Osmundaceae

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Stephen Mcloughlin - One of the best experts on this subject based on the ideXlab platform.

  • Figure S1
    2016
    Co-Authors: Guido W. Grimm, Benjamin Bomfleur, Stephen Mcloughlin, Pashalia Kapli, Susanne S. Renner
    Abstract:

    The ML tree for Osmundaceae from the same data as used for the tree in Fig. 1 with bootstrap support at the nodes

  • osmunda pulchella sp nov from the jurassic of sweden reconciling molecular and fossil evidence in the phylogeny of modern royal ferns Osmundaceae
    BMC Evolutionary Biology, 2015
    Co-Authors: Benjamin Bomfleur, Guido W. Grimm, Stephen Mcloughlin
    Abstract:

    The classification of royal ferns (Osmundaceae) has long remained controversial. Recent molecular phylogenies indicate that Osmunda is paraphyletic and needs to be separated into Osmundastrum and Osmunda s.str. Here, however, we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of both Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Osmunda pulchella and five additional Jurassic rhizome species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as probable ancestral members of modern genera and subgenera, which accords with recent evidence from Bayesian dating. Osmunda pulchella is likely a precursor of the Osmundastrum lineage. The recently proposed root placement in Osmundaceae—based solely on molecular data—stems from possibly misinformative outgroup signals in rbcL and atpA genes. We conclude that the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can instead be elegantly reconciled under the assumption that Osmunda is indeed monophyletic.

  • Osmunda pulchella sp. nov. from the Jurassic of Swedenreconciling molecular and fossil evidence in the phylogeny of Osmundaceae
    2014
    Co-Authors: Benjamin Bomfleur, Guido W. Grimm, Stephen Mcloughlin
    Abstract:

    The systematic classification of Osmundaceae has long remained controversial. Recent molecular data indicate that Osmunda is paraphyletic, and needs to be separated into Osmundastrum and Osmunda s. str. Here we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Osmunda pulchella and five additional, newly identified Jurassic Osmunda species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as ancestral members of modern genera and subgenera. Altogether, the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can be elegantly reconciled under the assumption that Osmunda is indeed monophyletic; the recently proposed root-placement in Osmundaceae—based solely on molecular data—likely results from un- or misinformative out-group signals.

  • a fossil osmunda from the jurassic of sweden reconciling molecular and fossil evidence in the phylogeny of Osmundaceae
    bioRxiv, 2014
    Co-Authors: Benjamin Bomfleur, Guido W. Grimm, Stephen Mcloughlin
    Abstract:

    ABSTRACT The systematic classification of Osmundaceae has long remained controversial. Recent molecular data indicate that Osmunda is paraphyletic, and needs to be separated into Osmundastrum and Osmunda s. str. Here we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Osmunda pulchella and five additional, newly identified Jurassic Osmunda species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as ancestral members of modern genera and subgenera. Altogether, the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can be elegantly reconciled under the assumption that Osmunda is indeed monophyletic; the recently proposed root-placement in Osmundaceae—based solely on molecular data—likely results from un- or misinformative out-group signals.

James R. Manhart - One of the best experts on this subject based on the ideXlab platform.

Guido W. Grimm - One of the best experts on this subject based on the ideXlab platform.

  • Figure S1
    2016
    Co-Authors: Guido W. Grimm, Benjamin Bomfleur, Stephen Mcloughlin, Pashalia Kapli, Susanne S. Renner
    Abstract:

    The ML tree for Osmundaceae from the same data as used for the tree in Fig. 1 with bootstrap support at the nodes

  • osmunda pulchella sp nov from the jurassic of sweden reconciling molecular and fossil evidence in the phylogeny of modern royal ferns Osmundaceae
    BMC Evolutionary Biology, 2015
    Co-Authors: Benjamin Bomfleur, Guido W. Grimm, Stephen Mcloughlin
    Abstract:

    The classification of royal ferns (Osmundaceae) has long remained controversial. Recent molecular phylogenies indicate that Osmunda is paraphyletic and needs to be separated into Osmundastrum and Osmunda s.str. Here, however, we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of both Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Osmunda pulchella and five additional Jurassic rhizome species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as probable ancestral members of modern genera and subgenera, which accords with recent evidence from Bayesian dating. Osmunda pulchella is likely a precursor of the Osmundastrum lineage. The recently proposed root placement in Osmundaceae—based solely on molecular data—stems from possibly misinformative outgroup signals in rbcL and atpA genes. We conclude that the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can instead be elegantly reconciled under the assumption that Osmunda is indeed monophyletic.

  • Osmunda pulchella sp. nov. from the Jurassic of Swedenreconciling molecular and fossil evidence in the phylogeny of Osmundaceae
    2014
    Co-Authors: Benjamin Bomfleur, Guido W. Grimm, Stephen Mcloughlin
    Abstract:

    The systematic classification of Osmundaceae has long remained controversial. Recent molecular data indicate that Osmunda is paraphyletic, and needs to be separated into Osmundastrum and Osmunda s. str. Here we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Osmunda pulchella and five additional, newly identified Jurassic Osmunda species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as ancestral members of modern genera and subgenera. Altogether, the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can be elegantly reconciled under the assumption that Osmunda is indeed monophyletic; the recently proposed root-placement in Osmundaceae—based solely on molecular data—likely results from un- or misinformative out-group signals.

  • a fossil osmunda from the jurassic of sweden reconciling molecular and fossil evidence in the phylogeny of Osmundaceae
    bioRxiv, 2014
    Co-Authors: Benjamin Bomfleur, Guido W. Grimm, Stephen Mcloughlin
    Abstract:

    ABSTRACT The systematic classification of Osmundaceae has long remained controversial. Recent molecular data indicate that Osmunda is paraphyletic, and needs to be separated into Osmundastrum and Osmunda s. str. Here we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Osmunda pulchella and five additional, newly identified Jurassic Osmunda species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as ancestral members of modern genera and subgenera. Altogether, the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can be elegantly reconciled under the assumption that Osmunda is indeed monophyletic; the recently proposed root-placement in Osmundaceae—based solely on molecular data—likely results from un- or misinformative out-group signals.

Mcloughlin Stephen - One of the best experts on this subject based on the ideXlab platform.

  • Disrupted vegetation as a response to Jurassic volcanism in southern Sweden
    'Geological Society of London', 2016
    Co-Authors: Vajda Vivi, Linderson Hans, Mcloughlin Stephen
    Abstract:

    Central Skåne (Scania) in southern Sweden hosts evidence of extensive Jurassic volcanism in the form of mafic volcanic plugs and associated volcaniclastic deposits that entomb well preserved macro-plant and spore–pollen assemblages. Palynological assemblages recovered from the Höör Sandstone are of Hettangian–Pliensbachian age and those from the overlying lahar deposits are dated as Pliensbachian–early Toarcian (?). Palynomorph assemblages from these units reveal significantly different ecosystems, particularly with respect to the gymnospermous components that represented the main canopy plants. Both palynofloras are dominated by osmundacean, marattiacean and cyatheacean fern spore taxa but, whereas the Höör Sandstone hosts abundant Chasmatosporites spp. pollen produced by plants related to cycadophytes, the volcanogenic deposits are dominated by cypress family pollen (Perinopollenites) with an understorey component rich in putative Erdtmanithecales (or possibly Gnetales), and collectively representing vegetation of disturbed habitats. Permineralized conifer wood attributed to Protophyllocladoxylon sp., belonging to plants that probably produced the abundant Perinopollenites grains, is abundant in the volcanigenic strata, and shows sporadic intraseasonal and multi-year episodes of growth disruption. Together with the relatively narrow but marked annual growth rings, and the annual and mean sensitivity values that span the complacent–sensitive domains, these features suggest growth within Mediterranean-type biomes subject to episodic disturbance.Part of the special issue Mesozoic Biotas of Scandinavia and its Arctic Territories edited by: Kear, B. P., Lindgren, J., Hurum, J. H., Milàn, J. & Vajda, V.

  • Disrupted vegetation as a response to Jurassic volcanism in southern Sweden
    'Geological Society of London', 2016
    Co-Authors: Vajda Vivi, Linderson Hans, Mcloughlin Stephen
    Abstract:

    Central Skåne (Scania) in southern Sweden hosts evidence of extensive Jurassic volcanism in the form of mafic volcanic plugs and associated volcaniclastic deposits that entomb wellpreserved macro-plant and spore-pollen assemblages. Palynological assemblages recovered from the Höör Sandstone are of Hettangian-Pliensbachian age and those from the overlying lahar deposits are dated as Pliensbachian-early Toarcian (?). Palynomorph assemblages from these units reveal significantly different ecosystems, particularly with respect to the gymnospermous components that represented the main canopy plants. Both palynofloras are dominated by osmundacean, marattiacean and cyatheacean fern spore taxa but, whereas the Höö r Sandstone hosts abundant Chasmatosporites spp. pollen produced by plants related to cycadophytes, the volcanogenic deposits are dominated by cypress family pollen (Perinopollenites) with an understorey component rich in putative Erdtmanithecales (or possibly Gnetales), and collectively representing vegetation of disturbed habitats. Permineralized conifer wood attributed to Protophyllocladoxylon sp., belonging to plants that probably produced the abundant Perinopollenites grains, is abundant in the volcanigenic strata, and shows sporadic intraseasonal and multi-year episodes of growth disruption. Together with the relatively narrow but marked annual growth rings, and the annual and mean sensitivity values that span the complacent-sensitive domains, these features suggest growth within Mediterranean-type biomes subject to episodic disturbance

  • Using more than the oldest fossils: Dating Osmundaceae with three Bayesian clock approaches
    'Oxford University Press (OUP)', 2015
    Co-Authors: Grimm Guido, Bomfleur Benjamin, Mcloughlin Stephen, Kapli Paschalia, Renner Susanne
    Abstract:

    A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved—“node dating” (ND) inBEAST, “total evidence” (TE) dating in MrBayes, and the “fossilized birth–death” (FBD) in FDPPDiv—to infer divergence times in the royal ferns. Osmundaceae have 16–17 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ∼17 genera. For ND, we used the five oldest fossils, whereas for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils,we included up to 36 rhizomes and frond compression/impression fossils, which for TE datingwere scored for 33morphological characters.We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence ages were generally greater than those inferred from ND; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We prefer the FBD-derived ages because they best fit the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Paleozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, the FBD approach yielded speciation and extinction rates that overlapped those obtained from just neontological data. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling; therefore, these estimates should be treated with caution.Exceptional permineralized biotas - windows into the evolution and functional diversity of terrestrial ecosystems through tim

  • Osmunda pulchella sp. nov. from the Jurassic of Sweden--reconciling molecular and fossil evidence in the phylogeny of modern royal ferns (Osmundaceae)
    'Springer Science and Business Media LLC', 2015
    Co-Authors: Bomfleur Benjamin, Grimm Guido, Mcloughlin Stephen
    Abstract:

    Background: The classification of royal ferns (Osmundaceae) has long remained controversial. Recent molecular phylogenies indicate that Osmunda is paraphyletic and needs to be separated into Osmundastrum and Osmunda s.str. Here, however, we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of both Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Results: Osmunda pulchella and five additional Jurassic rhizome species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as probable ancestral members of modern genera and subgenera, which accords with recent evidence from Bayesian dating. Conclusions: Osmunda pulchella is likely a precursor of the Osmundastrum lineage. The recently proposed root placement in Osmundaceae—based solely on molecular data—stems from possibly misinformative outgroup signals in rbcL and atpA genes. We conclude that the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can instead be elegantly reconciled under the assumption that Osmunda is indeed monophyletic.Exceptional permineralized biotas - windows into the evolution and functional diversity of terrestrial ecosystems through tim

  • Main matrices and dating results
    2014
    Co-Authors: Grimm, Guido W., Bomfleur Benjamin, Mcloughlin Stephen, Kapli Pashalia, Renner, Susanne S.
    Abstract:

    This archive includes the basic matrix files and the main result files of the various dating analyses. For a comprehensive phylogenetic analyses of these data, see Benjamin Bomfleur, Guido W Grimm, Stephen McLoughlin (2014) Osmunda pulchella sp. nov. from the Jurassic of Sweden—reconciling molecular and fossil evidence in the phylogeny of Osmundaceae. bioRxiv, doi: http://dx.doi.org/10.1101/005777

Bomfleur Benjamin - One of the best experts on this subject based on the ideXlab platform.

  • Using more than the oldest fossils: Dating Osmundaceae with three Bayesian clock approaches
    'Oxford University Press (OUP)', 2015
    Co-Authors: Grimm Guido, Bomfleur Benjamin, Mcloughlin Stephen, Kapli Paschalia, Renner Susanne
    Abstract:

    A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved—“node dating” (ND) inBEAST, “total evidence” (TE) dating in MrBayes, and the “fossilized birth–death” (FBD) in FDPPDiv—to infer divergence times in the royal ferns. Osmundaceae have 16–17 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ∼17 genera. For ND, we used the five oldest fossils, whereas for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils,we included up to 36 rhizomes and frond compression/impression fossils, which for TE datingwere scored for 33morphological characters.We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence ages were generally greater than those inferred from ND; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We prefer the FBD-derived ages because they best fit the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Paleozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, the FBD approach yielded speciation and extinction rates that overlapped those obtained from just neontological data. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling; therefore, these estimates should be treated with caution.Exceptional permineralized biotas - windows into the evolution and functional diversity of terrestrial ecosystems through tim

  • Osmunda pulchella sp. nov. from the Jurassic of Sweden--reconciling molecular and fossil evidence in the phylogeny of modern royal ferns (Osmundaceae)
    'Springer Science and Business Media LLC', 2015
    Co-Authors: Bomfleur Benjamin, Grimm Guido, Mcloughlin Stephen
    Abstract:

    Background: The classification of royal ferns (Osmundaceae) has long remained controversial. Recent molecular phylogenies indicate that Osmunda is paraphyletic and needs to be separated into Osmundastrum and Osmunda s.str. Here, however, we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of both Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Results: Osmunda pulchella and five additional Jurassic rhizome species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as probable ancestral members of modern genera and subgenera, which accords with recent evidence from Bayesian dating. Conclusions: Osmunda pulchella is likely a precursor of the Osmundastrum lineage. The recently proposed root placement in Osmundaceae—based solely on molecular data—stems from possibly misinformative outgroup signals in rbcL and atpA genes. We conclude that the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can instead be elegantly reconciled under the assumption that Osmunda is indeed monophyletic.Exceptional permineralized biotas - windows into the evolution and functional diversity of terrestrial ecosystems through tim

  • Main matrices and dating results
    2014
    Co-Authors: Grimm, Guido W., Bomfleur Benjamin, Mcloughlin Stephen, Kapli Pashalia, Renner, Susanne S.
    Abstract:

    This archive includes the basic matrix files and the main result files of the various dating analyses. For a comprehensive phylogenetic analyses of these data, see Benjamin Bomfleur, Guido W Grimm, Stephen McLoughlin (2014) Osmunda pulchella sp. nov. from the Jurassic of Sweden—reconciling molecular and fossil evidence in the phylogeny of Osmundaceae. bioRxiv, doi: http://dx.doi.org/10.1101/005777

  • TableS1_FossilListForDating
    2014
    Co-Authors: Grimm, Guido W., Bomfleur Benjamin, Mcloughlin Stephen, Kapli Pashalia, Renner, Susanne S.
    Abstract:

    Fossils of modern Osmundaceae used in the analyses

  • Fossilized nuclei and chromosomes reveal 180 millionyears of genomic stasis in Royal Ferns
    'American Association for the Advancement of Science (AAAS)', 2014
    Co-Authors: Bomfleur Benjamin, Mcloughlin Stephen, Vajda Vivi
    Abstract:

    Rapidly permineralized fossils can provide exceptional insights into the evolution of life over geological time. Here, we present an exquisitely preserved, calcified stem of a royal fern (Osmundaceae) from Early Jurassic lahar deposits of Sweden in which authigenic mineral precipitation from hydrothermal brines occurred so rapidly that it preserved cytoplasm, cytosol granules, nuclei, and even chromosomes in various stages of cell division. Morphometric parameters of interphase nuclei match those of extant Osmundaceae, indicating that the genome size of these reputed “living fossils” has remained unchanged over at least 180 million years—a paramount example of evolutionary stasis

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