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Evolutionary Cladistics and the origin of Angiosperms

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  • Nanjing Institute of Geology and paleontology, CAS
  • Oak Spring Garden Foundation
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... In contrast, coenocytes and their subsequent patterns of cellularization have provided explicit characters for inferring the phylogeny of seed plants ever since the earliest cladistic matrices were compiled. Regarding the coenocytic proembryo, when expanding on the earlier work of Hill and Crane (1982), Crane (1985) speculatively scored their bistate character "embryogenesis with a free-nuclear phase" as characterizing all spermatophytes, living and fossil, other than the gnetalean Welwitschia and angiosperms. All subsequent authors employed this character (e.g., Doyle andDonoghue 1986, 1992;Loconte and Stevenson 1990;Doyle et al. 1994;Nixon et al. 1994), but they were unwilling to speculate on its likely condition in fossil taxa. ...
... For the megagametophyte, Doyle and Donoghue (1986) introduced a second character (their character 60) that relates to megagametophyte cellularization. Inspired by discussions in Hill and Crane (1982) and (unlike embryogenesis) scorable for at least the better-known fossil taxa, the new character described whether the egg becomes cellularized shortly before fertilization and was consistently coded as a derived condition characterizing only Welwitschia and Gnetum. This megagametophytic character persisted in all subsequent morphological cladistic studies of spermatophytes until Doyle (1996, p. S35) drew on aspects of other characters previously employed by Doyle et al. (1994) and Rothwell and Serbet (1994) to generate a pair of characters, the first character tristate and the second bistate. ...
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Premise of research. The evolutionary origin of the seed habit coincided with profound physiological and structural changes associated with underlying developmental patterns. A coenocyte is formed during megagametophyte development in many vascular plants, including some lycophytes and all spermatophytes; this structure compares closely with similar free-nuclear growth phases during embryo development in gymnosperms and endosperm development in angiosperms. Methodology. We review the various free-nuclear growth phases that occur during development of the megaspore and of the ensuing seed of land plants in the context of phylogenies of extant embryophytes and recent studies of the genes that underlie plant development. Pivotal results. Two contrasting types of coenocyte are controlled by different genetic systems: coenocytic growth phases that subsequently become cellularized and contribute to the plant body (type a) and terminally differentiated multinucleate structures such as haustorial suspensor cells (type b). Conclusions. Coding decisions made for coenocytic characters may have contributed to the ongoing instability that characterizes morphological cladistic analyses of land plants. Coenocytic growth phases in lycophytes and spermatophytes probably have independent evolutionary origins. However, the strong similarity between them indicates similar underlying genetic machinery; we hypothesize that this type of growth is controlled by ancient regulatory factors that were recruited during the development of novel structures. Combined with heterospory and endospory, a free-nuclear proembryo likely represented a preadaptive factor that facilitated the evolutionary origin of the seed habit. We highlight a positive correlation between a coenocytic growth phase and increased ovule/seed size in early spermatophytes. In general terms, the relatively derived seed plant lineages—including extant conifers, gnetaleans, and angiosperms—have reverted to a smaller seed size and concomitantly restricted coenocytic growth phases that reflect heterochronic change. A positive correlation between coenocytic growth phases and the absence of a preprophase band indicates that suppression of cytokinesis is a significant aspect of early growth phases in spermatophyte life histories.
... ÿпàAE [73] . ¬dÍÿJÞdZ [48] ...
... Over the past few decades in various cladistic analyses, the extant sister group of the angiosperm crown group has been identified to be either Gnetophyta (the anthophyte hypothesis) (Crane 1985;Doyle & Donoghue 1986;Doyle et al., 1994;Rothwell & Serbet 1994;Hilton & Bateman 2006), a clade comprising Gnetum and Welwitschia (Nixon et al., 1994), a clade comprising conifers and Gnetophyta (Hill & Crane 1982;Soltis et al., 2002), a clade comprising conifers, cycads and Ginkgo (Magallón & Sanderson 2002;Rydin et al., 2002;Rai et al., 2003), or Cycadophyta (Doyle 2006). ...
Conference Paper
The explosive increase of molecular sequence data has produced unprecedented opportunities for addressing a number of evolutionary problems. Specially, the species divergence time estimation is fundamental because our understanding of history of life depends critically on knowledge of the ages of major clades. This thesis explores the use of molecular data (genome-scale datasets), combined with statistical summaries of the fossil record, to date the origin of angiosperms (flowering plants) and the divergence times of its major groups in an attempt to resolve the apparent conflict between the molecular dates and fossil evidence. Moreover, because fossil calibrations are the major source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis, several strategies for converting fossil calibrations into the prior on times are evaluated. Chapter one introduces the diversity and evolution of angiosperms, reviews the current literature that is based predominantly on systematics, phylogenetics, palaeobotany and plant molecular evolution. In introducing the early evolution of angiosperms this chapter highlights the questions associated with the origin of angiosperms and presents aims of the thesis. Chapter two focuses on molecular clock dating methods. It discusses different approaches for estimating divergence times, with emphasis on Bayesian molecular clock dating methods. Chapter three uses a powerful Bayesian method to analyze a molecular dataset of 83 genes from 644 taxa of vascular plants, combined with a suite of 52 fully-justified fossil calibrations to disentangle the pattern of angiosperm diversification. The results indicate that crown angiosperms originated during the Triassic to the Jurassic interval, long prior to the Cretaceous Terrestrial Revolution. This analysis demonstrates that even though many sources of uncertainty are explored, attempts to control for these factors still do not bring clock estimates and earliest confident fossil occurrences into agreement. A post-Jurassic origin of angiosperms was rejected, supporting the notion of a cryptic early history of angiosperms. The main factors affecting the estimates in this study are also discussed. Subsequently, in chapter four different strategies for summarizing fossil information to construct calibration priors were assessed employing an a priori procedure for deriving accurate calibration densities in Bayesian divergence dating. In general, truncation has a great impact on calibrations so that the effective priors on the calibration node ages after the truncation can be very different from the user-specified calibration densities. The different strategies for generating the effective prior also had considerable impact, leading to very different marginal effective priors. Arbitrary parameters used to implement minimum-bound calibrations were found to have a strong impact upon the prior and posterior of the divergence times. The results highlight the importance of inspecting the joint time prior used by the dating program before any Bayesian dating analysis. Finally, chapter five draws together key finding from chapters three and four, and reviews how this work advances our understanding of the origin and evolution of angiosperms and on molecular clock dating using fossil calibrations. This chapter also highlights new gaps in our understanding of early evolution of angiosperms and in the implementation of fossil calibrations in Bayesian molecular clock dating, and discusses several areas for future research. Overall, this thesis highlights that more room for improvement might lie in refining our knowledge and use of fossil calibrations, the resulting improvements to molecular estimates of timescales will lead to a better understanding of angiosperm evolution. I speculate that these results will also shed light on dating discrepancies in other major clades.
... 'Mesozoic pteridosperms' have figured prominently in discussions concerning the origin of flowering plants since the first part of the twentieth century (Thomas 1921(Thomas , 1925Gaussen 1946;Hill & Crane 1982;Frohlich 2002;Doyle 2006). The group is composed by four main orders (Taylor et al. 2006): Peltaspermales (Carboniferous-Triassic), Corystospermales (Permian-Triassic/Jurassic?), Petriellales (Triassic) and Caytoniales (Triassic-Cretaceous). ...
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Macrofossil impressions of caytonialean leaves and micro- and megasporangiate organs from the Early Jurassic Taquetrén locality in Patagonia, Argentina, are described based on more than 300 hand specimens. Leaves of the organ-genus Sagenopteris are described using both discrete and continuous features allowing us to erect the species Sagenopteris trapialensis sp. nov. Associated microsporangiate organs of Caytonanthus type are the first recorded for South America and are characterized by a unique combination of architecture, size and type of dehiscence. Two specimens, one resembling an isolated Caytonia cupule, and the other a Caytonia axis, are also described. The availability of a collection with numerous specimens has proven to be an important tool in order to fully understand the intraspecific morphological plasticity of the studied species. The striking morphological resemblance of both vegetative and reproductive organ-genera with their Northern Hemisphere counterparts suggests that they were part of the same lineage, which was widely distributed during the Jurassic. Well-defined whole-plant concepts are still needed to advance the goal of deciphering the internal relationships of caytonialeans in particular, and their relationships with other groups of seed-plants in general, and thorough macro-morphological characterization of the organs that compose them, as we present here, may be of valuable use in achieving it. © 2019, © The Trustees of the Natural History Museum, London 2019. All rights reserved.
... Before the advent of cladistics, some authors proposed that angiosperms and Gnetales were closest living relatives, while others argued that these two groups were strictly convergent and Gnetales were instead related to conifers (for a review, see Doyle and Donoghue 1986). However, since the earliest studies by Parenti (1980) and Hill and Crane (1982), which included only living taxa, the view that angiosperms are most closely related to Gnetales has appeared to be one of the most stable results of morphologically based parsimony analyses of seed plant phylogeny (Crane 1985a;Doyle andDonoghue 1986, 1992;Nixon et al. 1994;Rothwell and Serbet 1994;Doyle 1996Doyle , 2006Doyle , 2008Hilton and Bateman 2006;Friis et al. 2007;Rothwell et al. 2009;Rothwell and Stockey 2016; Fig. 1). The first analysis that included fossils (Crane 1985a) associated angiosperms and Gnetales with Mesozoic Bennettitales and Pentoxylon. ...
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The placement of angiosperms and Gnetales in seed plant phylogeny remains one of the most enigmatic problems in plant evolution, with morphological analyses (which have usually included fossils) and molecular analyses pointing to very distinct topologies. Almost all morphology-based phylogenies group angiosperms with Gnetales and certain extinct seed plant lineages, while most molecular phylogenies link Gnetales with conifers. In this study, we investigate the phylogenetic signal present in published seed plant morphological data sets. We use parsimony, Bayesian inference, and maximum-likelihood approaches, combined with a number of experiments with the data, to address the morphological–molecular conflict. First, we ask whether the lack of association of Gnetales with conifers in morphological analyses is due to an absence of signal or to the presence of competing signals, and second, we compare the performance of parsimony and model-based approaches with morphological data sets. Our results imply that the grouping of Gnetales and angiosperms is largely the result of long branch attraction (LBA), consistent across a range of methodological approaches. Thus, there is a signal for the grouping of Gnetales with conifers in morphological matrices, but it was swamped by convergence between angiosperms and Gnetales, both situated on long branches. However, this effect becomes weaker in more recent analyses, as a result of addition and critical reassessment of characters. Even when a clade including angiosperms and Gnetales is still weakly supported by parsimony, model-based approaches favor a clade of Gnetales and conifers, presumably because they are more resistant to LBA. Inclusion of fossil taxa weakens rather than strengthens support for a relationship of angiosperms and Gnetales. Our analyses finally reconcile morphology with molecules in favoring a relationship of Gnetales to conifers, and show that morphology may therefore be useful in reconstructing other aspects of the phylogenetic history of the seed plants.
... A notable palaeobotanist was Chris Hill. Hill wrote many articles on the subject of palaeontology and cladistics (Hill 1981a, b, Hill & Camus 1986, Hill & Crane 1982, even going so far as naming a fossil plant from the Wealden (Lower Cretaceous), southern England, Bevhalstia pebja (Hill 1996). Hill became good friends with David Hull. ...
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Ronald Brady was the first philosopher to defend pattern cladistics as an independent scientific field. That independence was achieved through the decoupling of biological systematics from phylogenetics––that is, inferred evolutionary processes (e.g. character transformation). Brady saw parallels between biological systematics and Wolfgang von Goethe's Morphology, an empirical scientific field that incorporates human observation and perception to discover coherent morphological structures. Goethe's Morphology and pre‐Darwinian systematics were independent from evolutionary narratives, a tradition that continued into the 20th Century through the work of biologists such as Agnes Arber. Most importantly, Brady provided the philosophical and historical foundations to an independent systematics by demonstrating the links between phenomenology, Goethe's Morphology and comparative biology.
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Phylogenetic definitions are provided for the names of 53 clades of vascular plants. Emphasis has been placed on well‐supported clades that are widely known to non‐specialists and/or have a deep origin within Tracheophyta or Angiospermae. These treatments follow the draft PhyloCode and illustrate the application of phylogenetic nomenclature in a variety of nomenclatural and phylogenetic contexts. Phylogenetic nomenclature promotes precision in distinguishing crown, apomorphy‐based, and total clades, thereby improving communication about character evolution and divergence times. To make these distinctions more transparent without increasing the number of entirely different names that must be learned, the following naming conventions (which have been adopted in the most recent draft of the PhyloCode) are employed here: widely known names are applied to crown clades, and the corresponding total clade (i.e., crown plus stem) is named “Pan‐X”, where “X” is the name of the crown (e.g., Pan‐Spermatophyta for the total clade of plants that share more recent ancestry with extant seed plants than with any other crown clade). If a name “X” that is based etymologically on an apomorphy is applied to the crown, the name “Apo‐X” is applied to the clade for which this trait is synapomorphic (e.g., Apo‐Spermatophyta for the clade originating from the first plant with seeds). Crown clade names can be defined by three kinds of definitions, two of which are used here: standard node‐based and branch‐modified node‐based. The latter is particularly useful when outgroup relationships of a crown clade are better known than basal relationships within the clade. Criteria and approaches used here to choose among competing preexisting names for a clade, to select a definition type, to choose appropriate specifiers, and (in some cases) to restrict the use of a name to certain phylogenetic contexts may be widely applicable when naming other clades. The phylogenetic definitions proposed here should help focus future discussions of the PhyloCode on real definitions rather than simplified hypothetical ones.
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