Article type : MS - Regular Manuscript Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events Ya Yang 1,4, Michael J. Moore2, Samuel F. Brockington3, Jessica Mikenas2, Julia Olivieri2, Joseph F. Walker1 and Stephen A. Smith1 1Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA; 2Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH 44074-1097, USA; 3Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK; 4Current address: Department of Plant and Microbial Biology, University of Minnesota, Twin Cities. 1445 Gortner Avenue, St Paul, MN 55108, USA Authors for correspondence: Ya Yang Tel: +1 612 625 6292 Email:
[email protected] Stephen A. Smith Tel: +1 734 764 7923 Email:
[email protected] Received: 30 May 2017 Accepted: 9 AugustAuthor Manuscript 2017 This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/nph.14812 This article is protected by copyright. All rights reserved Summary • Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. • We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one of the densest sampled genomic-scale datasets available.