The Importance of Biodiversity E-infrastructures for Megadiverse Countries

Addressing the challenges of biodiversity conservation and sustainable development requires global cooperation, support structures, and new governance models to integrate diverse initiatives and achieve massive, open exchange of data, tools, and technology. The traditional paradigm of sharing scientific knowledge through publications is not sufficient to meet contemporary demands that require not only the results but also data, knowledge, and skills to analyze the data. E-infrastructures are key in facilitating access to data and providing the framework for collaboration. Here we discuss the importance of e-infrastructures of public interest and the lack of long-term funding policies. We present the example of Brazil’s speciesLink network, an e-infrastructure that provides free and open access to biodiversity primary data and associated tools. SpeciesLink currently integrates 382 datasets from 135 national institutions and 13 institutions from abroad, openly sharing ~7.4 million records, 94% of which are associated to voucher specimens. Just as important as the data is the network of data providers and users. In 2014, more than 95% of its users were from Brazil, demonstrating the importance of local e-infrastructures in enabling and promoting local use of biodiversity data and knowledge. From the outset, speciesLink has been sustained through project-based funding, normally public grants for 2–4-year periods. In between projects, there are short-term crises in trying to keep the system operational, a fact that has also been observed in global biodiversity portals, as well as in social and physical sciences platforms and even in computing services portals. In the last decade, the open access movement propelled the development of many web platforms for sharing data. Adequate policies unfortunately did not follow the same tempo, and now many initiatives may perish

BioClimate: a Science Gateway for Climate Change and Biodiversity research in the EUBrazilCloudConnect project

[EN] Climate and biodiversity systems are closely linked across a wide range of scales. To better understand the mutual interaction between climate change and biodiversity there is a strong need for multidisciplinary skills, scientific tools, and access to a large variety of heterogeneous, often distributed, data sources. Related to that, the EUBrazilCloudConnect project provides a user-oriented research environment built on top of a federated cloud infrastructure across Europe and Brazil, to serve key needs in different scientific domains, which is validated through a set of use cases. Among them, the most data-centric one is focused on climate change and biodiversity research. As part of this use case, the BioClimate Science Gateway has been implemented to provide end-users transparent access to (i) a highly integrated user-friendly environment, (ii) a large variety of data sources, and (iii) different analytics & visualization tools to serve a large spectrum of users needs and requirements. This paper presents a complete overview of BioClimate and the related scientific environment, in particular its Science Gateway, delivered to the end-user community at the end of the project.This work was supported by the EU FP7 EUBrazilCloudConnect Project (Grant Agreement 614048), and CNPq/Brazil (Grant Agreement no 490115/2013-6).Fiore, S.; Elia, D.; Blanquer Espert, I.; Brasileiro, FV.; Nuzzo, A.; Nassisi, P.; Rufino, LAA.... (2019). BioClimate: a Science Gateway for Climate Change and Biodiversity research in the EUBrazilCloudConnect project. Future Generation Computer Systems. 94:895-909. https://doi.org/10.1016/j.future.2017.11.034S8959099

Convergent Evolution and the Diverse Ontogenetic Origins of Tendrils in Angiosperms

Climbers are abundant in tropical forests, where they constitute a major functional plant type. The acquisition of the climbing habit in angiosperms constitutes a key innovation. Successful speciation in climbers is correlated with the development of specialized climbing strategies such as tendrils, i.e., filiform organs with the ability to twine around other structures through helical growth. Tendrils are derived from a variety of morphological structures, e.g., stems, leaves, and inflorescences, and are found in various plant families. In fact, tendrils are distributed throughout the angiosperm phylogeny, from magnoliids to asterids II, making these structures a great model to study convergent evolution. In this study, we performed a thorough survey of tendrils within angiosperms, focusing on their origin and development. We identified 17 tendril types and analyzed their distribution through the angiosperm phylogeny. Some interesting patterns emerged. For instance, tendrils derived from reproductive structures are exclusively found in the Core Eudicots, except from one monocot species. Fabales and Asterales are the orders with the highest numbers of tendrilling strategies. Tendrils derived from modified leaflets are particularly common among asterids, occurring in Polemoniaceae, Bignoniaceae, and Asteraceae. Although angiosperms have a large number of tendrilled representatives, little is known about their origin and development. This work points out research gaps that should help guide future research on the biology of tendrilled species. Additional research on climbers is particularly important given their increasing abundance resulting from environmental disturbance in the tropics

Stinging Trichomes in Apocynaceae and Their Evolution in Angiosperms

Stinging trichomes are rare in plants, occurring only in angiosperms, where they are reported for a few genera belonging to six families. Although there is no report of stinging trichomes in Apocynaceae, previous fieldwork collections of Fischeria and Matelea caused us a mild allergic reaction on the skin when we contacted the dense indumentum of the plants. This fact associated with the well-known presence of glandular trichomes with acute apex in both genera raised suspicions that stinging trichomes could be present in the family. Hence, this study aimed to investigate the likely occurrence of stinging trichomes in Fischeria and Matelea. We analyzed vegetative shoots and leaves of Fischeria stellata and Matelea denticulata through the usual procedures of light and scanning electron microscopy. We also performed several histochemical tests to investigate the chemical composition of trichome secretion. We detected that glandular trichomes occur throughout the surface of the leaf and stem. They are multicellular, uniseriate with an apical secretory cell, which has a dilated base and a needle-shaped apex. The secretion is compressed into the acuminate portion of the apical cell by a large vacuole, and crystals are deposited in the cell wall in a subapical position, providing a preferential site of rupture. The secretion, composed of amino acids and/or proteins, is released under mechanical action, causing skin irritation. Based on our detailed morphological and anatomical analyses, and in the functional aspects observed, we concluded that the glandular trichomes in Fischeria and Matelea can indeed be classified as stinging. Thus, Apocynaceae is the seventh family for which this type of trichome has been reported. We also compiled information on stinging trichomes in all families of angiosperms. Their phylogenetic distribution indicates that they have evolved at least 12 times during angiosperm evolution and may represent an evolutionary convergence of plant defense against herbivory

Image1.PDF

<p>Climbers are abundant in tropical forests, where they constitute a major functional plant type. The acquisition of the climbing habit in angiosperms constitutes a key innovation. Successful speciation in climbers is correlated with the development of specialized climbing strategies such as tendrils, i.e., filiform organs with the ability to twine around other structures through helical growth. Tendrils are derived from a variety of morphological structures, e.g., stems, leaves, and inflorescences, and are found in various plant families. In fact, tendrils are distributed throughout the angiosperm phylogeny, from magnoliids to asterids II, making these structures a great model to study convergent evolution. In this study, we performed a thorough survey of tendrils within angiosperms, focusing on their origin and development. We identified 17 tendril types and analyzed their distribution through the angiosperm phylogeny. Some interesting patterns emerged. For instance, tendrils derived from reproductive structures are exclusively found in the Core Eudicots, except from one monocot species. Fabales and Asterales are the orders with the highest numbers of tendrilling strategies. Tendrils derived from modified leaflets are particularly common among asterids, occurring in Polemoniaceae, Bignoniaceae, and Asteraceae. Although angiosperms have a large number of tendrilled representatives, little is known about their origin and development. This work points out research gaps that should help guide future research on the biology of tendrilled species. Additional research on climbers is particularly important given their increasing abundance resulting from environmental disturbance in the tropics.</p

Image2.PDF

<p>Climbers are abundant in tropical forests, where they constitute a major functional plant type. The acquisition of the climbing habit in angiosperms constitutes a key innovation. Successful speciation in climbers is correlated with the development of specialized climbing strategies such as tendrils, i.e., filiform organs with the ability to twine around other structures through helical growth. Tendrils are derived from a variety of morphological structures, e.g., stems, leaves, and inflorescences, and are found in various plant families. In fact, tendrils are distributed throughout the angiosperm phylogeny, from magnoliids to asterids II, making these structures a great model to study convergent evolution. In this study, we performed a thorough survey of tendrils within angiosperms, focusing on their origin and development. We identified 17 tendril types and analyzed their distribution through the angiosperm phylogeny. Some interesting patterns emerged. For instance, tendrils derived from reproductive structures are exclusively found in the Core Eudicots, except from one monocot species. Fabales and Asterales are the orders with the highest numbers of tendrilling strategies. Tendrils derived from modified leaflets are particularly common among asterids, occurring in Polemoniaceae, Bignoniaceae, and Asteraceae. Although angiosperms have a large number of tendrilled representatives, little is known about their origin and development. This work points out research gaps that should help guide future research on the biology of tendrilled species. Additional research on climbers is particularly important given their increasing abundance resulting from environmental disturbance in the tropics.</p

Lacunas: a web interface to identify plant knowledge gaps to support informed decision-making

Scientists from megadiverse countries, such as Brazil, face huge challenges in gathering and analyzing information about species richness and abundance. In Brazil, speciesLink is an e-infrastructure that offers free and open access to data from more than 300 biological and data collections. SpeciesLink's thematic network, INCT-Virtual Herbarium of Plants and Fungi and the List of Species of the Brazilian Flora, are used as primary data sources to develop Lacunas, an information system with a public web interface that generates detailed reports of the status of plant species occurrence data. Lacunas also integrates information about endemism, conservation status, and collecting efforts over time. Here we describe the motivation and the functionality of this system, showing how it can be useful in detecting under-sampled plant species and geographic areas. We show examples of how knowledge can be extracted from biodiversity primary data using Lacunas. For instance, Lacunas report revealed that 111 angiosperm species (10.3 %), currently considered Data Deficient (DD) in the Official List of Threatened Brazilian Flora, have their distribution well characterized. In addition, the situation of Attalea funifera, a native palm classified as DD, was analyzed in detail, together with other use cases. Information presented in Lacunas reports can thus be used by scientists and policy-makers to help evaluate the status of species occurrence data and prioritize digitization and collecting efforts, as well as some features concerning its conservation status. As Lacunas offers a public online interface, it may also become a valuable tool for helping decision-making processes to become more dynamic and transparent. © 2013 Springer Science+Business Media Dordrecht.Scientists from megadiverse countries, such as Brazil, face huge challenges in gathering and analyzing information about species richness and abundance. In Brazil, speciesLink is an e-infrastructure that offers free and open access to data from more than231109131CNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO381021/2012-2; 573883/2008-4(2013) Atlas of Living Australia, , http://www.ala.org.au/, ALA. Accessed 16 Sept 2013Almeida, J.R.M., Aquino, R.C.M.P., Monteiro, S.N., Tensile mechanical properties, morphological aspects and chemical characterization of piassava (Attalea funifera) fibers (2006) Compos Part A, 37, pp. 1473-1479Anderson, R.P., Lew, D., Peterson, A.T., Evaluating predictive models of species' distributions: criteria for selecting optimal models (2003) Ecol Mod, 162, pp. 211-232Arzberger, P., Schroeder, P., Beaulieu, A., Bowker, G., Casey, K., Laaksonen, L., Moorman, D., Wouters, P., An international framework to promote access to data (2004) Science, 303, pp. 1777-1778Bachman, S., Moat, J., Hill, A.W., de la Torre, J., Scott, B., Supporting Red List threat assessments with GeoCAT: geospatial conservation assessment tool (2011) Zookeys, 150, pp. 117-126(2005) Lista da flora brasileira ameaçada de extinção, , http://www.biodiversitas.org.br/floraBr/, Biodiversitas Foundation. Accessed 20 May 2012Butchart, S.H.M., Bird, J.P., Data Deficient birds on the IUCN Red List: what don't we know and why does it matter? (2010) Biol Conserv, 143, pp. 239-247Costa, C.M.R., Herrmann, G., Martins, C.S., Lins, L.V., Lamas, I.R., (1998) Biodiversidade Em Minas Gerais-Um Atlas Para Sua conservação, , Belo Horizonte: Fundação Biodivesitas(2013) SpeciesLink, , http://splink.cria.org.br/, CRIA. Accessed 20 Feb 2012(2013) SpeciesLink, , http://splink.cria.org.br/, CRIA. Accessed 16 Sept 2013(2013) Biogeografia da Flora do Brasil, , http://biogeo.inct.florabrasil.net/, CRIA. Accessed 23 Feb 2013Cunningham, A.B., Opportunities and constraints on sustainable harvest: plant populations (2001) Applied Ethnobotany: People, Wild Plant Use and Conservation, pp. 144-191. , A. B. Cunningham (Ed.), New York: Earthscan PublicationsDavis, S.D., Heywood, V.H., Herrera-MacBryde, O., Villa-Lobos, J., Hamilton, A.C., (1997) Centres of Plant Diversity: A Guide and Strategy for Their Conservation, , Oxford: Information PressFarber, O., Kadmon, R., Assessment of alternative approaches for bioclimatic modeling with special emphasis on the Mahalanobis distance (2003) Ecol Model, 160, pp. 115-130Forzza, R.C., (2010) Catálogo das Plantas e Fungos do Brasil, , Andrea Jakobsson Estúdio, Rio de Janeiro Botanical Garden, Rio de JaneiroForzza, R.C., Leitman, P.M., Costa, A.F., (2012) Lista de espécies da flora do Brasil, , http://floradobrasil.jbrj.gov.br/2012, Accessed 10 May 2012Geeta, R., Levy, A., Thoch, J.M., Mark, M., Taxonomists and the CBD (2004) Science, 305, pp. 1105-1106Giulietti, A.M., Pirani, J.R., Patterns of geographic distribution of some plant species from the Espinhaço Range, Minas Gerais and Bahia, Brazil (1988) Proceedings of a workshop on neotropical distribution patterns, pp. 39-69. , In: Vanzolini PE, Heyer WR (eds). Academia Brasileira de Ciências, Rio de JaneiroHernandez, P.A., Graham, C.H., Master, L.L., Albert, D.L., The effect of sample size and species characteristics on performance of different species distribution modeling methods (2006) Ecography, 29, pp. 773-785Hirzel, A.H., Hausser, J., Chessel, D., Perrin, N., Ecological-niche factor analysis: how to compute habitat-suitability maps without absence data? (2002) Ecology, 83, pp. 2027-2036(2012) INCT Virtual Herbarium of Plants and Fungi, , http://inct.florabrasil.net, INCT-Virtual Herbarium. Accessed 20 Oct 2013(2011) Guidelines for using the IUCN Red List categories and criteria, , http://www.iucnredlist.org/documents/RedListGuidelines.pdf, IUCN Standards and Petitions SubcommitteeKadmon, R., Farber, O., Danin, A., A systematic analysis of factors affecting the performance of climatic envelope models (2003) Ecol Appl, 13, pp. 853-867Kamino, L.H.Y., Siqueira, M.F., Sánchez-Tapia, A., Stehmann, J.R., Reassessment of the extinction risk of endemic species in the Neotropics: how can modelling tools help us? (2012) Brazil J Nat Conserv, 10, pp. 191-198(2012) Lacunas de conhecimento da flora e dos fungos do Brasil-INCT-Virtual Herbarium, , http://lacunas.inct.florabrasil.net/, Lacunas. Accessed 10 Feb 2013Lastres, H.M.M., Albagli, S., Introdução: Chaves para ao terceiro milênio na era do conhecimento (1999) Informação E globalização Na Era Do Conhecimento, pp. 7-26. , H. M. M. Lastres and S. Albagli (Eds.), Rio de Janeiro: Editora Campus LtdaMaddison, D.R., Guralnick, R., Hill, A., Reysenbach, A.L., McDade, L.A., Ramping up biodiversity discovery via online quantum contributions (2012) Trends Ecol Evol, 27, pp. 72-77Mello-Silva, R., (2012) Velloziaceaein Lista de Espécies da Flora do Brasil, , http://checklist.florabrasil.net/public_20130301/2012/FB000245, Jardim Botânico do Rio de JaneiroMittermeier, R.A., (1997) Megadiversity: Earth's Biologically Wealthiest Nations, , Monterrey: CEMEX(2008) Normative Instruction No 06, from September 23, 2008, , MMA, Brasília: Ministério do Meio AmbienteMuñoz, M.E.S., Giovanni, R., Siqueira, M.F., OpenModeller: a generic approach to species' potential distribution modelling (2011) Geoinformatica, 15, pp. 111-135Myers, N., Mittermeier, R.A., Mittermeier, C.G., da Fonseca, G.A.B., Kent, J., Biodiversity hotspots for conservation priorities (2000) Nature, 403, pp. 853-860Paglia, A.P., Fonseca, G.A.B., Assessing changes in the conservation status of threatened Brazilian vertebrates (2009) Biodivers Conserv, 18, pp. 3563-3577Peterson, A.T., Soberón, J., Pearson, R.G., Anderson, R.P., Martínez-Meyer, E., Nakamura, M., Araújo, M.B., (2011) Ecological Niches and Geographic Distributions, , Princeton: Princeton University PressPhillips, S.J., Anderson, R.P., Shapire, R.E., Maximum entropy modelling of species geographic distributions (2006) Ecol Model, 190, pp. 231-259Porembski, S., Barthlott, W., Granitic and gneissic outcrops (inselbergs) as centers of diversity for desiccation-tolerant vascular plants (2000) Plant Ecol, 151, pp. 19-28Reichman, O.J., Jones, M.B., Schildhauer, M.P., Challenges and opportunities of open data in ecology (2011) Science, 331, pp. 703-705Rivers, M.C., Taylor, L., Brummitt, N.A., Meagher, T.R., Roberts, D.L., Lughadha, E.N., How many herbarium specimens are needed to detect threatened species? (2011) Biol Conserv, 144, pp. 2541-2547Santana, G., Tourism development in coastal areas-Brazil: economic, demand and environmental issues (2003) J Coast Res, 35, pp. 85-93Scarano, F.R., Martinelli, G., Brazilian list of threatened plant species: reconciling scientific uncertainty and political decision-making (2010) Nat Conserv, 8, pp. 13-18Schofield, P.N., Eppig, J., Huala, E., Angelis, M.H., Harvey, M., Davidson, D., Weaver, T., Hancock, J.M., Sustaining the data and bioresource commons (2010) Science, 330, pp. 592-593Schölkopf, B., Platt, J., Shawe-Taylor, J., Smola, A.J., Williamson, R.C., Estimating the support of a high-dimensional distribution (2001) Neural Comput, 13, pp. 1443-1471Sousa-Baena, M.S., Attalea funifera (v1) in Biogeografia da Flora do Brasil (2012) INCT-virtual herbarium of plants and fungi, , http://biogeo.inct.florabrasil.net/proc/200Sousa-Baena, M.S., Astronium fraxinifolium (v1) in Biogeografia da Flora do Brasil (2012) INCT-virtual herbarium of plants and fungi, , http://biogeo.inct.florabrasil.net/proc/200Sousa-Baena, M.S., Garcia, L.C., Peterson, A.T., Completeness of digital accessible knowledge of the plants of Brazil and priorities for survey and inventory (2013) Divers Distrib., , doi: 10. 1111/ddi. 12136Sousa-Baena, M.S., Garcia, L.C., Peterson, A.T., Knowledge behind conservation status decisions: Data basis for 'Data Deficient' Brazilian plant species (2013) Biol Conserv., , doi: 10. 1016/j. biocon. 2013. 06. 034Stockwell, D.R.B., Peterson, A.T., Effects of sample size on accuracy of species distribution models (2002) Ecol Model, 148, pp. 1-13(2007) Access to biological collections data-ABCD, , http://www.tdwg.org/activities/abcd/, TDWG. Biodiversity Information Standards-TDWGVamosi, J., Vamosi, S.M., Extinction risk escalates in the tropics (2008) PLoS ONE, 3, pp. 1-6Voeks, R.A., Extraction and tropical rain forest conservation in eastern Brazil (1996) Tropical Rainforest Research-Current Issues, pp. 477-487. , D. S. Edwards, W. E. Booth, and S. C. Choy (Eds.), Dordrecht: Kluwer AcademicWheeler, Q.D., Raven, P.H., Wilson, E.O., Response GEETA ET AL (2004) Science, 305, p. 1105Wheeler, Q.D., Raven, P.H., Wilson, E.O., Taxonomy: impediment or expedient? (2004) Science, 303, p. 285Wisz, M.S., Hijmans, R.J., Li, J., Peterson, A.T., Graham, C.H., Guisan, A., Effects of sample size on the performance of species distribution models (2008) Divers Distrib, 14, pp. 763-77

Research infrastructure and biodiversity data usage in Brazil.

<p>(A) Distribution of Rede Nacional de Ensino e Pesquisa (RNP) metropolitan networks (December 2014). (B) Distribution of <i>species</i>Link’s data providers (per institution) and amount of records shared (December 2014). (C) <i>species</i>Link data usage (sessions) across Brazil (2014). <i>Image credit</i>: <i>Eduardo G</i>. <i>Baena</i>.</p