Multigene Analyses of Monocot Relationships

Abstract

We present an analysis of supra-familial relationships of monocots based on a combined matrix of nuclear ISS and partial 26S rONA, plastid atpB, matK, ndhF, and rbcL, and mitochondrial atpl DNA sequences. Results are highly congruent with previous analyses and provide higher bootstrap support for nearly all relationships than in previously published analyses. Important changes to the results of previous work are a well-supported position of Petrosaviaceae as sister to all monocots above Acorales and Alismatales and much higher support for the commelinid clade. For the first time, the spine of the monocot tree has some bootstrap support, although support for paraphyly of liliids is still only low to moderate (79-82%). Dioscoreales and Pandanales are sister taxa (moderately supported, 87-92%), and Asparagales are weakly supported (79%) as sister to the commelinids. Analysis of just the four plastid genes reveals that addition of data from the other two genomes contributes to generally better support for most clades, particularly along the spine. A new collection reveals that previous material of Petermannia was misidentified, and now Petermanniaceae should no longer be considered a synonym of Colchicaceae. Arachnitis (Corsiaceae) falls into Liliales, but its exact position is not well supported. Sciaphila (Triuridaceae) falls with Pandanales. Trithuria (Hydatellaceae) falls in Poales near Eriocaulaceae, Mayacaceae, and Xyridaceae, but until a complete set of genes are produced for this taxon, its placement will remain problematic. Within the commelinid clade, Dasypogonaceae are sister to Poales and Arecales sister to the rest of the commelinids, but these relationships are only weakly supported.

Floral Anatomy of Xyrids (Poales): Contributions to Their Reproductive Biology, Taxonomy, and Phylogeny

“…Xyridaceae and Eriocaulaceae are identified as sister groups in most of the phylogenetic analyses of Poales (Givnish et al 1999(Givnish et al , 2005(Givnish et al , 2006Chase et al 2000Chase et al , 2006Bremer 2002;Christin et al 2008). Mayacaceae is clustered as a sister group to Eriocaulaceae (Givnish et al 2010); the cyperid clade, which includes Cyperaceae, Juncaceae, and Thurniaceae (Chase et al 2000;Christin et al 2008); or the clade formed by the cyperids plus Eriocaulaceae-Xyridaceae (Givnish et al 2005(Givnish et al , 2006Chase et al 2006).…”

Conserved differential expression of paralogous DEFICIENS‐ and GLOBOSA‐like MADS‐box genes in the flowers of Orchidaceae: refining the ‘orchid code’

“…To test it more extensively we present here a comparative analysis of the expression of DEF-and GLO-like genes in Vanilla planifolia (Vanilloideae) and Phragmipedium longifolium (Cypripedioideae), as well as in wild-type and peloric flowers from the Phalaenopsis hybrid 'Athens' (Epidendroideae) (Chase et al, 2006) (Figure 1d,e). In this analysis we employed quantitative real-time PCR (qRT-PCR) with a well-validated normalization approach based on the stable expression of three independent reference genes (Vandesompele et al, 2002;Hellemans et al, 2007).…”

Phylogeny, Adaptive Radiation, and Historical Biogeography of Bromeliaceae Inferred from ndhF Sequence Data

“…Givnish et al (1999) inferred that bromeliads arose in the Guayana Shield based on an analysis of rbcL sequence variation showing an apparent sister relationship between Bromeliaceae and Rapateaceae; the latter clearly originated in the Guayana Shield and remains mostly endemic to that region (Givnish et al 2000). However, more powerful molecular evidence based on an analysis of rbcL, atpB, and 18S sequences (Chase et al 2000), ndhF sequence variation ), a 7-gene analysis , and a 17-gene analysis (Graham et al 2006) indicates that Bromeliaceae and Rapateaceae occupy adjacent rungs at the base of order Poales instead of being sister to each other.…”