Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes

By Y. Qiu, O. Dombrovska, Jungho Lee, Libo Li, Barbara A. Whitlock, F. Bernasconi‐Quadroni, J. Rest, Charles C. Davis, Thomas Borsch, K. Hilu and 10 more. INTERNATIONAL JOURNAL PLANT SCIENCES, 2005

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DNA sequences of nine genes (plastid: atpB, matK, and rbcL; mitochondrial: atp1, matR, mtSSU, and mtLSU; nuclear: 18S and 26S rDNAs) from 100 species of basal angiosperms and gymnosperms were analyzed using parsimony, Bayesian, and maximum likelihood methods. All of these analyses support the following consensus of relationships among basal angiosperms. First, Amborella, Nymphaeaceae, and Austrobaileyales are strongly supported as a basal grade in the angiosperm phylogeny, with either Amborella or Amborella and Nymphaeales as sister to all other angiosperms. An examination of nucleotide substitution patterns of all nine genes ruled out any possibility of analytical artifacts because of RNA editing and GC‐content bias in placing these taxa at the base of the angiosperm phylogeny. Second, Magnoliales are sister to Laurales and Piperales are sister to Canellales. These four orders together constitute the magnoliid clade. Finally, the relationships among Ceratophyllum, Chloranthaceae, monocots, magnoliids, and eudicots are resolved in different ways in various analyses, mostly with low support. Our study indicates caution in total evidence approaches in that some of the genes employed (e.g., mtSSU, mtLSU, and nuclear 26S rDNA) added signal that conflicted with the other genes in resolving certain parts of the phylogenetic tree.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/68173fa1422982c475ff93119887866308052365

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Citations in the corpus

Flower Structure and Trends of Evolution in Eudicots and Their Major Subclades1 (2010, background): “Proteales, the third clade of basal eudicots (found by Chase et al., 1993), has three seemingly unrelated families (Fig.”
Monetianthus mirus gen. et sp. nov., a Nymphaealean Flower from the Early Cretaceous of Portugal (2009, unknown): “…analyses using molecular data place Nymphaeales between Amborellaceae and Austrobaileyales (Austrobaileyaceae, Illiciaceae, Schisandraceae, and Trimeniaceae), two lineages of woody angiosperms (Qiu 1999, 2005; Qiu et al. 2000, 2006; Soltis et al. 2000; Zanis et al. 2003; Saarela et al. 2007).”
Phylogeny of Nymphaea (Nymphaeaceae): Evidence from Substitutions and Microstructural Changes in the Chloroplast trnT‐trnF Region (2007, background): “An alternative hypothesis suggesting that a clade consisting of Amborella and Nymphaeales is sister to all other angiosperms (Barkman et al. 2000; Mathews and Donoghue 2000) has been favored by recent likelihood-based inferences (Leebens-Mack et al. 2005; Qiu et al. 2005).”
Angiosperm phylogeny: 17 genes, 640 taxa. (2011, unknown): “In agreement with other recent analyses (e.g., Zanis et al., 2002 ; Hilu et al., 2003 ; Qiu et al., 1999 , 2005 ; Soltis et al., 2007 ; Moore et al., 2010 ), Magnoliidae comprises two well-supported clades, each with BS = 100%: Magnoliales + Lau-rales and Piperales + Canellales.”
Phylogenetic analysis of Nymphaeales using fast-evolving and noncoding chloroplast markers (2007, background): “…Nymphaeales clade is most probably the second branch of the angiosperm tree, diverging after Amborella, and followed by Austrobaileyales (Parkinson, Adams & Palmer, 1999; Mathews & Donoghue, 2000; Soltis et al., 2000; Borsch et al., 2003; Hilu et al., 2003; Borsch et al., 2005; Qiu et al., 2005).”
Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1 (2010, background): “The latter, multigene strategy has proven the more productive approach (e.g., see Chase et al., 2000; Soltis et al., 2000; Qiu et al., 2005), partly due to the difficulty of aligning rapidly evolving regions across highly divergent taxa, and to the inherently higher rate of homoplasy associated…”
Systematics of Pipevines: Combining Morphological and Fast‐Evolving Molecular Characters to Investigate the Relationships within Subfamily Aristolochioideae (Aristolochiaceae) (2006, background): “Aristolochiaceae, a member of the Piperales (Borsch et al. 2005; Qiu et al. 2005), consists of ca. 550 species, most of which are tropical or subtropical.”