title: Another look at the phylogenetic position of the grape order Vitales: Chloroplast phylogenomics with an expanded sampling of key lineages.
abstract: Vitales is well-known for including the economically important fruit crop, the wine grape (Vitis vinifera). However, the position of the Vitales in the higher eudicots has been a subject of much debate. It has been variously reported to be sister to the Saxifragales and together as sister to the rest of rosids, or sister to the fabids-malvids clade, or sister to the Santalales, or sister to the fabids-malvids-Saxifragales clade. However, in all of these scenarios, the support values for the relationship of Vitales on the phylogenies were only low to moderate. Additionally, all previous studies sampled only Vitis vinifera as the representative of the Vitales. We herein expanded the sampling of the Vitales to include representatives of all major clades of the order, as well as representatives of other key lineages including Saxifragales, Dilleniales, and Santalales. Extensive likelihood and Bayesian analyses were conducted to test the position of Vitales, using different numbers of genes, a variety of partitioning strategies, and both nucleotide and amino acid sequences. With the expanded sampling strategy, almost all analyses supported the relationship of Vitales as sister to Saxifragales. This relationship was supported in a 72-gene data set with a bootstrap value of 91%, the highest support value reported to date. Based on this topology, we discuss possible morphological synapomorphies shared between Vitales and Saxifragales. Furthermore, a hypothesis of reticulate evolution was postulated as an explanation for the incongruence of Vitales' position when comparing plastid and nuclear gene phylogenies.
authors.affiliation: Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA. Electronic address: wenj@si.edu.
authors.forename: Jun
authors.initials: J
authors.lastname: Wen
authors.affiliation: Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA. Electronic address: zimmerl@si.edu.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Zimmer
mesh_terms: D001499:Bayes Theorem; D002736:Chloroplasts / Q000145:classification / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D017422:Sequence Analysis, DNA; D027843:Vitis / Q000145:classification* / Q000235:genetics
chemical_list: D018744:DNA, Plant
keywords: Phylogenomics; Plastid genome; Saxifragales; Vitales