Using phylogenetic information to impute missing functional trait values in ecological databases

Bastazini, 2017, Untangling the tangled bank: a novel method for partitioning the effects of phylogenies and traits on ecological networks, Evol. Biol., 44, 312, 10.1007/s11692-017-9409-8 Bastazini, 2019, Loss of generalist plant species and functional diversity decreases the robustness of a seed dispersal network, Environ. Conserv., 46, 52, 10.1017/S0376892918000334 Blomberg, 2003, Testing for phylogenetic signal in comparative data: behavioral traits are more labile, Evolution (N. Y.), 57, 717 Breiman, 2001, Random forests, Mach. Learn., 45, 5, 10.1023/A:1010933404324 Bruggeman, 2009, PhyloPars: estimation of missing parameter values using phylogeny, Nucleic Acids Res., 37, 179, 10.1093/nar/gkp370 Cardillo, 2005, Evolution: multiple causes of high extinction risk in large mammal species, Science (80-.), 309, 1239, 10.1126/science.1116030 Cardillo, 2008, The predictability of extinction: biological and external correlates of decline in mammals, Proc. R. Soc. B Biol. Sci., 275, 1441, 10.1098/rspb.2008.0179 Catford, 2019, Traits linked with species invasiveness and community invasibility vary with time, stage and indicator of invasion in a long-term grassland experiment, Ecol. Lett., 22, 593, 10.1111/ele.13220 Céréghino, 2018, Constraints on the functional trait space of aquatic invertebrates in bromeliads, Funct. Ecol., 32, 2435, 10.1111/1365-2435.13141 Davies, 2012, Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism, Ecology, 93, 242, 10.1890/11-1360.1 de Bello, 2010, The partitioning of diversity: showing Theseus a way out of the labyrinth, J. Veg. Sci., 21, 992, 10.1111/j.1654-1103.2010.01195.x de Bello, 2017, Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly, Methods Ecol. Evol., 8, 1200, 10.1111/2041-210X.12735 De’ath, 2000, Classification and regression trees: a powerful yet simple technique for ecological data analysis, Ecology, 81, 3178, 10.1890/0012-9658(2000)081[3178:CARTAP]2.0.CO;2 Debastiani, 2017, Evolutionary models and phylogenetic signal assessment via mantel test, Evol. Biol., 44, 135, 10.1007/s11692-016-9396-1 Díaz, 2016, The global spectrum of plant form and function, Nature, 529, 167, 10.1038/nature16489 Diniz-Filho, 1998, An eigenvector method for estimating phylogenetic inertia, Evolution (N. Y)., 52, 1247 Diniz-Filho, 2012, On the selection of phylogenetic eigenvectors for ecological analyses, Ecography (Cop.), 35, 239, 10.1111/j.1600-0587.2011.06949.x Felsenstein, 1985, Phylogenies and the comparative method, Am. Nat., 125, 1, 10.1086/284325 Fournier, 2019, Predicting future invaders and future invasions, Proc. Natl. Acad. Sci. U. S. A., 116, 7905, 10.1073/pnas.1803456116 Freckleton, 2006, Detecting non-brownian trait evolution in adaptive radiations, PLoS Biol., 4, 2104, 10.1371/journal.pbio.0040373 Glasser, 1964, Linear regression analysis with missing observations among the independent variables, J. Am. Stat. Assoc., 59, 834, 10.1080/01621459.1964.10480730 Goberna, 2016, Predicting microbial traits with phylogenies, ISME J., 10, 959, 10.1038/ismej.2015.171 Grafen, 1989, The phylogenetic regression, Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci., 326, 119 Guénard, 2013, Phylogenetic eigenvector maps: a framework to model and predict species traits, Methods Ecol. Evol., 4, 1120, 10.1111/2041-210X.12111 Harmon, 2009 Harmon, 2008, GEIGER: investigating evolutionary radiations, Bioinformatics, 24, 129, 10.1093/bioinformatics/btm538 Hastie, 2009 James, 2013, 10.1007/978-1-4614-7138-7 Johnson, 2007, An emerging synthesis between community ecology and evolutionary biology, Trends Ecol. Evol., 22, 250, 10.1016/j.tree.2007.01.014 Johnson, 2021, Handling missing values in trait data, Glob. Ecol. Biogeogr., 30, 51, 10.1111/geb.13185 Kim, 2018, Transcending data gaps: a framework to reduce inferential errors in ecological analyses, Ecol. Lett., 21, 1200, 10.1111/ele.13089 Laliberté, 2010, A distance-based framework for measuring functional diversity from multiple traits, Ecology, 91, 299, 10.1890/08-2244.1 Lefcheck, 2015, Choosing and using multiple traits in functional diversity research, Environ. Conserv., 42, 104, 10.1017/S0376892914000307 Legendre, 2012 Liaw, 2002, Classification and regression by randomForest, R News, 2, 18 Májeková, 2016, Evaluating functional diversity: missing trait data and the importance of species abundance structure and data transformation, PLoS One, 11, 10.1371/journal.pone.0149270 McGill, 2006, Rebuilding community ecology from functional traits, Trends Ecol. Evol., 21, 178, 10.1016/j.tree.2006.02.002 Molina-Venegas, 2017, Revisiting phylogenetic signal; strong or negligible impacts of polytomies and branch length information?, BMC Evol. Biol., 17, 1 Molina-Venegas, 2018, Assessing among-lineage variability in phylogenetic imputation of functional trait datasets, Ecography (Cop.), 41, 1740, 10.1111/ecog.03480 Naeem, 2003, Disentangling biodiversity effects on ecosystem functioning: deriving solutions to a seemingly insurmountable problem, Ecol. Lett., 6, 567, 10.1046/j.1461-0248.2003.00471.x Nakagawa, 2008, Missing inaction: the dangers of ignoring missing data, Trends Ecol. Evol., 23, 592, 10.1016/j.tree.2008.06.014 Oba, 2003, A Bayesian missing value estimation method for gene expression profile data, Bioinformatics, 19, 2088, 10.1093/bioinformatics/btg287 Pagel, 1999, Inferring the historical patterns of biological evolution, Nature, 401, 877, 10.1038/44766 Pakeman, 2014, Functional trait metrics are sensitive to the completeness of the species’ trait data?, Methods Ecol. Evol., 5, 9, 10.1111/2041-210X.12136 Paradis, 2004, APE: analyses of phylogenetics and evolution in R language, Bioinformatics, 20, 289, 10.1093/bioinformatics/btg412 Penone, 2014, Imputation of missing data in life-history trait datasets: which approach performs the best?, Methods Ecol. Evol., 5, 1, 10.1111/2041-210X.12232 Peres-Neto, 2005, How many principal components? Stopping rules for determining the number of non-trivial axes revisited, Comput. Stat. Data Anal., 49, 974, 10.1016/j.csda.2004.06.015 Pillar, 2009, Discriminating trait-convergence and trait-divergence assembly patterns in ecological community gradients, J. Veg. Sci., 20, 334, 10.1111/j.1654-1103.2009.05666.x Purvis, 2000, Predicting extinction risk in declining species, Proc. R. Soc. B Biol. Sci., 267, 1947, 10.1098/rspb.2000.1234 R Core Team, 2019 Revell, 2012, phytools: an R package for phylogenetic comparative biology (and other things), Methods Ecol. Evol., 3, 217, 10.1111/j.2041-210X.2011.00169.x Revell, 2008, Phylogenetic signal, evolutionary process, and rate, Syst. Biol., 57, 591, 10.1080/10635150802302427 Rohlf, 2001, Comparative methods for the analysis of continuous variables: geometric interpretations, Evolution (N. Y)., 55, 2143 Santos, 2018 Schmitz, 2015 Shmueli, 2010, To explain or to predict?, Stat. Sci., 25, 289, 10.1214/10-STS330 Stekhoven, 2012, Missforest-non-parametric missing value imputation for mixed-type data, Bioinformatics, 28, 112, 10.1093/bioinformatics/btr597 Swenson, 2014, Phylogenetic imputation of plant functional trait databases, Ecography (Cop.), 37, 105, 10.1111/j.1600-0587.2013.00528.x Swenson, 2017, Phylogeny and the prediction of tree functional diversity across novel continental settings, Glob. Ecol. Biogeogr., 26, 553, 10.1111/geb.12559 Troyanskaya, 2001, Missing value estimation methods for DNA microarrays, Bioinformatics, 17, 520, 10.1093/bioinformatics/17.6.520 van Buuren, 2011, mice: multivariate imputation by chained equations in R, J. Stat. Softw., 45, 1 Vellend, 2010, Conceptual synthesis in community ecology, Q. Rev. Biol., 85, 183, 10.1086/652373 Villéger, 2008, New multidimensional functional diversity indices for a multifaceted framework in functional ecology, Ecology, 89, 2290, 10.1890/07-1206.1 Violle, 2007, Let the concept of trait be functional!, Oikos, 116, 882, 10.1111/j.0030-1299.2007.15559.x Violle, 2014, The emergence and promise of functional biogeography, Proc. Natl. Acad. Sci. U. S. A., 111, 13690, 10.1073/pnas.1415442111 Webb, 2002, Phylogenies and community ecology, Annu. Rev. Ecol. Syst., 33, 475, 10.1146/annurev.ecolsys.33.010802.150448 Wilcox, 2017 Wilkes, 2020, Trait-based ecology at large scales: assessing functional trait correlations, phylogenetic constraints and spatial variability using open data, Glob. Chang. Biol., 26, 7255, 10.1111/gcb.15344 Wright, 2004, The worldwide leaf economics spectrum, Nature, 428, 821, 10.1038/nature02403