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T Standard phylogenetic approaches and Three-taxon statement analysis remain as tools of discovery: Cryptic genera in Atraphaxis (Polygonaceae) Olga V.Yurtseva1, Evgeny V.Mavrodiev2 1 Department of Higher Plants, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1-12, , Moscow, Russia, 2 Florida Museum of Natural History, University of Florida, Gainesville, Florida, U.S.A., Purpose We aim to reveal relationships within Atraphaxis L. s.l. as broadly circumscribed by Tavakkoli et al. (2015) using standard phylogenetic techniques and Three-taxon statement analysis (3TA). Methods Maximum Likelihood analysis (ML) and Bayesian Inference (BI) of the tribe Polygoneae based on nuclear (ITS) and combined plastid (three loci) datasets; Standard Maximum Parsimony (MP) and 3TA of 27 morphological characters Results Distributional areas of Bactria, Persepolium and Atraphaxis Bactria lazkovii Atraphaxis Bactria ovczinnikovii Peerspolium Nuclear phylogeny of the tribe Polygoneae (ML, BI) Plastid phylogeny of the tribe Polygoneae (ML, BI) Monophyly vs paraphyly of Bactria (plastid vs nuclear topology) The aLRT support values ≥ 0.8 from ML analysis / posterior probabilities ≥ 0.9 from the BI The aLRT support values ≥ 0.8 from ML analysis/ posterior probabilities ≥ 0.9 from the BI Morphological phylogeny of Atraphaxis s.l. (standard MP) Nested most parsimonious hierarchy of patterns (3TA, morphology) Bactria B. lazkovii B. ovczinnikovii P. salicornioides Persepolium Atraphaxis A. toktogulica A. virgata Conclusions The almost fully congruent topologies that result from (1.) ML and BI of the molecular datasets and (2.) from both standard MP and 3TA analyses of the morphological data elucidate the discovery of the generic rank of traditionally circumscribed Atraphaxis s.str., as well as Bactria and Persepolium, and suggest potential hybridization processes within the tribe Polygoneae. MP Bootstrap support values ≥ 50%
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Atraphaxis teretifolia
Post Scriptum. New intriguing story of Atraphaxis s.str. and allies: congruencies, incongruences and new species The best tree from ML analysis of the combined plastid dataset: trnL intron, trnL-trnF IGS, and rpl32–trnL(UAG) IGS regions of cpDNA Atraphaxis spinosa (A. sect. Atraphaxis) Atraphaxis virgata (A. sect. Tragopyrum) Atraphaxis teretifolia (A. sect. Physopyrum) The aLRT support values ≥ 0.8 from ML analysis / posterior probabilities ≥ 0.9 from the BI Persepolium salicornioides (Persepolium) References Farris JS 1983 The logical basis of phylogenetic analysis. Platnick, N I and V a Funk (Eds) Advances in Cladistics, Vol 2 Proceedings of the 2nd Meeting of the WilliHennig Society; Ann Arbor, Mich, USA, Oct 1-4, 1981 Xi+218p Columbia University Press: New York, NY, USA Illus: P7-36. Felsenstein J 2004 Inferring phylogenies.Sinauer Associates, Inc: i-xx, Guindon S, JF Dufayard, V Lefort, M Anisimova, W Hordijk, O Gascuel 2010 A new algorithms and methods to estimate Maximum-Likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology 59: Huelsenbeck JP, F Ronquist 2001 MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: Mavrodiev EV, A Madorsky 2012 TAXODIUM version 1.0: A simple way to generate uniform and fractionally weighted three-item matrices from various kinds of biological data. PLoS ONE7(11): e doi: /journal.pone Nelson G, NI Platnick 1991 Three-taxon statements - a more precise use of parsimony? Cladistics 7: Swofford DL PAUP*. Phylogenetic analysis using parsimony (*and other methods).Sinauer Associates, Sunderland, Massachusetts. Tavakkoli S, SK Osaloo, V Mozaffarian, AA Maassoumi 2015 Molecular phylogeny of Atraphaxis and the woody Polygonum species (Polygonaceae): Taxonomic implications based on molecular and morphological evidence. Plant Systematics and Evolution 301: Yurtseva OV, OI Kuznetsova, ME Mavrodieva, EV Mavrodiev 2016 What is Atraphaxis l. (Polygonaceae, Polygoneae): Cryptic taxa and resolved taxonomic complexity instead of the formal lumping and the lack of morphological synapomorphies.PeerJ 4:e1977; doi: /peerj.1977 Yurtseva OV,Severova EA, EV Mavrodiev 2017 Persepolium (Polygoneae): A new genus in Polygonaceae based on conventional Maximum Parsimony and Three-taxon statement analyses of a comprehensive morphological dataset. Phytotaxa (accepted). Yurtseva OV, OI Kuznetsova, EV Mavrodiev A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: I. Atraphaxis kamelinii spec. nov. from Mongolia. Phytotaxa. 268: 1-24
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