The main goal of this review is to recapitulate what has been done, where we are now, and where should we move towards in regards to this hypothesis. Despite evidence in support of the abundance-distance to niche centroid relationship, its usefulness has been highly debated, although with little consideration of the underlying theory regarding the circumstances that might break down the relationship. We address some key points about the conditions needed to test the hypothesis in correlative studies, specifically in relation to nichecharacterization and configurations of the Biotic-Abiotic-Mobility (BAM) framework to illustrate the problem of unfilled niches. Using a created supraspecific modeling unit, we show that species for which only a portion of their fundamental niche is represented in their area of historical accessibility (M)—i.e., when the environmental equilibrium condition is violated—it is impossible to characterize their true niche centroid. Therefore, we strongly recommend to analyze this assumption prior toassess the abundant niche-centroid hypothesis. Finally, we discuss the potential of using modeling units above the species level for cases in which environmental conditions associated with species’ occurrences may not be sufficient to fully characterize their fundamental niches.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"158 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121399741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}