Increased sampling of both genes and taxa improves resolution of phylogenetic relationships within Magnoliidae, a large and early-diverging clade of angiosperms.

Magnoliidae have been supported as a clade in the majority of large-scale molecular phylogenetic studies of angiosperms. This group consists of about 10,000 species assigned to 20 families and four orders, Canellales, Piperales, Laurales, and Magnoliales. Some relationships among the families are still largely debated. Here, we reconstruct the phylogenetic relationships of Magnoliidae as a whole, sampling 199 species (representing ca. 75% of genera) and 12 molecular markers from the three genomes (plastid atpB, matK, trnL intron, trnL-trnF spacer, ndhF, rbcL; mitochondrial atp1, matR, mtSSU, mtLSU; nuclear 18s rDNA, 26S rDNA). Maximum likelihood, Bayesian and maximum parsimony analyses yielded congruent trees, with good resolution and high support values for higher-level relationships. This study further confirms, with greater levels of support, two major clades in Magnoliidae: Canellales+Piperales and Laurales+Magnoliales. Relationships among the 20 families are, in general, well resolved and supported. Several previously ambiguous relationships are now well supported. For instance, the Aristolochiaceae s.l. (incl. Asaroideae, Aristolochioideae, and Lactoris) are monophyletic with high support when Hydnoraceae are excluded. The latter family was not included in most previous studies because of the lack of suitable plastid sequences, a consequence of the parasitic habit of its species. Here, we confirm that it belongs in Aristolochiaceae. Our analyses also provide moderate support for a sister group relationship between Lauraceae and Monimiaceae. Conversely, the exact position of Magnoliaceae remains very difficult to determine. This study provides a robust phylogenetic background to address the evolutionary history of an important and highly diverse clade of early-diverging angiosperms.

Massoni J ，Forest F ，Sauquet H 《-》

Five major shifts of diversification through the long evolutionary history of Magnoliidae (angiosperms).

Massoni J ，Couvreur TL ，Sauquet H 《BMC EVOLUTIONARY BIOLOGY》

Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids.

Cai Z ，Penaflor C ，Kuehl JV ，Leebens-Mack J ，Carlson JE ，dePamphilis CW ，Boore JL ，Jansen RK ... -  《BMC EVOLUTIONARY BIOLOGY》

Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences.

Savolainen V ，Chase MW ，Hoot SB ，Morton CM ，Soltis DE ，Bayer C ，Fay MF ，de Bruijn AY ，Sullivan S ，Qiu YL ... -  《SYSTEMATIC BIOLOGY》

Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids.

Rosids are a major clade in the angiosperms containing 13 orders and about one-third of angiosperm species. Recent molecular analyses recognized two major groups (i.e., fabids with seven orders and malvids with three orders). However, phylogenetic relationships within the two groups and among fabids, malvids, and potentially basal rosids including Geraniales, Myrtales, and Crossosomatales remain to be resolved with more data and a broader taxon sampling. In this study, we obtained DNA sequences of the mitochondrial matR gene from 174 species representing 72 families of putative rosids and examined phylogenetic relationships and phylogenetic utility of matR in rosids. We also inferred phylogenetic relationships within the "rosid clade" based on a combined data set of 91 taxa and four genes including matR, two plastid genes (rbcL, atpB), and one nuclear gene (18S rDNA). Comparison of mitochondrial matR and two plastid genes (rbcL and atpB) showed that the synonymous substitution rate in matR was approximately four times slower than those of rbcL and atpB; however, the nonsynonymous substitution rate in matR was relatively high, close to its synonymous substitution rate, indicating that the matR has experienced a relaxed evolutionary history. Analyses of our matR sequences supported the monophyly of malvids and most orders of the rosids. However, fabids did not form a clade; instead, the COM clade of fabids (Celastrales, Oxalidales, Malpighiales, and Huaceae) was sister to malvids. Analyses of the four-gene data set suggested that Geraniales and Myrtales were successively sister to other rosids, and that Crossosomatales were sister to malvids. Compared to plastid genes such as rbcL and atpB, slowly evolving matR produced less homoplasious but not less informative substitutions. Thus, matR appears useful in higher-level angiosperm phylogenetics. Analysis of matR alone identified a novel deep relationship within rosids, the grouping of the COM clade of fabids and malvids, which was not resolved by any previous molecular analyses but recently suggested by floral structural features. Our four-gene analysis supported the placements of Geraniales, Myrtales at basal nodes of the rosid clade and placed Crossosomatales as sister to malvids. We also suggest that the core part of rosids should include fabids, malvids and Crossosomatales.

Zhu XY ，Chase MW ，Qiu YL ，Kong HZ ，Dilcher DL ，Li JH ，Chen ZD ... -  《BMC EVOLUTIONARY BIOLOGY》