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      A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses

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          Abstract

          Abstract

          Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology.

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          Most cited references 88

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          Use of DNA barcodes to identify flowering plants.

          Methods for identifying species by using short orthologous DNA sequences, known as "DNA barcodes," have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short ( approximately 450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.
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            The age and diversification of the angiosperms re-revisited.

            • It has been 8 years since the last comprehensive analysis of divergence times across the angiosperms. Given recent methodological improvements in estimating divergence times, refined understanding of relationships among major angiosperm lineages, and the immense interest in using large angiosperm phylogenies to investigate questions in ecology and comparative biology, new estimates of the ages of the major clades are badly needed. Improved estimations of divergence times will concomitantly improve our understanding of both the evolutionary history of the angiosperms and the patterns and processes that have led to this highly diverse clade. • We simultaneously estimated the age of the angiosperms and the divergence times of key angiosperm lineages, using 36 calibration points for 567 taxa and a "relaxed clock" methodology that does not assume any correlation between rates, thus allowing for lineage-specific rate heterogeneity. • Based on the analysis for which we set fossils to fit lognormal priors, we obtained an estimated age of the angiosperms of 167-199 Ma and the following age estimates for major angiosperm clades: Mesangiospermae (139-156 Ma); Gunneridae (109-139 Ma); Rosidae (108-121 Ma); Asteridae (101-119 Ma). • With the exception of the age of the angiosperms themselves, these age estimates are generally younger than other recent molecular estimates and very close to dates inferred from the fossil record. We also provide dates for all major angiosperm clades (including 45 orders and 335 families [208 stem group age only, 127 both stem and crown group ages], sensu APG III). Our analyses provide a new comprehensive source of reference dates for major angiosperm clades that we hope will be of broad utility.
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              Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms.

              Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the last great question remaining in basal angiosperm phylogeny involves the branching order among the five major clades of mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, magnoliids, and monocots). Previous analyses have found no consistent support for relationships among these clades. In an effort to resolve these relationships, we performed phylogenetic analyses of 61 plastid genes ( approximately 42,000 bp) for 45 taxa, including members of all major basal angiosperm lineages. We also report the complete plastid genome sequence of Ceratophyllum demersum. Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularly Ceratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable. Total evidence ML analyses recovered a clade of Chloranthaceae + magnoliids as sister to a well supported clade of monocots + (Ceratophyllum + eudicots). ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 +/- 4.8 and 140.3 +/- 4.8 Mya.
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                Author and article information

                Contributors
                Journal
                Biodivers Data J
                Biodivers Data J
                1
                urn:lsid:arphahub.com:pub:F9B2E808-C883-5F47-B276-6D62129E4FF4
                urn:lsid:zoobank.org:pub:245B00E9-BFE5-4B4F-B76E-15C30BA74C02
                Biodiversity Data Journal
                Pensoft Publishers
                1314-2828
                2020
                21 January 2020
                : 8
                Affiliations
                [1 ] Botanic Garden Meise, Meise, Belgium Botanic Garden Meise Meise Belgium
                [2 ] Laboratory for Plant Conservation and Population Biology, KULeuven, Leuven, Belgium Laboratory for Plant Conservation and Population Biology, KULeuven Leuven Belgium
                [3 ] DIADE, IRD, Univ. Montpellier, Montpellier, France DIADE, IRD, Univ. Montpellier Montpellier France
                [4 ] AMAP Lab, IRD, CIRAD, CNRS, INRA, Univ Montpellier, Montpellier, France AMAP Lab, IRD, CIRAD, CNRS, INRA, Univ Montpellier Montpellier France
                [5 ] RMCA, Tervuren, Belgium RMCA Tervuren Belgium
                [6 ] University of Johannesburg, Johannesburg, South Africa University of Johannesburg Johannesburg South Africa
                [7 ] Royal Botanic Gardens, Kew, United Kingdom Royal Botanic Gardens Kew United Kingdom
                [8 ] Department of Plant Sciences, University of Oxford, Oxford, United Kingdom Department of Plant Sciences, University of Oxford Oxford United Kingdom
                [9 ] Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom Department of Plant Sciences, University of Cambridge Cambridge United Kingdom
                [10 ] Université de Bangui – Cerphameta, Bangui, Central African Republic Université de Bangui – Cerphameta Bangui Central African Republic
                [11 ] Ministère des Eaux, Forêts, Chasse et Pêche, Bangui, Central African Republic Ministère des Eaux, Forêts, Chasse et Pêche Bangui Central African Republic
                [12 ] Department of Evolutionary and Population Biology, University of Amsterdam, Amsterdam, Netherlands Department of Evolutionary and Population Biology, University of Amsterdam Amsterdam Netherlands
                [13 ] Understanding Evolution Group, Naturalis Biodiversity Center, Leiden, Netherlands Understanding Evolution Group, Naturalis Biodiversity Center Leiden Netherlands
                [14 ] Natural History Museum, University of Oslo, Oslo, Norway Natural History Museum, University of Oslo Oslo Norway
                [15 ] Universite Libre de Bruxelles, Brussels, Belgium Universite Libre de Bruxelles Brussels Belgium
                Author notes
                Corresponding author: Steven B. Janssens ( steven.janssens@ 123456plantentuinmeise.be ).

                Academic editor: Stephen Boatwright

                Article
                39677 12476
                10.3897/BDJ.8.e39677
                6987248
                Steven B. Janssens, Thomas L.P. Couvreur, Arne Mertens, Gilles Dauby, Leo-Paul M. J. Dagallier, Samuel Vanden Abeele, Filip Vandelook, Maurizio Mascarello, Hans Beeckman, Marc Sosef, Vincent Droissart, Michelle van der Bank, Olivier Maurin, William Hawthorne, Cicely Marshall, Maxime Réjou-Méchain, Denis Beina, Fidele Baya, Vincent Merckx, Brecht Verstraete, Olivier Hardy

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Page count
                Figures: 1, Tables: 1, References: 118
                Categories
                Research Article

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