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.

With the technological advent of bioinformatics, next-generation sequencing, and population genomics, recent studies can rely on high-throughput molecular data to investigate the evolution and diversification of Neotropical plant lineages. Here, we review one of the most widespread and dominant plant groups in the Neotropics based on a multidisciplinary approach. We integrate molecular data based on next-generation sequencing, morphological and functional data to unveil the evolutionary history of Protium heptaphyllum (Aubl.) Marchand, a plant taxon recently classified as one of the top hyperdominant trees in Amazonia. The results have direct implications for biodiversity conservation, taxonomy, and systematics of tropical plants. The dissertation chapters are described below.

The first chapter aimed to perform the most comprehensive review ever done in a hyperdominant taxa, long considered to be a taxonomically difficult group. By using morphological, genomic, and functional data, we showed that P. heptaphyllum sensu lato represents eight separately evolving lineages warranting species status. In addition, most of these newly discovered lineages are rare and threatened; few if any of them could be considered hyperdominant on their own. There is an urgent need to improve the classification of hyperdominant taxa in order to avoid oversimplified assumptions regarding diversity and functional aspects of tropical regions.

The second chapter comprises a taxonomic review and a detailed description of P. cordatum. Molecular phylogeny indicates that populations of P. cordatum should not be classified as an intraspecific taxon within Protium heptaphyllum (Burseraceae), while morphology and near-infrared spectroscopy data provide additional support for the recognition of a separate entity. Species delimitation remains a challenge worldwide and this study demonstrates the importance of using multiple tools to characterize and distinguish plant species in highly diverse tropical regions.

In the third chapter, I aimed to generate a novel genomic resource for Burseraceae, a family globally recognized for producing resins and essential oils with medical properties and economic values. In this section, I provide the transcriptome assembly of Protium copal, a widespread aromatic tree in Central America, and describe the functional annotation of terpene biosynthetic genes. Most of the aromatic and non-aromatic properties of Burseraceae resins are composed by terpene and terpenoid chemicals. The identification of terpene genes will be relevant for understanding the synthesis of economically important chemicals in Burseraceae.