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Catarina Rydin - One of the best experts on this subject based on the ideXlab platform.

James A. Doyle - One of the best experts on this subject based on the ideXlab platform.

  • Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of the relationship of angiosperms and Gnetales
    Paleobiology, 2018
    Co-Authors: Mario Coiro, Guillaume Chomicki, James A. Doyle
    Abstract:

    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.

  • Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of seed plant phylogeny
    bioRxiv, 2017
    Co-Authors: Mario Coiro, Guillaume Chomicki, James A. Doyle
    Abstract:

    The phylogeny of seed plants remains one of the most enigmatic problems in evolutionary plant biology, with morphological phylogenies (which include fossils) and molecular phylogenies pointing to very distinct topologies. Almost all morphology-based phylogenies support the so-called anthophyte hypothesis, grouping the angiosperms with Gnetales and several extinct seed plant lineages, while most molecular phylogenies link Gnetales with conifers. In this study, we investigate the phylogenetic signal present in seed plant morphological datasets. We use maximum parsimony and Bayesian inference, combined with a number of experiments with all available seed plant morphological matrices 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 Bayesian approaches with morphological datasets. Our results imply that the grouping of Gnetales and angiosperms is largely the result of long branch attraction, consistent across a range of methodological approaches. Thus, the signal for the grouping of Gnetales with conifers in morphological matrices was swamped by convergence between angiosperms and Gnetales, both situated on long branches, in previous analyses. However, this effect becomes weaker in more recent analyses, as a result of addition and critical reassessment of characters. Bayesian inference proves to be more resistant to long branch attraction, and the use of parsimony is largely responsible for persistence of the anthophyte topology. Our analyses finally reconcile morphology with molecules in the context of the seed plant phylogeny, and show that morphology may therefore be useful in reconstructing other aspects of the phylogenetic history of the seed plants.

  • Evolutionary significance of granular exine structure in the light of phylogenetic analyses.
    Review of Palaeobotany and Palynology, 2009
    Co-Authors: James A. Doyle
    Abstract:

    In 1973 Van Campo and Lugardon recognized granular structure as a third major type of exine structure in seed plants, in addition to columellar (restricted to angiosperms) and alveolar (restricted to other seed plants, such as cycads and saccate conifers). Because they found granular structure both in other seed plants (non-saccate conifers, Gnetales) and in angiosperms (some Magnoliales, monocots, and “Amentiferae”), they suggested it might be ancestral in angiosperms. This suggestion was elaborated by other workers and supported by studies of Le Thomas and Lugardon on Annonaceae (Magnoliales), which appeared to show origin of columellae by various modifications of granules. Phylogenetic (cladistic) analyses of seed plants based on morphological and molecular data modify this scheme considerably but reaffirm the systematic interest of granular structure. In conifers and Gnetales (which probably form a clade), granular structure appears to be derived from alveolar (as in Pinaceae, Podocarpaceae and extinct outgroups of conifers). Molecular analyses root the phylogenetic tree of angiosperms among Amborella, Nymphaeales, and Austrobaileyales, which have columellar and related exine structures, implying that granular exines were derived within angiosperms. This contradicts earlier views that granular structure provides evidence for a relationship between angiosperms and outgroups such as Gnetales and Bennettitales. Phylogenetic analyses indicate that granular structure was derived from columellar within Magnoliales and Laurales, in each of which it is an important synapomorphy of a major subgroup; the same may also be true for Fagales. However, phylogenetic analyses of Annonaceae confirm that granular structure is ancestral in this group and columellar is derived, essentially as a reversal to the ancestral state in angiosperms. In Fagales granular structure is associated with wind pollination, but not in Magnoliales and Laurales; however, in all three cases it may be correlated with reduction in exine thickness.

  • Seed plant phylogeny: Demise of the anthophyte hypothesis?
    Current Biology, 2000
    Co-Authors: Michael J. Donoghue, James A. Doyle
    Abstract:

    Recent molecular phylogenetic studies indicate, surprisingly, that Gnetales are related to conifers, or even derived from them, and that no other extant seed plants are closely related to angiosperms. Are these results believable? Is this a clash between molecules and morphology?

  • Molecules, morphology, fossils, and the relationship of angiosperms and Gnetales.
    Molecular Phylogenetics and Evolution, 1998
    Co-Authors: James A. Doyle
    Abstract:

    Morphological analyses of seed plant phylogeny agree that Gnetales are the closest living relatives of angiosperms, but some studies indicate that both groups are monophyletic, while others indicate that angiosperms are nested within Gnetales. Molecular analyses of several genes agree that both groups are monophyletic, but differ on whether they are related. Conflicts among morphological trees depend on the interpretation of certain characters; when these are analyzed critically, both groups are found to be monophyletic. Conflicts among molecular trees may reflect the rapid Paleozoic radiation of seed plant lines, aggravated by the long branches leading to extant taxa. Trees in which angiosperms are not related to Gnetales conflict more with the stratigraphic record. Even if molecular data resolve the relationships among living seed plant groups, understanding of the origin of angiosperm organs will require integration of fossil taxa, necessarily using morphology.

Sarah Mathews - One of the best experts on this subject based on the ideXlab platform.

  • Assessing Systematic Error in the Inference of Seed Plant Phylogeny
    International Journal of Plant Sciences, 2007
    Co-Authors: J. Gordon Burleigh, Sarah Mathews
    Abstract:

    We used parametric bootstrapping to assess the performance of maximum parsimony and maximum likelihood phylogenetic analyses of a 12‐locus seed plant data set. Evidence of biases in maximum parsimony analyses of single‐locus data sets may explain some of the locus‐specific variation among DNA‐based hypotheses of seed plant phylogeny. In particular, there is strong evidence of bias in maximum parsimony analyses, especially of plastid loci, that favors placing Gnetales sister to other seed plants. We concatenated simulated single‐locus data sets to examine biases in analyses of a 12‐locus data set in which each locus is simulated with different substitution parameters and branch lengths. Maximum parsimony analyses of the simulated 12‐locus data set also show evidence of biases in favor of recovering trees with Gnetales sister to other seed plants and against recovering anthophyte, gnepine, and gnetifer trees. These biases are most evident in analyses that include the fastest‐evolving characters. In the maxi...

  • phylogenetic signal in nucleotide data from seed plants implications for resolving the seed plant tree of life
    American Journal of Botany, 2004
    Co-Authors: Gordon J Burleigh, Sarah Mathews
    Abstract:

    Effects of taxonomic sampling and conflicting signal on the inference of seed plant trees supported in previous molecular analyses were explored using 13 single-locus data sets. Changing the number of taxa in single-locus analyses had limited effects on log likelihood differences between the gnepine (Gnetales plus Pinaceae) and gnetifer (Gnetales plus conifers) trees. Distinguishing among these trees also was little affected by the use of different substitution parameters. The 13-locus combined data set was partitioned into nine classes based on substitution rates. Sites evolving at intermediate rates had the best likelihood and parsimony scores on gnepine trees, and those evolving at the fastest rates had the best parsimony scores on Gnetales-sister trees (Gnetales plus other seed plants). When the fastest evolving sites were excluded from parsimony analyses, well-supported gnepine trees were inferred from the combined data and from each genomic partition. When all sites were included, Gnetales-sister trees were inferred from the combined data, whereas a different tree was inferred from each genomic partition. Maximum likelihood trees from the combined data and from each genomic partition were well-supported gnepine trees. A preliminary stratigraphic test highlights the poor fit of Gnetales-sister trees to the fossil data.

Else Marie Friis - One of the best experts on this subject based on the ideXlab platform.

  • RESEARCH ARTICLE Open Access
    2013
    Co-Authors: A Early, Catarina Rydin, Cretaceous Gnetales, Else Marie Friis
    Abstract:

    Background: Knowledge on fossil and evolutionary history of the Gnetales has expanded rapidly; Ephedra and ephedroids as well as the Gnetum-Welwitschia clade are now well documented in the Early Cretaceous. However, hypotheses on evolutionary relationships among living and fossil species are hampered by restricted knowledge of morphological variation in living groups and recent studies indicate that gnetalean diversity and character evolution may be more complex than previously assumed and involve additional extinct groups (Bennettitales, Erdtmanithecales and unassigned fossil taxa). Results: Here we describe a new fossil related to Gnetales, Siphonospermum simplex from the Early Cretaceous Yixian Formation, an impression/compression of a reproductive shoot. The slender main axis bears one pair of opposite and linear leaves with primary parallel venation. The reproductive units are ovoid, without supporting bracts and borne on one median and two lateral branches. The most conspicuous feature of the fossil is the long, thread-like micropylar tube formed by the integument. Each ovule is surrounded by two different layers representing one or two seed envelopes; an inner sclerenchymatous layer and an outer probably parenchymatous layer. Conclusions: The vegetative and reproductive features of Siphonospermum simplex exclude a relationship to any other group than the Gnetales. A combination of opposite phyllotaxis, linear leaves and ovules surrounded by see

  • Phase-contrast X-ray microtomography links Cretaceous seeds with Gnetales and Bennettitales
    Nature, 2007
    Co-Authors: Else Marie Friis, Peter R. Crane, Kaj Raunsgaard Pedersen, Stefan Bengtson, Philip C. J. Donoghue, Guido W. Grimm, Marco Stampanoni
    Abstract:

    The study of the emergence of flowering plants has been revolutionized over the past 25 years by the discovery of many exquisitely preserved fossil flowers. But fossil gymnosperms (conifers) have received less attention. Friis et al. have used a recently developed synchrotron radiation X-ray tomographic technique to redress the balance. Their images reveal internal structures at very high resolution. The seed structures of some Cretaceous gymnosperms suggest evolutionary links with Gnetales (an obscure and evolutionarily hard-to-place gymnosperm group with three living genera) and the Bennettitales (an important extinct group of cycad-like plants). A relatively new imaging technique is used to reveal that some Cretaceous gymnosperm seeds have evolutionary links with Gnetales (an evolutionarily hard-to-place gymnosperm group with three living genera) and the Bennetitales (an extinct group of cycad-like plants). The link between Gnetales and Bennetitales may have important consequences for our understanding of the evolution of seed plants, including flowering plants. Over the past 25 years the discovery and study of Cretaceous plant mesofossils has yielded diverse and exquisitely preserved fossil flowers that have revolutionized our knowledge of early angiosperms1, but remains of other seed plants in the same mesofossil assemblages2,3 have so far received little attention. These fossils, typically only a few millimetres long, have often been charred in natural fires and preserve both three-dimensional morphology and cellular detail. Here we use phase-contrast-enhanced synchrotron-radiation X-ray tomographic microscopy to clarify the structure of small charcoalified gymnosperm seeds from the Early Cretaceous of Portugal and North America. The new information links these seeds to Gnetales (including Erdtmanithecales, a putatively closely related fossil group2), and to Bennettitales—important extinct Mesozoic seed plants with cycad-like leaves and flower-like reproductive structures. The results suggest that the distinctive seed architecture of Gnetales, Erdtmanithecales and Bennettitales defines a clade containing these taxa. This has significant consequences for hypotheses of seed plant phylogeny by providing support for key elements of the controversial anthophyte hypothesis, which links angiosperms, Bennettitales and Gnetales.

  • Former diversity of Ephedra (Gnetales): evidence from Early Cretaceous seeds from Portugal and North America
    Annals of Botany, 2006
    Co-Authors: Catarina Rydin, Peter R. Crane, Kaj Raunsgaard Pedersen, Else Marie Friis
    Abstract:

    • Background and Aims The extant species of the seed plant group Gnetales (Ephedra, Gnetum and Welwitschia) have been considered a remnant of a much greater, now extinct, diversity due to the pronounced differences in form and ecology among the genera. Until recently, this hypothesis has not been supported by evidence from the fossil record. This paper adds to the expanding information on Gnetales from the Early Cretaceous and describes coalified seeds from Barremian-Albian localities in Portugal and USA. • Methods The fossils were extracted from sediment samples by sieving in water. Adhering mineral matrix was removed by chemical treatment. Seeds were investigated using light and scanning electron microscopy. Morphology and anatomy of the seeds were documented and compared with those of extant species. • Key Results The fossils share characters with extant Ephedra, for example papillae on the inner surface of the seed envelope and in situ polyplicate pollen grains that shed the exine during germination. They differ from extant Ephedra seeds in morphological and anatomical details as well as in their smaller size. Two new species of Ephedra are described together with one species assigned to a new genus of Gnetales. Other Ephedra-like seeds, for which pollen and critical morphological details are currently unknown, are also present in the samples. • Conclusions These Cretaceous seeds document that key reproductive characters and pollen germination processes have remained unchanged within Ephedra for about 120 million years or more. There is sufficient variety in details of morphology to suggest that a diversity of Ephedra and Ephedra-like species were present in the Early Cretaceous flora. Their presence in Portugal and eastern North America indicates that they were widespread on the Laurasian continent. The fossil seeds are similar to seeds of Erdtmanithecales and this supports the previously suggested relationship between Erdtmanithecales and Gnetales.

  • Pollen germination in Welwitschia mirabilis Hook. f.: comparing differences between the polyplicate pollen producing genera of the Gnetales
    Grana, 2005
    Co-Authors: Catarina Rydin, Else Marie Friis
    Abstract:

    Pollen grains of the seed plant genera   Ephedra L. and Welwitschia Hook. f. (Gnetales) are of similar size, shape, and have a polyplicate exine with alternating thicker and thinne ...

  • Cratonia cotyledon gen. et sp. nov. : a unique seedling related to Welwitschia
    2003
    Co-Authors: Catarina Rydin, Barbara A. R. Mohr, Else Marie Friis
    Abstract:

    The phylogeny of seed plants has been debated for more than a hundred years and is still not fully understood. Morphological analyses have consistently resulted in a phylogeny in which cycads are the earliest diverging seed plants, and Gnetales and angiosperms are sisters. Molecular data has, however, rarely supported this result. Mitochondrial data resolves Gnetales as sister to the conifer family Pinaceae, but results from the nuclear and chloroplast genomes are ambiguous. My studies showed a conflict between transitions and transversions within the chloroplast genes rbcL and atpB, and consequently, different topologies are obtained from different substitution models and character codings. Transversion parsimony as well as maximum likelihood using GTR-model results in an association between Gnetales and conifers, whereas equally weighted parsimony and a simpler model (F81) resolves Gnetales as sister to all other seed plants. Taxon sampling error may be another problem. I could easily obtain seemingly well-supported, but conflicting, topologies simply by substituting a few terminals in bayesian and parsimony analyses of rbcL. These problems do not only concern the systematic position of the Gnetales, but other fundamental issues such as the monophyly of conifers and gymnosperms, the sister group of Ginkgo etc. The most recent articles on the subject argue that monophyletic gymnosperms and a sister relationship between Gnetales and Pinaceae is the most probable scenario because this topology is supported by mitochondrial data and by chloroplast data from which the fastest evolving sites (i.e. transitions or third codon positions) have been removed or down-weighted.The Gnetales have often been considered a small remnant of a former much greater diversity due to the pronounced morphological and ecological differences between the genera. But until recently, megafossils, which could support this were rare. We have described a seedling from the Early Cretaceous of Brazil that shares several synapomorphies with Welwitschia and dates the split between Gnetum and Welwitschia to before 110 Myr. Ephedra, the sister group of the Gnetum-Welwitschia clade, comprises a homogenous group of species; very similar in gross morphology and with few informative characters in the investigated gene regions. The similarities made it difficult to resolve relationships within the group and to assign fossils to subgroups within Ephedra. We have studied Early Cretaceous fossils from Portugal, Virginia and China and they share several unique features with modern Ephedra, e.g. the peculiar naked male gametophyte. They differ in detailed morphology, however, indicating that a diversity of Ephedra species was present in the Early Cretaceous flora. We have compared the fossils to extant species and to the extinct Erdtmanispermum, and discuss character evolution within the ephedroid lineage. The paucity of information in most gene regions has indicated a very young age (8-32 Myr) for modern species in molecular dating analyses. The fossils document that the characteristic Ephedra features were present and widespread in the Early Cretaceous and they indicate that the crown group may be of Mesozoic origin (110-127 Myr). A recently published fossil from China, which possesses a character only present in a few extant species, further supports this idea. Ephedra might once again demonstrate the absence of a linear correlation between the amount of substitutions and time.

Chen Hou - One of the best experts on this subject based on the ideXlab platform.

  • PacBio Long-Read Sequencing Reveals the Transcriptomic Complexity and Aux/IAA Gene Evolution in Gnetum (Gnetales)
    Forests, 2019
    Co-Authors: Chen Hou, Nan Deng
    Abstract:

    The genus Gnetum includes pantropical trees, shrubs and lianas, with unresolved phylogenetic relationships with other seed plant groups. Despite the reference genome for this genus being recently published, the molecular mechanisms that regulate the reproductive organ development of Gnetum remain unclear. A previous study showed that indole-3-acetic acid is involved in the regulation of female strobili of Gnetum, while the diversity and evolution of indole-3-acetic acid-related genes—the Aux/IAA genes—have never been investigated in Gnetales. Thus, a pooled sample from different developmental stages of female strobili in Gnetum luofuense C.Y. Cheng was sequenced using PacBio single-molecular long-read technology (SMRT) sequencing. PacBio SMRT sequencing generated a total of 53,057 full-length transcripts, including 2043 novel genes. Besides this, 10,454 alternative splicing (AS) events were detected with intron retention constituting the largest proportion (46%). Moreover, 1196 lncRNAs were identified, and 8128 genes were found to possess at least one poly (A) site. A total of 3179 regulatory proteins, including 1413 transcription factors (e.g., MADS-box and bHLHs), 477 transcription regulators (e.g., SNF2), and 1289 protein kinases (e.g., RLK/Pelles) were detected, and these protein regulators probably participated in the female strobili development of G. luofuense. In addition, this is the first study of the Aux/IAA genes of the Gnetales, and we identified 6, 7 and 12 Aux/IAA genes from Gnetum luofuense, Welwitschia mirabilis, and Ephedra equistina, respectively. Our phylogenetic analysis reveals that Aux/IAA genes from the gymnosperms tended to cluster and possessed gene structures as diverse as those in angiosperms. Moreover, the Aux/IAA genes of the Gnetales might possess higher molecular evolutionary rates than those in other gymnosperms. The sequencing of the full-length transcriptome paves the way to uncovering molecular mechanisms that regulate reproductive organ development in gymnosperms.

  • pacbio long read sequencing reveals the transcriptomic complexity and aux iaa gene evolution in gnetum Gnetales
    Forests, 2019
    Co-Authors: Chen Hou, Nan Deng
    Abstract:

    The genus Gnetum includes pantropical trees, shrubs and lianas, with unresolved phylogenetic relationships with other seed plant groups. Despite the reference genome for this genus being recently published, the molecular mechanisms that regulate the reproductive organ development of Gnetum remain unclear. A previous study showed that indole-3-acetic acid is involved in the regulation of female strobili of Gnetum, while the diversity and evolution of indole-3-acetic acid-related genes—the Aux/IAA genes—have never been investigated in Gnetales. Thus, a pooled sample from different developmental stages of female strobili in Gnetum luofuense C.Y. Cheng was sequenced using PacBio single-molecular long-read technology (SMRT) sequencing. PacBio SMRT sequencing generated a total of 53,057 full-length transcripts, including 2043 novel genes. Besides this, 10,454 alternative splicing (AS) events were detected with intron retention constituting the largest proportion (46%). Moreover, 1196 lncRNAs were identified, and 8128 genes were found to possess at least one poly (A) site. A total of 3179 regulatory proteins, including 1413 transcription factors (e.g., MADS-box and bHLHs), 477 transcription regulators (e.g., SNF2), and 1289 protein kinases (e.g., RLK/Pelles) were detected, and these protein regulators probably participated in the female strobili development of G. luofuense. In addition, this is the first study of the Aux/IAA genes of the Gnetales, and we identified 6, 7 and 12 Aux/IAA genes from Gnetum luofuense, Welwitschia mirabilis, and Ephedra equistina, respectively. Our phylogenetic analysis reveals that Aux/IAA genes from the gymnosperms tended to cluster and possessed gene structures as diverse as those in angiosperms. Moreover, the Aux/IAA genes of the Gnetales might possess higher molecular evolutionary rates than those in other gymnosperms. The sequencing of the full-length transcriptome paves the way to uncovering molecular mechanisms that regulate reproductive organ development in gymnosperms.

  • Evolutionary studies of the Gnetales
    2016
    Co-Authors: Chen Hou
    Abstract:

    The Gnetales consist of three distinct genera, Ephedra, Gnetum and Welwitschia with considerable divergence among them regarding morphological, ecological and molecular characters. A longstanding d ...

  • Proteome of pollination drops in Ephedra (Gnetales)
    2016
    Co-Authors: Chen Hou, Catarina Rydin
    Abstract:

    Proteins are important in many physiological and ecological processes. In pollination drops of gymnosperms, proteins take part in a number of pollen-ovule interactions and aid for example in ovule ...

  • The chloroplast genome of Ephedra foeminea (Ephedraceae, Gnetales), an entomophilous gymnosperm endemic to the Mediterranean area.
    Mitochondrial DNA Part A, 2015
    Co-Authors: Chen Hou, Niklas Wikström, Catarina Rydin
    Abstract:

    This study presents the chloroplast genome of Ephedra foeminea, an entomophilous gymnosperm, sister to the remaining (wind-pollinated) species of Ephedra (Ephedraceae, Gnetales). Based on the refer ...