GEMTraits: A database and R package for accessing and analyzing plant functional traits from the Global Ecosystems Monitoring Network

Shenkin, A; Bentley, L; Asner, G; Diaz, S; Enquist, B; Malhi, Y; Girardin, C

Documentation:: This dataset contains a POSTGRESQL database with demographic and functional trait data on trees from 10 1-hectare permanent plots across an elevation transect from 3500m to 200m in SE Peru. They comprise part of the Global Ecosystems Monitoring Network (GEM; http://gem.tropicalforests.ox.ac.uk) and are operated by the Andes Biodiversity Ecosystems Research Group (ABERG, http://www.andesconservation.org). Further site details are described by Malhi (2017, in prep). Functional trait data includes leaf chemistry, leaf morphology, leaf venation, branch architecture, and 3D crown architecture measurements. Both sun and shade leaves were sampled where available. Microenvironmental data includes vertical light profiles from crown top to forest floor in a subset of trees, light availability at each measured branch, and the location of sampled branches within crowns. An R package ("gemtraits") for data access and analysis is also provided. AS and LPB contributed equally to the database construction.

Although this data is under embargo, any parties that wish to request access to it should contact the depositor (Dr Alexander Shenkin, Environmental Change Institute, Oxford University Centre for the Environment).

Version:: version 1

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APA Style

Shenkin, A., Bentley, L., Asner, G., Diaz, S., Enquist, B., Malhi, Y., & Girardin, C. (2017). GEMTraits: A database and R package for accessing and analyzing plant functional traits from the Global Ecosystems Monitoring Network. University of Oxford.

MLA Style

Shenkin, A., et al. GEMTraits: A Database and R Package for Accessing and Analyzing Plant Functional Traits from the Global Ecosystems Monitoring Network. University of Oxford, 2017.

Chicago Style

Shenkin, A, L Bentley, G Asner, S Diaz, B Enquist, Y Malhi, and C Girardin. 2017. “GEMTraits: A Database and R Package for Accessing and Analyzing Plant Functional Traits from the Global Ecosystems Monitoring Network.” University of Oxford.
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Authors/Creators

+ Shenkin, A More by this author/creator

Institution:: University of Oxford
Division:: SSD
Department:: SOGE
Role:: Project member, Data curator, Creator
ORCID:: 0000-0003-2358-9367

+ Bentley, L More by this author/creator

Institution:: Sonoma State University
Role:: Project member, Data curator, Creator

+ Asner, G More by this author/creator

Institution:: Carnegie Institution for Science
Role:: Project member, Principal Investigator (PI), Data curator, Creator

+ Diaz, S More by this author/creator

Institution:: IMBIV (CONICET - UNC) and FCEFyN, Universidad Nacional de Córdoba
Role:: Principal Investigator (PI), Project member, Data curator, Creator

+ Enquist, B More by this author/creator

Institution:: University of Arizona
Role:: Principal Investigator (PI), Project member, Data curator, Creator

More authors...

Contributors

+ Silman, M

Institution:: Wake Forest University
Role:: Contributor

+ Wu, M

Institution:: Department of Earth Sciences, University of Southern California, 3651 Trousdale Pkwy, Los Angeles, CA 90089, USA
Role:: Contributor

+ Boyle, B

Institution:: University of Arizona
Role:: Contributor

+ Farfan-Rios, W

Institution:: Wake Forest University
Role:: Contributor

+ Feakins, S

Institution:: Department of Earth Sciences, University of Southern California, 3651 Trousdale Pkwy, Los Angeles, CA 90089, USA
Role:: Contributor

More contributors...

+ U.S. National Science Foundation More from this funder

Funder identifier:: https://ror.org/021nxhr62
Funding agency for:: Asner, G
Grant:: DEB-1146206

+ Jackson Foundation More from this funder

Funder identifier:: https://ror.org/00jkq3860
Funding agency for:: Malhi, Y

+ European Research Council More from this funder

Funder identifier:: https://ror.org/0472cxd90
Grant:: 321131

+ Natural Environment Research Council More from this funder

Funder identifier:: https://ror.org/02b5d8509
Grant:: NE/D01025X/1; NE/D014174/1

+ John D. and Catherine T. MacArthur Foundation More from this funder

Funder identifier:: https://ror.org/00dxczh48
Funding agency for:: Asner, G

More funders...

Publisher:: University of Oxford
Publication date:: 2017
Spatial coverage:: SE Peru
Version number:: version 1
DOI:: 10.5287/bodleian:v0BD04N7o
Data collected:: 1983-08-09 - 2013-10-28

Language:: English
Keywords:: traits

carbon cycle

Peru
Subjects:: Cloud forests

Rain forests
Pubs id:: 1480869
UUID:: uuid:4101e249-3cf5-443f-9c29-9204604c667b
Local pid:: pubs:1480869
Deposit date:: 2017-03-28

Related item:: Altitude effect on leaf wax carbon isotopic composition in humid tropical forests
Description:: The carbon isotopic composition of plant leaf wax biomarkers is commonly used to reconstruct paleoenvironmental conditions. Adding to the limited calibration information available for modern tropical forests, we analyzed plant leaf and leaf wax carbon isotopic compositions in forest canopy trees across a highly biodiverse, 3.3 km elevation gradient on the eastern flank of the Andes Mountains. We sampled the dominant tree species and assessed their relative abundance in each tree community. In total, 405 sunlit canopy leaves were sampled across 129 species and nine forest plots along the elevation profile for bulk leaf and leaf wax n-alkane (C27–C33) concentration and carbon isotopic analyses (δ13C); a subset (76 individuals, 29 species, five forest plots) were additionally analyzed for n-alkanoic acid (C22–C32) concentrations and δ13C. δ13C values display trends of +0.87 ± 0.16‰ km−1 (95% CI, r2 = 0.96, p < 0.01) for bulk leaves and +1.45 ± 0.33‰ km−1 (95% CI, r2 = 0.94, p < 0.01) for C29n-alkane, the dominant chain length. These carbon isotopic gradients are defined in multi-species sample sets and corroborated in a widespread genus and several families, suggesting the biochemical response to environment is robust to taxonomic turnover. We calculate fractionations and compare to adiabatic gradients, environmental variables, leaf wax n-alkane concentrations, and sun/shade position to assess factors influencing foliar chemical response. For the 4 km forested elevation range of the Andes, 4–6‰ higher δ13C values are expected for upland versus lowland C3 plant bulk leaves and their n-alkyl lipids, and we expect this pattern to be a systematic feature of very wet tropical montane environments. This elevation dependency of δ13C values should inform interpretations of sedimentary archives, as 13C-enriched values may derive from C4 grasses, petrogenic inputs or upland C3 plants. Finally, we outline the potential for leaf wax carbon isotopes to trace biomarker sourcing within catchments and for paleoaltimetry.
Related item:: Production of leaf wax n-alkanes across a tropical forest elevation transect
Description:: Waxy compounds form the boundary layer of the living leaf and contribute biomarkers to soils, and lake and marine sediments. Cataloging the variation in leaf wax traits between species and across environmental gradients may contribute to the understanding of plant functional processes in modern ecosystems, as well as to calibration efforts supporting reconstruction of past ecosystems and environments from the sedimentary archives of leaf wax biomarkers. Towards these goals, we have surveyed the distributions of leaf wax n-alkanes in trees from the lowland tropical rainforest (TR) and montane cloud forest (TMCF) of Perú. Molecular abundances were quantified via gas chromatography flame ionization detection (GC-FID) for 632 individuals, 152 species, 99 genera and 51 families across 9 forest plots spanning 0.2–3.6 km elevation. We found the expected abundance distributions; for example, they were dominated by long chain, odd numbered n-alkanes, especially C29 and C31. New observations included a tendency to increasing total alkane concentration at higher elevation. We propose that the well known leaf economic strategy to increase leaf mass per unit area with elevation, provides a theoretical basis for understanding the increase in leaf wax n-alkane abundance with elevation: we infer an increased investment in foliar defense associated with increased leaf lifespan and in response to environmental pressures including cloud immersion and declining temperature. Furthermore, we combined measurements of n-alkane concentration with estimates of forest productivity to provide new ways to quantify ecosystem-scale forest alkane productivity. We introduce a new concept of n-alkane net primary productivity (NPPalk; the product of alkane concentration and leaf NPP) and find that alkane productivity estimates range from 300 to 5000 g C/ha/yr, associated with ecological and environmental changes across the elevation profile.
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Related item:: Predicting trait-environment relationships for venation networks along an Andes-Amazon elevation gradient
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Related item:: Examining variation in the leaf mass per area of dominant species across two contrasting tropical gradients in light of community assembly
Description:: Understanding variation in key functional traits across gradients in high diversity systems and the ecology of community changes along gradients in these systems is crucial in light of conservation and climate change. We examined inter- and intraspecific variation in leaf mass per area (LMA) of sun and shade leaves along a 3330-m elevation gradient in Peru, and in sun leaves across a forest–savanna vegetation gradient in Brazil. We also compared LMA variance ratios (T-statistics metrics) to null models to explore internal (i.e., abiotic) and environmental filtering on community structure along the gradients. Community-weighted LMA increased with decreasing forest cover in Brazil, likely due to increased light availability and water stress, and increased with elevation in Peru, consistent with the leaf economic spectrum strategy expected in colder, less productive environments. A very high species turnover was observed along both environmental gradients, and consequently, the first source of variation in LMA was species turnover. Variation in LMA at the genus or family levels was greater in Peru than in Brazil. Using dominant trees to examine possible filters on community assembly, we found that in Brazil, internal filtering was strongest in the forest, while environmental filtering was observed in the dry savanna. In Peru, internal filtering was observed along 80% of the gradient, perhaps due to variation in taxa or interspecific competition. Environmental filtering was observed at cloud zone edges and in lowlands, possibly due to water and nutrient availability, respectively. These results related to variation in LMA indicate that biodiversity in species rich tropical assemblages may be structured by differential niche-based processes. In the future, specific mechanisms generating these patterns of variation in leaf functional traits across tropical environmental gradients should be explored.
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Notes:: Although this data is under embargo, any parties that wish to request access to it should contact the depositor (Dr Alexander Shenkin, Environmental Change Institute, Oxford University Centre for the Environment).

Licence:: Terms and Conditions of Use for Oxford University Research Archive

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GEMTraits: A database and R package for accessing and analyzing plant functional traits from the Global Ecosystems Monitoring Network

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