Filling the gap in functional trait databases: Use of ecological hypotheses to replace missing data

Ecology and Evolution

Volumn 4, Issue 7, 2014, Pages 944-958

  Taugourdeau, Simon ^a,b,c   Villerd, Jean ^a,b   Plantureux, Sylvain ^a,b   Huguenin Elie, Olivier ^c   Amiaud, Bernard ^a,d  

^a UNIVERSITÉ DE LORRAINE   (France)

^b UNIVERSITÉ DE LORRAINE   (France)

^c AGROSCOPE RECKENHOLZ TÄNIKON RESEARCH STATION ART   (Switzerland)

^d LERFoB   (France)

Author keywords

Functional diversity; Imputation methods; LEDA database; Missing data; Plant functional trait

Indexed keywords

EID: 84897953396     PISSN: None     EISSN: 20457758     Source Type: Journal    
DOI: 10.1002/ece3.989     Document Type: Article

References (50)

1. Ackerly, D. D., and W. K. Cornwell. 2007. A trait-based approach to community assembly: partitioning of species trait values into within- and among-community components. Ecol. Lett. 10:135-145.
2. Albert, C. H., W. Thuiller, N. G. Yoccoz, R. Douzet, S. Aubert, and S. Lavorel. 2010a. A multi-trait approach reveals the structure and the relative importance of intra- vs. interspecific variability in plant traits. Funct. Ecol. 24:1192-1201.
3. Albert, C. H., W. Thuiller, N. G. Yoccoz, A. Soudant, F. Boucher, P. Saccone, et al. 2010b. Intraspecific functional variability: extent, structure and sources of variation. J. Ecol. 98:604.
4. Azur, M. J., E. A. Stuart, C. Frangakis, and P. J. Leaf. 2011. Multiple Imputation by Chained Equations: what is it and how does it work? Int. J. Methods Psychiatr. Res. 20:40-49.
5. de Bello, F., J. A. N. Leps, and M.-T. Sebastian. 2005. Predictive value of plant traits to grazing along a climatic gradient in the Mediterranean. J. Appl. Ecol. 42:824-833.
6. de Bello, F., S. Lavorel, S. Diaz, R. Harrington, J. H. C. Cornelissen, R. D. Bardgett, et al. 2010. Towards an assessment of multiple ecosystem processes and services via functional traits. Biodivers. Conserv. 19:2873-2893.
7. Boeken, B., and S. Moshe. 2006. Linking community and ecosystem processes: the role of minor species. Ecosystems 9:119-127.
8. Cornelissen, J. H. C., S. Lavorel, E. Garnier, S. Diaz, N. Buchmann, D. E. Gurvich, et al. 2003. A handbook of protocols for standardised and easy measurement of plant functional traits worldwide. Aust. J. Bot. 51:335-380.
9. Diaz, S., J. G. Hodgson, K. Thompson, M. Cabido, J. H. C. Cornelissen, A. Jalili, et al. 2004. The plant traits that drive ecosystems: evidence from three continents. J. Veg. Sci. 15:295-304.
10. Fried, G., E. Kazakou, and S. Gaba. 2012. Trajectories of weed communities explained by traits associated with species' response to management practices. Agric. Ecosyst. Environ. 158:147-155.
11. Garnier, E., J. Cortez, G. Billas, M. L. Navas, C. Roumet, M. Debussche, et al. 2004. Plant functional markers capture ecosystem properties during secondary succession. Ecology 85:2630-2637.
12. Gower, J. C. 1971. A general coefficient of similarity and some of its properties. Biometrics 27:857-871.
13. Gunton, M. G., S. Petit, and S. Gaba. 2011. Functional traits relating arable weed communities to crop characteristics. J. Veg. Sci. 22:541-550.
14. Hyndman, R. J., and A. B. Koehler. 2006. Another look at measures of forecast accuracy. Int. J. Forecast. 22:678-688.
15. Kattge, J., S. Diaz, S. Lavorel, C. Prentice, P. Leadley, G. Bonisch, et al. 2011. TRY - a global database of plant traits. Glob. Change Biol. 17:2905-2935.
16. Kleyer, M., R. M. Bekker, I. C. Knevel, J. P. Bakker, K. Thompson, M. Sonnenschein, et al. 2008. The LEDA Traitbase: a database of life-history traits of the Northwest European flora. J. Ecol. 96:1266-1274.
17. Klumpp, K., and J. F. Soussana. 2009. Using functional traits to predict grassland ecosystem change: a mathematical test of the response-and-effect trait approach. Glob. Change Biol. 15:2921-2934.
18. Lin, B. B., D. F. B. Flynn, D. E. Bunker, M. Uriarte, and S. Naeem. 2011. The effect of agricultural diversity and crop choice on functional capacity change in grassland conversions. J. Appl. Ecol. 48:609-618.
19. Louault, F., V. D. Pillar, J. Aufrere, E. Garnier, and J. F. Soussana. 2005. Plant traits and functional types in response to reduced disturbance in a semi-natural grassland. J. Veg. Sci. 16:151-160.
20. Mason, N. W. H., D. Mouillot, W. G. Lee, and J. B. Wilson. 2005. Functional richness, functional evenness and functional divergence: the primary components of functional diversity. Oikos 111:112-118.
21. Michaud, A., S. Plantureux, B. Amiaud, P. Carrère, P. Cruz, M. Duru, et al. 2012. Identification of the environmental factors which drive the botanical and functional composition of permanent grasslands. J. Agric. Sci. 150:219-236.
22. Mokany, K., J. Ash, and S. Roxburgh. 2008. Functional identity is more important than diversity in influencing ecosystem processes in a temperate native grassland. J. Ecol. 96:884-893.
23. Mouchet, M., F. Guilhaumon, S. Villéger, N. W. H. Mason, J.-A. Tomasini, and D. Mouillot. 2008. Towards a consensus for calculating dendrogram-based functional diversity indices. Oikos 117:794-800.
24. Mouchet, M. A., S. Villeger, N. W. H. Mason, and D. Mouillot. 2010. Functional diversity measures: an overview of their redundancy and their ability to discriminate community assembly rules. Funct. Ecol. 24:867-876.
25. Mouillot, D., S. Villéger, M. Scherer-Lorenzen, and N. W. H. Mason. 2011. Functional Structure of Biological Communities Predicts Ecosystem Multifunctionality. PLoS ONE 6:e17476.
26. Nakagawa, S., and R. P. Freckleton. 2008. Missing inaction: the danger of ignoring missing data. Trends Ecol. Evol. 11:592-596.
27. Ordoñez, J. C., P. M. van Bodegom, J.-P. M. Witte, I. J. Wright, P. B. Reich, and R. Aerts. 2009. A global study of relationships between leaf traits, climate and soil measures of nutrient fertility. Glob. Ecol. Biogeogr. 18:137-149.
28. Pakeman, R., and H. Quested. 2007. Sampling plant functional traits: what proportion of the species need to be measured? Appl. Veg. Sci. 10:91-96.
29. Pérez-Harguindeguy, N., S. Díaz, E. Garnier, S. Lavorel, H. Poorter, P. Jaureguiberry, et al. 2013. New handbook for standardised measurement of plant functional traits worldwide. Aust. J. Bot. 61:167-234.
30. Petchey, O. L., and K. J. Gaston. 2002. Functional diversity (FD), species richness and community composition. Ecol. Lett. 5:402-411.
31. Petchey, O. L., and K. J. Gaston. 2006. Functional diversity: back to basics and looking forward. Ecol. Lett. 9:741-758.
32. Peter, M., P. J. Edwards, P. Jeanneret, D. Kampmann, and A. Lüscher. 2008a. Changes over three decades in the floristic composition of fertile permanent grasslands in the Swiss Alps. Agric. Ecosyst. Environ. 125:204-212.
33. Peter, M., A. Gigon, P. J. Edwards, and A. Lüscher. 2008b. Changes over three decades in the floristic composition of nutrient-poor grasslands in the Swiss Alps. Biodivers. Conserv. 18:547-567.
34. Plantureux, S., and G. Thorion. 2005. Combined prediction of forage production and biodiversity of permanent pastures in Vosges Mountains (France). Pp. 221-229 Conference of the FAO-CIHEAM Sub-Network of Mountain pasture "quality production and quality of the environment in the mountain pastures of an enlarged Europe". Udine, Italy.
35. R Development Core Team. 2013. R : A language and Environment for Statistical Computing. R foundation for Statistical Computing, Vienna, Austria. Available at: http://www.R-project.org.
36. Rao, C. R. 1982. Diversity and dissimilarity coefficients - a unified approach. Theor. Popul. Biol. 21:24-43.
37. Rubin, D. B. 1996. Multiple imputation after 18+ years. J. Am. Stat. Assoc. 91:473-489.
38. Schafer, J. L., and J. W. Graham. 2002. Missing Data: our view of the state of the art. Psychol. Methods 7:147-177.
39. Schleuter, D., M. Daufresne, F. Massol, and C. Argillier. 2010. A user's guide to functional diversity indices. Ecol. Monogr. 80:469-484.
40. Shan, H., J. Kattge, P. B. Reich, A. Banerjee, F. Schordt, and M. Reichstein. 2012. Gap Filling in the Plant Kingdom-Trait Prediction Using Hierarchical Probabilistic Matrix Factorization. 29 th International Conferenceon Machine Learning. Edinburgh, U.K.
41. Siegel, S., and N. J. Castellan. 1988. Non parametric statistics for the behavioural sciences. MCGraw-Hill, New York, NY.
42. Spiegelberger, T., F. Gillet, B. Amiaud, A. Thébault, P. Mariotte, and A. Buttler. 2012. How do plant community ecologists consider the complementarity of observational, experimental and theoretical modelling approaches? Plant Ecol. Evol. 145:4-12.
43. Van Buuren, S. 2007. Multiple imputation of discrete and continuous data by fully conditional specification. Stat. Methods Med. Res. 16:219-242.
44. Van Buuren, S., and Groothuis-Oudshoorn K. 2011. Mice: multivariate imputation by chained equations in R. J. Stat. Softw. 45:1-67.
45. Van Buuren, S., J. P. L. Brands, C. G. M. Groothuis-Oudshoorn, and D. B. Rubin. 2006. Fully conditional specification in multivariate imputation. J. Stat. Comput. Simul. 76:1049-1064.
46. Villeger, S., N. W. H. Mason, and D. Mouillot. 2008. New multidimensional functional diversity indices for a multifaceted framework in functional ecology. Ecology 89:2290-2301.
47. Walker, B., A. Kinzig, and J. Langridge. 1999. Plant attribute diversity, resilience, and ecosystem function: the nature and significance of dominant and minor species. Ecosystems 2:95-113.
48. Westoby, M., D. S. Falster, A. T. Moles, P. A. Vesk, and I. J. Wright. 2002. PLANT ECOLOGICAL STRATEGIES: some leading dimensions of variation between species. Annu. Rev. Ecol. Syst. 33:125-159.
49. Wright, I. J., P. B. Reich, M. Westoby, D. D. Ackerly, Z. Baruch, F. Bongers, et al. 2004. The worldwide leaf economics spectrum. Nature 428:821-827.
50. Wright, J. P., S. Naeem, A. Hector, C. Lehman, P. B. Reich, B. Schmid, et al. 2006. Conventional functional classification schemes underestimate the relationship with ecosystem functioning. Ecol. Lett. 9:111-120.