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Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

Joseph F. Walker, Ya Yang, Michael J. Moore, Jessica Mikenas, Alfonso Timoneda, Samuel F. Brockington, Stephen A. Smith
doi: https://doi.org/10.1101/115741
Joseph F. Walker
2Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
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  • For correspondence: jfwalker@umich.edu eebsmith@umich.edu
Ya Yang
2Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
5Department of Plant Biology, University of Minnesota-Twin Cities. 1445 Gortner Avenue, St. Paul, MN 55108
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Michael J. Moore
3Department of Biology, Oberlin College, Science Center K111, 119 Woodland St., Oberlin, Ohio 44074-1097 USA
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Jessica Mikenas
3Department of Biology, Oberlin College, Science Center K111, 119 Woodland St., Oberlin, Ohio 44074-1097 USA
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Alfonso Timoneda
4Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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Samuel F. Brockington
4Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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Stephen A. Smith
2Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
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  • For correspondence: jfwalker@umich.edu eebsmith@umich.edu
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ABSTRACT

  • The carnivorous members of the large, hyperdiverse Caryophyllales (e.g. Venus flytrap, sundews and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved.

  • To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced ten transcriptomes, including all the carnivorous genera except those in the rare West African liana family (Dioncophyllaceae). We used a variety of methods to infer the species tree, examine gene tree conflict and infer paleopolyploidy events.

  • Phylogenomic analyses support the monophyly of the carnivorous Caryophyllales, with an origin of 68-83 mya. In contrast to previous analyses recover the remaining non-core Caryophyllales as non-monophyletic, although there are multiple reasons this result may be spurious and node supporting this relationship contains a significant amount gene tree discordance. We present evidence that the clade contains at least seven independent paleopolyploidy events, previously debated nodes from the literature have high levels of gene tree conflict, and taxon sampling influences topology even in a phylogenomic data set.

  • Our data demonstrate the importance of carefully considering gene tree conflict and taxon sampling in phylogenomic analyses. Moreover, they provide a remarkable example of the propensity for paleopolyploidy in angiosperms, with at least seven such events in a clade of less than 2500 species.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted March 10, 2017.
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Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales
Joseph F. Walker, Ya Yang, Michael J. Moore, Jessica Mikenas, Alfonso Timoneda, Samuel F. Brockington, Stephen A. Smith
bioRxiv 115741; doi: https://doi.org/10.1101/115741
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Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales
Joseph F. Walker, Ya Yang, Michael J. Moore, Jessica Mikenas, Alfonso Timoneda, Samuel F. Brockington, Stephen A. Smith
bioRxiv 115741; doi: https://doi.org/10.1101/115741

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