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 data set of transcriptomes and genomes from 168 species in Caryophyllales, of which 43 transcriptomes were newly generated for this study, representing one of the most densely sampled genomic-scale data sets available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped the phylogenetic distribution of polyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for allopolyploidy. We identified 26 ancient and more recent polyploidy events distributed throughout Caryophyllales. Two of these events were inferred to be allopolyploidy. Through dense phylogenomic sampling, we show the propensity of polyploidy throughout the evolutionary history of Caryophyllales. We also provide a framework for utilizing transcriptome data to detect allopolyploidy, which is important as it may have different macroevolutionary implications compared with autopolyploidy.
Bibliographical noteFunding Information:
The authors thank H. Flores Olvera, H. Ochoterena, N. Douglas, S. Lavergne, T. Stoughton, L. Crawford, G. Kadereit, R. Puente, L. Majure, M. Howard, D. Anderson, M. Palmer, and K. Thiele for assisting with obtaining plant material; the Cambridge University Botanic Gardens, Bureau of Land Management, White Sands Missile Range, US Forest Service, California State Parks, Rancho Santa Ana Botanic Garden, Desert Botanical Garden, Millennium Seed Bank, and Booderee National Park for granting access to their plant material; M. R. M. Marchán-Rivadeneira and M. Parks for help with laboratory work; L. Y. Chen for help revising the manuscript; and three anonymous reviewers for constructive suggestions. The molecular work of this study was conducted in part in the Genomic Diversity Laboratory at the University of Michigan. Support came from the University of Michigan, Oberlin College, the National Geographic Society, the US National Science Foundation (DEB 1054539, DEB 1352907, and DEB 1354048), and a Natural Environment Research Council Independent Research Fellowship (NERC RG69516).
- Ks plot
- genome duplication
- modified phylome