171
Acknowledgments We are grateful to Shan Kothari, Laura Williams, and Jesús Pinto-Ledezma
for their feedback on an early version of this manuscript. We are also grateful to the National
Institute for Mathematical and Biological Synthesis (NIMBioS) for funding the “Remotely
Sensing Biodiversity” working group.
References
Adams DC, Otárola-Castillo E (2013) Geomorph: an R package for the collection and analysis of
geometric morphometric shape data. Methods Ecol Evol 4(4):393–399
Antonelli A, Hettling H, Condamine FL, Vos K, Henrik Nilsson R, Sanderson MJ, Sauquet H et al
(2016) Toward a self-updating platform for estimating rates of speciation and migration, ages,
and relationships of taxa. Syst Biol 66(2):152–166. Oxford University Press: syw066
Asner G, Martin R (2011) Canopy phylogenetic, chemical and spectral assembly in a lowland
Amazonian forest. New Phytol 189:999–1012
Blomberg SP, Garland T, Ives AR (2003) Testing for phylogenetic signal in comparative data:
behavioral traits are more labile. Evolution 57(4):717–745
Burnham KP, Anderson DR (2002) Model selection and multimodel inference: a practical
information- theoretic. Springer, New York, NY
Butler MA, King AA (2004) Phylogenetic comparative analysis: a modeling approach for adaptive
evolution. Am Nat 164(6):683–695. The University of Chicago Press
Cavender-Bares J, Kozak KH, Fine PV, Kembel SW (2009) The merging of community ecology
and phylogenetic biology. Ecol Lett 12:693–715
Cavender-Bares J, Meireles JE, Couture JJ, Kaproth MA, Kingdon CC, Singh A, Serbin SP et al
(2016) Associations of leaf spectra with genetic and phylogenetic variation in oaks: prospects
for remote detection of biodiversity. Remote Sens 8(3):221
Clark M, Roberts D, Clark D (2005) Hyperspectral discrimination of tropical rain 10 forest tree
species at leaf to crown scales. Remote Sens Environ 96:375–398
Cornwell WK, Westoby M, Falster DS, FitzJohn RG, O’Meara BC, Pennell MW, McGlinn DJ
et al (2014) Functional distinctiveness of major plant lineages. Edited by Amy Austin. J Ecol
102(2):345–356
Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125(1):1–15
Felsenstein J (2008) Comparative methods with sampling error and within-species variation: contrasts revisited and revised. Am Nat 171(6):713–725
Hinchliff CE, Smith SA, Allman JF, Gordon Burleigh J, Chaudhary R, Coghill LM, Crandall KA
et al (2015) Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proc Natl
Acad Sci U S A 112(41):12764–12769
Ives AR, Midford PE, Garland T (2007) Within-species variation and measurement error in phylogenetic comparative methods. Syst Biol 56(2):252–270
McManus K, Asner GP, Martin RE, Dexter KG, John Kress W, Field C (2016) Phylogenetic structure of foliar spectral traits in tropical forest canopies. Remote Sens 8(3):196
O’Meara BC (2012) Evolutionary inferences from phylogenies: a review of methods. Ann Rev
Ecol Evol 43:267–285
O’Meara BC, Ané C, Sanderson MJ, Wainwright PC (2006) Testing for different rates of continuous trait evolution using likelihood. Evolution 60(5):922–933
Pagel M (1999) Inferring the historical patterns of biological evolution. Nature 401(6756):877–884
Pearse WD, Purvis A (2013) PhyloGenerator: an automated phylogeny generation tool for ecologists. Edited by Emmanuel Paradis. Methods Ecol Evol 4(7):692–698
7 Linking Leaf Spectra to the Plant Tree of Life
Acknowledgments We are grateful to Shan Kothari, Laura Williams, and Jesús Pinto-Ledezma
for their feedback on an early version of this manuscript. We are also grateful to the National
Institute for Mathematical and Biological Synthesis (NIMBioS) for funding the “Remotely
Sensing Biodiversity” working group.
References
Adams DC, Otárola-Castillo E (2013) Geomorph: an R package for the collection and analysis of
geometric morphometric shape data. Methods Ecol Evol 4(4):393–399
Antonelli A, Hettling H, Condamine FL, Vos K, Henrik Nilsson R, Sanderson MJ, Sauquet H et al
(2016) Toward a self-updating platform for estimating rates of speciation and migration, ages,
and relationships of taxa. Syst Biol 66(2):152–166. Oxford University Press: syw066
Asner G, Martin R (2011) Canopy phylogenetic, chemical and spectral assembly in a lowland
Amazonian forest. New Phytol 189:999–1012
Blomberg SP, Garland T, Ives AR (2003) Testing for phylogenetic signal in comparative data:
behavioral traits are more labile. Evolution 57(4):717–745
Burnham KP, Anderson DR (2002) Model selection and multimodel inference: a practical
information- theoretic. Springer, New York, NY
Butler MA, King AA (2004) Phylogenetic comparative analysis: a modeling approach for adaptive
evolution. Am Nat 164(6):683–695. The University of Chicago Press
Cavender-Bares J, Kozak KH, Fine PV, Kembel SW (2009) The merging of community ecology
and phylogenetic biology. Ecol Lett 12:693–715
Cavender-Bares J, Meireles JE, Couture JJ, Kaproth MA, Kingdon CC, Singh A, Serbin SP et al
(2016) Associations of leaf spectra with genetic and phylogenetic variation in oaks: prospects
for remote detection of biodiversity. Remote Sens 8(3):221
Clark M, Roberts D, Clark D (2005) Hyperspectral discrimination of tropical rain 10 forest tree
species at leaf to crown scales. Remote Sens Environ 96:375–398
Cornwell WK, Westoby M, Falster DS, FitzJohn RG, O’Meara BC, Pennell MW, McGlinn DJ
et al (2014) Functional distinctiveness of major plant lineages. Edited by Amy Austin. J Ecol
102(2):345–356
Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125(1):1–15
Felsenstein J (2008) Comparative methods with sampling error and within-species variation: contrasts revisited and revised. Am Nat 171(6):713–725
Hinchliff CE, Smith SA, Allman JF, Gordon Burleigh J, Chaudhary R, Coghill LM, Crandall KA
et al (2015) Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proc Natl
Acad Sci U S A 112(41):12764–12769
Ives AR, Midford PE, Garland T (2007) Within-species variation and measurement error in phylogenetic comparative methods. Syst Biol 56(2):252–270
McManus K, Asner GP, Martin RE, Dexter KG, John Kress W, Field C (2016) Phylogenetic structure of foliar spectral traits in tropical forest canopies. Remote Sens 8(3):196
O’Meara BC (2012) Evolutionary inferences from phylogenies: a review of methods. Ann Rev
Ecol Evol 43:267–285
O’Meara BC, Ané C, Sanderson MJ, Wainwright PC (2006) Testing for different rates of continuous trait evolution using likelihood. Evolution 60(5):922–933
Pagel M (1999) Inferring the historical patterns of biological evolution. Nature 401(6756):877–884
Pearse WD, Purvis A (2013) PhyloGenerator: an automated phylogeny generation tool for ecologists. Edited by Emmanuel Paradis. Methods Ecol Evol 4(7):692–698
7 Linking Leaf Spectra to the Plant Tree of Life