Phylogeny of the Liliales (Monocotyledons) with special emphasis on data partition congruence and RNA editing

@article{Petersen2013PhylogenyOT,
  title={Phylogeny of the Liliales (Monocotyledons) with special emphasis on data partition congruence and RNA editing},
  author={Gitte Petersen and Ole Seberg and Jerrold I. Davis},
  journal={Cladistics},
  year={2013},
  volume={29}
}
A phylogenetic analysis of the monocot order Liliales was performed using sequence data from three mitochondrial (atp1, cob, nad5) and two plastid genes (rbcL, ndhF). The complete data matrix includes 46 terminals representing all 10 families currently included in Liliales. The two major partitions, mitochondrial and plastid data, were congruent, and parsimony analysis resulted in 50 equally parsimonious trees and a well resolved consensus tree confirming monophyly of all families… 

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References

SHOWING 1-10 OF 74 REFERENCES

Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes

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.

Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences.

It seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.

Molecular phylogeny of monocotyledons inferred from combined analysis of plastid matK and rbcL gene sequences

Using matK and rbcL sequences from 113 genera of 45 families, a combined analysis to contribute to the understanding of major evolutionary relationships in the monocotyledons finds that Acorus (Acorales) is a sister group to the rest of themonocots, which receives 100% bootstrap support.

Phylogeny of the Asparagales based on three plastid and two mitochondrial genes.

Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families, whereas support for many families increases, and the increased support is dominated by plastid data.

Mitochondrial Data in Monocot Phylologenetics

RNA editing of mitochondrial genes is regarded only as a mechanism that may increase variability at edited sites and change the codon position bias accordingly in phylogenetic reconstruction, and edited sites may prove a valuable tool in identifying processed paralogs.

Phylogenetic Analyses of the Diploid Species of Hordeum (Poaceae) and a Revised Classification of the Genus

A new infrageneric classification of Hordeum including only monophyletic groups is presented, and one new taxon, Hordeum L. sect.

Phylogenetic Relationships of Monocots Based on the Highly Informative Plastid Gene ndhF

The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales-Pandanales in the strict consensus; Pandanales are sister to Dioscoreale in the bootstrap majority-rule tree, just above Petrosaviales.

Multigene Analyses of Monocot Relationships

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.

Rna editing and phylogenetic reconstruction in two monocot mitochondrial genes

Using mtDNA sequence data encoding for apocytochrome B and the alpha subunit of F1-ATP synthase (atp1) across the monocots, and in two subclades, alismatids and Agavaceae, it is shown that edited sites, despite being more homoplasious than non-edited sites, perform well on the trees.

Phylogenetic Information in the Mitochondrial nad5 Gene of Pteridophytes: RNA Editing and Intron Sequences

Placement of Psilotum in a class of its own receives no support from the mitochondrial sequences, which rather suggest its inclusion among eusporangiate ferns (Ophioglossales).
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