Molecular phylogenetic analysis of Passifloraceae sensu lato (Malpighiales) based on plastid and nuclear DNA sequences.

A phylogenetic analysis of Passifloraceae sensu lato was performed using rbcL, atpB, matK, and 18S rDNA sequences from 25 genera and 42 species. Parsimony analyses of combined data sets resulted in a single most parsimonious tree, which was very similar to the 50% majority consensus tree from the Bayesian analysis. All nodes except three were supported by more than 50% bootstrap. The monophyly of Passifloraceae s.l. as well as the former families, Malesherbiaceae, Passifloraceae sensu stricto, and Turneraceae were strongly supported. Passifloraceae s.s. and the Turneraceae are sisters, and form a strongly supported clade. Within Passifloraceae s.s., the tribes Passifloreae and Paropsieae are both monophyletic. The intergeneric relationships within Passifloraceae s.s. and Turneraceae are roughly correlated with previous classification systems. The morphological character of an androgynophore/gynophore is better used for characterizing genera grouping within Passifloraceae s.s. Other morphological characters such as the corona and aril are discussed.

Molecular phylogenetic analysis of Violaceae (Malpighiales) based on plastid and nuclear DNA sequences.

A phylogenetic analysis of Violaceae is presented using sequences from rbcL, atpB, matK and 18S rDNA from 39 species and 19 genera. The combined analysis of four molecular markers resulted in only one most parsimonious tree, and 33 of all 38 nodes within Violaceae are supported by a bootstrap proportion of more than 50%. Fusispermum is in a basal-most position and Rinorea, Decorsella, Rinoreocarpus and the other Violaceae are successively diverged. The monogeneric subfamily Fusispermoideae is supported, and it shares a number of plesiomorphies with Passifloraceae (a convolute petal aestivation, actinomorphic flowers and connate filaments). The other monogeneric subfamily Leonioideae is sunken within the subfamily Violoideae and is sister to Gloeospermum, sharing some seed morphological characteristics. The present molecular phylogenetic analysis suggests that the convolute, apotact and quincuncial petal aestivation is successively derived within the family. The evolutionary trends of the other morphological characteristics, such as a filament connation, the number of carpels and floral symmetry, are discussed.

Molecular phylogenetic analysis of Euphorbiaceae sensu stricto based on plastid and nuclear DNA sequences and ovule and seed character evolution.

A phylogenetic analysis of Euphorbiaceae sensu stricto is presented using sequences from rbcL, atpB, matK and 18S rDNA from 85 species and 83 genera. The combined analysis of four molecular markers resulted in only one most parsimonious tree and also generated new supported clades, which include Euphorbioideae + Acalyphoideae s.s., subclades A2 + A3, subclades A5 + A6 and a clade uniting subclades A2-A8 within Acalyphoideae s.s. A palisadal exotegmen is a possible synapomorphy for all the Euphorbiaceae, except for the subfamily Peroideae. The presence of vascular bundles in the inner integument and a thick inner integument were shown to be synapomorphies for the clade of inaperturate and articulated crotonoids and for the large clade of Euphorbioideae, Acalyphoideae s.s., inaperturate and articulated crotonoids, respectively. Characters of the aril and vascular bundles in the outer integument are discussed. The selected embryological characters were seen to be highly correlated with the molecular phylogeny. When the results of molecular phylogenetic analysis of a previous study and this study were adjusted along with the selected embryological characters, all clades within Euphorbiaceae were supported except for a clade comprising Euphorbioideae + Acalyphoideae s.s. + inaperturate crotonoids + articulated crotonoids + Adenoclineae s.l. and a clade uniting subclades A4-A8 within Acalyphoideae s.s.

Phylogenetic analyses of Malpighiales using plastid and nuclear DNA sequences, with particular reference to the embryology of Euphorbiaceae sens. str.

We present phylogenetic analyses of Malpighiales, which are poorly understood with respect to relationships within the order, using sequences from rbcL, atpB, matK and 18SrDNA from 103 genera in 23 families. From several independent and variously combined analyses, a four-gene analysis using all sequence data provided the best resolution, resulting in the single most parsimonious tree. In the Malpighiales [bootstrap support (BS) 100%], more than eight major clades comprising a family or group of families successively diverged, but no clade containing more than six families received over 50% BS. Instead, ten terminal clades that supported close relationships between and among families (>50% BS) were obtained, between, for example, Balanopaceae and Chrysobalanaceae; Lacistemataceae and Salicaceae; and Phyllanthaceae and Picrodendraceae. The monophyly of Euphorbiaceae sens. str. were strongly supported (BS 100%), but its sister group was unclear. Euphorbiaceae sens. str. comprised two basally diverging clades (BS 100%): one leading to the Clutia group (Chaetocarpus, Clutia, Pera and Trigonopleura), and the other leading to the rest of the family. The latter shared a palisadal, instead of a tracheoidal exotegmen as a morphological synapomorphy. While both Acalyphoideae (excluding Dicoelia and the Clutia group) and Euphorbioideae are monophyletic, Crotonoideae were paraphyletic, requiring more comprehensive analyses.

Phylogeography of the genus Cardiandra based on genetic variation in cpDNA sequences.

We investigated the phylogenetic relationships within the genus Cardiandra based on plastid DNA sequences. The phylogenetic tree showed that Cardiandra populations from the Ryukyu Islands (Japan) and Taiwan were monophyletic (Ryukyu-Taiwan clade), whereas taxa from China and mainland Japan were sisters to this clade. The divergence time between the Ryukyu-Taiwan clade and the other species was estimated to be 0.082 MYA, i.e., the late Pleistocene. The infrageneric and/or infraspecific differentiation of Cardiandra is estimated to have depended largely on allopatric differentiation caused by the presence or division of the past landbridge of the Ryukyu Islands, which connected mainland Japan to the Asian Continent during the Quaternary.

Molecular evidence for the inclusion of the Korean endemic genus " Echinosophora" in Sophora (Fabaceae), and embryological features of the genus.

Although Echinosophora Nakai has been known as a monotypic and endemic genus of Papillionoideae of Fabaceae in Korea, it has been controversial whether it is distinct from or merged with Sophora. To resolve this matter, we conducted molecular phylogenetic analyses using nucleotide sequence data from the plastid rbcL gene and trnL (UAA) intron. Parsimony analysis, using a total of 53 taxa of the Papillionoideae (including E. koreensis [Nakai] Nakai and several species of Sophora and related genera) and using 20 taxa of Caesalpinioideae and Mimosoideae as outgroups, showed that, although the examined species of Sophora are split into two clades, E. koreensis formed a common clade with S. tomentosa (the type species of the genus) and S. flavescens. E. koreensis therefore should be treated as S. koreensis Nakai, and the generic name Echinosophora be eliminated. We also investigated the embryology of S. koreensis (= E. koreensis) and S. flavescens and found that no differences existed between them. Our molecular study, like other studies, strongly suggested that Sophora is polyphyletic. In this study we presented a summary of embryological features of the core Sophora for future critical comparison with related and unrelated taxa.

Ovules and seeds in Acalyphoideae (Euphorbiaceae): structure and systematic implications.

Acalyphoideae, the largest subfamily of Euphorbiaceae, are investigated with respect to ovule and seed structure on the basis of 172 species of 80 genera in all 20 tribes of Acalyphoideae sensu Webster. All species of Acalyphoideae examined have bitegmic ovules with a non-vascularized inner integument. However, noticeable differences exist among and sometimes within the genera in the thickness of the inner and outer integument, the presence or absence of vascular bundles in the outer integument, whether ovules are pachychalazal or not, the presence or absence of an aril, seed coat structure (in terms of the best-developed mechanical cell-layer), and the shape of cells constituting the exotegmen. For the latter two characters, two different types of seed coat (i.e., "exotegmic" and "exotestal") and three different types of exotegmic cell (i.e., palisadal, tracheoidal and ribbon-like) were distinguished. Comparisons showed that three tribes Clutieae, Chaetocarpeae and Pereae are distinct from the other Acalyphoideae as well as from the other Euphorbiaceae in having an exotestal seed coat with a tracheoidal exotegmen. The tribe Dicoelieae is also distinct from the other Acalyphoideae in having an exotegmic seed that is composed of ribbon-like cells of exotegmen (i.e., cells both longitudinally and radially elongated, sclerotic and pitted). The tribe Galearieae, which should be treated as a distinct family Pandaceae, is also distinct from the other Acalyphoideae in having an exotegmic seed with a tracheoidal exotegmen (i.e., cells longitudinally elongated, sclerotic and pitted). The remaining genera of Acalyphoideae always have an exotegmic seed with a palisadal exotegmen (i.e., cells radially elongated, sclerotic and pitted). The shared palisadal exotegmen supports the close affinity of Acalyphoideae (excluding five tribes) with Crotonoideae and Euphorbioideae. Within the remaining genera of Acalyphoideae, a significant diversity is found in ovule and seed morphology with respect to the thickness of the inner and outer integument, the size of chalaza, vascularization of an outer integument and an aril.

Ovules and seeds in Euphorbioideae (Euphorbiaceae): structure and systematic implications.

Ovule and seed structure in Euphorbioideae, one of the five euphorbiaceous subfamilies, is surveyed to evaluate its systematic implications on the basis of 79 species representing four of five tribes. All Euphorbioideae, like two other "uniovulate" subfamilies Acalyphoideae and Crotonoideae, but unlike most of two "biovulate" subfamilies Oldfieldioideae and Phyllanthoideae, consistently have a persistent and palisadal exotegmen composed of radially elongate, sclerotic, and pitted cells. Within Euphorbioideae, the tribe Stomatocalyceae (also with the palisadal exotegmen) is unusual in having vascular bundles in outer integument and clearly distinct from the remaining Euphorbioideae and the other "uniovulate" subfamilies. With the exclusion of Stomatocalyceae, Euphorbioideae are not anatomically divided into major groups such as a pseudanthial and a non-pseudanthial clade, but instead have some remarkable diversity within a tribe, a subtribe, and even a genus in the three ovule and seed characters: (1) the thickness of the inner integument, (2) the thickness of the outer integument, and (3) the presence or absence of an aril. Groups of genera and species wrapped by different combinations of their characteristics, however, are not necessarily harmonized with tribal or subtribal classifications available. Anatomical similarities and dissimilarities presented in this paper, as well as relationships among taxa presented in the classifications available, will be critically evaluated in the light of results of ongoing molecular phylogenetic analyses.