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      Conceptual and empirical advances in Neotropical biodiversity research

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          Abstract

          The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of “trans-disciplinary biogeography,” which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow’s ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.

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          Rebuilding community ecology from functional traits.

          There is considerable debate about whether community ecology will ever produce general principles. We suggest here that this can be achieved but that community ecology has lost its way by focusing on pairwise species interactions independent of the environment. We assert that community ecology should return to an emphasis on four themes that are tied together by a two-step process: how the fundamental niche is governed by functional traits within the context of abiotic environmental gradients; and how the interaction between traits and fundamental niches maps onto the realized niche in the context of a biotic interaction milieu. We suggest this approach can create a more quantitative and predictive science that can more readily address issues of global change.
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            Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness

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              Cryptic species as a window on diversity and conservation.

              The taxonomic challenge posed by cryptic species (two or more distinct species classified as a single species) has been recognized for nearly 300 years, but the advent of relatively inexpensive and rapid DNA sequencing has given biologists a new tool for detecting and differentiating morphologically similar species. Here, we synthesize the literature on cryptic and sibling species and discuss trends in their discovery. However, a lack of systematic studies leaves many questions open, such as whether cryptic species are more common in particular habitats, latitudes or taxonomic groups. The discovery of cryptic species is likely to be non-random with regard to taxon and biome and, hence, could have profound implications for evolutionary theory, biogeography and conservation planning.
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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Francisco, USA )
                2167-8359
                4 October 2018
                2018
                : 6
                : e5644
                Affiliations
                [1 ]Department of Biological and Environmental Sciences, University of Gothenburg , Gothenburg, Sweden
                [2 ]Gothenburg Global Biodiversity Centre , Gothenburg, Sweden
                [3 ]Gothenburg Botanical Garden , Gothenburg, Sweden
                [4 ]Department of Organismic Biology and Evolutionary Biology, Museum of Comparative Zoology, Harvard University , Cambridge, MA, USA
                [5 ]Laboratory Ecologie et Biologie des Interactions, Team “Ecologie, Evolution, Symbiose”, Université de Poitiers , Poitiers, France
                [6 ]Department of Biology, University of Louisiana at Lafayette , Lafayette, LA, USA
                [7 ]Federal University of São Paulo , Diadema, Brazil
                [8 ]Museum of Zoology, University of São Paulo , São Paulo, Brazil
                [9 ]Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam , Amsterdam, Netherlands
                [10 ]Universidad Regional Amazonica IKIAM , Napo, Ecuador
                [11 ]Instituto de Biociências, Departamento de Botânica, Universidade de São Paulo , São Paulo, Brazil
                [12 ]Integrative Biology, University of California , Berkeley, CA, USA
                [13 ]Real Jardin Botanico , Madrid, Spain
                [14 ]Department of Computational Biology, University of Lausanne , Lausanne, Switzerland
                [15 ]Swiss Institute of Bioinformatics , Lausanne, Switzerland
                [16 ]Instituto Patagónico de Geología y Paleontología , Puerto Madryn, Guatemala
                [17 ]Naturalis Biodiversity Center , Leiden, Netherlands
                [18 ]Systems Ecology, Free University , Amsterdam, Netherlands
                [19 ]Department of Biology, University of Turku , Turku, Finland
                [20 ]Instituto Nacional de Pesquisas da Amazônia , Manaus, Brazil
                [21 ]Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden
                Author information
                http://orcid.org/0000-0003-1842-9297
                http://orcid.org/0000-0002-0932-1623
                http://orcid.org/0000-0003-2341-2705
                http://orcid.org/0000-0003-3318-7193
                http://orcid.org/0000-0003-4960-0587
                http://orcid.org/0000-0002-3371-7425
                http://orcid.org/0000-0001-6104-9658
                http://orcid.org/0000-0003-0100-0961
                http://orcid.org/0000-0002-8779-2607
                http://orcid.org/0000-0002-1680-9192
                http://orcid.org/0000-0003-2535-6217
                Article
                5644
                10.7717/peerj.5644
                6174874
                30310740
                b7c08fb8-6799-401b-8660-48866c223ce7
                © 2018 Antonelli et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 21 July 2017
                : 27 August 2018
                Funding
                Funded by: Chalmers University of Technology and the University of Gothenburg
                Funded by: The Swedish Research Council
                Award ID: B0569601
                Funded by: The European Research Council under the European Union’s Seventh Framework Programme
                Award ID: FP/2007-2013, ERC Grant Agreement 331024
                Funded by: The Swedish Foundation for Strategic Research, a Wallenberg Academy Fellowship, the Faculty of Sciences at the University of Gothenburg, the Wenner-Gren Foundations, and the David Rockefeller Center for Latin American Studies at Harvard University
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico
                Award ID: CNPq 249064/2013-8
                Funded by: Swedish Research Council
                Award ID: 2015-04748
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico, the Fundação de Amparo à Pesquisa do Amazonas, the Partnerships for Enhanced Engagement in Research from the U.S. National Academy of Sciences (PEER NAS/USAID, USA)
                Funded by: The L’Oréal-UNESCO for Women in Science Awards (Brazil and France)
                Funded by: MINECO/FEDER
                Award ID: CGL2015-67849-P
                Funded by: National Science Foundation
                Award ID: NSF 0614334, 0741450, and 1354511
                Funded by: Dimensions of Biodiversity-NSF/Biota-FAPESP grant
                Award ID: FAPESP 2012/50260-6
                Funded by: The Fundação de Amparo à Pesquisa do Estado de São Paulo
                Award ID: 2017/12797-1
                Funded by: Marie Skłodowska-Curie fellowship
                Award ID: 704035
                Funded by: Fundação de Amparo à Pesquisa do Estado de São Paulo
                Award ID: FAPESP, 2013/04170-8 and 2014/18837-7
                The workshop “Origins of Biodiversity” was funded by Chalmers University of Technology and the University of Gothenburg. The following researchers are supported by scholarship or research grants from the following agencies: Alexandre Antonelli by the Swedish Research Council (B0569601), the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013, ERC Grant Agreement 331024), the Swedish Foundation for Strategic Research, a Wallenberg Academy Fellowship, the Faculty of Sciences at the University of Gothenburg, the Wenner-Gren Foundations, and the David Rockefeller Center for Latin American Studies at Harvard University; Camila D. Ritter by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq 249064/2013-8); Daniele Silvestro by the Swedish Research Council (2015-04748); Fernanda P. Werneck by the Conselho Nacional de Desenvolvimento Científico e Tecnológico, the Fundação de Amparo à Pesquisa do Amazonas, the Partnerships for Enhanced Engagement in Research from the U.S. National Academy of Sciences (PEER NAS/USAID, USA), and the L’Oréal-UNESCO for Women in Science Awards (Brazil and France); Isabel Sanmartín by MINECO/FEDER (CGL2015-67849-P); James S. Albert by the National Science Foundation (NSF 0614334, 0741450, and 1354511); Josué A. R. Azevedo by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (99999.001292/2015-03); Lúcia G. Lohmann by a collaborative Dimensions of Biodiversity-NSF/Biota-FAPESP grant (FAPESP 2012/50260-6) and by the Fundação de Amparo à Pesquisa do Estado de São Paulo (2017/12797-1); Pável Matos-Maraví by a Marie Skłodowska-Curie fellowship (704035); Thaís Guedes by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, 2013/04170-8 and 2014/18837-7). No additional external funding was received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Biodiversity
                Biogeography
                Ecology
                Evolutionary Studies
                Genomics

                biogeography,biotic diversification,landscape evolution,phylogeny,scale,biodiversity,community ecology,phylogeography,phylogenetics,tropics

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