Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns.
Robert K. Jansen,Zhengqiu Cai,Linda A. Raubeson,Henry Daniell,Claude W. dePamphilis,Jim Leebens-Mack,Kai F. Müller,Mary Guisinger-Bellian,Rosemarie C. Haberle,Anne K. Hansen,Timothy W. Chumley,Seung Bum Lee,Rhiannon M. Peery,Joel R. McNeal,Jennifer V. Kuehl,Jeffrey L. Boore,Jeffrey L. Boore +16 more
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TLDR
Phylogenetic trees from multiple methods provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales, and the plastid genome trees also provide strongSupport for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids.Abstract:
Angiosperms are the largest and most successful clade of land plants with >250,000 species distributed in nearly every terrestrial habitat. Many phylogenetic studies have been based on DNA sequences of one to several genes, but, despite decades of intensive efforts, relationships among early diverging lineages and several of the major clades remain either incompletely resolved or weakly supported. We performed phylogenetic analyses of 81 plastid genes in 64 sequenced genomes, including 13 new genomes, to estimate relationships among the major angiosperm clades, and the resulting trees are used to examine the evolution of gene and intron content. Phylogenetic trees from multiple methods, including model-based approaches, provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales. The plastid genome trees also provide strong support for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids. Resolution of relationships among the major clades of angiosperms provides the necessary framework for addressing numerous evolutionary questions regarding the rapid diversification of angiosperms. Gene and intron content are highly conserved among the early diverging angiosperms and basal eudicots, but 62 independent gene and intron losses are limited to the more derived monocot and eudicot clades. Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements.read more
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An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II
TL;DR: A revised and updated classification for the families of the flowering plants is provided in this paper, which includes Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales.
Journal ArticleDOI
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
TL;DR: TreeGraph 2, a GUI-based graphical editor for phylogenetic trees, is developed, which allows automatically combining information from different phylogenetic analyses of a given dataset (or from different subsets of the dataset), and helps to identify and graphically present incongruences.
Journal ArticleDOI
Polyploidy and angiosperm diversification
Douglas E. Soltis,Victor A. Albert,Jim Leebens-Mack,Charles D. Bell,Andrew H. Paterson,Chunfang Zheng,David Sankoff,Claude W. dePamphilis,P. Kerr Wall,Pamela S. Soltis +9 more
TL;DR: Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae, but additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages.
Journal ArticleDOI
Phylotranscriptomic analysis of the origin and early diversification of land plants
Norman J. Wickett,Siavash Mirarab,Nam Nguyen,Tandy Warnow,Eric J. Carpenter,Naim Matasci,Saravanaraj Ayyampalayam,Michael S. Barker,J. Gordon Burleigh,Matthew A. Gitzendanner,Brad R. Ruhfel,Brad R. Ruhfel,Eric K. Wafula,Joshua P. Der,Sean W. Graham,Sarah Mathews,Michael Melkonian,Douglas E. Soltis,Douglas E. Soltis,Pamela S. Soltis,Pamela S. Soltis,Nicholas W. Miles,Carl J. Rothfels,Carl J. Rothfels,Lisa Pokorny,Lisa Pokorny,A. Jonathan Shaw,Lisa DeGironimo,Dennis W. Stevenson,Barbara Surek,Juan Carlos Villarreal,Béatrice Roure,Hervé Philippe,Hervé Philippe,Claude W. dePamphilis,Tao Chen,Michael K. Deyholos,Regina S. Baucom,Toni M. Kutchan,Megan M. Augustin,Jun Wang,Yong Zhang,Zhijian Tian,Zhixiang Yan,Xiaolei Wu,Xiao Sun,Gane Ka-Shu Wong,Jim Leebens-Mack +47 more
TL;DR: Strong and robust support is found for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
Journal ArticleDOI
The evolution of the plastid chromosome in land plants: gene content, gene order, gene function.
Susann Wicke,Susann Wicke,Gerald M. Schneeweiss,Claude W. dePamphilis,Kai F. Müller,Dietmar Quandt +5 more
TL;DR: This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors and suggests that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms.
References
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An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II
TL;DR: A revised and updated classification for the families of the flowering plants is provided in this paper, which includes Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales.
Journal ArticleDOI
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