Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms

By Michael J. Moore, C. Bell, Pamela S. Soltis, D. Soltis. Proceedings of the National Academy of Sciences of the United States of America, 2007

655 citations recorded by the source corpus.

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

View Paper: https://www.semanticscholar.org/paper/bfeaf3ae34d5fb617f061b9855461bc04664305c

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology, Evolution, Behavior and Systematics

In Molecular Biology

Citations in the corpus

The Linear Angiosperm Phylogeny Group (LAPG) III: A linear sequence of the families in APG III (2009, background): “Ceratophyllaceae have moved from within magnoliids and are now sister to the eudicots (Jansen et al., 2007; Moore et al., 2007).”
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV (2016, background): “Chloranthaceae are probably sister to magnoliids (Moore et al., 2007).”
Evolution of Gene Duplication in Plants1[OPEN] (2016, background): “The g duplication likely took place approximately 140 MYA (Bowers et al., 2003; Moore et al., 2007), and 4.4% of duplicates are still retained (Maere et al., 2005).”
A phylogenetic classification of the land plants to accompany APG III (2009, methodology): “We have therefore opted for an intermediate solution and have thus not given formal rank to the larger clades such as eudicots, mesangiosperms (Moore et al., 2007) or smaller clades such as fabids (eurosid I), malvids (eurosid II), lamiids (euasterid I) and campanulids (eurosid II) used in the APG…”
Xylem heterochrony: an unappreciated key to angiosperm origin and diversifications. (2009, methodology): “A simplified phylogenetic tree of angiosperms, based on Moore et al. (2007), and typical of recent phylogenetic”
Phylotranscriptomic analysis of the origin and early diversification of land plants (2014, background): “Ceratophyllaceae were not included in our analysis, but the Phylobayes CAT+GTR analyses of amino acid supported a magnoliid+Chloranthales (represented by Sarcandra glabra) clade sister to eudicots+ monocots (Fig.”
Angiosperm phylogeny inferred from sequences of four mitochondrial genes (2010, methodology): “…Qiu et al., 1999, 2005, 2006a; Barkman et al., 2000; Graham & Olmstead, 2000; Soltis et al., 2000; Zanis et al., 2002; Borsch et al., 2003; Hilu et al., 2003; Stefanovic et al., 2004; LeebensMack et al., 2005; Jansen et al., 2007; Moore et al., 2007; Saarela et al., 2007; Goremykin et al., 2009).”
Phylogenetic Analysis of the Plastid Inverted Repeat for 244 Species: Insights into Deeper-Level Angiosperm Relationships from a Long, Slowly Evolving Sequence Region (2011, methodology): “Support for relationships among these clades has been low or moderate even with gene-rich plastid genome data sets (Soltis et al. 2005, 2007; Jansen et al. 2007; Moore et al. 2007, 2010; Worberg et al. 2007; Burleigh et al. 2009; Wang et al. 2009).”
Phylogenetics, divergence times and diversification from three genomic partitions in monocots (2015, methodology): “In addition to this unconstrained analysis, we performed the same ML reconstruction with outgroup topology constrained to the current best estimate of relationships (Moore et al., 2007; Soltis & Soltis, 2013) to improve placement of fossil taxa for divergence time analyses (see below).”
Polyploidy and angiosperm diversification. (2009, background): “Because phylogenetic analyses (e.g., P. Soltis et al., 1999 ; reviewed in D. Soltis et al., 2005 , Leebens-Mack et al., 2005 ; Jansen et al., 2007; Moore et al., 2007 ) identify Amborella trichopoda (Amborellaceae) as the probable single sister species to all other living fl owering plants,…”
Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects (2010, methodology): “…of plants, such as Nandina domestica Thunb., Platanus occidentalis L., and Ceratophyllum demersum L., using the Roche/454 platform (Moore et al., 2006; Moore et al., 2007), and eight coniferous plastid genomes have been sequenced using the Illu- mina/Solexa Genome Analyzer (Cronn et al., 2008).”
Integrating Early Cretaceous Fossils into the Phylogeny of Living Angiosperms: ANITA Lines and Relatives of Chloranthaceae (2014, background): “…2008; Qiu et al. 2010; Moore et al. 2011; Zhang et al. 2012), although most indicate different relationships, such as analyses of whole chloroplast genomes (Jansen et al. 2007; Moore et al. 2007), in which Chloranthaceae are sister to the magnoliid clade and Ceratophyllum is sister to eudicots.”
Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots (2010, background): “S5 and Table S2) are similar to those of several other recent dating analyses (12, 34, 35), we stress that estimates of diversification dates are also susceptible to error, even when based on large data sets.”
Flower Evolution: The Origin and Subsequent Diversification of the Angiosperm Flower (2009, background): “Angiosperm relationships are from Soltis et al. (2008) summarizing Jansen et al. (2007) and Moore et al. (2007).”
Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA (2009, background): “…Moore et al. 2006), several complete chloroplast genomes of green plants are now generated every year (e.g., Wolf et al. 2003; Goremykin et al. 2004; Leebens-Mack et al. 2005; Chang et al. 2006; Chumley et al. 2006; Pombert et al. 2006; Jansen et al. 2007; Moore et al. 2007; Haberle et al. 2008).”