Mitochondrial Data in Monocot Phylologenetics

Abstract

Mitochondrial sequences are an important source of data in animal phylogenetics, equivalent in importance to plastid sequences in plants. However, in recent years plant systematists have begun exploring the mitochondrial genome as a source of phylogenetically useful characters. The plant mitochondrial genome is renowned for its variability in size, structure, and gene organization, but this need not be of concern for the application of sequence data in phylogenetics. However, the incorporation of reverse transcribed mitochondrial genes ("processed paralogs") and the recurring transfer of genes from the mitochondrion to the nucleus are evolutionary events that must be taken into account. RNA editing of mitochondrial genes is sometimes considered a problem in phylogenetic reconstruction, but we regard it only as a mechanism that may increase variability at edited sites and change the codon position bias accordingly. Additionally, edited sites may prove a valuable tool in identifying processed paralogs. An overview of genes and sequences used in phylogenetic studies of angiosperms is presented. In the monocots, a large amount of mitochondrial sequence data is being collected together with sequence data from plastid and nuclear genes, thus offering an opportunity to compare data from different genomic compartments. The mitochondrial and plastid data are incongruent when organelle gene trees are reconstructed. Possible reasons for the observed incongruence involve sampling of paralogous sequences and highly divergent substitution rates, potentially leading to longbranch attraction. The above problems are addressed in Acorales, Alismatales, Poales, Liliaceae, the "Anthericum clade" (in Agavaceae), and in some achlorophyllous taxa.

Multigene Analyses of Monocot Relationships

“…Therefore, as long as the results of combined analysis with genes from all three genomes appear to be improvements over their predecessors, this route should continue to be followed. However, performing combined analyses should not prevent us from exploring the patterns produced by the individual compartments or the potential causes of deviations in pattern, as in Petersen et al (2006). It is also clear that there are problems with the mitochondrial and nuclear genes as indicators of relationships for the achlorophyllous taxa (Burmanniaceae, Corsiaceae, and Triuridaceae) plus Trithuria (Hydatellaceae), the last of which is photosynthetic but which has also been problematic in other studies (Bremer 2002;Davis et al 2004).…”

“…Previous studies have demonstrated that although incongruence-as measured by, e.g., the partition homogeneity test-is present, direct combination provides greater resolution and higher bootstrap percentages Reeves et al 2001). We will not address these issues in depth here, but Petersen et al (2006) do examine this question with respect to the two mitochondrial genes, atp 1 and cob. Davis et al (2004) also discussed these issues with respect to atp 1 and rbcL.…”

“…We present in this paper results of a combined analysis of seven genes representing all three genomic compartments (including 18S rDNA, atpB, and rbcL, plus those listed above except for cob, results of which are described in Petersen et al 2006).…”

Phylogeny, Genome Size, and Chromosome Evolution of Asparagales

“…As in Fay et al (2000), representatives of Commelinales, Liliales, Pandanales, and Zingiberales were included as outgroups. For the most part, voucher information for the taxa used in these analyses was previously published (Table 1, Fay et al 2000; or will be published in forthcoming articles (see also Chase et al 2006;Petersen et al 2006).…”

“…GenBank numbers for rbcL, atpB, and trnL-F have been previously published Pireset al 2004). GenBank numbers for matK, ndhF, and atp1 are in press or will be presented in forthcoming publications and will not be provided here (see Davis et al 2004;Chase et al 2006;Givnish et al 2006;Petersen et al 2006). This analysis focuses on only 79 taxa of Asparagales and outgroups, but we are preparing a future analysis of ca.…”