The origin of angiosperms

The claim of monophyletic origin of angiosperms arose from the confusion of phylogenetic and taxonomic concepts. Unpreconceived studies of extant angiosperms point to more than one archetype. Several lines of angiosperms have simultaneously entered the fossil record; the monocotyledons, proto-Hamamelidales, proto-Laurales and “proteophylls” (possibly ancestral to the Rosidae) are recognized among them. Three groups of Mesozoic seed plants — the Caytoniales, Czekanowskiales and Dirhopalostachyaceae — are distinguished as major sources of angiosperm characters (proangiosperms). Other Mesozoic lineages probably also contributed to the angiosperm character pool. Angiospermization is related to Mammalization and other processes involved in development of the Cenozoic lithosphere and biosphere.     

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.     

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.     

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.     

Age at maturity and diversification in woody angiosperms

Angiosperm diversification has been associated with plant-animal interactions such as seed dispersal and pollination and life-history characters such as rapid growth and fast reproduction. This paper relates a life-history character (age at maturity) to woody angiosperm diversification. Here I present a comparative analysis of data drawn from the literature, indicating that time to first reproduction is shorter in woody angiosperms than in gymnosperms. In addition, age at maturity is negatively correlated with the rate of diversification (measured as the number of species per genus) at all the taxonomic levels analyzed and also when phylogenetically independent contrasts were conducted. This correlation suggests that early reproduction promotes diversification in woody angiosperms. Furthermore, this correlation is not a confounding effect of the association between age at maturity and other ecological factors that promote angiosperm diversification, such as pollination and seed dispersal systems.     

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.     

The origin and diversification of Galapagos mockingbirds

Abstract Evolutionary radiations of colonists on archipelagos provide valuable insight into mechanisms and modes of speciation. The apparent diversification of Galapagos mockingbirds (Nesomimus) provoked Darwin's initial conception of adaptive radiation, but the monophyly of this historically important exemplar has not been evaluated with molecular data. Additionally, as with most Galapagos organisms, we have a poor understanding of the temporal pattern of diversification of the mockingbirds following colonization(s) from source populations. Here we present a molecular phylogeny of Galapagos and other mockingbird populations based on mitochondrial sequence data. Monophyly of Galapagos mockingbirds was supported, suggesting a single colonization of the archipelago followed by diversification. Our analyses also indicate that Nesomimus is nested within the traditional genus Mimus, making the latter paraphyletic, and that the closest living relatives of Galapagos mockingbirds appear to be those currently found in North America, northern South America, and the Caribbean, rather than the geographically nearest species in continental Ecuador. Thus, propensity for over‐water dispersal may have played a more important role than geographic proximity in the colonization of Galapagos by mockingbirds. Within Galapagos, four distinct mitochondrial DNA clades were identified. These four clades differ from current taxonomy in several important respects. In particular, mockingbirds in the eastern islands of the archipelago (Española, San Cristóbal, and Genovesa) have very similar mitochondrial DNA sequences, despite belonging to three different nominal species, and mockingbirds from Isabela, in the west of the archipelago, are more phylogenetically divergent than previously recognized. Consistent with current taxonomy is the phylogenetic distinctiveness of the Floreana mockingbird (N. trifasciatus) and close relationships among most mockingbirds from the central and northern region of the archipelago (currently considered conspecific populations of N. parvulus). Overall, phylogeographic patterns are consistent with a model of wind‐based dispersal within Galapagos, with colonization of more northerly islands by birds from more southern populations, but not the reverse. Further radiation in Galapagos would require coexistence of multiple species on individual islands, but this may be prevented by relatively limited morphological divergence among mockingbirds and by lack of sufficient habitat diversity in the archipelago to support more than one omnivorous mimid     

Nonstochastic variation of species-level diversification rates within angiosperms

Variations in the origination and extinction rates of species over geological time often are linked with a range of factors, including the evolution of key innovations, changes in ecosystem structure, and environmental factors such as shifts in climate and physical geography. Before hypothesizing causality of a single factor, it is critical to demonstrate that the observed variation in diversification is significantly greater than one would expect due to natural stochasticity in the evolutionary branching process. Here, we use a likelihood-ratio test to compare taxonomic rate heterogeneity to a neutral birth-death model, using data on well-supported sister pairs of taxa and their species richness. We test the likelihood that the distribution of extant species among angiosperm genera and families could be the result of constant diversification rates. Results strongly support the conclusion that there is significantly more heterogeneity in diversity at the species level within angiosperms than would be expected due to stochastic processes. This result is consistent in datasets of genus pairs and family pairs and is not affected significantly by degrading pairs to simulate inaccuracy in the assumption of simultaneous origin of sister taxa. When we parse taxon pairs among higher groups of angiosperms, results indicate that a constant rates model is not rejected by rosid and basal eudicot pairs but is rejected by asterid and eumagnoliid pairs. These results provide strong support for the hypothesis that species-level rates of origination and/or extinction have varied nonrandomly within angiosperms and that the magnitude of heterogeneity varies among major groups within angiosperms.     

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.     

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.     

Evolutionary origin and functional diversification of aminotransferases

Aminotransferases (ATs) are pyridoxal 5′-phosphate–dependent enzymes that catalyze the transamination reactions between amino acid donor and keto acid acceptor substrates. Modern AT enzymes constitute ∼2% of all classified enzymatic activities, play central roles in nitrogen metabolism, and generate multitude of primary and secondary metabolites. ATs likely diverged into four distinct AT classes before the appearance of the last universal common ancestor and further expanded to a large and diverse enzyme family. Although the AT family underwent an extensive functional specialization, many AT enzymes retained considerable substrate promiscuity and multifunctionality because of their inherent mechanistic, structural, and functional constraints. This review summarizes the evolutionary history, diverse metabolic roles, reaction mechanisms, and structure–function relationships of the AT family enzymes, with a special emphasis on their substrate promiscuity and multifunctionality. Comprehensive characterization of AT substrate specificity is still needed to reveal their true metabolic functions in interconnecting various branches of the nitrogen metabolic network in different organisms.     

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.     

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.     

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.     

The role of Asia in the origin and diversification of hystricognathous rodents

In the absence of a comprehensive pre‐Oligocene fossil record, the origin and early evolution of hystricognathous rodents have long been the subject of much uncertainty. Baluchimyinae (Rodentia) were initially interpreted as a subfamily of the ctenodactyloid Chappatimyidae (sciurognathous), a group considered to be endemic to the Indian subcontinent and to be closely related to hystricognathous rodents. A newly discovered early Oligocene hystricognathous rodent, Bugtimys zafarullahi gen. n. et sp. n., described herein, from the Bugti Hills (Balochistan, Pakistan) sheds new light on the higher level taxonomy of the previously described Baluchimyinae. As a contribution to the phylogenetic debates regarding the origin of Hystricognathi, we present a cladistic assessment of the dental evidence for the Palaeogene hystricognathous rodent cladogenesis. Our phylogenetic results consistently support the monophyly of the Hystricognathiformes clade (including Tsaganomyidae plus Hystricognathi) of which baluchimyine rodents are clearly members. There is, however, no support for the monophyly of a baluchimyine clade. Nonetheless, ‘baluchimyines’ are for the moment reinterpreted as Hystricognathi incertae sedis. Hystricognathous rodents appear to be well diversified at least since the early Oligocene, both in Africa and South America (phiomorphs and caviomorphs, respectively), and also now in south Asia. Furthermore, our phylogenetic results support close relationships between early hystricognathous and Asian ‘ctenodactyloid’ rodents, which clearly points to an Asian origin for Hystricognathi. In this phylogenetic framework, ‘baluchimyines’ and tsaganomyids are representatives of an initial phase of diversification of hystricognathous rodents in Asia. Oligocene phiomorphs and caviomorphs (sister groups) seem therefore to share a common ‘Asian’ hystricognathous ancestor. This reinforces the possibility that the early dispersal of hystricognathous rodents to South America was not from Africa but from Asia.