Organellar data sets confirm overall angiosperm relationships if problematic RNA-edit sites are accounted for in mitochondrial genomes
bioRxiv (Cold Spring Harbor Laboratory)
Abstract
Premise Plastid-based data sets continue to play a major role in our understanding of early flowering-plant relationships, although organellar genomes of major lineages outside the monocots and eudicots remain under-sampled. A tendency of mitochondrial RNA-edit sites to mislead phylogenetic analysis in mixed transcriptomic/genomic data sets needs attention in angiosperm-wide studies, which only rarely consider mitochondrial genomes. Methods We compared mitochondrial- vs. plastid-based phylogenomic inferences, examined the effect of removing putative RNA-edit sites from mitochondrial data, and performed combined organellar analysis (plastid plus filtered mitochondrial genomes). We expanded taxon sampling for multiple angiosperm lineages for phylogenomic analysis using both organellar genomes, representing several poorly sampled lineages (in particular Degeneriaceae, Trimeniaceae) with smaller (few-gene) data sets. Results Plastid-based inferences recover well-supported relationships that align with and build upon previous studies, and recover well-supported internal relationships for two ANA-grade families (Hydatellaceae, Trimeniaceae) sampled for nearly all species. By contrast, unfiltered mitochondrial inferences of angiosperm phylogeny are generally poorly supported, and recover anomalous relationships compared to plastid-based inferences. However, removing putative mitochondrial RNA-edit sites dramatically reduces inter-organellar conflict and improves overall branch support. Conclusions We accounted for phylogenomic discordance between the two organellar genomes regarding overall angiosperm-wide relationships and filled in taxonomic gaps (poorly sampled lineages). Removing RNA edit sites substantially improves congruence in interorganellar inferences by effectively correcting a systematic bias in mitochondrial data. Uncertain relationships persist among five major mesangiosperm lineages in plastid-based inferences, but a clade comprising Chloranthales, Ceratophyllales and eudicots is well supported by filtered mitochondrial data.
Authors 17
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University of British Columbia
Affiliation as printed
University of British Columbia;
Deprtment of Botny, University of British Columbi, 6270 University Boulevrd, Vncouver, BC, Cnd, V6T 1Z4
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Goethe University Frankfurt · Technische Universität Dresden
Affiliation as printed
Goethe-Universitat Frankfurt;
Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, Dresden, Germany, D-01062
Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, 60438 Frankfurt am Main, Germany
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University of Lisbon · University of British Columbia
Affiliation as printed
University of Lisbon;
Deprtment of Botny, University of British Columbi, 6270 University Boulevrd, Vncouver, BC, Cnd, V6T 1Z4
Instituto Superior e Agronomia, University of Lisbon, Tapaa a Ajua, Lisbon, Portugal, 1349-017
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Affiliation as printed
University of Connecticut;
Dpartmnt of Ecology & Evolutionary Biology, Univrsity of Conncticut, 375 Torry Lif Scincs Building, 75 North Eaglvill Road, Storrs, CT 06269-3043, USA
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University of British Columbia
Affiliation as printed
University of British Columbia;
Genome Science and Technology Program, University o British Columbia, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada
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Affiliation as printed
University of Victoria;
Centre for Forest Bioloy, University of Victoria, 3800 Finnerty Road, Victoria, BC, Canada, V8P 5C2
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Affiliation as printed
Otterbein University;
Department of Biology and Eart Science, Otterbein University, 1 Sout Grove Street, Westerville, OH, 43081, USA
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Russian Academy of Sciences · Tel Aviv University · Department of Biological Sciences
Affiliation as printed
Tel Aviv University;
Department of Biological Sciences, Russian Academy of Sciences, Moscow 119991, Russia
School of Plant Scences and Food Securty, Faculty of Lfe Scences, Tel Avv Unversty, Tel Avv 6997801, Israel
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Department of Biodiversity, Conservation and Attractions
Affiliation as printed
Western Australian Herbarium;
Western Australian Herbarium, Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Loced Bag 104, Bentley Delivery Centre, Western Australia 6983 Australia
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University of British Columbia
Affiliation as printed
University of British Columbia;
Deprtment of Botny, University of British Columbi, 6270 University Boulevrd, Vncouver, BC, Cnd, V6T 1Z4
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Affiliation as printed
New College of Florida;
Natura Sciences Division, New Coege of Forida, E256 Heiser Natura Sciences Compex, 500 Coege Dr, Sarasota, FL, 34243, USA
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Affiliation as printed
Louisiana State University;
Departent of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
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Affiliation as printed
Oberlin College;
Departmet of Biology, Oberli College, 119 Woodlad St, Oberli, OH, 44074, USA
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Naturalis Biodiversity Center · Institut de Recherche pour le Développement · Diversité, adaptation et développement des plantes · Institut de Recherche pour le Développement
Affiliation as printed
Institut de Recherche pour le Developpement;
IRD, DIADE, Univ Montellier, Montellier, France
Naturalis Bidiversity Center, Leiden 2333 CR, The Netherlands
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Affiliation as printed
National Herbarium of NSW
National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, NSW, Australia
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Goethe University Frankfurt · Senckenberg - Leibniz Institution for Biodiversity and Earth System Research · Technische Universität Dresden · Universidad Nacional Autónoma de México
Affiliation as printed
Goethe-Universitat Frankfurt;
Abteilung Botanik und molekulae Evolutionsfoschung, Senckenbeg Gesellschaft fü Natufoschung, 60325 Fankfut am Main, Gemany
Departamento de Botánica, Intituto de Biología, Univeridad Nacional Autónoma de México, 70-367 Mexico City, Mexico
Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, Dresden, Germany, D-01062
Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, 60438 Frankfurt am Main, Germany
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Sean W. Graham corresponding
University of British Columbia
Affiliation as printed
University of British Columbia;
Deprtment of Botny, University of British Columbi, 6270 University Boulevrd, Vncouver, BC, Cnd, V6T 1Z4
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