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Impact of whole-genome duplication events on diversification rates in angiosperms.
Am J Bot. 2018 03; 105(3):348-363.AJ

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.

Authors+Show Affiliations

Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California, 92521, USA.Department of Biology, University of Florida, Gainesville, Florida, 32611, USA. Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA. Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA.Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA.Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA.Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA.Department of Biological Sciences, University of Idaho, Moscow, Idaho, 83844, USA. Stillinger Herbarium, University of Idaho, Moscow, Idaho, 83844, USA.Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA. Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

29719043

Citation

Landis, Jacob B., et al. "Impact of Whole-genome Duplication Events On Diversification Rates in Angiosperms." American Journal of Botany, vol. 105, no. 3, 2018, pp. 348-363.
Landis JB, Soltis DE, Li Z, et al. Impact of whole-genome duplication events on diversification rates in angiosperms. Am J Bot. 2018;105(3):348-363.
Landis, J. B., Soltis, D. E., Li, Z., Marx, H. E., Barker, M. S., Tank, D. C., & Soltis, P. S. (2018). Impact of whole-genome duplication events on diversification rates in angiosperms. American Journal of Botany, 105(3), 348-363. https://doi.org/10.1002/ajb2.1060
Landis JB, et al. Impact of Whole-genome Duplication Events On Diversification Rates in Angiosperms. Am J Bot. 2018;105(3):348-363. PubMed PMID: 29719043.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Impact of whole-genome duplication events on diversification rates in angiosperms. AU - Landis,Jacob B, AU - Soltis,Douglas E, AU - Li,Zheng, AU - Marx,Hannah E, AU - Barker,Michael S, AU - Tank,David C, AU - Soltis,Pamela S, Y1 - 2018/05/02/ PY - 2017/09/11/received PY - 2017/12/12/accepted PY - 2018/5/3/pubmed PY - 2019/3/1/medline PY - 2018/5/3/entrez KW - BAMM KW - MEDUSA KW - MuSSE KW - diversification rates KW - lag phase KW - polyploidy KW - sister-clade comparison SP - 348 EP - 363 JF - American journal of botany JO - Am. J. Bot. VL - 105 IS - 3 N2 - 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. SN - 1537-2197 UR - https://www.unboundmedicine.com/medline/citation/29719043/Impact_of_whole_genome_duplication_events_on_diversification_rates_in_angiosperms_ L2 - https://doi.org/10.1002/ajb2.1060 DB - PRIME DP - Unbound Medicine ER -