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Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages.
Am J Bot. 2020 05; 107(5):790-805.AJ

Abstract

PREMISE

Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well-documented phenomenon at shallow evolutionary levels but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes, but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome.

METHODS

We present a phylogenomic examination of a major angiosperm clade (Asteridae) based on sequence data from the nuclear, plastid, and mitochondrial genomes as a means of evaluating currently accepted relationships inferred from the plastome and exploring potential sources of genomic conflict in this group.

RESULTS

We recovered at least five instances of well-supported cytonuclear discordance concerning the placements of major asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis, and Icacinaceae). We attribute this conflict to a combination of incomplete lineage sorting and hybridization, the latter supported in part by previously inferred whole-genome duplications.

CONCLUSIONS

Our results challenge several long-standing hypotheses of asterid relationships and have implications for morphological character evolution and for the importance of ancient whole-genome duplications in early asterid evolution. These findings also highlight the value of reevaluating broad-scale angiosperm and green-plant phylogeny with nuclear genomic data.

Authors+Show Affiliations

Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China. Department of Botany, Smithsonian Institution, Washington, D.C., 20013, USA.Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA. Biodiversity Institute, 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 Biology, University of Florida, Gainesville, Florida, 32611, USA.Department of Biology, University of Florida, Gainesville, Florida, 32611, USA.Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA.

Pub Type(s)

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

Language

eng

PubMed ID

32406108

Citation

Stull, Gregory W., et al. "Nuclear Phylogenomic Analyses of Asterids Conflict With Plastome Trees and Support Novel Relationships Among Major Lineages." American Journal of Botany, vol. 107, no. 5, 2020, pp. 790-805.
Stull GW, Soltis PS, Soltis DE, et al. Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages. Am J Bot. 2020;107(5):790-805.
Stull, G. W., Soltis, P. S., Soltis, D. E., Gitzendanner, M. A., & Smith, S. A. (2020). Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages. American Journal of Botany, 107(5), 790-805. https://doi.org/10.1002/ajb2.1468
Stull GW, et al. Nuclear Phylogenomic Analyses of Asterids Conflict With Plastome Trees and Support Novel Relationships Among Major Lineages. Am J Bot. 2020;107(5):790-805. PubMed PMID: 32406108.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages. AU - Stull,Gregory W, AU - Soltis,Pamela S, AU - Soltis,Douglas E, AU - Gitzendanner,Matthew A, AU - Smith,Stephen A, Y1 - 2020/05/13/ PY - 2019/10/26/received PY - 2020/02/26/accepted PY - 2020/5/15/pubmed PY - 2020/7/14/medline PY - 2020/5/15/entrez KW - Aquifoliales KW - Ericales KW - asterids KW - cytonuclear discordance KW - incomplete lineage sorting KW - phylogenomics KW - whole-genome duplication SP - 790 EP - 805 JF - American journal of botany JO - Am. J. Bot. VL - 107 IS - 5 N2 - PREMISE: Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well-documented phenomenon at shallow evolutionary levels but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes, but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome. METHODS: We present a phylogenomic examination of a major angiosperm clade (Asteridae) based on sequence data from the nuclear, plastid, and mitochondrial genomes as a means of evaluating currently accepted relationships inferred from the plastome and exploring potential sources of genomic conflict in this group. RESULTS: We recovered at least five instances of well-supported cytonuclear discordance concerning the placements of major asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis, and Icacinaceae). We attribute this conflict to a combination of incomplete lineage sorting and hybridization, the latter supported in part by previously inferred whole-genome duplications. CONCLUSIONS: Our results challenge several long-standing hypotheses of asterid relationships and have implications for morphological character evolution and for the importance of ancient whole-genome duplications in early asterid evolution. These findings also highlight the value of reevaluating broad-scale angiosperm and green-plant phylogeny with nuclear genomic data. SN - 1537-2197 UR - https://www.unboundmedicine.com/medline/citation/32406108/Nuclear_phylogenomic_analyses_of_asterids_conflict_with_plastome_trees_and_support_novel_relationships_among_major_lineages_ L2 - https://doi.org/10.1002/ajb2.1468 DB - PRIME DP - Unbound Medicine ER -
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