@article {273,
	title = {RNA editing and phylogenetic reconstruction in two monocot mitochondrial genes},
	journal = {TaxonTaxon},
	volume = {55},
	number = {4},
	year = {2006},
	pages = {871-886},
	abstract = {The mitochondrial genome of land plants has a high level of evolutionary plasticity that may impair its use in phylogenetic analyses. Among the most challenging properties are RNA editing and retroprocessing of edited mRNA into the mitochondrial and/or nuclear genome as processed paralogs. Using mtDNA sequence data encoding for apocytochrome B (cob) 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, and that they are not randomly distributed among taxa but have a clade specific distribution. Indirect evidence for the presence of processed paralogs is presented and their likely evolutionary fate discussed. },
	keywords = {Agavaceae, Alismatales, Calycanthaceae, Monocotyledones, phylogeny, RNA editing, processed paralogs},
	author = {Petersen, Gitte and Seberg, Ole and Davis, Jerrold I. and Stevenson, Dennis W.}
}
@article {85,
	title = {Are mitochondrial genes useful for the analysis of monocot relationships?},
	journal = {TaxonTaxon},
	volume = {55},
	number = {4},
	year = {2006},
	pages = {857-870},
	abstract = {A phylogenetic analysis of monocots and related dicots was conducted, using a four-gene matrix consisting of two genes from the plastid genome (matK and rbcL) and two from the mitochondrial genome (atpA/atp1 and cob). The taxon sample includes 101 monocots and 36 dicots, and all four genes were sampled for all 137 taxa. Jackknife support was assessed for clades resolved by the four-gene analysis, and compared to support for the same clades by each of the four three-gene subset matrices, in order to quantify the degree to which each gene contributed to or detracted from support for each clade. Instances of positively and negatively correlated support for clades by genes of the same and different genomes were observed. In particular, the placement of Acorus within a clade that also includes Tofieldiaceae, Araceae, and Alismatales s.s., as opposed to its frequent placement as sister of all other monocots, is supported by atpA and matK. The results indicate that genes from the mitochondrial genome provide a unique test of relationships that have been inferred with plastid-encoded genes. },
	keywords = {atpA, cob, mitochondrial genes, matK, monocots, phylogenetics, plastid genes, rbcL},
	author = {Davis, Jerrold I. and Petersen, Gitte and Seberg, Ole and Stevenson, Dennis W. and Hardy, Christopher R. and Simmons, Mark P. and Michelangeli, Fabian A. and Goldman, Douglas H. and Campbell, Lisa M. and Specht, Chelsea D. and Cohen, James I.}
}
