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  1. Article ; Online: Getting inside the oldest known vertebrate skull.

    Gai, Zhikun / Donoghue, Philip C J

    Nature

    2023  Volume 621, Issue 7980, Page(s) 696–698

    MeSH term(s) Skull ; Head
    Language English
    Publishing date 2023-09-20
    Publishing country England
    Document type News
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-023-02865-2
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  2. Article ; Online: Plant evolution: Streptophyte multicellularity, ecology, and the acclimatisation of plants to life on land.

    Donoghue, Philip C J / Clark, James W

    Current biology : CB

    2024  Volume 34, Issue 3, Page(s) R86–R89

    Abstract: Land plants are celebrated as one of the three great instances of complex multicellularity, but new phylogenomic and phenotypic analyses are revealing deep evolutionary roots of multicellularity among algal relatives, prompting questions about the causal ...

    Abstract Land plants are celebrated as one of the three great instances of complex multicellularity, but new phylogenomic and phenotypic analyses are revealing deep evolutionary roots of multicellularity among algal relatives, prompting questions about the causal basis of this major evolutionary transition.
    MeSH term(s) Plants ; Biological Evolution ; Phylogeny ; Embryophyta ; Acclimatization
    Language English
    Publishing date 2024-01-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2023.12.036
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  3. Article ; Online: Author Correction: Evolutionary analysis of swimming speed in early vertebrates challenges the 'New Head Hypothesis'.

    Ferrón, Humberto G / Donoghue, Philip C J

    Communications biology

    2023  Volume 6, Issue 1, Page(s) 786

    Language English
    Publishing date 2023-07-28
    Publishing country England
    Document type Published Erratum
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-023-05164-8
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  4. Article ; Online: Fossil cells.

    Donoghue, Philip C J

    Current biology : CB

    2020  Volume 30, Issue 10, Page(s) R485–R490

    Abstract: Philip Donoghue introduces the fossil record of cells. ...

    Abstract Philip Donoghue introduces the fossil record of cells.
    MeSH term(s) Biological Evolution ; Cells/cytology ; Fossils ; Genomics ; Origin of Life
    Language English
    Publishing date 2020-05-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2020.02.063
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  5. Article ; Online: Constraining Whole-Genome Duplication Events in Geological Time.

    Clark, James W / Donoghue, Philip C J

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2545, Page(s) 139–154

    Abstract: The timing of whole-genome duplication (WGD) events is crucial to understanding their role in evolution and underpins many hypotheses linking WGD to increased diversity and complexity. As such, means of estimating the timing of the WGD events relative to ...

    Abstract The timing of whole-genome duplication (WGD) events is crucial to understanding their role in evolution and underpins many hypotheses linking WGD to increased diversity and complexity. As such, means of estimating the timing of the WGD events relative to their macroevolutionary outcomes are of considerable importance. Molecular clock methods facilitate direct estimation of the absolute timing of WGD events, integrating information on the rate of sequence evolution between species while accommodating the uncertainty inherent to the fossil record. We present an explanation of the best practice for constructing fossil calibrations and estimating the age of WGD events via molecular clock methods in the program MCMCtree, with an example dataset based on a well-characterized WGD event within the flowering dogwoods (Cornus). The approach presented herein allows for the estimation of the age of WGD events and subsequent speciation events, allowing the relationship between WGD and the macroevolutionary outcomes to be explored. In our example, we show that in the case of flowering dogwoods, the WGD event long predates the end-Cretaceous mass extinction and that the two events may be independent.
    MeSH term(s) Gene Duplication ; Calibration ; Extinction, Biological ; Fossils
    Language English
    Publishing date 2023-01-11
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2561-3_7
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  6. Article ; Online: The unbearable uncertainty of panarthropod relationships.

    Wu, Ruolin / Pisani, Davide / Donoghue, Philip C J

    Biology letters

    2023  Volume 19, Issue 1, Page(s) 20220497

    Abstract: Panarthropoda, the clade comprising the phyla Onychophora, Tardigrada and Euarthropoda, encompasses the largest majority of animal biodiversity. The relationships among the phyla are contested and resolution is key to understanding the evolutionary ... ...

    Abstract Panarthropoda, the clade comprising the phyla Onychophora, Tardigrada and Euarthropoda, encompasses the largest majority of animal biodiversity. The relationships among the phyla are contested and resolution is key to understanding the evolutionary assembly of panarthropod bodyplans. Molecular phylogenetic analyses generally support monophyly of Onychophora and Euarthropoda to the exclusion of Tardigrada (Lobopodia hypothesis), which is also supported by some analyses of morphological data. However, analyses of morphological data have also been interpreted to support monophyly of Tardigrada and Euarthropoda to the exclusion of Onychophora (Tactopoda hypothesis). Support has also been found for a clade of Onychophora and Tardigrada that excludes Euarthropoda (Protarthropoda hypothesis). Here we show, using a diversity of phylogenetic inference methods, that morphological datasets cannot discriminate statistically between the Lobopodia, Tactopoda and Protarthropoda hypotheses. Since the relationships among the living clades of panarthropod phyla cannot be discriminated based on morphological data, we call into question the accuracy of morphology-based phylogenies of Panarthropoda that include fossil species and the evolutionary hypotheses based upon them.
    MeSH term(s) Animals ; Phylogeny ; Arthropods/genetics ; Arthropods/anatomy & histology ; Uncertainty ; Biological Evolution ; Tardigrada/genetics ; Tardigrada/anatomy & histology
    Language English
    Publishing date 2023-01-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2135022-X
    ISSN 1744-957X ; 1744-9561
    ISSN (online) 1744-957X
    ISSN 1744-9561
    DOI 10.1098/rsbl.2022.0497
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    Zs.A 1364 -Letters-: Show issues Location:
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  7. Article ; Online: Cryogenian Origins of Multicellularity in Archaeplastida.

    Bowles, Alexander M C / Williamson, Christopher J / Williams, Tom A / Donoghue, Philip C J

    Genome biology and evolution

    2024  Volume 16, Issue 2

    Abstract: Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship ...

    Abstract Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution.
    MeSH term(s) Phylogeny ; Biological Evolution ; Plants ; Embryophyta ; Chlorophyta ; Fossils ; Evolution, Molecular
    Language English
    Publishing date 2024-02-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2495328-3
    ISSN 1759-6653 ; 1759-6653
    ISSN (online) 1759-6653
    ISSN 1759-6653
    DOI 10.1093/gbe/evae026
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  8. Article ; Online: Fossilization can mislead analyses of phenotypic disparity.

    Smith, Thomas J / Sansom, Robert S / Pisani, Davide / Donoghue, Philip C J

    Proceedings. Biological sciences

    2023  Volume 290, Issue 2004, Page(s) 20230522

    Abstract: Analyses of morphological disparity can incorporate living and fossil taxa to facilitate the exploration of how phenotypic variation changes through time. However, taphonomic processes introduce non-random patterns of data loss in fossil data and their ... ...

    Abstract Analyses of morphological disparity can incorporate living and fossil taxa to facilitate the exploration of how phenotypic variation changes through time. However, taphonomic processes introduce non-random patterns of data loss in fossil data and their impact on perceptions of disparity is unclear. To address this, we characterize how measures of disparity change when simulated and empirical data are degraded through random and structured data loss. We demonstrate that both types of data loss can distort the disparity of clades, and that the magnitude and direction of these changes varies between the most commonly employed distance metrics and disparity indices. The inclusion of extant taxa and exceptionally preserved fossils mitigates these distortions and clarifies the full extent of the data lost, most of which would otherwise go uncharacterized. This facilitates the use of ancestral state estimation and evolutionary simulations to further control for the effects of data loss. Where the addition of such reference taxa is not possible, we urge caution in the extrapolation of general patterns in disparity from datasets that characterize subsets of phenotype, which may represent no more than the traits that they sample.
    MeSH term(s) Phylogeny ; Biological Evolution ; Fossils ; Phenotype
    Language English
    Publishing date 2023-08-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209242-6
    ISSN 1471-2954 ; 0080-4649 ; 0962-8452 ; 0950-1193
    ISSN (online) 1471-2954
    ISSN 0080-4649 ; 0962-8452 ; 0950-1193
    DOI 10.1098/rspb.2023.0522
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  9. Article ; Online: Evolution of fungal phenotypic disparity.

    Smith, Thomas J / Donoghue, Philip C J

    Nature ecology & evolution

    2022  Volume 6, Issue 10, Page(s) 1489–1500

    Abstract: Organismal-grade multicellularity has been achieved only in animals, plants and fungi. All three kingdoms manifest phenotypically disparate body plans but their evolution has only been considered in detail for animals. Here we tested the general ... ...

    Abstract Organismal-grade multicellularity has been achieved only in animals, plants and fungi. All three kingdoms manifest phenotypically disparate body plans but their evolution has only been considered in detail for animals. Here we tested the general relevance of hypotheses on the evolutionary assembly of animal body plans by characterizing the evolution of fungal phenotypic variety (disparity). The distribution of living fungal form is defined by four distinct morphotypes: flagellated; zygomycetous; sac-bearing; and club-bearing. The discontinuity between morphotypes is a consequence of extinction, indicating that a complete record of fungal disparity would present a more homogeneous distribution of form. Fungal disparity expands episodically through time, punctuated by a sharp increase associated with the emergence of multicellular body plans. Simulations show these temporal trends to be non-random and at least partially shaped by hierarchical contingency. These trends are decoupled from changes in gene number, genome size and taxonomic diversity. Only differences in organismal complexity, characterized as the number of traits that constitute an organism, exhibit a meaningful relationship with fungal disparity. Both animals and fungi exhibit episodic increases in disparity through time, resulting in distributions of form made discontinuous by extinction. These congruences suggest a common mode of multicellular body plan evolution.
    MeSH term(s) Animals ; Biological Evolution ; Fungi/genetics ; Phenotype ; Plants
    Language English
    Publishing date 2022-08-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2397-334X
    ISSN (online) 2397-334X
    DOI 10.1038/s41559-022-01844-6
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  10. Article: Internal anatomy of a fossilized embryonic stage of the Cambrian-Ordovician scalidophoran

    Dong, Xi-Ping / Duan, Baichuan / Liu, Jianbo / Donoghue, Philip C J

    Royal Society open science

    2022  Volume 9, Issue 10, Page(s) 220115

    Abstract: The Wangcun fossil Lagerstätte in Hunan, South China, has yielded hundreds of fossilized embryos ... ...

    Abstract The Wangcun fossil Lagerstätte in Hunan, South China, has yielded hundreds of fossilized embryos of
    Language English
    Publishing date 2022-10-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2787755-3
    ISSN 2054-5703
    ISSN 2054-5703
    DOI 10.1098/rsos.220115
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