The age and diversification of the angiosperms re-revisited

? Premise of the study: It has been 8 years since the last comprehensive analysis of divergence times across the angiosperms. Given recent methodological improvements in estimating divergence times, refined understanding of relationships among major angiosperm lineages, and the immense interest in using large angiosperm phylogenies to investigate questions in ecology and comparative biology, new estimates of the ages of the major clades are badly needed. Improved estimations of divergence times will concomitantly improve our understanding of both the evolutionary history of the angiosperms and the patterns and processes that have led to this highly diverse clade. ? Methods: We simultaneously estimated the age of the angiosperms and the divergence times of key angiosperm lineages, using 36 calibration points for 567 taxa and a relaxed clock methodology that does not assume any correlation between rates, thus allowing for lineage-specific rate heterogeneity. ? Key results: Based on the analysis for which we set fossils to fit lognormal priors, we obtained an estimated age of the angiosperms of 167-199 Ma and the following age estimates for major angiosperm clades: Mesangiospermae (139-156 Ma); Gunneridae (109-139 Ma); Rosidae (108-121 Ma); Asteridae (101-119 Ma). ? Conclusions: With the exception of the age of the angiosperms themselves, these age estimates are generally younger than other recent molecular estimates and very close to dates inferred from the fossil record. We also provide dates for all major angiosperm clades (including 45 orders and 335 families [208 stem group age only, 127 both stem and crown group ages], sensu APG III). Our analyses provide a new comprehensive source of reference dates for major angiosperm clades that we hope will be of broad utility.     

Evolutionary diversification of the flowers in angiosperms

Angiosperms and their flowers have greatly diversified into an overwhelming array of forms in the past 135 million years. Diversification was shaped by changes in climate and the biological environment (vegetation, interaction with other organisms) and by internal structural constraints and potentials. This review focuses on the development and structural diversity of flowers and structural constraints. It traces floral diversification in the different organs and organ complexes (perianth, androecium, gynoecium) through the major clades of extant angiosperms. The continuously improved results of molecular phylogenetics provide the framework for this endeavor, which is necessary for the understanding of the biology of the angiosperms and their flowers. Diversification appears to work with innovations and modifications of form. Many structural innovations originated in several clades and in special cases could become key innovations, which likely were hot spots of diversification. Synorganization between organs was an important process to reach new structural levels, from which new diversifications originated. Complexity of synorganization reached peaks in Orchidaceae and Apocynaceae with the independent evolution of pollinaria. Such a review throughout the major clades of angiosperms also shows how superficial and fragmentary our knowledge on floral structure in many clades is. Fresh studies and a multidisciplinary approach are needed.     

Phylogenetic evidence for pollinator-driven diversification of angiosperms

Since Darwin, the diversity of flowers has been attributed to selection by pollinators. Although pollinators commonly act as selective agents on floral traits, determining the extent to which they have influenced angiosperm diversification requires a historical perspective. Here we review recent studies that combine species-level phylogenies with pollinator data and show that pollinator shifts are common, being associated with at least a quarter of documented divergence events. However, shift frequency and directionality vary extensively, owing to variation in intrinsic factors such as floral features and phylogenetic history, as well as extrinsic factors such as interactions with local pollinator assemblages. Despite technical advances, phylogenies remain limited in their power to distinguish among various pollinator-driven evolutionary processes.     

The evolutionary origin and diversification of feathers

Progress on the evolutionary origin and diversification of feathers has been hampered by conceptual problems and by the lack of plesiomorphic feather fossils. Recently, both of these limitations have been overcome by the proposal of the developmental theory of the origin of feathers, and the discovery of primitive feather fossils on nonavian theropod dinosaurs. The conceptual problems of previous theories of the origin of feathers are reviewed, and the alternative developmental theory is presented and discussed. The developmental theory proposes that feathers evolved through a series of evolutionary novelties in developmental mechanisms of the follicle and feather germ. The discovery of primitive and derived fossil feathers on a diversity of coelurosaurian theropod dinosaurs documents that feathers evolved and diversified in nonavian theropods before the origin of birds and before the origin of flight. The morphologies of these primitive feathers are congruent with the predictions of the developmental theory. Alternatives to the theropod origin of feathers are critique and rejected. Hypotheses for the initial function of feathers are reviewed. The aerodynamic theory of feather origins is falsified, but many other functions remain developmentally and phylogenetically plausible. Whatever their function, feathers evolved by selection for a follicle that would grow an emergent tubular appendage. Feathers are inherently tubular structures. The homology of feathers and scales is weakly supported. Feathers are composed of a suite of evolutionary novelties that evolved by the duplication, hierarchical organization, interaction, dissociation, and differentiation of morphological modules. The unique capacity for modular subdivision of the tubular feather follicle and germ has fostered the evolution of numerous innovations that characterize feathers. The evolution of feather keratin and the molecular basis of feather development are also discussed.     

The origin of angiosperms: New and old problems

Recent palaeobotanical discoveries assisted by the thorough morphological analysis of 'living fossils'-archaic extant plants-have brought to light many unexpected features of the early angiosperms and their immediate precursors, while studies in palaeoecology have provided a basis for deciphering the chronology of evolutionary events and their environmental forcing. Our previous ideas of what is primitive and what angiosperm ancestors looked like are presently under revision. We now have a clearer picture of how macroevolution proceeds and how a large taxon could come into being.     

Genome duplication and the origin of angiosperms

Despite intensive research, little is known about the origin of the angiosperms and their rise to ecological dominance during the Early Cretaceous. Based on whole-genome analyses of Arabidopsis thaliana, there is compelling evidence that angiosperms underwent two whole-genome duplication events early during their evolutionary history. Recent studies have shown that these events were crucial for the creation of many important developmental and regulatory genes found in extant angiosperm genomes. Here, we argue that these ancient polyploidy events might have also had an important role in the origin and diversification of the angiosperms.     

The endosymbiotic origin,diversification and fate of plastids

Plastids and mitochondria each arose from a single endosymbiotic event and share many similarities in how they were reduced and integrated with their host. However, the subsequent evolution of the two organelles could hardly be more different: mitochondria are a stable fixture of eukaryotic cells that are neither lost nor shuffled between lineages, whereas plastid evolution has been a complex mix of movement, loss and replacement. Molecular data from the past decade have substantially untangled this complex history, and we now know that plastids are derived from a single endosymbiotic event in the ancestor of glaucophytes, red algae and green algae (including plants). The plastids of both red algae and green algae were subsequently transferred to other lineages by secondary endosymbiosis. Green algal plastids were taken up by euglenids and chlorarachniophytes, as well as one small group of dinoflagellates. Red algae appear to have been taken up only once, giving rise to a diverse group called chromalveolates. Additional layers of complexity come from plastid loss, which has happened at least once and probably many times, and replacement. Plastid loss is difficult to prove, and cryptic, non-photosynthetic plastids are being found in many non-photosynthetic lineages. In other cases, photosynthetic lineages are now understood to have evolved from ancestors with a plastid of different origin, so an ancestral plastid has been replaced with a new one. Such replacement has taken place in several dinoflagellates (by tertiary endosymbiosis with other chromalveolates or serial secondary endosymbiosis with a green alga), and apparently also in two rhizarian lineages: chlorarachniophytes and Paulinella (which appear to have evolved from chromalveolate ancestors). The many twists and turns of plastid evolution each represent major evolutionary transitions, and each offers a glimpse into how genomes evolve and how cells integrate through gene transfers and protein trafficking.     

Phylogenetic evidence for the herbaceous origin of angiosperms

The ancestral angiosperm is commonly interpreted as an arborescent to shrubby magnolialean with large, multiparted, complex flowers. We examined this hypothesis using a phylogenetic analysis of new and reevaluated characters polarizabled with outgroup comparison. Our cladistic analysis of basal angiosperms placed the nonmagnolialeanChloranthaceae andPiperaceae at the bottom of the tree. We further inferred the probable ancestral states of characters not polarizable with outgroup comparison by examining their distribution among taxa at the base of our cladogram. The sum of ancestral character states suggests that the protoangiosperm was a diminutive, rhizomatous to scrambling perennial herb, with small, simple flowers.     

Cretaceous diversification of angiosperms in the western part of the Iberian Peninsula

The classic leaf fossil floras from the Cretaceous of the Lusitanian Basin, Portugal, which were first described more than one hundred years ago, have played an important role in the development of ideas on the early evolution of angiosperms. Insights into the nature of vegetational change in the Lusitanian Basin through the Cretaceous have also come from studies of fossil pollen and spores, but the discovery of a series of mesofossil floras containing well-preserved angiosperm reproductive structures has provided a new basis for understanding the systematic relationships and biology of angiosperms at several stratigraphic levels through the Cretaceous. In the earliest mesofossil floras from the Torres Vedras locality, which are of probable Late Barremian-Early Aptian age, angiosperms are surprisingly diverse with about 50 different taxa. In slightly later mesofossil floras, which are of probable Late Aptian-Early Albian age, the diversity of angiosperms is still more substantial with more than hundred different kinds of angiosperm reproductive structures recognized from the Famalicão locality alone. However, this early diversity is largely among angiosperm lineages that produced monoaperturate pollen (e.g., Chloranthaceae, Nymphaeales) and early diverging monocots (Alismatales). Eudicots are rare in these Early Cretaceous mesofossil floras, but already by the Late Cenomanian the vegetation of the western Iberian Peninsula is dominated by angiosperms belonging to various groups of core eudicots. The Normapolles complex is a particularly conspicuous element in both mesofossil floras and in palynological assemblages. In the Late Cretaceous mesofossil floras from Esgueira and Mira, which are of Campanian-Maastrichtian age, core eudicots are also floristically dominant and flowers show great organisational similarity to fossil flowers from other Late Cretaceous floras described from other localities in Asia, Europe and North America.     

Deep-sea origin and in-situ diversification of chrysogorgiid octocorals

The diversity, ubiquity and prevalence in deep waters of the octocoral family Chrysogorgiidae Verrill, 1883 make it noteworthy as a model system to study radiation and diversification in the deep sea. Here we provide the first comprehensive phylogenetic analysis of the Chrysogorgiidae, and compare phylogeny and depth distribution. Phylogenetic relationships among 10 of 14 currently-described Chrysogorgiidae genera were inferred based on mitochondrial (mtMutS, cox1) and nuclear (18S) markers. Bathymetric distribution was estimated from multiple sources, including museum records, a literature review, and our own sampling records (985 stations, 2345 specimens). Genetic analyses suggest that the Chrysogorgiidae as currently described is a polyphyletic family. Shallow-water genera, and two of eight deep-water genera, appear more closely related to other octocoral families than to the remainder of the monophyletic, deep-water chrysogorgiid genera. Monophyletic chrysogorgiids are composed of strictly (Iridogorgia Verrill, 1883, Metallogorgia Versluys, 1902, Radicipes Stearns, 1883, Pseudochrysogorgia Pante & France, 2010) and predominantly (Chrysogorgia Duchassaing & Michelotti, 1864) deep-sea genera that diversified in situ. This group is sister to gold corals (Primnoidae Milne Edwards, 1857) and deep-sea bamboo corals (Keratoisidinae Gray, 1870), whose diversity also peaks in the deep sea. Nine species of Chrysogorgia that were described from depths shallower than 200 m, and mtMutS haplotypes sequenced from specimens sampled as shallow as 101 m, suggest a shallow-water emergence of some Chrysogorgia species.     

Factors influencing diversification in angiosperms: at the crossroads of intrinsic and extrinsic traits

Recent studies indicate that both key innovations and available area influence species richness in angiosperms. Available area has been observed to have the greatest effect, however, and appears to alter the "carrying capacity" of a lineage rather than alter diversification rates. Here, we review and weigh the evidence of predictors of angiosperm diversification and further dissect how area can place ecological limits on diversification of angiosperms, specifically addressing the following: (1) theoretical mechanisms by which particular intrinsic and extrinsic traits may affect diversification in angiosperm families; (2) evidence that the amount of available area determines the ecological limits on lineages; and (3) geographical distribution of diversification hotspots in angiosperms, concentrating on the effects of zygomorphy, noncontiguous area, and latitude. While we found that dispersal to numerous noncontiguous areas is most important in spurring diversification, diversification of tropical and zygomorphic families appears to be elevated by the generation of more species per given area.     

Current views of the origin and diversification of tetrapods

In several recent decades, a wealth of evidence was obtained (including new fossils and new nucleotide sequences) that allows a revision of the current evolutionary theories. The primary structure was determined for orthologous regions from a variety of genomes. Complete genome sequences were established for some organisms. The review considers the modern concepts of the origin and diversification of tetrapods and of the formation of modern vertebrate classes.     

Fossil evidence for a herbaceous diversification of early eudicot angiosperms during the Early Cretaceous

Eudicot flowering plants comprise roughly 70% of land plant species diversity today, but their early evolution is not well understood. Fossil evidence has been largely restricted to their distinctive tricolpate pollen grains and this has limited our understanding of the ecological strategies that characterized their primary radiation. I describe megafossils of an Early Cretaceous eudicot from the Potomac Group in Maryland and Virginia, USA that are complete enough to allow reconstruction of important life-history traits. I draw on quantitative and qualitative analysis of functional traits, phylogenetic analysis and sedimentological evidence to reconstruct the biology of this extinct species. These plants were small and locally rare but widespread, fast-growing herbs. They had complex leaves and they were colonizers of bright, wet, disturbance-prone habitats. Other early eudicot megafossils appear to be herbaceous rather than woody, suggesting that this habit was characteristic of their primary radiation. A mostly herbaceous initial diversification of eudicots could simultaneously explain the heretofore sparse megafossil record as well as their rapid diversification during the Early Cretaceous because the angiosperm capacity for fast reproduction and fast evolution is best expressed in herbs.     

Cretaceous origin and repeated tertiary diversification of the redefined butterflies

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous-Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis, a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.     

Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach

We present a numerical cladistic (parsimony) analysis of seed plants plus progymnosperms, using characters from all parts of the plant body, outgroup comparison, and a method of character coding that avoids biases for or against alternative morphological theories. The robustness of the results was tested by construction of alternative trees and analysis of subsets of the data. These experiments show that although some clades are strongly supported, they can often be related to each other in very different but nearly equally parsimonious ways, apparently because of extensive homoplasy. Our results support Rothwell’s idea that coniferopsids are derived fromCallistophyton- like platyspermic seed ferns with saccate pollen, but the hypothesis that they evolved fromArchaeopteris- like progymnosperms and the seed arose twice is nearly as parsimonious. Meyen’s division of seed plants into radiospermic and primarily and secondarily platyspermic lines is highly unparsimonious, but his suggestion that ginkgos are related to peltasperms deserves attention. Angiosperms belong among the platyspermic groups, as the sister group of Bennettitales,Pentoxylon, and Gnetales, and this “anthophyte” clade is best related toCaytonia and glossopterids, although relationships with other combinations of Mesozoic seed fern taxa are nearly as parsimonious. These results imply that the angiosperm carpel can be interpreted as a modified pinnate sporophyll bearing anatropous cupules (=bitegmic ovules), while gnetalian strobili are best interpreted as aggregations of highly reduced bennettitalian flowers, as anticipated by Arber and Parkin and Crane. Our most parsimonious trees imply that the angiosperm line (though not necessarily all its modern features) extended back to the Triassic, but a later derivation of angiosperms from some species ofCaytonia or Bennettitales, which would be nearly as parsimonious, should also be considered. These results raise the possibility that many features considered key adaptations in the origin and rise of angiosperms (insectpollinated flowers, rapid reproduction, drought tolerance) were actually inherited from their gymnospermous precursors. The explosive diversification of angiosperms may instead have been a consequence of carpel closure, resulting in increased speciation rates due to potential for stigmatic isolating mechanisms and/or new means of dispersal. DNA sequencing of extant plants and better information on anatomy, chemistry, sporophyll morphology, and embryology of Bennettitales and Caytoniales and the morphological diversity of Mesozoic anthophytes could provide critical tests of relationships.     

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes.