Laboratório de Ecologia de Florestas Tropicais

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====== Neotropical Tree Communities database (TreeCo)  ======
{{:projetos:treeco:onlinelogomaker-083014-2224.png?125 |logo}} A project that aims to compile and synthesize the existing knowledge on the structure and diversity of neotropical tree communities and the functional traits of their species. Currently, the project mainly contains information from the forests and shrublands of eastern South America, including the Atlantic Forest, Cerrado, Caatinga and Pantanal domains (//i.e.// extra-Amazonian neotropical domains). It includes surveys of all vegetation types, successional stages and sampling methods. The database is currently in version 4.0. 
[[projetos:treeco:start:full|Read More]]

Follow us!  [[https://twitter.com/treeco_db?ref_src=twsrc%5Etfw|{{:projetos:treeco:twitter.png?35}}]] [[https://www.researchgate.net/project/Neotropical-Tree-Communities-database-TreeCo|{{:projetos:treeco:6a011168a6e300970c01bb09d0ebba970d-500wi.png?35|}}]] 


**__IMPORTANT NOTE__: This project currently has no funding and it is kept on the free time of its coordinators. Thus, replies to data requests may be delayed and priority is given to projects that can improve the quality of the database.**

=== People ===
  *Lead researchers: [[http://ecologia.ib.usp.br/let/doku.php?id=lima:start|Renato A. Ferreira de Lima]], [[http://labtrop.ib.usp.br/doku.php?id=equipe:adalardo:start|Alexandre Adalardo]] & [[http://ecologia.ib.usp.br/let/doku.php?id=engl:prado:start|Paulo Inácio Prado]] (USP)
  *Associate researchers: [[https://www.researchgate.net/profile/Luiz_Magnago|Luiz F.S. Magnago]] (UFSB) & [[https://www.ufrgs.br/levcamp/index.php/10-equipe/pesquisadores-associados/50-sandra-cristina-mueller|Sandra C. Müller]] (UFRGS)
  *Labs involved: [[http://ecologia.ib.usp.br/let/doku.php?id=let|LET/IB/USP]], [[http://labtrop.ib.usp.br/|LABTROP/IB/USP]] & [[https://www.ufrgs.br/leveg/grupo/|LEVEG/UFRGS]]

=== The database ===
So far, TreeCo is composed by two main bodies of information:
  * A cloud service used to store and share digital copies of the studies and documents related to TreeCo. 
  * A series of tables storing information on:
    * bibliographic references of quantitative tree community surveys
    * study methods: sampling methods, effort, ...
    * forest description: coordinates, fragment size, forest type, forest succession, ...
    * site environment: altitude, soil conditions, rainfall, temperature, ...
    * species abundances data: counts of trees and total basal area per species per site
    * species traits: wood density, maximum height, leaf area, seed/fruit size, among others, obtained mainly from the literature but also from (un)published field measurements 

=== Database overview - July 2020 ===

== Studies and inventories data ==
  * Number of quantitative plant community studies retrieved: 1790  
  * Number of inventories retrieved: 4466
    * Atlantic Forest: 3143
    * Cerrado: 852
    * Caatinga: 309
    * Pantanal: 113 
    * Amazon: 25
    * Pampa: 24

== Species abundance data == 
  * Number of inventories entered: 1982 
  * Number of abundance records: 139,761  
  * Overall sampling effort: 1735 hectares and 1,992,721 trees 
  * Number of families, genera and valid species: 139, 771 and 4006

== Species functional trait data (all sources) == 
  * Number of traits with information: 74
  * Overall number of trait records: 110,220 
  * Traits with higher species coverage within Treeco abundance data (~3500 spp):
    * Wood density: 91% (46% and 45% at species and genus level)
    * Maximum height: 92%
    * Leaf area: 56%
    * Leaf type: 63%
    * Leaf hairness: 51%
    * Leaf rigidness: 48%   
    * Seed size: 64%
    * Dispersal syndrome: 69%
    * Ecological groups: 53%
  

{{ :projetos:treeco:all_NABs_AGB_v1.jpg |}}
Figure 1. The current geographical extent covered by TreeCo (top left), the distribution of all the quantitative vegetation inventories stored in the database (top right), the inventories with species abundance data already entered in the database (bottom left), and the inventories with information on Tree Above-ground Biomass (AGB), excluding data from state forest inventories (bottom right). Thick lines present the official limits of Latin America, while the grey lines define the Brazilian states. The number of inventories with geographical coordinates (N) is given for each panel. 

  
=== Data sharing and collaboration ===

TreeCo is available upon reasonable request from researches interested in using the database for scientific purposes. We share all the data available as long as there is no overlap with ongoing projects, and if references and funding sources are properly cited. We are also more prone to share TreeCo data with researchers willing to give their input on the quantity/quality of the database than only using it. Young researchers willing to use the database in their grad or post-doc projects are especially welcome. 

TreeCo coordinators are also open for collaboration on the research topics listed below ('Future research topics'). We are glad to provide lists of references and to share pdf copies of any study we may have. The use of other information stored in the database, such as the species composition, abundance and trait information, is also possible. But in this case, it may imply the participation of the project coordinators in the investigation and related publications.

=== Ongoing projects ===

  * Lima, RAF et. al. The threat status of endemic Atlantic Forest trees. Marie Skłodowska-Curie Actions/European Commission (Project: 795114 H2020-MSCA-RISE-2018, acronym THREAT).
  * Lima, RAF et. al. Fragmentation effects on the commonness and rarity of Atlantic Forest trees. Naturalis Biodiversity Center.
  * Pyles, M.V. Drivers of ecosystem services and functional resilience as guides for the conservation and restoration of human-modified landscapes in the Atlantic Forest. PhD project, Federal University of Lavras.
  * Marjakangas, E.‐L. et al. Co-occurrences of tropical trees: disentangling abiotic and biotic forces. PhD project.
  * Lima, RAF & Prado, PI [[http://www.bv.fapesp.br/pt/bolsas/145695/o-papel-da-diversidade-funcional-na-estruturacao-de-comunidades-arboreas-tropicais-uma-abordagem-bas/|O papel da diversidade funcional na estruturação de comunidades arbóreas tropicais]].
  * Klipel, J et al. Climatic control of tree species distributions in the Atlantic Forest. MSc. project. Universidade Federal do Rio Grande do Sul.
  * Pitta, G, Prado, PI & Lima, RAF. The carbon balance in the Atlantic forest. A case study for SP-Brazil. MSc. project. Universidade de São Paulo (USP). 
  * Mori, DP, Lima, RAF & Prado, PI. O papel da fragmentação nos processos que estruturam comunidades arbóreas. MSc. project. Universidade de São Paulo (USP).

=== Future research topics ===
The main scientific questions we want to answer using TreeCo are related to the following topics:   
  * Environment effects on the parameters of the species abundance distribution (SAD)
  * Relationships between SAD built using counts of individuals and biomass
  * Environment and distance effects on beta-diversity
  * Environmental filtering on species traits (trait variation)
  * Trade-offs in functional traits of Atlantic Forest species
  * Phylogenetic structure along environmental gradients
  * Abundance-range size relationships and concept of rarity
  * Trait effect on species niche size/breath or geographical distribution
  * Indicator species of the Neotropical Forest subtypes
  * Differences and similarities in the structure and diversity of Neotropical Forest subtypes


=== Publications using TreeCo database===
  * Marjakangas, E.‐L. et al. 2019. [[https://doi.org/10.1111/ddi.13010|Fragmented tropical forests lose mutualistic plant–animal interactions]]. Diversity and Distributions 00: 1– 15. 
  * Lima, R.A.F. et al. 2018. [[http://www.scielo.br/scielo.php?pid=S1415-47572018000400661&script=sci_arttext| Can plant DNA barcoding be implemented in species-rich tropical regions? A perspective from São Paulo State, Brazil.]] Genetics and Molecular Biology, 41(3), 661-670.
  * Marjakangas, E.-L. et al. 2018. [[https://doi.org/10.1098/rstb.2017.0435|Estimating interaction credit for trophic rewilding in tropical forests]]. Philosophical Transactions of the Royal Society B: Biological Sciences 373(1761): 20170435.
  * Brancalion, P.H.S. et al. 2018. [[https://onlinelibrary.wiley.com/doi/abs/10.1111/conl.12454| Maximizing biodiversity conservation and carbon stocking in restored tropical forests.]] Conservation Letters 11(4): e12454.
  * Sobral-Souza, T. et al. 2017. [[https://www.sciencedirect.com/science/article/pii/S2530064417300731#ack0005| Rewilding defaunated Atlantic Forests with tortoises to restore lost seed dispersal functions.]] Perspectives in Ecology and Conservation, 15(4): 300-307.
  * Bello, C. et al. 2015. [[http://advances.sciencemag.org/content/advances/1/11/e1501105| Defaunation affects carbon storage in tropical forests.]] Science Advances, 1(11): e1501105.
  * Lima, RAF et al. 2015. [[http://dx.doi.org/10.1007/s10531-015-0953-1| How much do we know about the endangered Atlantic Forest? Reviewing nearly 70 years of information on tree community surveys.]] Biodiversity and Conservation, 24(9): 2135-2148. {{:projetos:treeco:accepted_manuscript.pdf|click here for the final draft}}
  

=== Acknowledgments ===

We are grateful for the hundreds of researchers, students and technicians that performed fieldwork, species identification and data analysis that resulted in the published and unpublished inventories that are included in TreeCo. 

We also thank all people that have directly contributed to surveys and species data compilation, namely Gregory Pitta, Danilo Mori, Luiz Magnago, Markus Gastauer, Carolina Bello, Renato Toledo, Natália Targhetta and Geison Castro.

We are also greatly in debt with the researchers that provided their (un)published tree data: André Amorim, Andréia A. Rezende, Bruno R. Ribeiro, João A. Meira-Neto, João L.F. Batista, Marcelo Pansonato, Márcia C.M. Marques, Maria T.Z. Toniato, Mariana C. Pardgurschi, Mario J. Marques-Azevedo, Markus Gastauer, Ricardo R. Rodrigues, Robson L. Capretz and Victor P. Zwiener.



=== Funding ===
 
TreeCo database was funded by the São Paulo Research Foundation (FAPESP) grant 2013/08722-5 and by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 795114.

The forest inventories compiled by TreeCo were funded by many different agencies, such as the Coordination for the Improvement of Higher Education Personnel (CAPES), by the National Council for Scientific and Technological Development (CNPQ) and by the many state-specific research funding agencies, such as FAPESP, FAPEMIG, FAPESC, FAPERJ, etc. These agencies funded the scholarships, fieldwork and/or equipment used to conduct these inventories. 

We acknowledge some specific funding that resulted in the (un)published data included in TreeCo: São Paulo Research Foundation (FAPESP), grants 1999/08515-0, 1999/09635-0 and 2004/04820-3. Santa Catarina Research Foundation (FAPESC), grant 2017TR1922. Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), grant 312075/2013-8 and 484747/2011-8. US Department of Energy grant DE-FC26-01NT411151 (US Department of Energy).

If you think there is a major funding that should be added to this list, please e-mail the funding agency and grant number to raflima@usp.br.

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Laboratório de Ecologia de Florestas Tropicais

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