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Taxonomy of Brazil's National Tree: Paubrasilia Echinata (Leguminosae)

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Taxonomy of Brazil's National Tree: Paubrasilia Echinata (Leguminosae) Taxonomy of Brazil’s national tree: Paubrasilia echinata (Leguminosae) Mathew Rees August 2019 School of Biological Sciences, University of Edinburgh & Royal Botanic Garden Edinburgh Thesis submitted in partial fulfilment for the MSc in the Biodiversity and Taxonomy of Plants 1 Abstract Background: Paubrasilia echinata (Lam.) E. Gagnon, H. C. Lima & G. P. Lewis is the national tree of Brazil and an endangered species endemic to the Mata Atlantica. Three morphotypes are commonly identified based on the size of the folioles but it is unclear if they represent distinct taxa or a single polymorphic species. This dissertation aims at clarifying the taxonomic position of the three morphotypes and informing conservation decisions. Methods: A comprehensive morphometric study based on 74 geographically representative herbarium specimens from the entire distribution of the species was coupled with phylogenomic investigation of genotyping-by-sequencing data and multivariate ecological analyses of climate data. Results: We found that the three morphotypes do not match separately evolving lineages. Rather, P.echinata is composed of five clades that are geographically structured and two lineages show signs of ongoing gene flow. Conclusions: P. echinata is best treated as a single species composed of evolutionary and geographically distinct lineages. Morphologically diagnosable characters are missing to describe sub-species that would help inform conservation measures whilst reflecting evolutionary history. Key words: Pau Brasil, Paubrasilia echinata, species delimitation, morphometric, genotyping-by- sequencing, conservation. 2 Acknowledgements I would like to sincerely thank Edeline Gagnon for inviting me to work on this project, supervising me throughout my work and transmitting her knowledge. Her patient explanations and calm attitude when dealing with rebellious software were invaluable. To Gwilym Lewis, a very warm thanks for receiving me at the Royal Botanic Gardens Kew, showing me the collections and the precious discussions concerning morphology, field observations and implications for conservation. Um agradecimento especial a Haroldo Lima por sua opinião especializada e contribução para questões de pesquias. I would like to thank Linda Neeves for her fine suggestions with the genomic data. I will now think of SNPs as Simply No Problems. I am extremely grateful to Michael Frohlich, whose generosity in unsurpassed and of whom I will forever be appreciative for helping me join the MSc course. Finally I thank my partner, Toral Shah, for her continuous support. 3 Table of contents Abstract ..................................................................................................................................1 Acknowledgements ................................................................................................................2 Table of contents ....................................................................................................................3 List of figures .........................................................................................................................5 List of tables ...........................................................................................................................5 List of appendices ...................................................................................................................6 List of acronyms and abbreviations .........................................................................................7 Introduction ............................................................................................................................9 Preamble ............................................................................................................................9 Historic and cultural background ........................................................................................9 Species biology................................................................................................................. 10 Taxonomic and nomenclatural background: ...................................................................... 13 Molecular biology and DNA fingerprinting ...................................................................... 18 Species concepts ............................................................................................................... 22 Aim and objectives ........................................................................................................... 25 Methodology ........................................................................................................................ 26 Taxon sampling ................................................................................................................ 26 DNA extraction and sequencing........................................................................................ 27 Data assembly .................................................................................................................. 27 Genetic clustering and population structure ....................................................................... 29 Phylogenetic inference ...................................................................................................... 30 Morphological analysis ..................................................................................................... 31 Ecological identity ............................................................................................................ 34 Results.................................................................................................................................. 35 Data assembly .................................................................................................................. 35 Genetic clustering ............................................................................................................. 35 Phylogenetic inference ...................................................................................................... 40 Morphometrics ................................................................................................................. 43 Ecological identity ............................................................................................................ 47 Discussion ............................................................................................................................ 49 Species concepts ............................................................................................................... 49 4 Genetics............................................................................................................................ 50 Morphology ...................................................................................................................... 53 Ecology ............................................................................................................................ 55 Conservation .................................................................................................................... 57 Conclusions .......................................................................................................................... 59 References ............................................................................................................................ 60 Appendices ........................................................................................................................... 70 5 List of figures Front cover: Flower and pollinator of Paubrasilia echinata. Photo credit: Marcos Sana Figure 1: Details of P.echinata trunk showing distinctive spines. .......................................... 10 Figure 2: Distribution of P. echinata in Brazil modified from De Lima (2019). .................... 12 Figure 3: Illustration of Paubrasilia echinata from Lewis, 1998 ........................................... 16 Figure 4: Paubrasilia echinata.............................................................................................. 17 Figure 5: Simplified assembly process used by ipyrad. ......................................................... 20 Figure 6: Classes of species concepts, their properties and advocates .................................... 22 Figure 7: Extent of sampling ................................................................................................. 26 Figure 8: DAPC of the min12b dataset identified five genetic clusters .................................. 36 Figure 9: STRUCTURE analysis identified five genetic clusters ........................................... 38 Figure 10: Neighbornet network identified five genetic clusters. ........................................... 39 Figure 11: Maximum Likelihood phylogeny using the min30 dataset. ................................... 41 Figure 12: Bayesian inference phylogeny using the min 30 dataset. ...................................... 42 Figure 13: Ward clustering dendrograms .............................................................................. 44 Figure 14: Estimating the optimal number of clusters ........................................................... 45 Figure 15: PCA of uncorrelated square root transformed morphological variables ................ 46 Figure 16: Classification tree and boxplots of the morphometric analysis ............................. 46 Figure 17: Geo-referencing collections of Pau Brasil ...........................................................
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