A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

@inproceedings{Davis2004APO,
  title={A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values},
  author={Jerrold I. Davis and Dennis W. Stevenson and Gitte Petersen and Ole Seberg and Lisa M. Campbell and John V Freudenstein and Douglas H. Goldman and Christopher R. Hardy and Fabi{\'a}n A. Michelangeli and Mark P. Simmons and Chelsea D. Specht and Francisco Vergara-Silva and Maria A. Gandolfo},
  year={2004}
}
Abstract A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid lineages (Canellales, Piperales, Magnoliales, and Laurales) as sister of the monocots, with the deepest branch… 
Angiosperm phylogeny inferred from sequences of four mitochondrial genes
TLDR
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Robust Inference of Monocot Deep Phylogeny Using an Expanded Multigene Plastid Data Set
TLDR
Despite substantial variation in the overall rate of molecular evolution among lineages, inferred amounts of change among codon-position data partitions are correlated with each other across the monocot tree, consistent with low incongruence between these partitions.
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TLDR
The results indicate that genes from the mitochondrial genome provide a unique test of relationships that have been inferred with plastid-encoded genes.
Monocot relationships: an overview.
  • M. Chase
  • Biology, Medicine
    American journal of botany
  • 2004
TLDR
Based on analyses of seven genes representing all three genomes, the following clades have high bootstrap support: Acorales (with the single genus Acorus) is sister to the rest of the monocots, followed successively by Alismatales (including Araceae and Tofieldiaceae), Petrosaviales, Dioscoreales/Pandanales, Liliale, Asparagales, and Arecales.
Plastid Phylogenomic Analyses Resolve Tofieldiaceae as the Root of the Early Diverging Monocot Order Alismatales
TLDR
The first complete plastid genomes from three key families in this order are sequenced, showing both strong support for Acorales as sister to the remaining monocots and monophyly of Alismatales and Tofieldiaceae was resolved as the most basal lineage within Alism atales.
Phylogenetic Inferences and the Evolution of Plastid DNA in Campynemataceae and the Mycoheterotrophic Corsia dispar D.L Jones & B. Gray (Corsiaceae)
TLDR
Functional plastid genes found in C. dispar may be applicable to other species in Corsiaceae, which will provide a basis for in-depth molecular analyses of interspecies relationships within the family, once molecular data from other members become available.
Phylogeny and evolution of Burmanniaceae (Dioscoreales) based on nuclear and mitochondrial data.
TLDR
Phylogenetic inference using nucleotide sequences of the nuclear 18S rDNA region and the mitochondrial nad1 b-c intron revealed two well-supported, major lineages within the Burmanniaceae, corresponding to the two tribes recognized in the family: Burmannieae and Thismieae.
Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes
TLDR
Comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloropleft genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.
Phylogeny of the Liliales (Monocotyledons) with special emphasis on data partition congruence and RNA editing
TLDR
It is argued that processed paralogs should not a priori be excluded from phylogenetic analysis and were more homoplasious than the other characters and increased incongruence among most data partitions.
Multigene Analyses of Monocot Relationships
TLDR
Analysis of supra-familial relationships of monocots based on a combined matrix of nuclear 18S and partial 26S rDNA, plastid atpB, matK, ndhF, and rbcL, and mitochondrial atpl DNA sequences provides higher bootstrap support for nearly all relationships than in previously published analyses.
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