Seventy-nine species representing 12 genera of Vitaceae were sequenced for the trnL-F spacer, 37 of which were subsequently sequenced for the atpB-rbcL spacer and the rps16 intron. Phylogenetic analysis of the combined data provided a fairly robust phylogeny for Vitaceae. Cayratia, Tetrastigma, and Cyphostemma form a clade. Cyphostemma and Tetrastigma are each monophyletic, and Cayratia may be paraphyletic. Ampelopsis is paraphyletic with the African Rhoicissus and the South American Cissus striata nested within it. The pinnately leaved Ampelopsis form a subclade, and the simple and palmately leaved Ameplopsis constitutes another with both subclades containing Asian and American species. Species of Cissus from Asia and Central America are monophyletic, but the South American C. striata does not group with other Cissus species. The Asian endemic Nothocissus and Pterisanthes form a clade with Asian Ampelocissus, and A. javalensis from Central America is sister to this clade. Vitis is monophyletic and forms a larger clade with Ampelocissus, Pterisanthes, and Nothocissus. The eastern Asian and North American disjunct Parthenocissus forms a clade with Yua austro-orientalis, a species of a small newly recognized genus from China to eastern Himalaya. Vitaceae show complex multiple intercontinental relationships within the northern hemisphere and between northern and southern hemispheres.

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The phylogenetic relationship among 30 accessions belonging to nine species of the genus Echinochloa Beauv. was studied on the basis of the sequence of three non-coding regions ( trn T-L, trn L-F intergenic spacers, and trn L intron) of chloroplast DNA (cpDNA). A strict consensus parsimonious tree of the three most parsimonious trees derived from 25 polymorphic sites (six indels and 19 substitutions) in the total sequences, ranging from 1715-1760 bp, represented five groups: (i) Echinochloa oryzicola Vasing. and Echinochloa stagnina Beauv. from Thailand; (ii) Echinochloa crus-galli Beauv. complex; (iii) Echinochloa crus-pavonis Schult; (iv) Echinochloa colonum Link. and Echinochloa frumentacea Link.; and (v) the African species, Echinochloa obtusiflora Stapf and Echinochloa stagnina . Japanese barnyard millet ( Echinochloa esculenta H. Scholz) and various weedy varieties of E. crus-galli and Echinochloa oryzoides Fritsch had quite similar sequences and formed the E. crus-galli complex, which was characterized by six substitutions. A cultivated form of E. oryzicola (Mosuo barnyard millet) and various morphological and agronomical forms of E. oryzicola were characterized by two indels. Indian barnyard millet ( E. frumentacea ) and its wild counterpart ( E. colonum ) were characterized by five substitutions. Domestication as millets and adaptation to paddy environments as mimic weeds might occur after the divergence of species in the Asian Echinochloa .

The phylogeny of Vitaceae was reconstructed sampling 114 accessions of Vitaceae and the outgroup Leea of Leeaceae, using three noncoding plastid markers: trnC-petN, trnH-psbA, and trnL-F. Six 5-merous genera including Parthenocissus, Yua, Ampelocissus, Vitis, Nothocissus, and Pterisanthes form a well-supported clade. Ampelopsis, Rhoicissus, and the Cissus striata complex form a clade sister to the clade containing all the other taxa of Vitaceae. The core Cissus clade is resolved to be sister to the Cayratia-Tetrastigma-Cyphostemma clade, forming a clade of taxa with 4-merous flowers. The Parthenocissus-Yua clade is sister to the Ampelocissus-Vitis-Nothocissus-Pterisanthes clade. The Old World Cissus is paraphyletic, with the New World core Cissus nested within it. The intercontinental disjunction between Africa and Asia may have evolved at least twice in Cissus. Cayratia is paraphyletic with four Asian species sampled grouping with Tetrastigma and the African species forming another clade.

The phylogeny of Nolana (Solanaceae), a genus primarily distributed in the coastal Atacama and Peruvian deserts with a few species in the Andes and one species endemic to the Galápagos Islands, was reconstructed using sequences of four plastid regions (ndhF, psbA-trnH, rps16-trnK, and trnC-psbM) and the nuclear LEAFY second intron. The monophyly of Nolana was strongly supported by all molecular data. The LEAFY data suggested that the Chilean species, including Nolana sessiliflora, the N. acuminata group and at least some members of the Alona group, are basally diverged, supporting the Chilean origin of the genus. Three well supported clades in the LEAFY tree were corroborated by the SINE (short interspersed elements) or SINE-like insertions. Taxa from Peru are grouped roughly into two clades. Nolana galapagensis from the Galápagos Island is most likely to have derived from a Peruvian ancestor. The monophyly of the morphologically well diagnosed Nolana acuminata group (N. acuminata, N. baccata, N. paradoxa, N. parviflora, N. pterocarpa, N. rupicola and N. elegans) was supported by both plastid and LEAFY data. Incongruence between the plastid and the LEAFY data was detected concerning primarily the positions of N. sessiliflora, N. galapagensis, taxa of the Alona group, and the two Peruvian clades. Such incongruence may be due to reticulate evolution or in some cases lineage sorting of plastid DNA. Incongruence between our previous GBSSI trees and the plastid -LEAFY trees was also detected concerning two well-supported major clades in the GBSSI tree. Duplication of the GBSSI gene may have contributed to this incongruence. ACCEPTED MANUSCRIPT3

The currently recognized eastern Asian-North American disjunct species A. pedatum needs to be segregated into three species, corresponding to populations in eastern North America, China, and Japan. The eastern Asian-North American disjunction in the complex is inferred to be the result of two intercontinental migrations, one from eastern Asia into North America in the late Tertiary and the other from North America back to eastern Asia in the Pleistocene.

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Phylogenetic analysis of 105 nuclear GAI1 sequences of Vitaceae provided a fairly robust phylogeny, largely congruent with the recently published chloroplast data of the family. In the GAI1 phylogeny, Cayratia Juss., Tetrastigma (Miq.) Planch., and Cyphostemma (Planch.) Alston form a clade. Cyphostemma and Tetrastigma are both monophyletic, and Cayratia is paraphyletic. Ampelopsis Michx is paraphyletic with the African Rhoicissus Planch. and the South American Cissus striata Ruiz & Pav. and its close relatives (e.g., Cissus simsiana Roem. & Schult.) nested within it. The pinnately leaved Ampelopsis forms a subclade, and the simple and palmately leaved Ampelopsis constitutes another subclade. All species of Cissus L. sampled from Asia, Africa, and Central and South America (except the C. striata complex) form a monophyletic group. Pterisanthes Blume of southeastern Asia forms a clade with the Asian Ampelocissus Planch. Vitis L. is monophyletic and forms a larger clade with the tropical Ampelocissus and Pterisanthes. Parthenocissus Planch., forms a clade with Yua C.L. Li, with each genus reportedly monophyletic. Cissus from the Old World is paraphyletic with the neotropical core Cissus nested within it. The basal grade of Cissus consists of taxa from Africa. The African-Asian biogeographic relationships are complex, with several intercontinental disjunctions. The Northern Hemisphere Ampelopsis is most closely related to the South American C. striata complex and the African Rhoicissus. Résumé : L'analyse phylogénétique de 105 séquences du GAII nucléique des Vitaceae conduit à une phylogénie passablement robuste, concordant avec les données récemment publiées sur les chloroplastes de la famille. Selon la phylogénie basée sur le GAII, les Cayatia Juss., Tetrastigma (Miq.) Planch. et Cyphostemma (Planch.) Alston forment un clade. Les Cyphostemma et Tetrastigma sont chacun monophylétiques, alors que le Cayratia est paraphylétiques. L'Ampelopsis Michx. est paraphylétique avec le Rhoicissius Planch. africain, le Cissus striata Ruiz. & Pav. sud-américain et ses proches parents (e.g. Cissus simsiana Roem. & Schult.), s'y retrouvant. Les Ampelopsis à feuilles pennées forment un sous-clade, et les Ampelopsis à feuilles simples ou palmées constituent un autre sous-clade. Toutes les espèces de Cissus L. échantillonnées en Asie, en Afrique et en Amérique centrale et du sud (sauf le complexe C. striata) forment un groupe monophylétique. Le Pterisanthes du sud-est asiatique forme un clade avec l'Ampelocissus asiatique. Le Vitis est monophylétique et forme un large clade avec les Ampelocissus et les Pterisanthes tropicales. Le Parthenocissus forme un clade avec le Yua C.L. Li, chaque genre étant monophylétique. Le Cissus de l'Ancien monde est paraphylétique, le noyau des Cissus néotropicaux s'y retrouvant. L'étage basal des Cissus est constitué de taxons provenant d'Afrique. Les relations biogéographiques Afrique-Asie apparaissent complexes et comportent plusieurs disjonctions intercontinentales. L'Ampelopsis de l'hémisphère nord e...