Toward a Global Phylogeny of the Brassicaceae

Abstract

The Brassicaceae is a large plant family (338 genera and 3,700 species) of major scientific and economic importance. The taxonomy of this group has been plagued by convergent evolution in nearly every morphological feature used to define tribes and genera. Phylogenetic analysis of 746 nrDNA internal transcribed spacer (ITS) sequences, representing 24 of the 25 currently recognized tribes, 146 genera, and 461 species of Brassicaceae, produced the most comprehensive, single-locus-based phylogenetic analysis of the family published to date. Novel approaches to nrDNA ITS analysis and extensive taxonomic sampling offered a test of monophyly for a large complement of the currently recognized tribes and genera of Brassicaceae. In the most comprehensive analysis, tribes Alysseae, Anchonieae plus Hesperideae, Boechereae, Cardamineae, Eutremeae, Halimolobeae, Iberideae, Noccaeeae, Physarieae, Schizopetaleae, Smelowskieae, and Thlaspideae were all monophyletic. Several broadly defined genera (e.g., Draba and Smelowskia) were supported as monophyletic, whereas others (e.g., Sisymbrium and Alyssum) were clearly polyphyletic. Analyses of ITS data identified several problematic sequences attributable to errors in sample identification or database submission. Results from parsimony ratchet and Bayesian analyses recovered little support for the backbone of the phylogeny, suggesting that many lineages of Brassicaceae have undergone rapid radiations that may ultimately be difficult to resolve with any single locus. However, the development of a preliminary supermatrix including the combination of 10 loci for 65 species provides an initial estimate of intertribal relations and suggests that broad application of such a method will provide greater understanding of relationships in the family.

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

“…2) derived from 1,048,889 fourfolddegenerate sites and using Carica papaya 38 as an outgroup was consistent with previously published phylogenies 31,39 . The total branch length of the tree (~1.5 substitutions per site) was similar to that for a set of nine diverse mammals (~1.3 substitutions per site) 40 used in the identification of conserved noncoding regions.…”

Molecular phylogeny and systematics of the tribe Chorisporeae (Brassicaceae)

“…Family-wide phylogenetic studies of the Brassicaceae (e.g., Bailey et al 2006;Beilstein et al 2006Beilstein et al , 2008Koch et al 2007;Franzke et al 2009;Koch and Al-Shehbaz 2009;Couvreur et al 2010;Warwick et al 2010) show a lack of resolution in the basal polytomy regardless of the molecular marker used. Similar results were observed within lineages (e.g., Warwick et al 2007) and speciose genera (e.g., Carlsen et al 2009).…”

“…It is often difficult to unravel phylogeny at various levels and to create a natural classification because of substantial homoplasy in almost all morphological characters (e.g., Koch et al 2003;Al-Shehbaz et al 2006;Warwick et al 2010). However, considerable progress has recently been made both in phylogeny and systematics at the generic and tribal levels Bailey et al 2006;Beilstein et al 2006Beilstein et al , 2008Al-Shehbaz and Warwick 2007;Koch et al 2007;Warwick et al 2007;German and Al-Shehbaz 2008a;Mandáková and Lysak 2008;Koch and Al-Shehbaz 2009;Franzke et al 2009;German et al 2009; Electronic supplementary material The online version of this article (doi:10.1007/s00606-011-0452-0) contains supplementary material, which is available to authorized users. Khosravi et al 2009;Mandáková et al 2010;Couvreur et al 2010).…”

The shrunken genome of Arabidopsis thaliana

“…The values were obtained from published sources Bailey 2006;Lysak et al 2003;Warwick and Al-Shehbaz 2006). For the MacClade TM analyses, the chromosome counts (2n) for each taxon were converted into a discrete character state (a range of 14 possible states) and treated as unordered or ordered as described earlier.…”