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  1. Article ; Online: Molecular phylogenies map to biogeography better than morphological ones.

    Oyston, Jack W / Wilkinson, Mark / Ruta, Marcello / Wills, Matthew A

    Communications biology

    2022  Volume 5, Issue 1, Page(s) 521

    Abstract: Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Currently, most phylogenies of extant taxa are inferred from molecules and when morphological and molecular trees conflict the latter are often ... ...

    Abstract Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Currently, most phylogenies of extant taxa are inferred from molecules and when morphological and molecular trees conflict the latter are often preferred. Although supported by simulations, the superiority of molecular trees has rarely been assessed empirically. Here we test phylogenetic accuracy using two independent data sources: biogeographic distributions and fossil first occurrences. For 48 pairs of morphological and molecular trees we show that, on average, molecular trees provide a better fit to biogeographic data than their morphological counterparts and that biogeographic congruence increases over research time. We find no significant differences in stratigraphic congruence between morphological and molecular trees. These results have implications for understanding the distribution of homoplasy in morphological data sets, the utility of morphology as a test of molecular hypotheses and the implications of analysing fossil groups for which molecular data are unavailable.
    MeSH term(s) Fossils ; Phylogeny
    Language English
    Publishing date 2022-05-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-022-03482-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Molecular phylogenies map to biogeography better than morphological ones

    Jack W. Oyston / Mark Wilkinson / Marcello Ruta / Matthew A. Wills

    Communications Biology, Vol 5, Iss 1, Pp 1-

    2022  Volume 12

    Abstract: Using biogeographical and phylogenetic data, it is shown that molecular trees fit species geographical data better than trees inferred from morphology, and that these differences are not simply due to better tree resolution. ...

    Abstract Using biogeographical and phylogenetic data, it is shown that molecular trees fit species geographical data better than trees inferred from morphology, and that these differences are not simply due to better tree resolution.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Why should we investigate the morphological disparity of plant clades?

    Oyston, Jack W / Hughes, Martin / Gerber, Sylvain / Wills, Matthew A

    Annals of botany

    2015  Volume 117, Issue 5, Page(s) 859–879

    Abstract: Background: Disparity refers to the morphological variation in a sample of taxa, and is distinct from diversity or taxonomic richness. Diversity and disparity are fundamentally decoupled; many groups attain high levels of disparity early in their ... ...

    Abstract Background: Disparity refers to the morphological variation in a sample of taxa, and is distinct from diversity or taxonomic richness. Diversity and disparity are fundamentally decoupled; many groups attain high levels of disparity early in their evolution, while diversity is still comparatively low. Diversity may subsequently increase even in the face of static or declining disparity by increasingly fine sub-division of morphological 'design' space (morphospace). Many animal clades reached high levels of disparity early in their evolution, but there have been few comparable studies of plant clades, despite their profound ecological and evolutionary importance. This study offers a prospective and some preliminary macroevolutionary analyses.
    Methods: Classical morphometric methods are most suitable when there is reasonable conservation of form, but lose traction where morphological differences become greater (e.g. in comparisons across higher taxa). Discrete character matrices offer one means to compare a greater diversity of forms. This study explores morphospaces derived from eight discrete data sets for major plant clades, and discusses their macroevolutionary implications.
    Key results: Most of the plant clades in this study show initial, high levels of disparity that approach or attain the maximum levels reached subsequently. These plant clades are characterized by an initial phase of evolution during which most regions of their empirical morphospaces are colonized. Angiosperms, palms, pines and ferns show remarkably little variation in disparity through time. Conifers furnish the most marked exception, appearing at relatively low disparity in the latest Carboniferous, before expanding incrementally with the radiation of successive, tightly clustered constituent sub-clades.
    Conclusions: Many cladistic data sets can be repurposed for investigating the morphological disparity of plant clades through time, and offer insights that are complementary to more focused morphometric studies. The unique structural and ecological features of plants make them ideally suited to investigating intrinsic and extrinsic constraints on disparity.
    MeSH term(s) Biodiversity ; Biological Evolution ; Ferns/anatomy & histology ; Ferns/classification ; Ferns/physiology ; Magnoliopsida/anatomy & histology ; Magnoliopsida/classification ; Magnoliopsida/physiology ; Species Specificity
    Language English
    Publishing date 2015-12-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1461328-1
    ISSN 1095-8290 ; 0305-7364
    ISSN (online) 1095-8290
    ISSN 0305-7364
    DOI 10.1093/aob/mcv135
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Why should we investigate the morphological disparity of plant clades?

    Oyston, Jack W / Hughes, Martin / Gerber, Sylvain / Wills, Matthew A

    Annals of botany. 2016 Apr., v. 117, no. 5

    2016  

    Abstract: Background Disparity refers to the morphological variation in a sample of taxa, and is distinct from diversity or taxonomic richness. Diversity and disparity are fundamentally decoupled; many groups attain high levels of disparity early in their ... ...

    Abstract Background Disparity refers to the morphological variation in a sample of taxa, and is distinct from diversity or taxonomic richness. Diversity and disparity are fundamentally decoupled; many groups attain high levels of disparity early in their evolution, while diversity is still comparatively low. Diversity may subsequently increase even in the face of static or declining disparity by increasingly fine sub-division of morphological ‘design’ space (morphospace). Many animal clades reached high levels of disparity early in their evolution, but there have been few comparable studies of plant clades, despite their profound ecological and evolutionary importance. This study offers a prospective and some preliminary macroevolutionary analyses. Methods Classical morphometric methods are most suitable when there is reasonable conservation of form, but lose traction where morphological differences become greater (e.g. in comparisons across higher taxa). Discrete character matrices offer one means to compare a greater diversity of forms. This study explores morphospaces derived from eight discrete data sets for major plant clades, and discusses their macroevolutionary implications. Key Results Most of the plant clades in this study show initial, high levels of disparity that approach or attain the maximum levels reached subsequently. These plant clades are characterized by an initial phase of evolution during which most regions of their empirical morphospaces are colonized. Angiosperms, palms, pines and ferns show remarkably little variation in disparity through time. Conifers furnish the most marked exception, appearing at relatively low disparity in the latest Carboniferous, before expanding incrementally with the radiation of successive, tightly clustered constituent sub-clades. Conclusions Many cladistic data sets can be repurposed for investigating the morphological disparity of plant clades through time, and offer insights that are complementary to more focused morphometric studies. The unique structural and ecological features of plants make them ideally suited to investigating intrinsic and extrinsic constraints on disparity.
    Keywords Angiospermae ; Carboniferous period ; Pinus ; conifers ; data collection ; evolution ; ferns and fern allies ; morphometry
    Language English
    Dates of publication 2016-04
    Size p. 859-879.
    Publishing place Oxford University Press
    Document type Article
    ZDB-ID 1461328-1
    ISSN 1095-8290 ; 0305-7364
    ISSN (online) 1095-8290
    ISSN 0305-7364
    DOI 10.1093/aob/mcv135
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: What limits the morphological disparity of clades?

    Oyston, Jack W / Hughes, Martin / Wagner, Peter J / Gerber, Sylvain / Wills, Matthew A

    Interface focus

    2015  Volume 5, Issue 6, Page(s) 20150042

    Abstract: The morphological disparity of species within major clades shows a variety of trajectory patterns through evolutionary time. However, there is a significant tendency for groups to reach their maximum disparity relatively early in their histories, even ... ...

    Abstract The morphological disparity of species within major clades shows a variety of trajectory patterns through evolutionary time. However, there is a significant tendency for groups to reach their maximum disparity relatively early in their histories, even while their species richness or diversity is comparatively low. This pattern of early high-disparity suggests that there are internal constraints (e.g. developmental pleiotropy) or external restrictions (e.g. ecological competition) upon the variety of morphologies that can subsequently evolve. It has also been demonstrated that the rate of evolution of new character states decreases in most clades through time (character saturation), as does the rate of origination of novel bodyplans and higher taxa. Here, we tested whether there was a simple relationship between the level or rate of character state exhaustion and the shape of a clade's disparity profile: specifically, its centre of gravity (CG). In a sample of 93 extinct major clades, most showed some degree of exhaustion, but all continued to evolve new states up until their extinction. Projection of states/steps curves suggested that clades realized an average of 60% of their inferred maximum numbers of states. Despite a weak but significant correlation between overall levels of homoplasy and the CG of clade disparity profiles, there were no significant relationships between any of our indices of exhaustion curve shape and the clade disparity CG. Clades showing early high-disparity were no more likely to have early character saturation than those with maximum disparity late in their evolution.
    Language English
    Publishing date 2015-04-13
    Publishing country England
    Document type Journal Article
    ISSN 2042-8898
    ISSN 2042-8898
    DOI 10.1098/rsfs.2015.0042
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The transcriptional landscape of age in human peripheral blood.

    Peters, Marjolein J / Joehanes, Roby / Pilling, Luke C / Schurmann, Claudia / Conneely, Karen N / Powell, Joseph / Reinmaa, Eva / Sutphin, George L / Zhernakova, Alexandra / Schramm, Katharina / Wilson, Yana A / Kobes, Sayuko / Tukiainen, Taru / Ramos, Yolande F / Göring, Harald H H / Fornage, Myriam / Liu, Yongmei / Gharib, Sina A / Stranger, Barbara E /
    De Jager, Philip L / Aviv, Abraham / Levy, Daniel / Murabito, Joanne M / Munson, Peter J / Huan, Tianxiao / Hofman, Albert / Uitterlinden, André G / Rivadeneira, Fernando / van Rooij, Jeroen / Stolk, Lisette / Broer, Linda / Verbiest, Michael M P J / Jhamai, Mila / Arp, Pascal / Metspalu, Andres / Tserel, Liina / Milani, Lili / Samani, Nilesh J / Peterson, Pärt / Kasela, Silva / Codd, Veryan / Peters, Annette / Ward-Caviness, Cavin K / Herder, Christian / Waldenberger, Melanie / Roden, Michael / Singmann, Paula / Zeilinger, Sonja / Illig, Thomas / Homuth, Georg / Grabe, Hans-Jörgen / Völzke, Henry / Steil, Leif / Kocher, Thomas / Murray, Anna / Melzer, David / Yaghootkar, Hanieh / Bandinelli, Stefania / Moses, Eric K / Kent, Jack W / Curran, Joanne E / Johnson, Matthew P / Williams-Blangero, Sarah / Westra, Harm-Jan / McRae, Allan F / Smith, Jennifer A / Kardia, Sharon L R / Hovatta, Iiris / Perola, Markus / Ripatti, Samuli / Salomaa, Veikko / Henders, Anjali K / Martin, Nicholas G / Smith, Alicia K / Mehta, Divya / Binder, Elisabeth B / Nylocks, K Maria / Kennedy, Elizabeth M / Klengel, Torsten / Ding, Jingzhong / Suchy-Dicey, Astrid M / Enquobahrie, Daniel A / Brody, Jennifer / Rotter, Jerome I / Chen, Yii-Der I / Houwing-Duistermaat, Jeanine / Kloppenburg, Margreet / Slagboom, P Eline / Helmer, Quinta / den Hollander, Wouter / Bean, Shannon / Raj, Towfique / Bakhshi, Noman / Wang, Qiao Ping / Oyston, Lisa J / Psaty, Bruce M / Tracy, Russell P / Montgomery, Grant W / Turner, Stephen T / Blangero, John / Meulenbelt, Ingrid / Ressler, Kerry J / Yang, Jian / Franke, Lude / Kettunen, Johannes / Visscher, Peter M / Neely, G Gregory / Korstanje, Ron / Hanson, Robert L / Prokisch, Holger / Ferrucci, Luigi / Esko, Tonu / Teumer, Alexander / van Meurs, Joyce B J / Johnson, Andrew D

    Nature communications

    2015  Volume 6, Page(s) 8570

    Abstract: Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ... ...

    Abstract Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age. The age-associated genes do not harbor more age-associated CpG-methylation sites than other genes, but are instead enriched for the presence of potentially functional CpG-methylation sites in enhancer and insulator regions that associate with both chronological age and gene expression levels. We further used the gene expression profiles to calculate the 'transcriptomic age' of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features linked to ageing, such as blood pressure, cholesterol levels, fasting glucose, and body mass index. The transcriptomic prediction model adds biological relevance and complements existing epigenetic prediction models, and can be used by others to calculate transcriptomic age in external cohorts.
    MeSH term(s) Aging/blood ; Biomarkers/blood ; DNA Methylation ; European Continental Ancestry Group ; Gene Expression Profiling ; Humans ; Transcriptome
    Chemical Substances Biomarkers
    Language English
    Publishing date 2015-10-22
    Publishing country England
    Document type Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/ncomms9570
    Database MEDical Literature Analysis and Retrieval System OnLINE

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