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Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution

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      • Through the lens of the fossil record, angiosperm diversification precipitated a Cretaceous Terrestrial Revolution ( KTR) in which pollinators, herbivores and predators underwent explosive co‐diversification. Molecular dating studies imply that early angiosperm evolution is not documented in the fossil record. This mismatch remains controversial.

      • We used a Bayesian molecular dating method to analyse a dataset of 83 genes from 644 taxa and 52 fossil calibrations to explore the effect of different interpretations of the fossil record, molecular clock models, data partitioning, among other factors, on angiosperm divergence time estimation.

      • Controlling for different sources of uncertainty indicates that the timescale of angiosperm diversification is much less certain than previous molecular dating studies have suggested. Discord between molecular clock and purely fossil‐based interpretations of angiosperm diversification may be a consequence of false precision on both sides.

      • We reject a post‐Jurassic origin of angiosperms, supporting the notion of a cryptic early history of angiosperms, but this history may be as much as 121 Myr, or as little as 23 Myr. These conclusions remain compatible with palaeobotanical evidence and a more general KTR in which major groups of angiosperms diverged later within the Cretaceous, alongside the diversification of pollinators, herbivores and their predators.

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      Most cited references 97

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      MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

      We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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        PAML 4: phylogenetic analysis by maximum likelihood.

         Ziheng Yang (2007)
        PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (
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          SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.

          We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees. In relation to the wide present offer of tools and algorithms for phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at

            Author and article information

            [ 1 ] Department of Genetics, Evolution and Environment University College London Darwin Building Gower Street London WC1E 6BT UK
            [ 2 ] School of Biological and Chemical Sciences Queen Mary University of London Mile End Road London E1 4NS UK
            [ 3 ] Center of Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Menglun Yunnan China
            [ 4 ] Department of Botany Natural History Museum Cromwell Road London SW7 5BD UK
            [ 5 ] School of Earth Sciences University of Bristol Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
            Author notes
            [* ] Authors for correspondence:

            Ziheng Yang

            Tel: +44 020 7679 2000, ext. 34379

            Email: z.yang@

            Philip C. J. Donoghue

            Tel: +44 011 7394 1209

            Email: phil.donoghue@

            New Phytol
            New Phytol
            The New Phytologist
            John Wiley and Sons Inc. (Hoboken )
            05 February 2018
            April 2018
            : 218
            : 2 ( doiID: 10.1111/nph.2018.218.issue-2 )
            : 819-834
            NPH15011 2017-24672
            © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust

            This is an open access article under the terms of the License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

            Figures: 6, Tables: 2, Pages: 16, Words: 11597
            Funded by: Biotechnology and Biosciences Research Council (UK)
            Award ID: BB/N000609/1
            Funded by: Natural Environment Research Council
            Award ID: NE/N002067/1
            Funded by: Royal Society
            Funded by: Wolfson Foundation
            Funded by: CONACyT‐Mexico and UCL scholarship
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            April 2018
            Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.4.3 mode:remove_FC converted:23.07.2018


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