A Biogeographical and Conservation Approach
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Integrating community phylogenetics and phylogenetic beta diversity to understand Amazonian trees community assembly: a biogeographical and conservation approach By Juan Ernesto Guevara Andino A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy In Integrative Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Paul V.A. Fine, Chair Professor David Ackerly Professor Rosemary Gillespie Professor Brent Mishler Spring 2017 Abstract Integrating community phylogenetics and phylogenetic beta diversity to understand Amazonian trees community assembly: a biogeographical and conservation approach By Juan Ernesto Guevara Andino Doctor of Philosophy in Biology University of California, Berkeley Professor Paul V.A. Fine, Chair Understanding the tree species composition and turnover in Amazon forests has fascinated ecologists and evolutionary biologists since the first botanical expeditions from the 19th century. More recently, the advent of community phylogenetics and phylogenetic beta diversity methods has been demonstrated to be powerful tools to investigate the patterns and causes of Amazonian tree species assemblies. However, the lack of a comprehensive sampling of tree species communities using well- standardized taxonomy across gradients of soils, geology and climate has precluded making conclusions about the relative importance of these environmental filters on the patterns of species and lineage composition and turnover. In addition, due to current threats that Amazon forests are experiencing an ecologically informed delineation of floristic boundaries is urgently needed to guide conservation decisions. In this dissertation, I present the results of intensive floristic sampling at two spatial scales continental and regional, and show that the complementary implementation of phylogenetic beta diversity and community phylogenetics can help us to better describe and analyze floristic patterns of Amazon tree communities. Additionally, I used this combination of methods to determine high priority conservation areas that are currently experiencing severe threats in Ecuador Amazon. 1 Table of contents Introduction………………………………………………………………….................................ii Acknowledgements…...……………………………………………………...................................v Chapter 1 Low Phylogenetic Beta Diversity and Geographic Neo-endemism in Amazonian White-sand Forests……………………………………………………………............................1 Abstract…………………………………………………………………………………….….......1 Introduction………………………………………………………………………………………..1 Methods……………………………………………………………………………………………2 Results………………………………………………………………………………………...…...5 Discussion…………………………………………………………………………………………7 Acknowledgements………………………………………………………………………………10 References………………………………………………………………………………………..11 Tables…………………………………………………………………………………………….16 Figure Legends……………...……………………………………………………………………17 Figures……………………………………………………………………………………………18 Appendices……………………………………………………………………………………….23 Chapter 2 Incorporating phylogenetic information for the definition of floristic subregions in hyper-diverse Amazon forests: implications for conservation............................................40 Abstract……………………………………………………………………………………...…...40 Introduction…………………………………………………………………………………........40 Methods………………………………………………………………………………………......42 Results………………………………………………………………………………………........46 Discussion…………………………………………………………………………………..........47 Acknowledgements…………………………………………………………………………........50 References……………………………………………………………………………………......50 Tables……………………………………………………………………………………….........56 Figure Legends……………………………………………………………………………...........59 Figures………………………………………………………………………………………........60 Appendices………………………………………………………………………………….........65 Chapter 3 Climatic and geomorphological control on the phylogenetic and taxonomic beta diversity patterns of Amazon tree communities………………………………......................117 Abstract………………………………………………………………………………………....117 Introduction…………………………………………………………………………………......117 Methods……………………………………………………………………………………........119 Results………………………………………………………………………………………......123 Discussion……………………………………………………………………………………....124 Acknowledgements…………………………………………………………………………......127 References…………………………………………………………………………………........127 Tables……………………………………………………………………………………….......132 Figure Legends...……………………………………………………………………………......134 Figures………………………………………………………………………………………......135 Appendices………………………………………………………………………………….......139 i Introduction The merging of community ecology and phylogenetics has been one of the major advances in evolutionary biology and ecology in the last 15 years. Because there is an intrinsic relation between the patterns of distribution and abundance of the species and the evolutionary processes that underlie them, the study of community phylogenetics is fundamental for our understanding about the emergence and maintenance of diversity. This relationship becomes evident when we consider evolutionary time in the origin and maintenance of biodiversity because the rate of change in diversity is intrinsically linked to the rates at which both a clade originates and goes extinct (Graham and Fine 2008). Community ecology attempts to explain the patterns and processes that determine the co-occurrence and abundance of species in a community and increasingly, a large amount of publications linking evolutionary history and genealogical relations of the species to patterns of community assembly and diversity. Since Darwin’s postulates in the Origin of Species, two basic trends have been strongly linked to phylogeny. The first one posits that “closely related species tend to not co-occur in the same community due to interspecific competition” (Elton 1946, Webb 2000) and the second states that if related species tend to co-occur in local communities they must exhibit similar ecological requirements (Darwin 1871, Ackerly 2003). However, this dichotomization ignores the complexity of the interplay between evolutionary and ecological processes on the spatial and taxonomic patterns of community assembly and phylogenetic community structure. For the sake of argument, processes like speciation important in the determination of regional diversity could determine that close relatives inhabit the same local community (i.e., phylogenetic clustering) with very divergent ecological traits (i.e., trait lability) if allopatric speciation is involved (Cavender-Bares et al. 2009, Vamosi et al. 2009). By the same token if sympatric populations experienced an adaptive radiation to novel, divergent environments, closely related species with divergent traits will inhabit the same region but distantly related species will occupy the same local community (i.e., phylogenetic eveness) (Guillespie et al. 2004). In this sense, the study of phylogenetic community structure allows us to explore what kinds of mechanisms are responsible for shaping the community assemblage. Furthermore, the link between community structure and phylogenetic structure is also related to the evolution of traits and the biogeographical sorting of lineages across heterogeneous environments (Ackerly 2003, Ackerly 2004). Nevertheless, because two communities could potentially exhibit a similar pattern of phylogenetic community structure but different species composition, the analysis of phylogenetic community structure per se could not provide accurate information about the role of evolutionary process as diversification and the role of geographic barriers and biotic interactions as drivers of composition of local communities (Graham et al. 2009) In this sense, the analysis of phylogenetic beta diversity (phylobetadiversity) allow us to analyze how the phylogenetic relatedness of regional or local communities changes across environmental and spatial gradients in response to different biogeographic histories of regional species pools (Webb 2000, Graham and Fine 2008, Kraft et al. 2007, Fine and Kembel 2011, Kembel and Hubbell 2006). Because phylobetadiversity takes into account changes in phylogenetic community assembly and the geographic distribution of phylogenetic diversity it adds an additional factor to the analysis, which is inherently linked to the quantification of changes in phylogenetic patterns across space as a function of environmental gradients and geographic barriers (Graham and Fine 2008). ii In this dissertation, I employ the complementary use of phylogenetic community structure and phylogenetic beta diversity metrics to describe and analyze floristic patterns of Amazonian tree communities from both biogeographic and conservation perspectives. At the same time, I aim to disentangle the drivers of both species and lineage composition of Amazon tree communities combining extensive fieldwork with community phylogenetics, geology and climatic data. The first chapter is focused on a biogeographical analysis of Amazonian white-sand forests at a regional scale. I present the results of the most comprehensive data set known to date for Amazonian white-sand forests in order to elucidate the biogeographic relationships of these tree communities across Amazon basin. First, I describe floristic relationships in Amazonian white sand forests at the regional scale by using the largest number of one-hectare plots ever compiled for these forests, including all Amazonian regions. Secondly, I evaluated the role of dispersal and putative in situ radiation using community phylogenetic methods and phylogenetic