James A. Doyle

Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree

Although the relationship of angiosperms to other seed plants remains controversial, great progress has been made in identifying the earliest extant splits in flowering-plant phylogeny, with the discovery that the New Caledonian shrub Amborella trichopoda, the water lilies (Nymphaeales), and the woody Austrobaileyales constitute a basal grade of lines that diverged before the main radiation in the clade. By focusing attention on these ancient lines, this finding has re-written our understanding of angiosperm structural and reproductive biology, physiology, ecology and taxonomy. The discovery of a new basal lineage would lead to further re-evaluation of the initial angiosperm radiation, but would also be unexpected, as nearly all of the ∼460 flowering-plant families have been surveyed in molecular studies. Here we show that Hydatellaceae, a small family of dwarf aquatics that were formerly interpreted as monocots, are instead a highly modified and previously unrecognized ancient lineage of angiosperms. Molecular phylogenetic analyses of multiple plastid genes and associated noncoding regions from the two genera of Hydatellaceae identify this overlooked family as the sister group of Nymphaeales. This surprising result is further corroborated by evidence from the nuclear gene phytochrome C (PHYC), and by numerous morphological characters. This indicates that water lilies are part of a larger lineage that evolved more extreme and diverse modifications for life in an aquatic habitat than previously recognized.

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.RésuméNous présentons une analyse cladistique numérique (de parcimonie, ou économie d’hypothèses) des Spermatophytes plus Progymnospermes, utilisant des caractères de tous les organes du corps végétal, la comparaison extra-groupe, et une méthode de codification de caractères qui évite des prédispositions en faveur de ou contre les théories morphologiques alternatives. La solidité des résultats a été testé par la construction d’arbres phylétiques alternatifs et l’analyse de sous-ensembles des données. Selon ces expériences, certains phylums sont bien appuyés, mais ils peuvent être reliés de façons très différentes mais presque également économiques, apparemment à cause d’homoplasie répandue. Nos résultats confirment le concept de Rothwell, selon lequel les Coniféropsides sont dérivées de Ptéridospermes platyspermiques à pollen saccate proches deCallistophyton, mais l’hypothèse d’une dérivation de Progymnospermes proches d’Archaeopteris et d’une origine diphylétique de la graine est presque aussi économique. La division de Meyen des Spermatophytes en lignées radiospermiques et primairement et secondairement platyspermiques est très peu économique, mais son concept d’une affinité entre les Ginkgoales et les Peltaspermes mérite de l’attention. Les Angiospermes se situent parmi les groupes platyspermiques, comme groupe-frère des Bennettitales,Pentoxylon, et Gnetales, et le phylum ainsi constitué (“Anthophytes”) est le mieux lié àCaytonia et aux Glossoptérides, bien que des rapports avec d’autres combinaisons de taxons de Ptéridospermes mésozoïques soient presque aussi économiques. Ces résultats indiquent que le carpelle des Angiospermes peut être interprété comme une sporophylle pennée modifiée portant des cupules anatropes (=ovules bitégumentés), puisque les strobiles des Gnetales sont le mieux interprétés comme des agglomérations de fleurs bennettitaliennes fort réduites, comme l’a proposé Arber et Parkin et Crane. Nos arbres phylétiques les plus économiques supposent que la lignée des Angiospermes (mais pas forcément tous ses traits modernes) s’étend jusqu’au Trias, mais une origine plus récente à partir de quelque espèce deCaytonia ou de Bennettitales, hypothèses presque aussi économiques, doit aussi être considérée. Ces résultats suggèrent que plusieurs traits considérés comme des adaptationsclés dans l’origine ou l’expansion des Angiospermes (fleurs entomophiles, rapidité de reproduction, tolérance de sécheresse) étaient en fait hérités de leurs ancêtres gymnospermiques. La diversification explosive des Angiospermes pourrait plutôt être une conséquence de la clôture du carpelle, conduisant à un taux de spéciation élevé dû au potential pour des mécanismes d’isolement stigmatiques et/ou de nouveaux moyens de dispersion. L’étude de séquences d’ADN des végétaux actuels et de meilleurs renseignements sur l’anatomie, la phytochimie, la morphologie des sporophylles, et l’embryologie des Bennettitales et Caytoniales pourraient fournir des testes critiques de rapports phylétiques.

Early cretaceous fossil evidence for angiosperm evolution

Morphological, stratigraphic, and sedimentological analyses of Early Cretaceous pollen and leaf sequences, especially from the Potomac Group of the eastern United States, support the concept of a Cretaceous adaptive radiation of the angiosperms and suggest pathways of their initial ecological and systematic diversification. The oldest acceptable records of angiosperms are rare monosulcate pollen grains with columellar exine structure from probable Barremian strata of England, equatorial Africa, and the Potomac Group, and small, simple, pinnately veined leaves with several orders of reticulate venation from the Neocomian of Siberia and the basal Potomac Group. The relatively low diversity and generalized character of these fossils and the subsequent coherent pattern of morphological diversification are consistent with a monophyletic origin of the angiosperms not long before the Barremian. PatuxentArundel floras (Barremian-early Albian?) of the Potomac Group include some pollen and leaves with monocotyledonous features as well as dicotyledonous forms. Patuxent angiosperm pollen is strictly monosulcate and has exine sculpture indicative of insect pollination. Rare Patuxent-Arundel angiosperm leaves are generally small, have disorganized venation, and are largely restricted to sandy stream margin lithofacies; the largest are comparable to and may include ancestors of woody Magnoliidae adapted to understory conditions. Patapsco floras (middle to late Albian?) contain rapidly diversifying tricolpate pollen and several new complexes of locally abundant angiosperm leaves. Ovate-cordate and peltate leaves in clayey pond lithofacies may includeancestors of aquatic Nymphaeales and Nelumbonales. Pinnatifid and later pinnately compound leaves with increasingly regular venation which are abundant just above rapid changes in sedimentation are interpreted as early successional “weed trees” transitional to but more primitive than the modern subclass Rosidae. Apparently related palmately lobed, palinactinodromous leaves which develop rigidly percurrent tertiary venation and become abundant in uppermost Potomac stream margin deposits (latest Albian-early Cenomanian?) are interpreted as riparian trees ancestral to the order Hamamelidales. Comparisons of dated pollen floras of other regions indicate that one major subgroup of angiosperms, tricolpate-producing dicots (i.e., excluding Magnoliidae of Takhtajan) originated in the Aptian of Africa-South America at a time of increasing aridity and migrated poleward into Laurasia and Australasia. However, the earlier (Barremian) monosulcate phase of the angiosperm record is represented equally in Africa-South America and Laurasia before marked climatic differentiation between the two areas. These trends are considered consistent with the hypothesis that the angiosperms originated as small-leafed shrubs of seasonally arid environments, and underwent secondary expansion of leaf area and radiated into consecutively later successional stages and aquatic habitats after entering mesic regions as riparian “weeds,” as opposed to the concept that they arose as trees of mesic forest environments.

Morphological Phylogenetic Analysis of Basal Angiosperms: Comparison and Combination with Molecular Data

We have amassed structural data for 108 characters and 52 taxa of magnoliids and basal monocots and eudicots, including observations by P. K. Endress and A. Igersheim on flowers. These data were analyzed separately and in combination with rbcL, 18S, and atpB sequences. Besides confirming agreements between previous analyses of both kinds of data (reduction of Magnoliales to six families; relation of Piperaceae, Saururaceae, Lactoris, and Aristolochiaceae), trees based on this data set show shifts toward molecular results (separation of Illiciaceae and Schisandraceae from Winteraceae and of Amborella, Austrobaileya, Trimeniaceae, and Chloranthaceae from Laurales; relation of Winteraceae and Canellaceae) plus continued conflicts (association of Chloranthaceae with Amborella and Trimeniaceae and of Nymphaeales with monocots). In cases where molecular and morphological trees conflict, combined analyses of morphological and molecular data generally yield the same topologies as molecular analyses, but morphology overcomes weak molecular evidence in indicating that Chloranthaceae belong just above the basal grade, that monocots are related to Piperales, and that Lauraceae are linked with Hernandiaceae. If angiosperms are rooted by molecular data, chloranthoid leaf teeth, two‐trace nodes, columellar (not granular) pollen, and ascidiate carpels sealed by secretion are ancestral. Vesselless xylem is primitive in Amborella but secondary in Winteraceae and Trochodendraceae.

Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data

Molecular estimates of the age of angiosperms have varied widely, and many greatly predate the Early Cretaceous appearance of angiosperms in the fossil record, but there have been few attempts to assess confidence limits on ages. Experiments with rbcL and 18S data using maximum likelihood suggest that previous angiosperm age estimates were too old because they assumed equal rates across sites-use of a gamma distribution of rates to correct for site-to-site variation gives 10-30 my (million years) younger ages-and relied on herbaceous angiosperm taxa with high rates of molecular evolution. Ages based on first and second codon positions of rbcL are markedly older than those based on third positions, which conflict with the fossil record in being too young, but all examined data partitions of rbcL and 18S depart substantially from a molecular clock. Age estimates are surprisingly insensitive to different views on seed-plant relationships. Randomization schemes were used to quantify confidence intervals due to phylogenetic uncertainty, substitutional noise, and lineage effects (deviations from a molecular clock). Estimates of the age of crown-group angiosperms range from 68 to 281 mya (million years ago), depending on data, tree, and assumptions, with most ∼140-190 mya (Early Jurassic-earliest Cretaceous). Approximate 95% confidence intervals on ages are wider for rbcL than 18S, ranging up to 160 my for phylogenetic uncertainty, 90 my for substitutional noise, and 70 my for lineage effects. These intervals overlap the oldest occurrences of angiosperms in the fossil record, as well as some estimates from previous molecular studies.

Reconstructing the ancestral angiosperm flower and its initial specializations.

Increasingly robust understanding of angiosperm phylogeny allows more secure reconstruction of the flower in the most recent common ancestor of extant angiosperms and its early evolution. The surprising emergence of several extant and fossil taxa with simple flowers near the base of the angiosperms-Chloranthaceae, Ceratophyllum, Hydatellaceae, and the Early Cretaceous fossil Archaefructus (the last three are water plants)-has brought a new twist to this problem. We evaluate early floral evolution in angiosperms by parsimony optimization of morphological characters on phylogenetic trees derived from morphological and molecular data. Our analyses imply that Ceratophyllum may be related to Chloranthaceae, and Archaefructus to either Hydatellaceae or Ceratophyllum. Inferred ancestral features include more than two whorls (or series) of tepals and stamens, stamens with protruding adaxial or lateral pollen sacs, several free, ascidiate carpels closed by secretion, extended stigma, extragynoecial compitum, and one or several ventral pendent ovule(s). The ancestral state in other characters is equivocal: e.g., bisexual vs. unisexual flowers, whorled vs. spiral floral phyllotaxis, presence vs. absence of tepal differentiation, anatropous vs. orthotropous ovules. Our results indicate that the simple flowers of the newly recognized basal groups are reduced rather than primitively simple.

Seed Plant Phylogeny and the Relationships of Gnetales

Most phylogenetic analyses of morphological data agree that Gnetales are a monophyletic group related to angiosperms and Bennettitales. However, they disagree on whether these groups (anthophytes) are related to coniferopsids or to Mesozoic seed ferns, and thus on whether the flowers of Gnetales are primitively simple or reduced. Molecular analyses indicate that both Gnetales and angiosperms are monophyletic but disagree on their relationship. The conclusion of Nixon et al. (1994) that Gnetales are paraphyletic, with angiosperms nested within them, is weakly supported; when several questionable embryological characters are redefined in a neutral manner, Gnetales are inferred to be monophyletic Jurassic reproductive structures associated with linear leaves and ephedroid pollen (Piroconites) consist of a bract and a scalelike sporophyll covered with Welwitschia-like microsynangia or ovules, recalling the bractsporophyll complex of glossopterids. An analysis of seed plants incorporating these fossils and other new data links Gnetales with Piroconites, angiosperms with Caytonia, and both groups (plus Bennettitales and Pentoxylon) with glossopterids, making up a clade called the glossophytes. These results imply that glossophytes originally had glossopterid-like leaves and bract-sporophyll complexes, which were transformed into carpels with bitegmic ovules in angiosperms, but reduced to single, terminal ovules in Gnetales; flowers arose independently in the two lines. The common ancestor of angiosperms and Gnetales may be as old as Permian, and some of their shared advances, such as double fertilization (without endosperm formation), may have arisen as adaptations to seasonal temperate climates in Gondwana.

Angiosperm pollen zonation of the continental Cretaceous of the Atlantic coastal plain and its application to deep wells in the Salisbury Embayment

Abstract This paper presents and illustrates an informal palynological zonation of the pre‐Magothy continental Cretaceous sediments of the Atlantic Coastal Plain (Potomac Group, Raritan Formation), based primarily on new and previously published studies of angiosperm pollen from two wells near Delaware City, Delaware, and from outcrop samples from Virginia through New Jersey, following lines established by Brenner (1963). Monosulcate angiosperm pollen (with columellar exine structure) is present from the base of Brenners Zone I (Patuxent Formation and Arundel Clay equivalents, Barremian‐lower Albian?). Reticulate tricolpates enter in upper Zone I and diversify in Brenners Subzones II‐A and II‐B (Patapsco Formation equivalents, middle‐upper Albian?); tricolporoidates appear in Subzone II‐B. Very small, psilate tricolporoidates and Rugubivesiculites rugosus enter in our Subzone II‐C (uppermost Albian?), larger triangular tricolporates and new tricolpates in Zone III (lower Cenomanian?); these two units ar...

Dark and disturbed: a new image of early angiosperm ecology

Abstract Better understanding of the functional biology of early angiosperms may clarify ecological factors surrounding their origin and early radiation. Phylogenetic studies identify Amborella, Nymphaeales (water lilies), Austrobaileyales, and Chloranthaceae as extant lineages that branched before the radiation of core angiosperms. Among living plants, these lineages may represent the best models for the ecology and physiology of early angiosperms. Here we combine phylogenetic reconstruction with new data on the morphology and ecophysiology of these plants to infer early angiosperm function. With few exceptions, Amborella, Austrobaileyales, and Chloranthaceae share ecophysiological traits associated with shady, disturbed, and wet habitats. These features include low and easily light-saturated photosynthetic rates, leaf anatomy related to the capture of understory light, small seed size, and clonal reproduction. Some Chloranthaceae, however, possess higher photosynthetic capacities and seedlings that recruit in canopy gaps and other sunny, disturbed habitats, which may have allowed Cretaceous Chloranthaceae to expand into more diverse environments. In contrast, water lilies possess ecophysiological features linked to aquatic, sunny habitats, such as absence of a vascular cambium, ventilating stems and roots, and floating leaves tuned for high photosynthetic rates in full sun. Nymphaeales may represent an early radiation into such aquatic environments. We hypothesize that the earliest angiosperms were woody plants that grew in dimly lit, disturbed forest understory habitats and/or shady streamside settings. This ecology may have restricted the diversity of pre-Aptian angiosperms and living basal lineages. The vegetative flexibility that evolved in the understory, however, may have been a key factor in their diversification in other habitats. Our inferences based on living plants are consistent with many aspects of the Early Cretaceous fossil record and can be tested with further study of the anatomy, chemistry, and sedimentological context of Early Cretaceous angiosperm fossils.

Integration of morphological and ribosomal RNA data on the origin of angiosperms

Previous phylogenetic analyses of morphological and rRNA data indicated that Gnetales are the closest living relatives of angiosperms but gave different basal angiosperm relationships. A two-step morphological analysis of seed plants (including fossils) and angiosperms rooted the latter near Magnoliales, with tricolpate eudicots and paleoherbs (herbaceous magnoliids and monocots) forming a clade, whereas analyses of rRNA sequences rooted angiosperms among paleoherbs, with eudicots and woody magnoliids forming a clade. Experiments with a revised seed plant morphological data set raise further questions: when angiosperms are scored like different angiosperm subgroups, they associate with different outgroups, although Gnetales are their closest living relatives