Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited

Abstract

The family Brassicaceae comprises 3710 species in 338 genera, 25 recently delimited tribes, and three major lineages based on phylogenetic results from the chloroplast gene ndhF. To assess the credibility of the lineages and newly delimited tribes, we sequenced an approximately 1.8‐kb region of the nuclear phytochrome A (PHYA) gene for taxa previously sampled for the chloroplast gene ndhF. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the approximately unbiased (AU) test to compare phylogenetic results from PHYA with findings from ndhF. We also combined ndhF and PHYA data and used a Bayesian mixed model approach to infer phylogeny. PHYA and combined analyses recovered the same three large lineages as those recovered in ndhF trees, increasing confidence in these lineages. The combined tree confirms the monophyly of most of the recently delimited tribes (only Alysseae, Anchonieae, and Descurainieae are not monophyletic), while 13 of the 23 sampled tribes are monophyletic in PHYA trees. In addition to phylogenetic results, we documented the trichome branching morphology of species across the phylogeny and explored the evolution of different trichome morphologies using the AU test. Our results indicate that dendritic, medifixed, and stellate trichomes likely evolved independently several times in the Brassicaceae.

Molecular phylogeny and systematics of the tribe Chorisporeae (Brassicaceae)

“…Recent family-wide studies (e.g., Beilstein et al 2006Beilstein et al , 2008Beilstein et al , 2010Warwick et al 2007Warwick et al , 2010; Koch et al 2007;Koch and Al-Shehbaz 2009;Franzke et al 2009;German et al 2009;Couvreur et al 2010;Zhao et al 2010) were congruent and showed that the vast majority of tribes can be assigned to three phylogenetic lineages (designated I, II, and III in Beilstein et al 2006). These studies are further congruent in the placement in lineage III of Chorisporeae C.A.…”

“…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 last authors also demonstrated the paraphyly of Parrya, with Pseudoclausia nested within, and Khosravi et al (2009) showed that Chorispora was polyphyletic. However, all studies that included the Chorisporeae (e.g., Koch et al 2007;Beilstein et al 2008;Franzke et al 2009;Lysak et al 2009;Couvreur et al 2010;Warwick et al 2010;Zhao et al 2010) collectively sampled only 16 of its species (25% of the tribe total), including six (out of ca. 40) Parrya species, and used in most cases a single marker.…”

Diversity of non-glandular trichomes in subtribe Lychnophorinae (Asteraceae: Vernonieae) and taxonomic implications

“…Also, trichome morphology has already been used to clarify tribal or sectional classifications (Webster et al 1996;Al-Shehbaz et al 2006) and, more recently, has been used as data in phylogenetic studies (e.g. Belstein et al 2006Belstein et al , 2008Caruzo et al 2011;van Ee and Berry 2011).…”