Jacob B Landis1, Douglas E Soltis2,3,4, Zheng Li5, Hannah E Marx5, Michael S Barker5, David C Tank6,7, Pamela S Soltis3,4. 1. Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California, 92521, USA. 2. Department of Biology, University of Florida, Gainesville, Florida, 32611, USA. 3. Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA. 4. Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA. 5. Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA. 6. Department of Biological Sciences, University of Idaho, Moscow, Idaho, 83844, USA. 7. Stillinger Herbarium, University of Idaho, Moscow, Idaho, 83844, USA.
Abstract
PREMISE OF THE STUDY: Polyploidy or whole-genome duplication (WGD) pervades the evolutionary history of angiosperms. Despite extensive progress in our understanding of WGD, the role of these events in promoting diversification is still not well understood. We seek to clarify the possible association between WGD and diversification rates in flowering plants. METHODS: Using a previously published phylogeny spanning all land plants (31,749 tips) and WGD events inferred from analyses of the 1000 Plants (1KP) transcriptome data, we analyzed the association of WGDs and diversification rates following numerous WGD events across the angiosperms. We used a stepwise AIC approach (MEDUSA), a Bayesian mixture model approach (BAMM), and state-dependent diversification analyses (MuSSE) to investigate patterns of diversification. Sister-clade comparisons were used to investigate species richness after WGDs. KEY RESULTS: Based on the density of 1KP taxon sampling, 106 WGDs were unambiguously placed on the angiosperm phylogeny. We identified 334-530 shifts in diversification rates. We found that 61 WGD events were tightly linked to changes in diversification rates, and state-dependent diversification analyses indicated higher speciation rates for subsequent rounds of WGD. Additionally, 70 of 99 WGD events showed an increase in species richness compared to the sister clade. CONCLUSIONS: Forty-six of the 106 WGDs analyzed appear to be closely associated with upshifts in the rate of diversification in angiosperms. Shifts in diversification do not appear more likely than random within a four-node lag phase following a WGD; however, younger WGD events are more likely to be followed by an upshift in diversification than older WGD events.
PREMISE OF THE STUDY: Polyploidy or whole-genome duplication (WGD) pervades the evolutionary history of angiosperms. Despite extensive progress in our understanding of WGD, the role of these events in promoting diversification is still not well understood. We seek to clarify the possible association between WGD and diversification rates in flowering plants. METHODS: Using a previously published phylogeny spanning all land plants (31,749 tips) and WGD events inferred from analyses of the 1000 Plants (1KP) transcriptome data, we analyzed the association of WGDs and diversification rates following numerous WGD events across the angiosperms. We used a stepwise AIC approach (MEDUSA), a Bayesian mixture model approach (BAMM), and state-dependent diversification analyses (MuSSE) to investigate patterns of diversification. Sister-clade comparisons were used to investigate species richness after WGDs. KEY RESULTS: Based on the density of 1KP taxon sampling, 106 WGDs were unambiguously placed on the angiosperm phylogeny. We identified 334-530 shifts in diversification rates. We found that 61 WGD events were tightly linked to changes in diversification rates, and state-dependent diversification analyses indicated higher speciation rates for subsequent rounds of WGD. Additionally, 70 of 99 WGD events showed an increase in species richness compared to the sister clade. CONCLUSIONS: Forty-six of the 106 WGDs analyzed appear to be closely associated with upshifts in the rate of diversification in angiosperms. Shifts in diversification do not appear more likely than random within a four-node lag phase following a WGD; however, younger WGD events are more likely to be followed by an upshift in diversification than older WGD events.
Authors: Gregory W Stull; Xiao-Jian Qu; Caroline Parins-Fukuchi; Ying-Ying Yang; Jun-Bo Yang; Zhi-Yun Yang; Yi Hu; Hong Ma; Pamela S Soltis; Douglas E Soltis; De-Zhu Li; Stephen A Smith; Ting-Shuang Yi Journal: Nat Plants Date: 2021-07-19 Impact factor: 15.793
Authors: Fay-Wei Li; Tomoaki Nishiyama; Manuel Waller; Eftychios Frangedakis; Jean Keller; Zheng Li; Noe Fernandez-Pozo; Michael S Barker; Tom Bennett; Miguel A Blázquez; Shifeng Cheng; Andrew C Cuming; Jan de Vries; Sophie de Vries; Pierre-Marc Delaux; Issa S Diop; C Jill Harrison; Duncan Hauser; Jorge Hernández-García; Alexander Kirbis; John C Meeks; Isabel Monte; Sumanth K Mutte; Anna Neubauer; Dietmar Quandt; Tanner Robison; Masaki Shimamura; Stefan A Rensing; Juan Carlos Villarreal; Dolf Weijers; Susann Wicke; Gane K-S Wong; Keiko Sakakibara; Péter Szövényi Journal: Nat Plants Date: 2020-03-13 Impact factor: 15.793