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Classification of Tropical Vegetation by Dominica Elaine Harrison A thesis submitted in partial fulfillment of the requirements for the degree of Master’s of Science Earth and Atmospheric Sciences University of Alberta © Dominica Elaine Harrison, 2016 Thesis abstract The increasing anthropogenic pressure on biodiversity in the tropics is resulting in changes to ecosystem structure and increasing species extinction rates (Collen et al. 2013). These issues are heightened in the tropics where 50% of the world’s biodiversity is held in 7% of the world’s terrestrial landmass (Urquhart 2001). The biodiversity of vegetation has been used as an indicator of the overall health and processes occurring in a biological system. This thesis explores ways to quantify the biodiversity of vegetation using different avenues of vegetation classification. In the second chapter of this thesis the leaf economic spectra (LES), a vegetation classification that attempts to provide a general framework to assess plant functional diversity, is used to explore the relationships between the conventional plant functional traits with the newly applied anatomical traits (Wright et al. 2004). This system uses economic principles to help understand plant ecology trade-offs and performance strategies. The LES was used to discern two plant functional groups (PFG), lianas and tree species, at two different Panamanian tropical sites, a tropical wet forest and a tropical dry forest. This was accomplished by examining the interactions between commonly used whole-leaf traits from the LES and newly applied anatomical traits. The addition of anatomical traits to the LES is a new approach (Reich 2014). The findings of this investigation support the hypothesis that trees are resource conservative when compared to their liana counterpart, which are thought to be resource acquisitive (Schnitzer 2005; Asner and Martin 2012). Additionally, the interaction of whole-leaf and anatomical traits provide insight into the foliar mechanisms and cellular organization such as: the amount of palisade and nutrients dictates leaf growth rates, the amount of airspace in the spongy mesophyll and potassium regulate water uptake, and cell size and cell numbers affects the defences against ii herbivores. Furthermore, variations across sites demonstrated that more resource availability will result in conservative traits and fewer resources will result in acquisitive traits. Future research in the field should focus on the implementation of anatomical traits on different PFGs and at different sites in the tropics. The third chapter of this thesis takes a remote sensing perspective to vegetation classification by exploring a region of the electromagnetic spectrum that has not been exploited extensively for vegetation investigations, namely the long-wave infrared (LWIR; 8.0 µm-12.5 µm; Ribeiro da Luz and Crowley 2007). Focusing on species discrimination through spectral signature sampling, a Fourier Transform Infrared (FTIR) spectrometer was used to collect the LWIR spectra of 26 tropical dry forest tree species in Costa Rica. To begin, a spectral library of cuticle and cell wall compounds collected by Ribeiro da Luz and Crowley (2007) was used to identify spectral features in the spectra of each species. Then the species were divided into groups based on similarities between spectral features and main compound(s) driving their spectra. Linear discriminant analysis (LDAs) was applied to each group to discriminate species within a group with accuracy rates ranging from 0-67% after validation. A random forest boot-strapping analysis was then applied to entire suite of species to discriminate species resulting in an out-of- bag error rate of 11%. This investigation is a first step in the application of LWIR to environmental monitoring. Advances in technology and airborne sensors will facilitate future remote sensing investigations in species discrimination from imagery and at regional scales. These two studies demonstrate different approaches to vegetation classification, PFT`s and RS. Together they emphasise the need to classify vegetation to assess damage resulting from biodiversity loss. Future research should focus on a standardization of wide-scale classification techniques. iii Preface This thesis is an original work completed by Dominica Elaine Harrison. Whole-leaf trait data for Chapter 2 was collected by Dr. Joseph Wright and company at the Smithsonian Tropical Research Institute in Panama. Leaf samples for Chapter 2 were collected by Dr. Karen Castro at the Smithsonian Tropical Research Institute in Panama. All sample histological preparations and data collection of the anatomical traits from Chapter 2 were prepared by me. All collection and preparation for Chapter 3 was my original work. iv Acknowledgements Foremost, I would like to acknowledge my co-supervisors, Dr. Benoit Rivard and Dr. Arturo Sanchez-Azofeifa for the constant support and guidance they have provided. This opportunity given to me would not otherwise be possible without their expertise and financial assistance. Thank you for all the time and effort put into this thesis with me, it has helped grow as a scientist and an individual. I greatly appreciate the advice and involvement of Dr. Janice Cooke, Dr. Joseph Wright and Dr. Andreas Hamann. A special thanks to Sofia Calvo-Rodriguez, Sandra Duran and Kayla Stan. I would also like to thank Mei Mei Chong and all my colleagues in the CEOS lab at the University of Alberta. I would like to acknowledge those who helped in the field when I was far from home: Julio Calvo-Alvarado, Mario Santos, Ana Julieta Calvo, Branko Hilje, Maria Rodriguez and Thiago Silva Furthermore, I would like to thank my friends and family who have been supporting me the entire two and a half years, specifically, to my parents for their constant proud support. Finally, I would like to acknowledge the financial and institutional support of the University of Alberta, NSERC and the Inter-American Institute for Global Change Research (IAI). v Table of Contents 1.0 Introduction ............................................................................................................................. 1 1.1 References .......................................................................................................................... 9 2.0 An anatomical application to Leaf Economic Spectrum through liana and tree whole- leaf trait analysis ......................................................................................................................... 13 2.1 Abstract........................................................................................................................... 13 2.2 Introduction .................................................................................................................... 14 2.3. Methods.......................................................................................................................... 18 2.3.1. Study area and sample preparation ...................................................................... 18 2.3.2 Leaf histology ......................................................................................................... 19 2.3.3 Leaf metrics ........................................................................................................... 19 2.3.4.2 Linear Mixed Models (LMMs) ............................................................................ 21 2.3.4.3 Analysis of covariance (ANCOVA) ..................................................................... 21 2.3.4.4 Standardized major axis regression ................................................................... 22 2.3.4.5 Linear discriminant analysis (LDA) .................................................................. 23 2.4 Results ............................................................................................................................. 23 2.4.1 Whole-leaf traits .................................................................................................... 23 2.4.2 Anatomical traits ................................................................................................... 24 2.4.3 Whole-leaf and anatomical interactions ................................................................ 25 2.5 Discussion ....................................................................................................................... 27 2.5.1 Palisade mesophyll functions ................................................................................ 28 2.5.2 Spongy mesophyll functions ................................................................................... 30 2.5.3 Infrastructure functions ......................................................................................... 32 2.5.4 Importance of mesophyll ........................................................................................ 34 2.6 Conclusions ..................................................................................................................... 35 2.7 References ....................................................................................................................... 37 3.0 Longwave infrared spectral feature characterization of tropical dry forest tree species and use for species discrimination ............................................................................................. 56 3.1 Abstract..........................................................................................................................
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    Anales del Jardín Botánico de Madrid Vol. 65(2): 343-352 julio-diciembre 2008 ISSN: 0211-1322 Araracuara, un nuevo género de Rhamnaceae de la Amazonía colombiana por José Luis Fernández-Alonso1 & María Victoria Arbeláez2 1 Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Apartado Aéreo 7495, Bogotá D.C., Colombia. [email protected] 2 Institute for Biodiversity and Ecosystem Dynamics (IBED), Universiteit van Amsterdam, Kruislaan 318, 1098 SM, Amsterdam, The Netherlands. [email protected] Resumen Abstract Fernández-Alonso, J.L., & Arbeláez, M.V. 2008. Araracuara, un Fernández-Alonso, J.L., & Arbeláez, M.V. 2008. Araracuara, the nuevo género de Rhamnaceae de la Amazonía colombiana. Ana- new genera of the Rhamnaceae from Colombian Amazon. Ana- les Jard. Bot. Madrid 65(2): 343-352. les Jard. Bot. Madrid 65(2): 343-352 (in Spanish). Se describe e ilustra Araracuara Fern. Alonso, un nuevo género de Araracuara Fern. Alonso, a new genus of Rhamnaceae only la familia Rhamnaceae conocido tan sólo de las mesetas de arenisca known from the sandstone plateaus of the Colombian Amazon, de la Amazonía colombiana. Se discuten sus posibles afinidades en is described and illustrated. Its possible affinities are discussed la familia y se sugiere que estaríamos ante un género relíctico, rela- and it is proposed that this is a relictual genus related to the pan- cionado con el pantropical Colubrina y en menor medida con el tropical Colubrina and to a lesser degree with the Amazonian amazónico Ampelozizyphus. Se incluye una clave para los géneros Ampelozizyphus. Also included are both a key to the Colombian de Rhamnaceae de Colombia y un apéndice con una muestra repre- genera of Rhamnaceae and a list of representative specimens of sentativa de especies de los géneros estudiados, algunos de ellos the genera studied (some of which have been poorly documen- pobremente documentados de territorio colombiano.