Understanding the evolution of Boraginales

Abstract

Boraginales are a medium-sized angiosperm order within Lamiids, with very diverse fruit morphology, which has been traditionally used for nomenclatural subdivisions. This thesis attempts to elucidate some aspects of the evolutionary history of Boraginales by pairing a morphological and a molecular perspective, since the interest comes from the shape and function of the organisms, in combination with a knowledge about their relationships. Specific research questions were developed around three main objectives. The first one is to improve our understanding of the evolutionary history of the basal grade of Boraginales II clade and provide additional support for the recognition of two families within it (i.e., Hydrophyllaceae and Namaceae), through phylogenetic and spatiotemporal studies. The second objective is to identify which particular processes and structures other than the ovule number transitions have been essential for fruit evolution of Boraginales. The third and final objective is to reconstruct an updated phylogeny of the entire order based on a phylogenomic approach, which will constitute a solid basis for understanding and discussing fruit evolution.<br /> To achieve these aims, the phylogenetic relationships of different taxonomic groups (between and within families in Chapter 2; at species level in Chapter 3; across the order in Chapter 6) are reconstructed using a variety of different methods. Specifically, in Chapter 2, the phylogeny and the historical biogeography of Hydrophyllaceae and Namaceae are inferred based on a plastid (<em>ndhF</em>) and a nuclear (ITS) dataset representing all major clades and biogeographic areas. Both likelihood and Bayesian methods are used for phylogenetic reconstruction. The estimation of divergence times and ancestral areas for all major clades, using a relaxed Bayesian uncorrelated molecular clock and the dispersal-extinction-cladogenesis approach is done based on the plastid dataset. In Chapter 3, a ddRAD sequencing approach is applied together with a classical taxonomic approach in order to re-evaluate morphological characters traditionally used for species delimitation of the highly diverse South American <em>Phacelia</em> taxa. Chapter 6 investigates the phylogenetic relationships across Boraginales by implementing a target enrichment sequencing strategy in order to collect phylogenomic data from 208 samples representing 10 Boraginales families and 79 % of genus diversity. To gain insight into the gynoecium/fruit evolution and diversification in the order two morphological studies are conducted (Chapters 4 and 5), investigating gynoecium and fruit development in relation to the other floral organs, in the tribe Hydrophylleae (Hydrophyllaceae) and in Lennoaceae and Ehretiaceae respectively, using scanning electron microscopy and micro-computed tomography.<br /> In summary, despite the clear and novel insights into the evolutionary history of Hydrophyllaceae and Namaceae, their treatment as separate families is not strongly supported. Their phylogenetic relationship remains ambiguous and their pleisiomorphic morphological traits are unable to provide clarification. Additionally, next generation sequencing approaches turned out to be very useful for resolving both interspecific relationships (ddRADseq) and relationships at higher taxonomic ranks (target enrichment sequencing). These methods combined with strategic taxon sampling in future studies are likely able to resolve most of the remaining issues. Furthermore, the morphological studies, along with data derived from the literature, reveal that among all the structures involved in the formation of complex internal ovary architecture in Boraginales, placentation and its plasticity seem to be key elements. Transitions from intrusive parietal to axile placentation were a fundamental basis for fruit diversification in the order. An evolutionary series for the boraginalean fruits is proposed, considering the results of Chapters 4, 5 and 6 as well as available literature data. Finally, remaining questions and future research directions related to this thesis are discussed.