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Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of seed plant phylogeny

Mario Coiro, Guillaume Chomicki, James A. Doyle
doi: https://doi.org/10.1101/134262
Mario Coiro
1Department of Systematic and Evolutionary Botany, University of Zurich, 8008 Zurich, Switzerland
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  • For correspondence: mario.coiro@systbot.uzh.ch
Guillaume Chomicki
2Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), D-80638 Munich, Germany
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James A. Doyle
3Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
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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.

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Posted June 07, 2017.
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Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of seed plant phylogeny
Mario Coiro, Guillaume Chomicki, James A. Doyle
bioRxiv 134262; doi: https://doi.org/10.1101/134262
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Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of seed plant phylogeny
Mario Coiro, Guillaume Chomicki, James A. Doyle
bioRxiv 134262; doi: https://doi.org/10.1101/134262

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