Cladistic parsimony analyses of rbcL nucleotide sequence data from 171 taxa representing nearly all tribes and subtribes of Orchidaceae are presented here. These analyses divide the family into five primary monophyletic clades: apostasioid, cypripedioid, vanilloid, orchidoid, and epidendroid orchids, arranged in that order. These clades, with the exception of the vanilloids, essentially correspond to currently recognized subfamilies. A distinct subfamily, based upon tribe Vanilleae, is supported for Vanilla and its allies. The general tree topology is, for the most part, congruent with previously published hypotheses of intrafamilial relationships; however, there is no evidence supporting the previously recognized subfamilies Spiranthoideae, Neottioideae, or Vandoideae. Subfamily Spiranthoideae is embedded within a single clade containing members of Orchidoideae and sister to tribe Diurideae. Genera representing tribe Tropideae are placed within the epidendroid clade. Most traditional subtribal units are supported within each clade, but few tribes, as currently circumscribed, are monophyletic. Although powerful in assessing monophyly of clades within the family, in this case rbcL fails to provide strong support for the interrelationships of the subfamilies (i.e., along the spine of the tree). The cladograms presented here should serve as a standard to which future morphological and molecular studies can be compared.

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An expanded plastid DNA phylogeny for Orchidaceae was generated from sequences of rbcL and matK for representatives of all five subfamilies. The data were analyzed using equally weighted parsimony, and branch support was assessed with jackknifing. The analysis supports recognition of five subfamilies with the following relationships: (Apostasioideae (Vanilloideae (Cypripedioideae (Orchidoideae (Epidendroideae))))). Support for many tribal-level groups within Epidendroideae is evident, but relationships among these groups remain uncertain, probably due to a rapid radiation in the subfamily that resulted in short branches along the spine of the tree. A series of experiments examined jackknife parameters and strategies to determine a reasonable balance between computational effort and results. We found that support values plateau rapidly with increased search effort. Tree bisection-reconnection swapping in a single search replicate per jackknife replicate and saving only two trees resulted in values that were close to those obtained in the most extensive searches. Although this approach uses considerably more computational effort than less extensive (or no) swapping, the results were also distinctly better. The effect of saving a maximal number of trees in each jackknife replicate can also be pronounced and is important for representing support accurately.

Phylogenetic relationships within the epidendroid orchids with emphasis on tribes Epidendreae and Arethuseae were assessed with parsimony and model-based analyses of individual and combined DNA sequence data from ITS nuclear ribosomal DNA and plastid trnL intron, the trnL-F spacer, matK (gene and spacers), and rbcL regions. Despite the absence of boostrap support for some of the relationships, a well-resolved and supported consensus was found, for which most clades were present in more than one individual analysis. Most clades of this consensus attained high posterior probabilities with a Bayesian approach. Circumscription of Arethuseae and Epidendreae are different from most orchid systems based on morphology, but they correspond to a combination of patterns from several less comprehensive orchid phylogenetic analyses previously published. A new circumscription of Epidendreae includes only Neotropical subtribes (Bletiinae, Chysiinae, Laeliinae, Ponerinae, and Pleurothallidinae), whereas Arethuseae include Coelogyninae (all Old World) and Arethusinae (pantropical). Many previously included genera will need to be moved to other tribes. Taxa previously assigned to be Old World Epidendreae are related to different groups of Old World orchids, and this study can serve as a guide for sampling strategies in future studies to resolve troublesome epidendroid orchid clades.

The most robust previously published phylogeny for the overall structure of the grass family (Poaceae) shows three early diverging lineages and two major derived clades, the BEP clade and the PACCAD clade (Grass Phylogeny Working Group 2001). A few key taxa were incompletely sampled, however, and support for the BEP clade was moderate at best and relationships among the major lineages within the PACCAD clade remained unresolved. In addition, recent studies indicated that the sister group to Poaceae may be Joinvilleaceae and/or Ecdeiocoleaceae, the latter of which were not previously sampled. In this study, missing structural data were determined and analyzed as well as sequence data for ndhF and rbcL, the two most complete plastid sequence data sets. Sampling was increased with a particular focus on key taxa such as Danthoniopsis, Eriachne, Micraira, and Streptogyna and a representative of the outgroup, Ecdeiocoleaceae. A total of 61 ingroup and two outgroup taxa were analyzed using maximum parsimony for total data, and maximum parsimony, Bayesian inference, and neighbor joining for the molecular data. A strongly supported clade of ((Eriachneae, Isachne) Micraira) was recovered as a sister subfamily to Arundinoideae and excluded from Panicoideae. Arundinaria was strongly united with Bambusoideae. The position of Streptogyna was weakly supported among Ehrhartoideae, and is still unresolved. An outgroup effect on ingroup topology was observed demonstrating that highly divergent outgroups may unpredictably alter ingroup relationships.

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.

The orchid genus Calopogon R.Br. (Orchidaceae), native to eastern North America and the northern Caribbean, currently contains five species and up to three varieties. Using nuclear internal transcribed spacer (ITS) ribosomal DNA sequences, amplified fragment length polymorphisms (AFLPs), chloroplast DNA restriction fragments, and chromosome counts, we present a phylogenetic and taxonomic study of the genus. Calopogon multiflorus and C. pallidus are consistently sister species, but the relationships of C. barbatus, C. oklahomensis, and C. tuberosus are not as clear. In the ITS analysis C. oklahomensis is sister to C. barbatus, whereas it is sister to C. tuberosus in the plastid restriction fragment analysis. Furthermore, all species were found to have chromosome numbers of 2n = 38 and 40, with the exception of the putatively hybrid-derived C. oklahomensis with 2n = 114 and 120. The hexaploidy of the latter, plus the discrepancy in its position between the ITS and plastid restriction fragment trees, could suggest that it is of hybrid origin. However, the presence of unique morphological and molecular characters might indicate that it is either an ancient hybrid or not of hybrid derivation at all. Finally, using these molecular methods all taxa appear to generally be discrete groups, with the exception of C. tuberosus vars. latifolius and tuberosus, the former of which is best combined with the latter.

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.