Reconstructing the ancestral female gametophyte of angiosperms: Insights from Amborella and other ancient lineages of flowering plants

For more than a century, the common ancestor of flowering plants was thought to have had a seven-celled, eight-nucleate Polygonum-type female gametophyte. It is now evident that not one, but in fact three, patterns of female gametophyte development and mature structure characterize the common ancestors of the four most ancient clades of extant angiosperms: Amborella-type, Nuphar/Schisandra-type and Polygonum-type. The Amborella-type female gametophyte is restricted to a single extant species, Amborella trichopoda, and at maturity consists of eight cells and nine nuclei. Development of the Amborella-type gametophyte is essentially identical to the Polygonum-type except that there is an additional and asynchronous cell division at the micropylar pole prior to maturation that produces a third synergid and the egg cell. The Nuphar/Schisandra-type female gametophyte is four-nucleate and four-celled and at maturity contains a typical three-celled egg apparatus and a central cell with a single haploid polar nucleus. This type of gametophyte appears to be universal among extant members of the Nymphaeales (including Hydatellaceae) and Austrobaileyales. Based on explicit reconstruction of character distribution and evolution, the Polygonum-type female gametophyte is certain to be representative of the common ancestors of monocots, eudicots, magnoliids, Ceratophyllaceae, and Chloranthaceae. There are compelling biological reasons to suggest that the four-celled, four-nucleate female gametophyte (as found in Nymphaeales and Austrobaileyales) is ancestral among angiosperms, with transitions to Polygonum-type female gametophytes separately in the Amborellales and in the ancient angiosperm clade that includes all angiosperms except Amborella, Nymphaeales, and Austrobaileyales. Subsequent to the evolution of a seven-celled, eight-nucleate Polygonum-type female gametophyte in the Amborellales, we hypothesize that a peramorphic increase in egg apparatus cell number took place and led to the unique situation in which there are three synergids in Amborella trichopoda.     

Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella is supported as sister and Observed Variability is biased

Identifying the extant sister group to the remaining angiosperms has been a subject of long debate, for which the primary currently competing hypotheses are that Amborella alone is sister or that the clade (Amborella, Nymphaeales) is sister. Both Xi et al. (Syst. Biol., 2014, 63, 919) and Goremykin et al. (Syst. Biol., 2015, 64, 879) identified Amborella as sister in concatenation‐based phylogenetic analyses of their 310 nuclear genes and 78 plastid genes, respectively. But after application of Observed Variability‐based character subsampling, both papers reported the clade (Amborella, Nymphaeales) as sister. Hence alternative character‐sampling strategies may produce highly supported yet mutually exclusive phylogenetic inferences when applied to nuclear and plastid genomic data sets. Edwards et al. (Mol. Phylogenet. Evol., 2016, 94, 447) defended Observed Variability and the (Amborella, Nymphaeales) hypothesis. In this study I respond to Edwards et al.'s (Mol. Phylogenet. Evol., 2016, 94, 447) criticisms of Simmons and Gatesy (Mol. Phylogenet. Evol., 2015, 91, 98) and use Edwards et al.'s (Mol. Phylogenet. Evol., 2016, 94, 447) and Goremykin et al.'s (Syst. Biol., 2015, 64, 879) own data to demonstrate that the best‐supported phylogenetic hypothesis is that Amborella alone is sister and that the competing evidence in favour of the (Amborella, Nymphaeales) hypothesis is caused primarily by methodological artifacts (biased character deletion by Observed Variability, MP‐EST and STAR generally not being robust to the highly divergent and mis‐rooted gene trees that were used).     

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.     

Convergent evolution and adaptive radiation of beetle-pollinated angiosperms

A literature review of 34 families of flowering plants containing at least one species pollinated primarily by beetles is presented. While the majority of species are represented by magnoliids and basal monocotyledons specialized, beetle-pollinated systems have evolved independently in 14 families of eudicotyldons and six families of petaloid monocots. Four, overlapping modes of floral presentation in plants pollinated exclusively by beetles (Bilabiate, Brush, Chamber Blossom and Painted Bowl) are described. Chamber Blossoms and Painted Bowls are the two most common modes. Chamber Blossoms, found in magnoliids, primitive monocotyledons and in some families of woody eudicots, exploit the greatest diversity of beetle pollinators. Painted Bowls are restricted to petaloid monocots and a few families of eudicots dependent primarily on hairy species of Scarabaeidae as pollen vectors. In contrast, generalist flowers pollinated by a combination of beetles and other animals are recorded in 22 families. Generalist systems are more likely to secrete nectar and exploit four beetle families absent in specialist flowers. Centers of diversity for species with specialized, beetle-pollinated systems are distributed through the wet tropics (centers for Brush and Chamber Blossoms) to warm temperate-Mediterranean zones (centers for Painted Bowls and a few Bilabiate flowers). It is unlikely that beetles were the first pollinators of angiosperms but specialized, beetlepollinated flowers must have evolved by the midlate Cretaceous to join pre-existing guilds of beetlepollinated gymnosperms. The floras of Australia and western North America suggest that mutualistic interactions between beetles and flowers has been a continuous and labile trend in angiosperms with novel interactions evolving through the Tertiary.     

The identification of fossil angiosperm pollen and its bearing on the time and place of the origin of angiosperms

Studies in the 1970's reporting the occurrence of fossil pollen types in the Cretaceous, coupled with surveys of extant pollen morphology of primitive flowering plants, laid the foundation for proposing a Lower Cretaceous origin of angiosperms. Over the last 30 years, morphological, ultrastructural, and ontogenetic studies of both extant and fossil pollen have provided an array of new characters, as well as greater resolution in defining character polarities. Moreover, a range of fossil pollen types exhibiting angiosperm characters occur in low frequency within Triassic and Jurassic sediments. The pollen data provide evidence of a pre-Cretaceous origin of angiosperms. Speciation and extinction rates were likely equal during the Triassic and Jurassic, resulting in the paucity of angiosperm pollen types from different geographic areas in the Atlantic – South American/African rift zone. It was not until the Lower Cretaceous that origination rates exceed extinction rates, resulting in the subsequent diversification of angiosperms and the origin of the eudicots.     

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 Amborella genome: an evolutionary reference for plant biology

The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.     

The ecophysiology of early angiosperms

Angiosperms first appeared during the Early Cretaceous, and within 30 million years they reigned over many floras worldwide. Associated with this rise to prominence, angiosperms produced a spectrum of reproductive and vegetative innovations, which produced a cascade of ecological consequences that altered the ecology and biogeochemistry of the planet. The pace, pattern and phylogenetic systematics of the Cretaceous angiosperm diversification are broadly sketched out. However, the ecophysiology and environmental interactions that energized the early angiosperm radiation remain unresolved. This constrains our ability to diagnose the selective pressures and habitat contexts responsible for the evolution of fundamental angiosperm features, such as flowers, rapid growth, xylem vessels and net-veined leaves, which in association with environmental opportunities, drove waves of phylogenetic and ecological diversification. Here, we consider our current understanding of early angiosperm ecophysiology. We focus on comparative patterns of ecophysiological evolution, emphasizing carbon- and water-use traits, by merging recent molecular phylogenetic studies with physiological studies focused on extant basal angiosperms. In doing so, we discuss how early angiosperms established a roothold in pre-existing Mesozoic plant communities, and how these events canalized subsequent bursts of angiosperm diversification during the Aptian-Albian.     

Leaf flavonoids of Amborella trichopoda

The leaf flavonoids of Amborella trichopoda were examined and two kaempterol glycosides were detected. Procyanidin was also present. These results are similar to the flavonoid pattern in other families of the Laurales and it is suggested that simple flavonol glycosides are a primitive feature in the order.     

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.     

The origin and diversification of angiosperms

The angiosperms, one of five groups of extant seed plants, are the largest group of land plants. Despite their relatively recent origin, this clade is extremely diverse morphologically and ecologically. However, angiosperms are clearly united by several synapomorphies. During the past 10 years, higher-level relationships of the angiosperms have been resolved. For example, most analyses are consistent in identifying Amborella, Nymphaeaceae, and Austrobaileyales as the basalmost branches of the angiosperm tree. Other basal lineages include Chloranthaceae, magnoliids, and monocots. Approximately three quarters of all angiosperm species belong to the eudicot clade, which is strongly supported by molecular data but united morphologically by a single synapomorphy-triaperturate pollen. Major clades of eudicots include Ranunculales, which are sister to all other eudicots, and a clade of core eudicots, the largest members of which are Saxifragales, Caryophyllales, rosids, and asterids. Despite rapid progress in resolving angiosperm relationships, several significant problems remain: (1) relationships among the monocots, Chloranthaceae, magnoliids, and eudicots, (2) branching order among basal eudicots, (3) relationships among the major clades of core eudicots, (4) relationships within rosids, (5) relationships of the many lineages of parasitic plants, and (6) integration of fossils with extant taxa into a comprehensive tree of angiosperm phylogeny.     

The late pollen-specific actins in angiosperms

The actin gene family of Arabidopsis has eight functional genes that are grouped into two ancient classes, vegetative and reproductive, and into five subclasses based on their phylogeny and mRNA expression patterns. Progress in deciphering the functional significance of this diversity is hindered by the lack of tools that can distinguish the highly conserved subclasses of actin proteins at the biochemical and cellular level. In order to address the functional diversity of actin isovariants, we have used Arabidopsis recombinant actins as immunogens and produced several new anti-actin monoclonal antibodies. One of them, MAb45a, specifically recognizes two closely related reproductive subclasses of actins. On immunoblots, MAb45a reacts strongly with actins expressed in mature pollen but not with actins in other Arabidopsis tissues. Moreover, immunocytochemical studies show that this antibody can distinguish actin filaments in pollen tubes from those in most vegetative tissues. Peptide competition analyses demonstrate that asparagine at position 79 (Asn79) within an otherwise conserved sequence is essential for MAb45a specificity. Actins with the Asn79 epitope are also expressed in the mature pollen from diverse angiosperms and Ephedra but not from lower gymnosperms, suggesting that this epitope arose in an ancestor common to angiosperms and advanced gymnosperms more than 220 million years ago. During late pollen development in angio- sperms there is a switch in expression of actins from vegetative to predominantly reproductive subclasses, perhaps to fulfil the unique functions of pollen in fertilization.     

The question of cotyledon homology in angiosperms

The flowering plants (Magnoliophyta) are separated into two large classes distinguished by the morphology of their embryos. The embryos of monocots (class Liliopsida) have a single terminal cotyledon, while the embryos of dicots (class Magnoliopsida) usually have two lateral cotyledons. The cotyledons of monocots and dicots also differ in form, and there are no true intermediates. In addition, the third leaf of Nymphaealean seedlings appears to be identical to the single cotyledon of monocots. From this it is concluded that the cotyledons of monocots and dicots are not homologous. In addition, dissimilarity of cotyledons and succeeding leaves in dicots, together with recent genetic studies, suggests that the two cotyledons of dicots are not homologous with the succeeding leaves of the same plant. This interpretation is consistent with the view that the Nymphaealean embryo’s third leaf is homologous to the first leaf (cotyledon) of monocots. Because dicotyledonous embryos are common among seed plants and are present in the Gnetopsids, the most likely scenario is that the dicots share a widespread seed plant symplesiomorphy and that the monocots have lost this character state. A less parsimonious hypothesis of monocotyledonous embryos as plesiomorphic for angiosperms is also discussed. Genetic analysis of early embryo development in a variety of vascular plants may be the only way to conclusively determine the evolutionary origin of the distinctive difference between monocot and dicot embryos.