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  • 1.
    Antonelli, Alexandre
    et al.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Biology, University of Oxford, Oxford, United Kingdom.
    Smith, Rhian J.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.
    Perrigo, Allison L.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.
    Crottini, Angelica
    CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
    Hackel, Jan
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Testo, Weston
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Field Museum of Natural History, IL, Chicago, United States.
    Farooq, Harith
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Faculty of Natural Sciences, Lúrio University, Pemba, Cabo Delgado Province, Mozambique.
    Torres Jiménez, Maria F.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Institute of Biosciences, Life Sciences Centre, Vilnius University, Vilnius, Lithuania.
    Andela, Niels
    School of Earth and Environmental Sciences, Cardiff University, Wales, Cardiff, United Kingdom.
    Andermann, Tobias
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden; Department of Biology, University of Fribourg, Fribourg, Switzerland.
    Andriamanohera, Andotiana M.
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Andriambololonera, Sylvie
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar.
    Bachman, Steven P.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Bacon, Christine D.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.
    Baker, William J.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Belluardo, Francesco
    CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
    Birkinshaw, Chris
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar; , Missouri Botanical Garden, MO, St. Louis, United States.
    Borrell, James S.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Cable, Stuart
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Canales, Nataly A.
    University of Copenhagen, Natural History Museum of Denmark, Copenhagen, Denmark.
    Carrillo, Juan D.
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Biology, University of Fribourg, Fribourg, Switzerland; CR2P, Muséum National d'Histoire Naturelle, Paris, France; Swiss Institute of Bioinformatics, Fribourg, Switzerland.
    Clegg, Rosie
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; Department of Geography, University of Exeter, Exeter, Devon, UK.
    Clubbe, Colin
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Cooke, Robert S C
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; UK Centre for Ecology and Hydrology, Wallingford, United Kingdom.
    Damasco, Gabriel
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Rio Grande do Norte, Natal, Brazil.
    Dhanda, Sonia
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics. Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.
    Faurby, Søren
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.
    de Lima Ferreira, Paola
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic.
    Fisher, Brian L.
    California Academy of Sciences, CA, San Francisco, United States.
    Forest, Félix
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Gardiner, Lauren M.
    Cambridge University Herbarium, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom.
    Goodman, Steven M.
    Field Museum of Natural History, IL, Chicago, United States; Association Vahatra, Antananarivo, Madagascar.
    Grace, Olwen M.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Guedes, Thaís B
    Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, São Paulo, Campinas, Brazil.
    Henniges, Marie C.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom.
    Hill, Rowena
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom.
    Lehmann, Caroline E R
    Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom; School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom.
    Lowry, Porter P.
    , Missouri Botanical Garden, MO, St. Louis, United States; Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Paris, France.
    Marline, Lovanomenjanahary
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar; Association Vahatra, Antananarivo, Madagascar.
    Matos-Maraví, Pável
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic.
    Moat, Justin
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Neves, Beatriz
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
    Nogueira, Matheus G C
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
    Onstein, Renske E.
    Naturalis Biodiversity Center, Darwinweg 2, Leiden, Netherlands; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
    Papadopulos, Alexander S T
    School of Natural Sciences, Bangor University, Bangor, Gwynedd, Wales, UK.
    Perez-Escobar, Oscar A.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Phelps, Leanne N.
    Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom; School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom.
    Phillipson, Peter B.
    , Missouri Botanical Garden, MO, St. Louis, United States; Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Paris, France.
    Pironon, Samuel
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, United Kingdom.
    Przelomska, Natalia A S
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; Department of Anthropology, Smithsonian National Museum of Natural History, WA, United States.
    Rabarimanarivo, Marina
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar.
    Rabehevitra, David
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Raharimampionona, Jeannie
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar.
    Rajaonah, Mamy Tiana
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Rajaonary, Fano
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar.
    Rajaovelona, Landy R.
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Rakotoarinivo, Mijoro
    Department of Plant Biology and Ecology, University of Antananarivo, Antananarivo, Madagascar.
    Rakotoarisoa, Amédée A
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Rakotoarisoa, Solofo E.
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Rakotomalala, Herizo N.
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Rakotonasolo, Franck
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Ralaiveloarisoa, Berthe A.
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Ramirez-Herranz, Myriam
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Instituto de Ecología y Biodiversidad, University of La Serena, La Serena, Chile; Programa de Doctorado en Biología y Ecología Aplicada, Universidad Católica del Norte, Universidad de La Serena, La Serena, Chile.
    Randriamamonjy, Jean Emmanuel N
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Randriamboavonjy, Tianjanahary
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Randrianasolo, Vonona
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Rasolohery, Andriambolantsoa
    Ileiry Geospatial Services, Antananarivo, Madagascar.
    Ratsifandrihamanana, Anitry N.
    WWF, Antananarivo, Madagascar.
    Ravololomanana, Noro
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar.
    Razafiniary, Velosoa
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Razanajatovo, Henintsoa
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Razanatsoa, Estelle
    Plant Conservation Unit, Department of Biological Sciences, University of Cape Town, South Africa.
    Rivers, Malin
    Botanic Gardens Conservation International, Kew, Richmond, Surrey, UK.
    Sayol, Ferran
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
    Silvestro, Daniele
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Biology, University of Fribourg, Fribourg, Switzerland; Swiss Institute of Bioinformatics, Fribourg, Switzerland.
    Vorontsova, Maria S.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Walker, Kim
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; Royal Holloway, University of London, Egham, Surrey, UK.
    Walker, Barnaby E.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Wilkin, Paul
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Williams, Jenny
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Ziegler, Thomas
    Cologne Zoo, Cologne, Germany; Institute of Zoology, University of Cologne, Cologne, Germany.
    Zizka, Alexander
    Department of Biology, Philipps-University Marburg, Marburg, Germany.
    Ralimanana, Hélène
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Madagascar's extraordinary biodiversity: Evolution, distribution, and use2022In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 378, no 6623, article id eabf0869Article, review/survey (Refereed)
    Abstract [en]

    Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique "living laboratory" for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth's biodiversity.

  • 2.
    Bohlin, Ludvig
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Lancichinetti, Andrea
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Rosval, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Community Detection and Visualization of Networks with the Map Equation Framework2014In: Measuring Scholarly Impact: Methods and Practice / [ed] Ying Ding, Ronald Rousseau, Dietmar Wolfram, Springer, 2014, p. 3-34Chapter in book (Refereed)
    Abstract [en]

    Large networks contain plentiful information about the organization of a system. The challenge is to extract useful information buried in the structure of myriad nodes and links. Therefore, powerful tools for simplifying and highlighting important structures in networks are essential for comprehending their organization. Such tools are called community-detection methods and they are designed to identify strongly intraconnected modules that often correspond to important functional units. Here we describe one such method, known as the map equation, and its accompanying algorithms for finding, evaluating, and visualizing the modular organization of networks. The map equation framework is very flexible and can identify two-level, multi-level, and overlapping organization in weighted, directed, and multiplex networks with its search algorithm Infomap. Because the map equation framework operates on the flow induced by the links of a network, it naturally captures flow of ideas and citation flow, and is therefore well-suited for analysis of bibliometric networks.

  • 3.
    Calvente, Alice
    et al.
    Laboratório de Botânica Sistemática, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Lagoa Nova, RN, Natal, Brazil.
    da Silva, Ana Paula Alves
    Laboratório de Botânica Sistemática, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Lagoa Nova, RN, Natal, Brazil.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics. Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Carvalho, Fernanda Antunes
    Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, MG, Belo Horizonte, Brazil.
    Fantinati, Mariana Ramos
    Departamento de Ciências Biológicas, Universidade Estadual Paulista–câmpus de Assis, Parque Universitário, SP, Assis, Brazil.
    Zizka, Alexander
    Biodiversity of plants, Philipps University Marburg, Marburg, Germany.
    Antonelli, Alexandre
    Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Royal Botanic Gardens Kew, Richmond, United Kingdom; Department of Biology, University of Oxford, Oxford, United Kingdom.
    Spiny but photogenic: amateur sightings complement herbarium specimens to reveal the bioregions of cacti2023In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 110, no 10, article id e16235Article in journal (Refereed)
    Abstract [en]

    Premise: Cacti are characteristic elements of the Neotropical flora and of major interest for biogeographic, evolutionary, and ecological studies. We tested global biogeographic boundaries for Neotropical Cactaceae using specimen-based occurrences, coupled with data from visual observations, as a means to tackle the known collection biases in the family.

    Methods: Species richness and record density were assessed for preserved specimens and human observations, and a bioregional scheme tailored to Cactaceae was produced using the interactive web application Infomap Bioregions, based on data from 261,272 point records cleaned through automated and manual steps.

    Results: We found that areas in Mexico and southwestern USA, in eastern Brazil, and along the Andean region have the greatest density of records and the highest species richness. Human observations complement information from preserved specimens substantially, especially along the Andes. We propose 24 cactus bioregions, among which the most species-rich are northern Mexico/southwestern USA, central Mexico, southern central Mexico, Central America, Mexican Pacific coast, central and southern Andes, northwestern Mexico/extreme southwestern USA, southwestern Bolivia, northeastern Brazil, and Mexico/Baja California.

    Conclusions: The bioregionalization proposed shows biogeographic boundaries specific to cacti and can thereby aid further evolutionary, biogeographic, and ecological studies by providing a validated framework for further analyses. This classification builds upon, and is distinctive from, other expert-derived regionalization schemes for other taxa. Our results showcase how observation data, including citizen-science records, can complement traditional specimen-based data for biogeographic research, particularly for taxa with specific specimen collection and preservation challenges and those that are threatened or internationally protected.

  • 4.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Mapping incomplete relational data: networks in ecology & evolution2022Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    We live in an interconnected world full of complex systems that cannot be understood simply by analyzing their components. From how genes regulate biological functions to the distribution of life on Earth, we need methods that can analyze systems as a whole.

    Networks are abstractions of complex systems, helping capture properties that emerge from patterns of interactions rather than from the individual parts. To understand the patterns of interactions in large networks, we need to simplify them by discovering their modular structure that often characterizes complex systems. A hierarchical modular structure functions as a map that lets us navigate relational data efficiently and helps us see the general patterns. But how reliable is the map if it is based on incomplete data?

    This thesis applies and builds upon the map equation, which is an information-theoretic method for detecting modular regularities in the flow patterns on networks. To robustly map incomplete data, we have developed three general approaches: (1) Adaptive resolution in both sampling of and dynamics on networks better fits the data. (2) Regularization avoids overfitting to random patterns. (3) Richer data can be included into the network for a more complete map. Methods that can include evolutionary relationships and handle incomplete data provide more powerful tools for mapping biodiversity in space and time.

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  • 5.
    Edler, Daniel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Bohlin, Ludvig
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Mapping Higher-Order Network Flows in Memory and Multilayer Networks with Infomap2017In: Algorithms, E-ISSN 1999-4893, Vol. 10, no 4, article id 112Article in journal (Refereed)
    Abstract [en]

    Comprehending complex systems by simplifying and highlighting important dynamical patterns requires modeling and mapping higher-order network flows. However, complex systems come in many forms and demand a range of representations, including memory and multilayer networks, which in turn call for versatile community-detection algorithms to reveal important modular regularities in the flows. Here we show that various forms of higher-order network flows can be represented in a unified way with networks that distinguish physical nodes for representing a complex system's objects from state nodes for describing flows between the objects. Moreover, these so-called sparse memory networks allow the information-theoretic community detection method known as the map equation to identify overlapping and nested flow modules in data from a range of different higher-order interactions such as multistep, multi-source, and temporal data. We derive the map equation applied to sparse memory networks and describe its search algorithm Infomap, which can exploit the flexibility of sparse memory networks. Together they provide a general solution to reveal overlapping modular patterns in higher-order flows through complex systems.

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  • 6.
    Edler, Daniel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics. Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Gothenburg, Sweden.
    Guedes, Thais
    Zizka, Alexander
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Antonelli, Alexandre
    Infomap Bioregions: Interactive Mapping of Biogeographical Regions from Species Distributions2017In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 66, no 2, p. 197-204Article in journal (Refereed)
    Abstract [en]

    Biogeographical regions (bioregions) reveal how different sets of species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology, and evolution. Several methods have been developed to identify bioregions based on species distribution data rather than expert opinion. One approach successfully applies network theory to simplify and highlight the underlying structure in species distributions. However, this method lacks tools for simple and efficient analysis. Here, we present Infomap Bioregions, an interactive web application that inputs species distribution data and generates bioregion maps. Species distributions may be provided as georeferenced point occurrences or range maps, and can be of local, regional, or global scale. The application uses a novel adaptive resolution method to make best use of often incomplete species distribution data. The results can be downloaded as vector graphics, shapefiles, or in table format. We validate the tool by processing large data sets of publicly available species distribution data of the world's amphibians using species ranges, and mammals using point occurrences. We then calculate the fit between the inferred bioregions and WWF ecoregions. As examples of applications, researchers can reconstruct ancestral ranges in historical biogeography or identify indicator species for targeted conservation.

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  • 7.
    Edler, Daniel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics. Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Holmgren, Anton
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Rojas, Alexis
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Antonelli, Alexandre
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Department of Biology, University of Oxford, Oxford, United Kingdom; Royal Botanical Gardens Kew, Richmond, Surrey, United Kingdom.
    Infomap Bioregions 2: exploring the interplay between biogeography and evolution2022Manuscript (preprint) (Other academic)
  • 8.
    Edler, Daniel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Klein, Johannes
    Antonelli, Alexandre
    Silvestro, Daniele
    raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML2021In: Methods in Ecology and Evolution, E-ISSN 2041-210X, Vol. 12, no 2, p. 373-377Article in journal (Refereed)
    Abstract [en]

    raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used softwares for phylogenetic inference using maximum likelihood. Here we present raxmlGUI 2.0, a complete rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front-end to setup and run phylogenetic analyses. Our program offers automated pipelines for analyses that require multiple successive calls of RAxML, built-in functions to concatenate alignment files while automatically specifying the appropriate partition settings, and one-click model testing to select the best substitution models using ModelTest-NG. In addition to RAxML 8.x, raxmlGUI 2.0 also supports the new RAxML-NG, which provides new functionality and higher performance on large datasets. raxmlGUI 2.0 facilitates phylogenetic analyses by coupling an intuitive interface with the unmatched performance of RAxML.

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  • 9.
    Edler, Daniel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Smiljanić, Jelena
    Umeå University, Faculty of Science and Technology, Department of Physics. Institute of Physics, University of Belgrade, Belgrade, Serbia.
    Holmgren, Anton
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Antonelli, Alexandre
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Department of Plant Sciences, University of Oxford, Oxford, United Kingdom; Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Variable Markov dynamics as a multifocal lens to map multiscale complex networksManuscript (preprint) (Other academic)
  • 10.
    Eriksson, Anton
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Rojas, Alexis
    Umeå University, Faculty of Science and Technology, Department of Physics.
    de Domenico, Manlio
    CoMuNe Lab, Fondazione Bruno Kessler, Povo (TN), Italy.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    How choosing random-walk model and network representation matters for flow-based community detection in hypergraphs2021In: Communications Physics, E-ISSN 2399-3650, Vol. 4, no 1, article id 133Article in journal (Refereed)
    Abstract [en]

    Hypergraphs offer an explicit formalism to describe multibody interactions in complex systems. To connect dynamics and function in systems with these higher-order interactions, network scientists have generalised random-walk models to hypergraphs and studied the multibody effects on flow-based centrality measures. Mapping the large-scale structure of those flows requires effective community detection methods applied to cogent network representations. For different hypergraph data and research questions, which combination of random-walk model and network representation is best? We define unipartite, bipartite, and multilayer network representations of hypergraph flows and explore how they and the underlying random-walk model change the number, size, depth, and overlap of identified multilevel communities. These results help researchers choose the appropriate modelling approach when mapping flows on hypergraphs.

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  • 11.
    Farage, Carmel
    et al.
    Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics. Gothenburg Global Biodiversity Centre, Gothenburg, Sweden; Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Eklöf, Anna
    Division of Theoretical Biology, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Pilosof, Shai
    Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
    Identifying flow modules in ecological networks using Infomap2021In: Methods in Ecology and Evolution, E-ISSN 2041-210X, Vol. 12, no 5, p. 778-786Article in journal (Refereed)
    Abstract [en]

    Analysing how species interact in modules is a fundamental problem in network ecology. Theory shows that a modular network structure can reveal underlying dynamic ecological and evolutionary processes, influence dynamics that operate on the network and affect the stability of the ecological system. Although many ecological networks describe flows, such as biomass flows in food webs or disease transmission, most modularity analyses have ignored network flows, which can hinder our understanding of the interplay between structure and dynamics. Here we present Infomap, an established method based on network flows to the field of ecological networks. Infomap is a flexible tool that can identify modules in virtually any type of ecological network and is particularly useful for directed, weighted and multilayer networks. We illustrate how Infomap works on all these network types. We also provide a fully documented repository with additional ecological examples. Finally, to help researchers to analyse their networks with Infomap, we introduce the open-source R package infomapecology. Analysing flow-based modularity is useful across ecology and transcends to other biological and non-biological disciplines. A dynamic approach for detecting modular structure has strong potential to provide new insights into the organisation of ecological networks.

  • 12.
    Holmgren, Anton
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Mapping change in higher-order networks with multilevel and overlapping communitiesManuscript (preprint) (Other academic)
    Abstract [en]

    New network models of complex systems use layers, state nodes, or hyperedges to capture higher-order interactions and dynamics. Simplifying how the higher-order networks change over time or depending on the network model would be easy with alluvial diagrams, which visualize community splits and merges between networks. However, alluvial diagrams were developed for networks with regular nodes assigned to non-overlapping flat communities. How should they be defined for nodes in layers, state nodes, or hyperedges? How can they depict multilevel, overlapping communities? Here we generalize alluvial diagrams to map change in higher-order networks and provide an interactive tool for anyone to generate alluvial diagrams. We use the alluvial generator to illustrate the effect of modeling network flows with memory in a citation network, distinguishing multidisciplinary from field-specific journals. 

  • 13.
    Holmgren, Anton
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics. Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Mapping change in higher-order networks with multilevel and overlapping communities2023In: Applied Network Science, E-ISSN 2364-8228, Vol. 8, no 1, article id 42Article in journal (Refereed)
    Abstract [en]

    New network models of complex systems use layers, state nodes, or hyperedges to capture higher-order interactions and dynamics. Simplifying how the higher-order networks change over time or depending on the network model would be easy with alluvial diagrams, which visualize community splits and merges between networks. However, alluvial diagrams were developed for networks with regular nodes assigned to non-overlapping flat communities. How should they be defined for nodes in layers, state nodes, or hyperedges? How can they depict multilevel, overlapping communities? Here we generalize alluvial diagrams to map change in higher-order networks and provide an interactive tool for anyone to generate alluvial diagrams. We use the alluvial diagram generator in three case studies to illustrate significant changes in the organization of science, the effect of modeling network flows with memory in a citation network and distinguishing multidisciplinary from field-specific journals, and the effects of multilayer representation of a collaboration hypergraph.

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  • 14.
    Ralimanana, Hélène
    et al.
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Perrigo, Allison L.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.
    Smith, Rhian J.
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Borrell, James S.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Faurby, Søren
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.
    Rajaonah, Mamy Tiana
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Randriamboavonjy, Tianjanahary
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Vorontsova, Maria S.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Cooke, Robert S. C.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; UK Centre for Ecology and Hydrology, Wallingford, United Kingdom.
    Phelps, Leanne N.
    School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom; Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom.
    Sayol, Ferran
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
    Andela, Niels
    School of Earth and Environmental Sciences, Cardiff University, Wales, Cardiff, United Kingdom.
    Andermann, Tobias
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden; Department of Biology, University of Fribourg, Fribourg, Switzerland.
    Andriamanohera, Andotiana M.
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Andriambololonera, Sylvie
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar.
    Bachman, Steven P.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Bacon, Christine D.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.
    Baker, William J.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Belluardo, Francesco
    CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
    Birkinshaw, Chris
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar; , Missouri Botanical Garden, MO, St. Louis, United States.
    Cable, Stuart
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Canales, Nataly A.
    University of Copenhagen, Natural History Museum of Denmark, Copenhagen, Denmark.
    Carrillo, Juan D.
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Biology, University of Fribourg, Fribourg, Switzerland; CR2P, Muséum National d'Histoire Naturelle, Paris, France; Swiss Institute of Bioinformatics, Fribourg, Switzerland.
    Clegg, Rosie
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; Department of Geography, University of Exeter, Exeter, Devon, UK.
    Clubbe, Colin
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Crottini, Angelica
    CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
    Damasco, Gabriel
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Rio Grande do Norte, Natal, Brazil.
    Dhanda, Sonia
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics. Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.
    Farooq, Harith
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Faculty of Natural Sciences, Lúrio University, Pemba, Cabo Delgado Province, Mozambique.
    de Lima Ferreira, Paola
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic.
    Fisher, Brian L.
    California Academy of Sciences, CA, San Francisco, United States.
    Forest, Félix
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Gardiner, Lauren M.
    Cambridge University Herbarium, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom.
    Goodman, Steven M.
    Association Vahatra, Antananarivo, Madagascar; Field Museum of Natural History, IL, Chicago, United States.
    Grace, Olwen M.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Guedes, Thaís B
    Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, São Paulo, Campinas, Brazil.
    Hackel, Jan
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Henniges, Marie C.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom.
    Hill, Rowena
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom.
    Lehmann, Caroline E R
    School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom; Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom.
    Lowry, Porter P.
    , Missouri Botanical Garden, MO, St. Louis, United States; Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Paris, France.
    Marline, Lovanomenjanahary
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Association Vahatra, Antananarivo, Madagascar.
    Matos-Maraví, Pável
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic.
    Moat, Justin
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Neves, Beatriz
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
    Nogueira, Matheus G C
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
    Onstein, Renske E.
    Naturalis Biodiversity Center, Leiden, Netherlands; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
    Papadopulos, Alexander S T
    School of Natural Sciences, Bangor University, Bangor, Gwynedd, Wales, UK.
    Perez-Escobar, Oscar A.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Phillipson, Peter B.
    , Missouri Botanical Garden, MO, St. Louis, United States; Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Paris, France.
    Pironon, Samuel
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, United Kingdom.
    Przelomska, Natalia A S
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; Department of Anthropology, Smithsonian National Museum of Natural History, WA, United States.
    Rabarimanarivo, Marina
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar.
    Rabehevitra, David
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Raharimampionona, Jeannie
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar.
    Rajaonary, Fano
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar.
    Rajaovelona, Landy R.
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Rakotoarinivo, Mijoro
    Department of Plant Biology and Ecology, University of Antananarivo, Antananarivo, Madagascar.
    Rakotoarisoa, Amédée A
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Rakotoarisoa, Solofo E.
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Rakotomalala, Herizo N.
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Rakotonasolo, Franck
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Ralaiveloarisoa, Berthe A.
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Ramirez-Herranz, Myriam
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Instituto de Ecología y Biodiversidad, University of La Serena, La Serena, Chile; Programa de Doctorado en Biología y Ecología Aplicada, Universidad Católica del Norte, Universidad de La Serena, La Serena, Chile.
    Randriamamonjy, Jean Emmanuel N
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Randrianasolo, Vonona
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Rasolohery, Andriambolantsoa
    Ileiry Geospatial Services, Antananarivo, Madagascar.
    Ratsifandrihamanana, Anitry N.
    WWF, Antananarivo, Madagascar.
    Ravololomanana, Noro
    Madagascar Program, Missouri Botanical Garden, Antananarivo, Madagascar.
    Razafiniary, Velosoa
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Razanajatovo, Henintsoa
    Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar.
    Razanatsoa, Estelle
    Plant Conservation Unit, Department of Biological Sciences, University of Cape Town, South Africa.
    Rivers, Malin
    Botanic Gardens Conservation International, Kew, Richmond, Surrey, UK.
    Silvestro, Daniele
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Biology, University of Fribourg, Fribourg, Switzerland; Swiss Institute of Bioinformatics, Fribourg, Switzerland.
    Testo, Weston
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Field Museum of Natural History, IL, Chicago, United States.
    Torres Jiménez, Maria F.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Institute of Biosciences, Life Sciences Centre, Vilnius University, Vilnius, Lithuania.
    Walker, Kim
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK; Royal Holloway, University of London, Egham, Surrey, UK.
    Walker, Barnaby E.
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Wilkin, Paul
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Williams, Jenny
    Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
    Ziegler, Thomas
    Cologne Zoo, Cologne, Germany; Institute of Zoology, University of Cologne, Cologne, Germany.
    Zizka, Alexander
    Department of Biology, Philipps-University Marburg, Marburg, Germany.
    Antonelli, Alexandre
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Royal Botanic Gardens, Kew, Richmond, Surrey, UK; Department of Biology, University of Oxford, Oxford, United Kingdom.
    Madagascar's extraordinary biodiversity: threats and opportunities2022In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 378, no 6623, article id eadf1466Article, review/survey (Refereed)
    Abstract [en]

    Madagascar's unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar's terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.

  • 15. Samoilenko, Anna
    et al.
    Karimi, Fariba
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Kunegis, Jerome
    Strohmaier, Markus
    Linguistic neighbourhoods: explaining cultural borders on Wikipedia through multilingual co-editing activity2016In: EPJ Data Science, ISSN 2193-1127, Vol. 5, article id 9Article in journal (Refereed)
    Abstract [en]

    In this paper, we study the network of global interconnections between language communities, based on shared co-editing interests of Wikipedia editors, and show that although English is discussed as a potential lingua franca of the digital space, its domination disappears in the network of co-editing similarities, and instead local connections come to the forefront. Out of the hypotheses we explored, bilingualism, linguistic similarity of languages, and shared religion provide the best explanations for the similarity of interests between cultural communities. Population attraction and geographical proximity are also significant, but much weaker factors bringing communities together. In addition, we present an approach that allows for extracting significant cultural borders from editing activity of Wikipedia users, and comparing a set of hypotheses about the social mechanisms generating these borders. Our study sheds light on how culture is reflected in the collective process of archiving knowledge on Wikipedia, and demonstrates that cross-lingual interconnections on Wikipedia are not dominated by one powerful language. Our findings also raise some important policy questions for the Wikimedia Foundation.

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  • 16.
    Samoilenko, Anna
    et al.
    GESIS - Leibniz-Institute for the Social Sciences, Germany.
    Karimi, Fariba
    GESIS - Leibniz-Institute for the Social Sciences, Germany.
    Kunegis, Jérôme
    University of Koblenz-Landau, Germany.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Strohmaier, Markus
    GESIS - Leibniz-Institute for the Social Sciences, Germany; University of Koblenz-Landau, Germany.
    Linguistic influence patterns within the global network of Wikipedia language editions2015In: WebSci '15: Proceedings of the 2015 ACM Web Science Conference, ACM Digital Library, 2015, article id 54Conference paper (Refereed)
    Abstract [en]

    The Internet is highly multilingual, and its content is created, shared, debated and shaped within many different language-speaking communities. These communities do not exist in isolation, but communicate and influence each other's interests, just as in the offline world. Quantifying this influence is however a non-trivial task, as these communities are usually spread across multiple heterogeneous platforms. In this work, we set out to measure the influence of languages on each other by observing concept overlap between the 110 largest Wikipedia language editions. We describe experiments to test if language overlap in concept coverage is a random process, and find that edition size is a strong predictor of higher concept overlap, with English-German being the most frequently co-occurring pair (45%). Both small and large editions co-occur more frequently than expected with editions of similar size, but co-occurrences across groups are below what is expected by chance. Additionally, by applying network analysis, we find that the hierarchy of language interconnections differs depending on the locality of topics: for interlingually popular topics, the dominance of English, German and French is pronounced, while for topics with a local reach, geographical and cultural proximity as well as common heritage are better explanators of co-occurrence.

  • 17.
    Smiljanic, Jelena
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics. Scientific Computing Laboratory, Center for the Study of Complex Systems, Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, Belgrade, Serbia.
    Blöcker, Christopher
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics. Gothenburg Global Biodiversity Centre, Box 461, Gothenburg, Sweden; Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs Gata 22B, Gothenburg, Sweden.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Mapping flows on weighted and directed networks with incomplete observations2021In: Journal of Complex Networks, ISSN 2051-1310, E-ISSN 2051-1329, Vol. 9, no 6, article id cnab044Article in journal (Refereed)
    Abstract [en]

    Detecting significant community structure in networks with incomplete observations is challenging because the evidence for specific solutions fades away with missing data. For example, recent research shows that flow-based community detection methods can highlight spurious communities in sparse undirected and unweighted networks with missing links. Current Bayesian approaches developed to overcome this problem do not work for incomplete observations in weighted and directed networks that describe network flows. To overcome this gap, we extend the idea behind the Bayesian estimate of the map equation for unweighted and undirected networks to enable more robust community detection in weighted and directed networks. We derive an empirical Bayes estimate of the transitions rates that can incorporate metadata information and show how an efficient implementation in the community-detection method Infomap provides more reliable communities even with a significant fraction of data missing.

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    errata
  • 18.
    Smiljanic, Jelena
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics. Scientific Computing Laboratory, Center for the Study of Complex Systems, Institute of Physics, University of Belgrade, Serbia.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics. Gothenburg Global Biodiversity Centre, Gothenburg, Sweden; Department of Biological and Environmental Sciences, University of Gothenburg, Sweden.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Mapping flows on sparse networks with missing links2020In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 102, no 1, article id 012302Article in journal (Refereed)
    Abstract [en]

    Unreliable network data can cause community-detection methods to overfit and highlight spurious structures with misleading information about the organization and function of complex systems. Here we show how to detect significant flow-based communities in sparse networks with missing links using the map equation. Since the map equation builds on Shannon entropy estimation, it assumes complete data such that analyzing undersampled networks can lead to overfitting. To overcome this problem, we incorporate a Bayesian approach with assumptions about network uncertainties into the map equation framework. Results in both synthetic and real-world networks show that the Bayesian estimate of the map equation provides a principled approach to revealing significant structures in undersampled networks.

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  • 19.
    Zizka, Alexander
    et al.
    German Center for Integrative Biodiversity Research Halle-Jena-Leipzig (iDiv), sDiv, University of Leipzig, Leipzig, Germany; Naturalis Biodiversity Center, Leiden University, Leiden, Netherlands.
    Rydén, Oskar
    Varieties of Democracy Institute, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Centre for Collective Action Research, University of Gothenburg, Gothenburg, Sweden; Department of Political Science, University of Gothenburg, Gothenburg, Sweden.
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics. Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Klein, Johannes
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.
    Perrigo, Allison
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Silvestro, Daniele
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Department of Biology, University of Fribourg, Fribourg, Switzerland; Swiss Institute of Bioinformatics, Fribourg, Switzerland.
    Jagers, Sverker C.
    Centre for Collective Action Research, University of Gothenburg, Gothenburg, Sweden; Department of Political Science, University of Gothenburg, Gothenburg, Sweden.
    Lindberg, Staffan I.
    Varieties of Democracy Institute, University of Gothenburg, Gothenburg, Sweden; Department of Political Science, University of Gothenburg, Gothenburg, Sweden.
    Antonelli, Alexandre
    Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden; Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Department of Plant Sciences, University of Oxford, Oxford, United Kingdom; Royal Botanic Gardens Kew, Richmond, United Kingdom.
    Bio-Dem, a tool to explore the relationship between biodiversity data availability and socio-political conditions in time and space2021In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 48, no 11, p. 2715-2726Article in journal (Refereed)
    Abstract [en]

    Aim: Geo-referenced species occurrence records are a prime example of biodiversity data and a cornerstone of biodiversity research. Yet, their availability depends on non-biological factors, including the political framework in the region of collection. Here we present Bio-Dem (www.bio-dem.surge.sh), an open-source software to explore the relationship between the availability of species occurrence records and the political framework in countries worldwide and through time.

    Location: Global.

    Taxon: Any.

    Methods: Bio-Dem accesses the number of occurrence records available from countries worldwide from the Global Biodiversity Information Facility (www.gbif.org) and socio-political information from these countries from the Varieties of Democracy database (www.v-dem.net) as well as information on colonial history from the Issue Correlates of War Project.

    Results: Bio-Dem is available as a free graphical user interface web application at www.bio-dem.surge.sh. Through three interactive graphs, Bio-Dem enables users to explore the relationship between species occurrence records and countries’ regime type, freedom of movement, freedom of association, gross domestic product, education length, political corruption, armed conflict and colonial history. We describe possible links of these specific political indicators with the collection and mobilization of biodiversity data. Illustrative examples and video tutorials explaining the use of Bio-Dem are available at www.bio-dem.surge.sh.

    Main conclusions: Bio-Dem provides a user-friendly way to explore the link between socio-political variables and the availability of species occurrence records in user-selected taxa and geographic regions, and to generate hypotheses on their connection. We envision Bio-Dem as a useful tool for teachers communicating the caveats of available biodiversity data, for biodiversity scientists exploring potential spatial and temporal bias in their data, and for social scientists exploring the impact of political systems on scientific data collection and biodiversity conservation.

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  • 20. Zizka, Alexander
    et al.
    Silvestro, Daniele
    Andermann, Tobias
    Azevedo, Josue
    Ritter, Camila Duarte
    Edler, Daniel
    Umeå University, Faculty of Science and Technology, Department of Physics. Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Göteborg, Sweden; .
    Farooq, Harith
    Herdean, Andrei
    Ariza, Maria
    Scharn, Ruud
    Svantesson, Sten
    Wengström, Niklas
    Zizka, Vera
    Antonelli, Alexandre
    CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases2019In: Methods in Ecology and Evolution, E-ISSN 2041-210X, Vol. 10, no 5, p. 744-751Article in journal (Refereed)
    Abstract [en]

    Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo-referencing or dating, can diminish their usefulness. Manual cleaning is time-consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records.

    Here, we present CoordinateCleaner, an r-package to scan datasets of species occurrence records for geo-referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo-referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio-temporal tests for fossils.

    We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic.

    All cleaning functions and the biodiversity institution database are open-source and available within the CoordinateCleaner r-package.

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