Research Disparity, diversity, and duplications in the Caryophyllales Stephen A. Smith1, Joseph W. Brown1, Ya Yang2, Riva Bruenn3, Chloe P. Drummond3, Samuel F. Brockington4, Joseph F. Walker1, Noah Last2, Norman A. Douglas3 and Michael J. Moore3 1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103, USA; 2Department of Plant Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St Paul, MN 55108, USA; 3Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH 44074-1097, USA; 4Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK Summary Author for correspondence: The role played by whole genome duplication (WGD) in plant evolution is actively debated. Stephen A. Smith WGDs have been associated with advantages such as superior colonization, various adapta- Tel: +1 734 615 5510 tions, and increased effective population size. However, the lack of a comprehensive mapping Email:
[email protected] of WGDs within a major plant clade has led to uncertainty regarding the potential association Received: 30 May 2017 of WGDs and higher diversification rates. Accepted: 28 July 2017 Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species. We phylogenetically New Phytologist (2017) mapped putative WGDs as identified from analyses on transcriptomic and genomic data and doi: 10.1111/nph.14772 analyzed these in conjunction with shifts in climatic occupancy and lineage diversification rate. Thirteen putative WGDs and 27 diversification shifts could be mapped onto the phylogeny. Key words: Caryophyllales, climatic occupancy, diversification rates, duplications, Of these, four WGDs were concurrent with diversification shifts, with other diversification phylogenomics.