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The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the notion that early diversifications of angiosperms and insects were inextricably linked. In this article, we examine (i) the discrepancies between dates of emergence for angiosperms and major clades of insects; (ii) the long history of gymnosperm-insect pollination modes, which likely shaped early angiosperm-insect pollination mutualisms; and (iii) how the K-Pg (Cretaceous-Paleogene) mass extinction event was vital in propelling modern angiosperm-insect mutualisms. We posit that the early diversifications of angiosperms and their insect pollinators were largely decoupled until the end of the Cretaceous.

Premise Significant paleobotanical discoveries in recent decades have considerably improved our understanding of the early evolution of angiosperms and their flowers. However, our ability to test the systematic placement of fossil flowers on the basis of phylogenetic analyses has remained limited, mainly due to the lack of an adequate, angiosperm-wide morphological data set for extant taxa. Earlier attempts to place fossil flowers phylogenetically were, therefore, forced to make prior qualitative assessments of the potential systematic position of fossils and to restrict phylogenetic analyses to selected angiosperm subgroups. Methods We conduct angiosperm-wide molecular backbone analyses of 10 fossil flower taxa selected from the Cretaceous record. Our analyses make use of a floral trait data set built within the framework of the eFLOWER initiative. We provide an updated version of this data set containing data for 28 floral and two pollen traits for 792 extant species representing 372 angiosperm families. Results We find that some fossils are placed congruently with earlier hypotheses while others are found in positions that had not been suggested previously. A few take up equivocal positions, including the stem branches of large clades. Conclusions Our study provides an objective approach to test for the phylogenetic position of fossil flowers across angiosperms. Such analyses may provide a complementary tool for paleobotanical studies, allowing for a more comprehensive understanding of fossil phylogenetic relationships in angiosperms. Ongoing work focused on extending the sampling of extant taxa and the number of floral traits will further improve the applicability and accuracy of our approach.

Pseudanthia are widespread and have long been postulated to be a key innovation responsible for some of the angiosperm radiations. The aim of our study was to analyze macroevolutionary patterns of these flower-like inflorescences and their potential correlation with diversification rates in Apiaceae subfamily Apioideae. In particular, we were interested to investigate evolvability of pseudanthia and evaluate their potential association with changes in the size of floral display.The framework for our analyses consisted of a time-calibrated phylogeny of 1734 representatives of Apioideae and a morphological matrix of inflorescence traits encoded for 847 species. Macroevolutionary patterns in pseudanthia were inferred using Markov models of discrete character evolution and stochastic character mapping, and a principal component analysis was used to visualize correlations in inflorescence architecture. The interdependence between net diversification rates and the occurrence of pseudocorollas was analyzed with trait-independent and trait-dependent approaches.Pseudanthia evolved in 10 major clades of Apioideae with at least 36 independent origins and 46 reversals. The morphospace analysis recovered differences in color and compactness between floral and hyperfloral pseudanthia. A correlation between pseudocorollas and size of inflorescence was also strongly supported. Contrary to our predictions, pseudanthia are not responsible for variation in diversification rates identified in this subfamily.Our results suggest that pseudocorollas evolve as an answer to the trade-off between enlargement of floral display and costs associated with production of additional flowers. The high evolvability and architectural differences in apioid pseudanthia may be explained on the basis of adaptive wandering and evolutionary developmental biology.

The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ~140 million years (Ma; Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both macroevolutionary analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their divergence with acrogymnosperms (stem age); the age(s) of emergence of their unique, distinctive features including flowers (morphological age); and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior distribution (typically a calibration density set by the user in Bayesian analyses). Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as largely unknown (140–270 Ma) and that contrasting age estimates in the literature mostly reflect conflicting prior distributions. We also suggest that future work that depends on the time scale of flowering plant diversification be designed to integrate over this vexing uncertainty.

Summary Morphological diversity (disparity) is an essential but often neglected aspect of biodiversity. Hence, it seems timely and promising to re‐emphasize morphology in modern evolutionary studies. Disparity is a good proxy for the diversity of functions and interactions with the environment of a group of taxa. In addition, geographical and ecological patterns of disparity are crucial to understand organismal evolution and to guide biodiversity conservation efforts.Here, we analyse floral disparity across latitudinal intervals, growth forms, climate types, types of habitats, and regions for a large and representative sample of the angiosperm order Ericales.We find a latitudinal gradient of floral disparity and a decoupling of disparity from species richness. Other factors investigated are intercorrelated, and we find the highest disparity for tropical trees growing in African and South American forests.Explanations for the latitudinal gradient of floral disparity may involve the release of abiotic constraints and the increase of biotic interactions towards tropical latitudes, allowing tropical lineages to explore a broader area of the floral morphospace. Our study confirms the relevance of biodiversity parameters other than species richness and is consistent with the importance of species interactions in the tropics, in particular with respect to angiosperm flowers and their pollinators.

Contents Summary 1170 I. Introduction 1170 II. Six key questions 1172 III. Three key challenges 1177 IV. Conclusions 1181 Acknowledgements 1182 References 1183 SUMMARY: The origin and rapid diversification of angiosperms (flowering plants) represent one of the most intriguing topics in evolutionary biology. Despite considerable progress made in complementary fields over the last two decades (paleobotany, phylogenetics, ecology, evo-devo, genomics), many important questions remain. For instance, what has been the impact of mass extinctions on angiosperm diversification? Are the angiosperms an adaptive radiation? Has morphological evolution in angiosperms been gradual or pulsed? We propose that the recent and ongoing revolution in macroevolutionary methods provides an unprecedented opportunity to explore long-standing questions that probably hold important clues to understand present-day biodiversity. We present six key questions that explore the origin and diversification of angiosperms. We also identify three key challenges to address these questions: (1) the development of new integrative models that include diversification, multiple intrinsic and environmental traits, biogeography and the fossil record all at once, whilst accounting for sampling bias and heterogeneity of macroevolutionary processes through time and among lineages; (2) the need for large and standardized synthetic databases of morphological variation; and (3) continuous effort on sampling the fossil record, but with a revolution in current paleobotanical practice.

Recent advances in molecular phylogenetics and a series of important palaeobotanical discoveries have revolutionized our understanding of angiosperm diversification. Yet, the origin and early evolution of their most characteristic feature, the flower, remains poorly understood. In particular, the structure of the ancestral flower of all living angiosperms is still uncertain. Here we report model-based reconstructions for ancestral flowers at the deepest nodes in the phylogeny of angiosperms, using the largest data set of floral traits ever assembled. We reconstruct the ancestral angiosperm flower as bisexual and radially symmetric, with more than two whorls of three separate perianth organs each (undifferentiated tepals), more than two whorls of three separate stamens each, and more than five spirally arranged separate carpels. Although uncertainty remains for some of the characters, our reconstruction allows us to propose a new plausible scenario for the early diversification of flowers, leading to new testable hypotheses for future research on angiosperms., Nature Communications, 8, ISSN:2041-1723

The Early Cretaceous (145-100 million years ago (Ma)) witnessed the rise of flowering plants (angiosperms), which ultimately lead to profound changes in terrestrial plant communities. However, palaeobotanical evidence shows that the transition to widespread angiosperm-dominated biomes was delayed until the Palaeocene (66-56 Ma). Important aspects of the timing and geographical setting of angiosperm diversification during this period, and the groups involved, remain uncertain. Here we address these aspects by constructing and dating a new and complete family-level phylogeny, which we integrate with 16 million geographic occurrence records for angiosperms on a global scale. We show substantial time lags (mean, 37-56 Myr) between the origin of families (stem age) and the diversification leading to extant species (crown ages) across the entire angiosperm tree of life. In turn, our results show that families with the shortest lags are overrepresented in temperate and arid biomes compared with tropical biomes. Our results imply that the diversification and ecological expansion of extant angiosperms was geographically heterogeneous and occurred long after most of their phylogenetic diversity originated during the Cretaceous Terrestrial Revolution.

Species diversity is remarkably unevenly distributed among flowering plant lineages. Despite a growing toolbox of research methods, the reasons underlying this patchy pattern have continued to perplex plant biologists for the past two decades. In this review, we examine the present understanding of transitions in flowering plant evolution that have been proposed to influence speciation and extinction. In particular, ploidy changes, transitions between tropical and nontropical biomes, and shifts in floral form have received attention and have offered some surprises in terms of which factors influence speciation and extinction rates. Mating systems and dispersal characteristics once predominated as determining factors, yet recent evidence suggests that these changes are not as influential as previously thought or are important only when paired with range shifts. Although range extent is an important correlate of speciation, it also influences extinction and brings an applied focus to diversification research. Recent studies that find that past diversification can predict present-day extinction risk open an exciting avenue for future research to help guide conservation prioritization.

Ancestral state reconstruction is an important tool to study morphological evolution and often involves estimating transition rates among character states. However, various factors, including taxonomic scale and sampling density, may impact transition rate estimation and indirectly also the probability of the state at a given node. Here, we test the influence of rate heterogeneity using maximum likelihood methods on five binary perianth characters, optimized on a phylogenetic tree of angiosperms including 1230 species sampled from all families. We compare the states reconstructed by an equal-rate (Mk1) and a two-rate model (Mk2) fitted either with a single set of rates for the whole tree or as a partitioned model, allowing for different rates on five partitions of the tree. We find strong signal for rate heterogeneity among the five subdivisions for all five characters, but little overall impact of the choice of model on reconstructed ancestral states, which indicates that most of our inferred ancestral states are the same whether heterogeneity is accounted for or not.

The staggering diversity of angiosperms and their flowers has fascinated scientists for centuries. However, the quantitative distribution of floral morphological diversity (disparity) among lineages and the relative contribution of functional modules (perianth, androecium and gynoecium) to total floral disparity have rarely been addressed. Focusing on a major angiosperm order (Ericales), we compiled a dataset of 37 floral traits scored for 381 extant species and nine fossils. We conducted morphospace analyses to explore phylogenetic, temporal and functional patterns of disparity. We found that the floral morphospace is organized as a continuous cloud in which most clades occupy distinct regions in a mosaic pattern, that disparity increases with clade size rather than age, and that fossils fall in a narrow portion of the space. Surprisingly, our study also revealed that among functional modules, it is the androecium that contributes most to total floral disparity in Ericales. We discuss our findings in the light of clade history, selective regimes as well as developmental and functional constraints acting on the evolution of the flower and thereby demonstrate that quantitative analyses such as the ones used here are a powerful tool to gain novel insights into the evolution and diversity of flowers.

center dot Background and Aims The basal eudicot family Proteaceae (approx. 1700 species) shows considerable variation in floral symmetry but has received little attention in studies of evolutionary development at the genetic level. A framework for understanding the shifts in floral symmetry in Proteaceae is provided by reconstructing ancestral states on an upated phylogeny of the family, and homologues of CYCLOIDEA (CYC), a key gene for the control of floral symmetry in both monocots and eudicots, are characterized. center dot Methods Perianth symmetry transitions were reconstructed on a new species-level tree using parsimony and maximum likelihood. CYC-like genes in 35 species (31 genera) of Proteaceae were sequenced and their phylogeny was reconstructed. Shifts in selection pressure following gene duplication were investigated using nested branch-site models of sequence evolution. Expression patterns of CYC homologues were characterized in three species of Grevillea with different types of floral symmetry. center dot Key Results Zygomorphy has evolved 10-18 times independently in Proteaceae from actinomorphic ancestors, with at least four reversals to actinomorphy. A single duplication of CYC-like genes occurred prior to the diversification of Proteaceae, with putative loss or divergence of the ProtCYC1 paralogue in more than half of the species sampled. No shifts in selection pressure were detected in the branches subtending the two ProtCYC paralogues. However, the amino acid sequence preceding the TCP domain is strongly divergent in Grevillea ProtCYC1 compared with other species. ProtCYC genes were expressed in developing flowers of both actinomorphic and zygomorphic Grevillea species, with late asymmetric expression in the perianth of the latter. center dot Conclusion Proteaceae is a remarkable family in terms of the number of transitions in floral symmetry. Furthermore, although CYC-like genes in Grevillea have unusual sequence characteristics, they display patterns of expression that make them good candidates for playing a role in the establishment of floral symmetry.

Dating the Tree of Life has now become central to relating patterns of biodiversity to key processes in Earth history such as plate tectonics and climate change. Regions with a Mediterranean climate have long been noted for their exceptional species richness and high endemism. How and when these biota assembled can only be answered with a good understanding of the sequence of divergence times for each of their components. A critical aspect of dating by using molecular sequence divergence is the incorporation of multiple suitable age constraints. Here, we show that only rigorous phylogenetic analysis of fossil taxa can lead to solid calibration and, in turn, stable age estimates, regardless of which of 3 relaxed clock-dating methods is used. We find that Proteaceae, a model plant group for the Mediterranean hotspots of the Southern Hemisphere with a very rich pollen fossil record, diversified under higher rates in the Cape Floristic Region and Southwest Australia than in any other area of their total distribution. Our results highlight key differences between Mediterranean hotspots and indicate that Southwest Australian biota are the most phylogenetically diverse but include numerous lineages with low diversification rates.

Background With 10,000 species, Magnoliidae are the largest clade of flowering plants outside monocots and eudicots. Despite an ancient and rich fossil history, the tempo and mode of diversification of Magnoliidae remain poorly known. Using a molecular data set of 12 markers and 220 species (representing >75% of genera in Magnoliidae) and six robust, internal fossil age constraints, we estimate divergence times and significant shifts of diversification across the clade. In addition, we test the sensitivity of magnoliid divergence times to the choice of relaxed clock model and various maximum age constraints for the angiosperms. Results Compared with previous work, our study tends to push back in time the age of the crown node of Magnoliidae (178.78-126.82 million years, Myr), and of the four orders, Canellales (143.18-125.90 Myr), Piperales (158.11-88.15 Myr), Laurales (165.62-112.05 Myr), and Magnoliales (164.09-114.75 Myr). Although families vary in crown ages, Magnoliidae appear to have diversified into most extant families by the end of the Cretaceous. The strongly imbalanced distribution of extant diversity within Magnoliidae appears to be best explained by models of diversification with 6 to 13 shifts in net diversification rates. Significant increases are inferred within Piperaceae and Annonaceae, while the low species richness of Calycanthaceae, Degeneriaceae, and Himantandraceae appears to be the result of decreases in both speciation and extinction rates. Conclusions This study provides a new time scale for the evolutionary history of an important, but underexplored, part of the tree of angiosperms. The ages of the main clades of Magnoliidae (above the family level) are older than previously thought, and in several lineages, there were significant increases and decreases in net diversification rates. This study is a new robust framework for future investigations of trait evolution and of factors influencing diversification in this group as well as angiosperms as a whole. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0320-6) contains supplementary material, which is available to authorized users.

International audience; Background and Aims Fumarioideae (20 genera, 593 species) is a clade of Papaveraceae (Ranunculales) characterized by flowers that are either disymmetric (i.e. two perpendicular planes of bilateral symmetry) or zygomorphic (i.e. one plane of bilateral symmetry). In contrast, the other subfamily of Papaveraceae, Papaveroideae (23 genera, 230 species), has actinomorphic flowers (i.e. more than two planes of symmetry). Understanding of the evolution of floral symmetry in this clade has so far been limited by the lack of a reliable phylogenetic framework. Pteridophyllum (one species) shares similarities with Fumarioideae but has actinomorphic flowers, and the relationships among Pteridophyllum, Papaveroideae and Fumarioideae have remained unclear. This study reassesses the evolution of floral symmetry in Papaveraceae based on new molecular phylogenetic analyses of the family. Methods : Maximum likelihood, Bayesian and maximum parsimony phylogenetic analyses of Papaveraceae were conducted using six plastid markers and one nuclear marker, sampling Pteridophyllum, 18 (90 %) genera and 73 species of Fumarioideae, 11 (48 %) genera and 11 species of Papaveroideae, and a wide selection of outgroup taxa. Floral characters recorded from the literature were then optimized onto phylogenetic trees to reconstruct ancestral states using parsimony, maximum likelihood and reversible-jump Bayesian approaches. Key Results : Pteridophyllum is not nested in Fumarioideae. Fumarioideae are monophyletic and Hypecoum (18 species) is the sister group of the remaining genera. Relationships within the core Fumarioideae are well resolved and supported. Dactylicapnos and all zygomorphic genera form a well-supported clade nested among disymmetric taxa. Conclusions : Disymmetry of the corolla is a synapomorphy of Fumarioideae and is strongly correlated with changes in the androecium and differentiation of middle and inner tepal shape (basal spurs on middle tepals). Zygomorphy subsequently evolved from disymmetry either once (with a reversal in Dactylicapnos) or twice (Capnoides, other zygomorphic Fumarioideae) and appears to be correlated with the loss of one nectar spur.

Summary The Proteaceae is a large angiosperm family displaying the common pattern of uneven distribution of species among genera. Previous studies have shown that this disparity is a result of variation in diversification rates across lineages, but the reasons for this variation are still unclear. Here, we tested the impact of floral symmetry and occurrence in Mediterranean climate regions on speciation and extinction rates in the Proteaceae. A rate shift analysis was conducted on dated genus-level phylogenetic trees of the Proteaceae. Character-dependent analyses were used to test for differences in diversification rates between actinomorphic and zygomorphic lineages and between lineages located within or outside Mediterranean climate regions. The rate shift analysis identified 5–10 major diversification rate shifts in the Proteaceae tree. The character-dependent analyses showed that speciation rates, extinction rates and net diversification rates of the Proteaceae were significantly higher for lineages occurring in Mediterranean hotspots. Higher speciation and extinction rates were also detected for zygomorphic species, but net diversification rates appeared to be similar in actinomorphic and zygomorphic Proteaceae. Presence in Mediterranean hotspots favors Proteaceae diversification. In contrast with observations at the scale of angiosperms, floral symmetry is not a trait that strongly influences their evolutionary success.

Objectives Identify patterns of change in species distributions, diversity, concentrations of evolutionary history, and assembly of Australian rainforests. Methods We used the distribution records of all known rainforest woody species in Australia across their full continental extent. These were analysed using measures of species richness, phylogenetic diversity (PD), phylogenetic endemism (PE) and phylogenetic structure (net relatedness index; NRI). Phylogenetic structure was assessed using both continental and regional species pools. To test the influence of growth-form, freestanding and climbing plants were analysed independently, and in combination. Results Species richness decreased along two generally orthogonal continental axes, corresponding with wet to seasonally dry and tropical to temperate habitats. The PE analyses identified four main areas of substantially restricted phylogenetic diversity, including parts of Cape York, Wet Tropics, Border Ranges, and Tasmania. The continental pool NRI results showed evenness (species less related than expected by chance) in groups of grid cells in coastally aligned areas of species rich tropical and sub-tropical rainforest, and in low diversity moist forest areas in the south-east of the Great Dividing Range and in Tasmania. Monsoon and drier vine forests, and moist forests inland from upland refugia showed phylogenetic clustering, reflecting lower diversity and more relatedness. Signals for evenness in Tasmania and clustering in northern monsoon forests weakened in analyses using regional species pools. For climbing plants, values for NRI by grid cell showed strong spatial structuring, with high diversity and PE concentrated in moist tropical and subtropical regions. Conclusions/Significance Concentrations of rainforest evolutionary history (phylo-diversity) were patchily distributed within a continuum of species distributions. Contrasting with previous concepts of rainforest community distribution, our findings of continuous distributions and continental connectivity have significant implications for interpreting rainforest evolutionary history and current day ecological processes, and for managing rainforest diversity in changing circumstances.

The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subsampling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest divergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon sampling, significant methodological changes, and new information from the fossil record. [Angiospermae, chloroplast, genome, molecular dating, Triassic.].

Progress has been made recently towards the elucidation of phylogenetic relationships among subfamilies and tribes of the Ranunculaceae – the most recent hypothesis was published in 2016 by our team. Although relationships among the 10 tribes of the subfamily Ranunculoideae remain incompletely supported, this hypothesis provides an interesting framework to address the key issue of the ancestral vs. derived nature of a differentiated perianth within the family, and at the level of Ranunculales as a whole. Here, we present ancestral state reconstructions for several perianth characters, such as differentiation into sepals and petals, shape of petals, presence/absence of nectaries, and petaloid or sepaloid aspect of sepals. Characters were scored using the PROTEUS database and optimized on the most recent phylogeny of Ranunculaceae using parsimony and maximum likelihood methods. The results are discussed with regard to recent evo-devo studies focused on identifying genes involved in floral organs identity (the so-called ABC model) in Ranunculales.

Magnoliidae have been supported as a clade in the majority of large-scale molecular phylogenetic studies of angiosperms. This group consists of about 10,000 species assigned to 20 families and four orders, Canellales, Piperales, Laurales, and Magnoliales. Some relationships among the families are still largely debated. Here, we reconstruct the phylogenetic relationships of Magnoliidae as a whole, sampling 199 species (representing ca. 75% of genera) and 12 molecular markers from the three genomes (plastid atpB, matK, trnL intron, trnL-trnF spacer, ndhF, rbcL; mitochondrial atp1, matR, mtSSU, mtLSU; nuclear 18s rDNA, 26S rDNA). Maximum likelihood, Bayesian and maximum parsimony analyses yielded congruent trees, with good resolution and high support values for higher-level relationships. This study further confirms, with greater levels of support, two major clades in Magnoliidae: Canellales+Piperales and Laurales+Magnoliales. Relationships among the 20 families are, in general, well resolved and supported. Several previously ambiguous relationships are now well supported. For instance, the Aristolochiaceae s.l. (incl. Asaroideae, Aristolochioideae, and Lactoris) are monophyletic with high support when Hydnoraceae are excluded. The latter family was not included in most previous studies because of the lack of suitable plastid sequences, a consequence of the parasitic habit of its species. Here, we confirm that it belongs in Aristolochiaceae. Our analyses also provide moderate support for a sister group relationship between Lauraceae and Monimiaceae. Conversely, the exact position of Magnoliaceae remains very difficult to determine. This study provides a robust phylogenetic background to address the evolutionary history of an important and highly diverse clade of early-diverging angiosperms.

Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using "early but risky" fossil constraints in addition to "safe but late" constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.

The angiosperm family Proteaceae is a distinct component of the Cape Floristic Region biodiversity hot-spot with 330 endemic species. Phylogenetic analyses of subfamily Proteoideae using sequence data from one nuclear and six plastid loci show that most of this diversity is contained in two distinct Cape floral clades. Molecular dating analyses, using Bayesian and penalized likelihood methods and four phylogenetically supported fossil age constraints. reveal contrasting histories for these two clades. The genus Protea belongs to a lineage that may have been in Africa since the Late Cretaceous but began to diversify in the Cape only 5-18 Myr ago. In contrast, the Leucadendrinae clade presumably arrived in the region no earlier than 46 Myr ago by long-distance dispersal from an Australian ancestor and the extant members of this clade began to diversify in the Cape 22-39 Myr ago. These results join a growing number of case studies that challenge the commonly accepted view that most of the Cape flora radiated synchronously in the Late Miocene and Early Pliocene when a Mediterranean climate settled in the region. (C) 2008 Elsevier Inc. All rights reserved.

We investigated higher-level phylogenetic relationships within the genus Halictus based on parsimony and maximum likelihood (ML) analysis of elongation factor-1α DNA sequence data. Our data set includes 41 OTUs representing 35 species of halictine bees from a diverse sample of outgroup genera and from the three widely recognized subgenera of Halictus (Halictus s.s., Seladonia, and Vestitohalictus). We analyzed 1513 total aligned nucleotide sites spanning three exons and two introns. Equal-weights parsimony analysis of the overall data set yielded 144 equally parsimonious trees. Major conclusions supported in this analysis (and in all subsequent analyses) included the following: (1) Thrincohalictus is the sister group to Halictus s.l., (2) Halictus s.l. is monophyletic, (3) Vestitohalictus renders Seladonia paraphyletic but together Seladonia + Vestitohalictus is monophyletic, (4) Michener's Groups 1 and 3 are monophyletic, and (5) Michener's Group 1 renders Group 2 paraphyletic. In order to resolve basal relationships within Halictus we applied various weighting schemes under parsimony (successive approximations character weighting and implied weights) and employed ML under 17 models of sequence evolution. Weighted parsimony yielded conflicting results but, in general, supported the hypothesis that Seladonia + Vestitohalictus is sister to Michener's Group 3 and renders Halictus s.s. paraphyletic. ML analyses using the GTR model with site-specific rates supported an alternative hypothesis: Seladonia + Vestitohalictus is sister to Halictus s.s. We mapped social behavior onto trees obtained under ML and parsimony in order to reconstruct the likely historical pattern of social evolution. Our results are unambiguous: the ancestral state for the genus Halictus is eusociality. Reversal to solitary behavior has occurred at least four times among the species included in our analysis.

Biodiversity today has the unusual property that 85% of plants and animal species live on land rather than in the sea, and half of these in tropical rainforests. An explosive boost to terrestrial diversity occurred from ca. 100-50 million years ago, the Late Cretaceous and early Palaeogene. During this interval, the Earth-life system on land was reset, and the biosphere expanded to a new level of productivity, enhancing the capacity and species diversity of terrestrial environments. This boost in terrestrial biodiversity coincided with innovations in flowering plant biology and evolutionary ecology, including their (1) flowers and efficiencies in reproduction, (2) coevolution with animals, especially pollinators and herbivores, (3) photosynthetic capacities, (4) adaptability, and (5) ability to modify habitats. The rise of angiosperms triggered a macroecological revolution on land and drove modern biodiversity in a secular, prolonged shift to new, high levels, a series of processes we name here the Angiosperm Terrestrial Revolution.

Deep phylogenetic relationships in the angiosperms had long been uncertain. However, by the end of the 1990s, large-scale studies contributed to the current well resolved picture of the tree of flowering plants, in which eudicots, monocots, and magnoliids are the three largest clades. Whereas monocots and eudicots have been recognized since the very first phylogenetic analyses, the monophyly of magnoliids (Canellales, Laurales, Magnoliales, and Piperales) is a more recent result. Magnoliidae, as now circumscribed, consist of 20 families and ca. 10,000 species mostly distributed in the tropics. Before the present thesis, several parts of the magnoliid tree had been well studied, but little was known about the evolutionary history of Magnoliidae as a whole. The first chapter of this thesis is a phylogenetic study conducted to clarify the relationships among families and orders of Magnoliidae. To do so, I sampled 199 species of Magnoliidae and 12 molecular markers from the three genomes and conducted phylogenetic analyses using parsimony, maximum likelihood, and Bayesian methods. The results confirm, with a greater level of support, two clades in Magnoliidae: Canellale + Piperales, and Laurales + Magnoliales. In addition, the relationships among the 20 families are generally well supported, and Lactoridaceae and Hydnoraceae are nested within Aristolochiaceae (Piperales). In the second chapter, the ages and phylogenetic positions of 10 fossils attributed to Magnoliidae were reviewed in detail. The goal of this study was to provide new reliable calibration points in order to conduct molecular dating analyses. These fossils were selected from the rich fossil record of the group because of their previous inclusion in phylogenetic analyses with extant taxa. The resulting calibration scheme provides six solid, internal minimum age constraints. The third chapter includes molecular dating analyses using the present calibration scheme and the same molecular dataset of Chapter 1. This study tends to push back in time the ages of the crown nodes of Magnoliidae (127.1-198.9 Ma), and of the four orders, Canellales (126.3-141.0 Ma), Piperales (88.2-157.7 Ma), Laurales (111.8-165.6 Ma), and Magnoliales (115.0-164.2 Ma). In the same chapter, I investigated the mode of diversification in the group. The strongly imbalanced distribution of species appears to be best explained by models of diversification with 6 to 14 diversification rate shifts. Finally, in the last chapter, I traced the evolution of 26 floral characters to reconstruct the ancestral flowers in key nodes of Magnoliidae. I used the phylogeny of Chapter 1 and an exemplar approach. Our results show that the most recent common ancestor of all Magnoliidae was a tree bearing actinomorphic, bisexual flowers with a differentiated perianth of two alternate, trimerous whorls of free perianth parts (outer and inner tepals) and probably three free stamens. This work provides key results on the evolution of Magnoliidae and raises several new questions such as the impact of geological crises on diversification of the group or the influence of pollinators and the environment on the evolution of floral morphology.; Les relations de parentés profondes au sein des Angiospermes ont été longtemps incertaines. A la fin des années 90, les études phylogénétiques à grande échelle ont contribué à l’obtention de l’arbre actuel des Plantes à fleurs, dans lequel Eudicotylédones, Monocotylédones et Magnoliidae forment les trois plus grands clades. Contrairement aux Monocotylédones et aux Eudicotylédones, la monophylie des Magnoliidae (Canellales, Laurales, Magnoliales et Piperales) n’a été soutenue que plus récemment. Les Magnoliidae contiennent actuellement 20 familles et environ 10 000 espèces majoritairement présentes sous les tropiques. Avant cette thèse, de nombreuses parties de ce groupe avaient été étudiées en détail mais l’histoire évolutive du groupe dans son ensemble était encore mal connue. Le premier chapitre est une étude phylogénétique des relations entre les familles et les ordres de Magnoliidae. Pour réaliser cette étude, j’ai échantillonné 199 espèces du groupe et 12 marqueurs moléculaires issus des trois génomes. J’ai ensuite mené des analyses phylogénétiques avec les méthodes de parcimonie, d’inférence bayésienne et de maximum de vraisemblance. Les résultats confirment avec un plus fort soutien la présence de deux clades dans ce groupe : Canellales + Piperales et Laurales + Magnoliales. De plus, les relations entre les 20 familles sont généralement bien soutenues, les Lactoridaceae et les Hydnoraceae étant incluses dans les Aristolochiaceae (Piperales). Dans le second chapitre, j’ai révisé l’âge et la position de 10 fossiles identifiés comme appartenant aux Magnoliidae. Le but de cette étude était de fournir de nouveaux points de calibration fiables afin de conduire de nouvelles analyses de datation moléculaire. Parmi les nombreux fossiles du groupe, nous avons choisi ces espèces car elles avaient été placées phylogénétiquement par des études antérieures. Le schéma de calibration résultant de ce travail inclut six contraintes fiables d’âges minimum. Le troisième chapitre est une étude de datation moléculaire utilisant ce schéma de calibration et le même jeu de données moléculaires que le chapitre 1. Les résultats tendent à repousser l’âge des Magnoliidae (127.1-198.9 Ma), et des quatre ordres Canellales (126.3-141.0 Ma), Piperales (88.2-157.7 Ma), Laurales (111.8-165.6 Ma) et Magnoliales (115.0-164.2 Ma). Dans ce même chapitre, j’ai également étudié le mode de diversification du groupe. Les variations importantes du nombre d’espèces entre les différentes parties de l’arbre s’expliquent le mieux par des modèles de diversification incluant 6 à 14 transition du taux net de diversification. Enfin, dans le dernier chapitre de la thèse, j’ai retracé l’histoire évolutive de 26 caractères floraux pour reconstruire les fleurs ancestrales de nœuds-clés des Magnoliidae. Pour ce faire, j’ai tiré parti de la phylogénie du premier chapitre et utilisé les mêmes espèces dans ma matrice morphologique. Les résultats montrent que l’ancêtre commun le plus récent des Magnoliidae présentait des fleurs bisexuées et actinomorphes avec un périanthe différencié de deux cycles trimères à tépales libres et probablement trois étamines libres. Ce travail de thèse apporte des résultats importants sur l’évolution des Magnoliidae et soulève de nombreuses questions telles que l’impact des crises géologiques sur la diversification du groupe ou l’influence des pollinisateurs et de l’environnement sur l’évolution de la morphologie florale.

Deep phylogenetic relationships in the angiosperms had long been uncertain. However, by the end of the 1990s, large-scale studies contributed to the current well resolved picture of the tree of flowering plants, in which eudicots, monocots, and magnoliids are the three largest clades. Whereas monocots and eudicots have been recognized since the very first phylogenetic analyses, the monophyly of magnoliids (Canellales, Laurales, Magnoliales, and Piperales) is a more recent result. Magnoliidae, as now circumscribed, consist of 20 families and ca. 10,000 species mostly distributed in the tropics. Before the present thesis, several parts of the magnoliid tree had been well studied, but little was known about the evolutionary history of Magnoliidae as a whole. The first chapter of this thesis is a phylogenetic study conducted to clarify the relationships among families and orders of Magnoliidae. To do so, I sampled 199 species of Magnoliidae and 12 molecular markers from the three genomes and conducted phylogenetic analyses using parsimony, maximum likelihood, and Bayesian methods. The results confirm, with a greater level of support, two clades in Magnoliidae: Canellale + Piperales, and Laurales + Magnoliales. In addition, the relationships among the 20 families are generally well supported, and Lactoridaceae and Hydnoraceae are nested within Aristolochiaceae (Piperales). In the second chapter, the ages and phylogenetic positions of 10 fossils attributed to Magnoliidae were reviewed in detail. The goal of this study was to provide new reliable calibration points in order to conduct molecular dating analyses. These fossils were selected from the rich fossil record of the group because of their previous inclusion in phylogenetic analyses with extant taxa. The resulting calibration scheme provides six solid, internal minimum age constraints. The third chapter includes molecular dating analyses using the present calibration scheme and the same molecular dataset of Chapter 1. This study tends to push back in time the ages of the crown nodes of Magnoliidae (127.1-198.9 Ma), and of the four orders, Canellales (126.3-141.0 Ma), Piperales (88.2-157.7 Ma), Laurales (111.8-165.6 Ma), and Magnoliales (115.0-164.2 Ma). In the same chapter, I investigated the mode of diversification in the group. The strongly imbalanced distribution of species appears to be best explained by models of diversification with 6 to 14 diversification rate shifts. Finally, in the last chapter, I traced the evolution of 26 floral characters to reconstruct the ancestral flowers in key nodes of Magnoliidae. I used the phylogeny of Chapter 1 and an exemplar approach. Our results show that the most recent common ancestor of all Magnoliidae was a tree bearing actinomorphic, bisexual flowers with a differentiated perianth of two alternate, trimerous whorls of free perianth parts (outer and inner tepals) and probably three free stamens. This work provides key results on the evolution of Magnoliidae and raises several new questions such as the impact of geological crises on diversification of the group or the influence of pollinators and the environment on the evolution of floral morphology.; Les relations de parentés profondes au sein des Angiospermes ont été longtemps incertaines. A la fin des années 90, les études phylogénétiques à grande échelle ont contribué à l’obtention de l’arbre actuel des Plantes à fleurs, dans lequel Eudicotylédones, Monocotylédones et Magnoliidae forment les trois plus grands clades. Contrairement aux Monocotylédones et aux Eudicotylédones, la monophylie des Magnoliidae (Canellales, Laurales, Magnoliales et Piperales) n’a été soutenue que plus récemment. Les Magnoliidae contiennent actuellement 20 familles et environ 10 000 espèces majoritairement présentes sous les tropiques. Avant cette thèse, de nombreuses parties de ce groupe avaient été étudiées en détail mais l’histoire évolutive du groupe dans son ensemble était encore mal connue. Le premier chapitre est une étude phylogénétique des relations entre les familles et les ordres de Magnoliidae. Pour réaliser cette étude, j’ai échantillonné 199 espèces du groupe et 12 marqueurs moléculaires issus des trois génomes. J’ai ensuite mené des analyses phylogénétiques avec les méthodes de parcimonie, d’inférence bayésienne et de maximum de vraisemblance. Les résultats confirment avec un plus fort soutien la présence de deux clades dans ce groupe : Canellales + Piperales et Laurales + Magnoliales. De plus, les relations entre les 20 familles sont généralement bien soutenues, les Lactoridaceae et les Hydnoraceae étant incluses dans les Aristolochiaceae (Piperales). Dans le second chapitre, j’ai révisé l’âge et la position de 10 fossiles identifiés comme appartenant aux Magnoliidae. Le but de cette étude était de fournir de nouveaux points de calibration fiables afin de conduire de nouvelles analyses de datation moléculaire. Parmi les nombreux fossiles du groupe, nous avons choisi ces espèces car elles avaient été placées phylogénétiquement par des études antérieures. Le schéma de calibration résultant de ce travail inclut six contraintes fiables d’âges minimum. Le troisième chapitre est une étude de datation moléculaire utilisant ce schéma de calibration et le même jeu de données moléculaires que le chapitre 1. Les résultats tendent à repousser l’âge des Magnoliidae (127.1-198.9 Ma), et des quatre ordres Canellales (126.3-141.0 Ma), Piperales (88.2-157.7 Ma), Laurales (111.8-165.6 Ma) et Magnoliales (115.0-164.2 Ma). Dans ce même chapitre, j’ai également étudié le mode de diversification du groupe. Les variations importantes du nombre d’espèces entre les différentes parties de l’arbre s’expliquent le mieux par des modèles de diversification incluant 6 à 14 transition du taux net de diversification. Enfin, dans le dernier chapitre de la thèse, j’ai retracé l’histoire évolutive de 26 caractères floraux pour reconstruire les fleurs ancestrales de nœuds-clés des Magnoliidae. Pour ce faire, j’ai tiré parti de la phylogénie du premier chapitre et utilisé les mêmes espèces dans ma matrice morphologique. Les résultats montrent que l’ancêtre commun le plus récent des Magnoliidae présentait des fleurs bisexuées et actinomorphes avec un périanthe différencié de deux cycles trimères à tépales libres et probablement trois étamines libres. Ce travail de thèse apporte des résultats importants sur l’évolution des Magnoliidae et soulève de nombreuses questions telles que l’impact des crises géologiques sur la diversification du groupe ou l’influence des pollinisateurs et de l’environnement sur l’évolution de la morphologie florale.