Analysis of phylogenetic relationships of Brassicaceae species based on Chs sequences

Sequences of nuclear chalcone synthase gene (Chs) were analyzed for species of the Brassicaceae family to reconstruct phylogenetic relationships. The phylogeny for 106 species of 60 genera was reconstructed, and assigned to 24 tribes, using maximum parsimony, maximum likelihood, and neighbor-joining methods. Most of the tribes can be assigned to the major lineages (Lineages I–III) suggested by Beilstein et al. (2006). The tribe Camelineae was not monophyletic. Conringia planisiliqua together with Orychophragmus violaceus would not be recognized as a new tribe proposed by the previous studies, and C. planisiliqua should be a member of tribe Isatideae. The genera delimitation and monophyly of the expanded Solms-laubachia were also confirmed by our data. Furthermore, one parent of inter-tribal allopolyploid Pachycladon appeared to be most closely associated with Crucihimalaya, Transberingia and tribes Boechereae and Halimolobeae, another parent was proved to be in tribe Smelowskieae.     

Resolving robust phylogenetic relationships of core Brassicaceae using genome skimming data

The Brassicaceae is an economically and scientifically important family distributed globally, including oilseed rape and the model plant, Arabidopsis thaliana. Although growing molecular data have been used in phylogenetic studies, the relationships among major clades and tribes of Brassicaceae are still controversial. Here, we investigated the core Brassicaceae phylogenetics using 222 plastomes and 235 nrDNA cistrons, including 106 plastomes and 112 nrDNA cistrons assembled from newly sequenced genome skimming data of 112 taxa. The sampling covered 73 genera from 61.5% tribes and four unassigned genera and species. Three well supported lineages LI, LII, and LIII were revealed in our plastomic analyses, with LI sister to LII + LIII. In addition, the monophyly of the newly delimitated LII was strongly supported by three different partition strategies, concatenated methods under Bayesian and Maximum Likelihood analyses. LII comprised 13 tribes, including four tribes previously unassigned to any lineage, that is Biscutelleae as the earliest diverging clade and Cochlearieae as the sister to Megacarpaeeae + Anastaticeae. Within LII, the intertribal relationships were also well resolved, except that a conflicting position of Orychophragmus was detected among different datasets. In LIII, Shehbazia was resolved as a member of Chorisproreae, but Chorisproreae, Dontostemoneae, and Euclidieae were all resolved as paraphyletic, which was also confirmed by nrDNA analyses. Moreover, the loss of the rps16 gene was detected as likely to be a synapomorphy of the tribes Arabideae and Alysseae. Overall, using genome skimming data, we resolved robust phylogenetic relationships of core Brassicaceae and shed new light on the complex evolutionary history of this family.     

Phylogenetic relationships of Old World Brassicaceae from Iran based on nuclear ribosomal DNA sequences

Phylogenetic analysis of 155 nuclear rDNA ITS sequences among them 19 Iranian endemic genera were used to elucidate phylogenetic relationships of Old World Brassicaceae from Iran in the context of the most recent tribal system suggested by Al-Shehbaz et al. [Al-Shehbaz, I.A., Beilstein, M.A, Kellogg, E.A., 2006. Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview. Plant Syst. Evol. 259, 89–120]. Iranian endemic taxa are assigned to 16 clades, 15 of these correspond to recognized tribes. Our data support the recent tribal recognition of Calepina and relatives and further indicate that the Orychophragmus clade (with Conringia planisiliqua and Orychophragmus) may be recognized as a new tribe. Our data also support the inclusion of 13 genera not previously studied, or with unresolved positions in previous phylogenetic analyses in 10 tribes with the tribal assignment given in parentheses: Acanthocardamum (Aethionemeae), Alyssopsis (Camelineae), Anastatica (Malcolmieae), Asperuginoides (Cochlearieae), Camelinopsis (Thlaspideae), Didymophysa (Thlaspideae), Dielsiocharisi (Camelineae), Lachnoloma (Anchonieae), Micrantha (Anchonieae), Noccidium (Camelineae), Octoceras (Euclidieae), Pseudofortuynia (Sisymbrieae) and Streptoloma (Euclidieae). ITS data and morphological characters further indicate that the remaining five genera, i.e., Acanthocardamum, Olimarabidopsis, Brossardia, Noccidium and Zuvanda may be subsumed under Aethionema, Alyssopsis, Noccaea, Capsella and Conringia, respectively. Alyssum, Chorispora, Fibigia and Goldbachia are paraphyletic and Conringia, Malcolmia, Matthiola are polyphyletic taxa.     

Molecular phylogeny and systematics of the tribe Chorisporeae (Brassicaceae)

Sequence data from nuclear (ITS) and chloroplast (trnL-F) regions for 89 accessions representing 56 out of 64 species from all five genera of the tribe Chorisporeae (plus Dontostemon tibeticus) have been studied to test the monophyly of the tribe and its component genera, clarify its boundaries, and elucidate its phylogenetic position in the family. Both data sets showed strong support for the monophyly of the Chorisporeae as currently delimited, though the position of its tentative member D. tibeticus was not resolved by ITS. Parrya and Pseudoclausia are poly- and paraphyletic with regard to each other, and Chorispora is either polyphyletic or at least paraphyletic (comprising Diptychocarpus) within a weakly supported monophyletic clade. The incongruence in branching pattern among the markers was most likely caused by hybridization and possibly influenced by incomplete lineage sorting. The present results suggest uniting Pseudoclausia, Clausia podlechii, and Achoriphragma with Parrya and transferring P. beketovii and P. saposhnikovii to Leiospora (Euclidieae). We also obtained support for splitting Chorispora into two geographically defined groups, one of which is closer to Diptychocarpus. Both data sets revealed a close relationship of the Chorisporeae to Dontostemoneae, while ITS also indicated affinity to Hesperideae. Therefore, the position of Chorisporeae needs further verification.     

Glucosinolate spectrum of some AlgerianCruciferae

Seventeen glucosinolates were identified and quantified by micro-scale GC analysis in Algerian samples fromSisymbrieae, Arabideae, Lepidieae, andBrassiceae tribes of theCruciferae. Major glucosinolates and their amino acid precursors allowed species to fall naturally into tribes as classified byJanchen.     

Molecular phylogenetic studies of Brassica, rorippa, arabidopsis and allied genera based on the internal transcribed spacer region of 18S-25S rDNA

The phylogenetic relationships of nine genera in four tribes of the family Brassicaceae were estimated from the sequences of the internal transcribed spacer region (ITS) of the 18S-25S nuclear ribosomal DNA. The entire ITS region of 16 accessions belonging to 10 species of seven genera was sequenced. Eight published sequences of Brassicaceae were also used. A total of 27 sequences were included in this study; four of them were found to be pseudogenes. Both the neighbor-joining and the parsimony trees suggest that the nine genera can be divided into three groups: (1) Arabidopsis, Cardaminopsis, Capsella, and Lepidium; (2) Rorippa and Cardamine; and (3) Brassica, Sinapis, and Raphanus. In contradiction to the proposal that Cardaminopsis and Arabidopsis be put into an expanded tribe Arabideae, our data show that these two genera are more closely related to Capsella and Lepidium (tribe Lepidieae) than to Rorippa and Cardamine (tribe Arabideae). Further, our data show that within the tribe Brassiceae, Raphanus is more closely related to B. nigra than to the B. oleracea/B. rapa clade. This result is in agreement with the nuclear data obtained in several studies, but is in conflict with the RFLP data of mitochondrial and chloroplast DNA. As pointed out by previous authors, it is possible that Raphanus is a hybrid between the B. nigra and B. oleracea/B. rapa lineages with the latter as the maternal parent.     

Phylogeny and taxonomy of casebearer moths (Lepidoptera,Coleophoridae) based on morphological and molecular genetic data. 1. Reconstruction of phylogeny of coleophoridae using analysis of <Emphasis Type="Italic">COI</Emphasis> gene variability

A phylogenetic study of representatives of the family Coleophoridae was conducted using a comprehensive approach, including methods of morphological and molecular genetic analyses. The existent data on the family system were compared with the results of phylogenetic analysis of the COI mitochondrial gene sequences. Four of the five studied subfamilies (Coleophorinae, Ischnophaninae, Augasminae, and Tolleophorinae) corresponded to their location on the phylogram; representatives of Metriotinae were part of Coleophorinae. According to the aggregate data from molecular phylogeny and morphology, the most numerous subfamily of casebearers, Coleophorinae, is polyphyletic within its current boundaries. The results of our analysis of COI molecular divergence does not refute the monophyly of the tribes Casignetellini, Carpochenini, Klinzigedini, Goniodomini, Casasini, and Atractulini from the subfamily Coleophorinae. The allocation of the tribes Aporipturini and Sistrophoecini within the subfamily does not correspond to the molecular data. Monophyly of the genera Ecebalia, Perygra, and Casignetella was confirmed. These genera are well isolated, which reflects the evolutionary significance of the morphological characters chosen for their taxonomic division. The boundaries of the cluster containing these genera correspond to those of the tribe Casignetellini, justifying the allocation of this tribe within the subfamily. The existence of monophyletic tribes Goniodomini (genus Goniodoma) and Carpochenini (genera Ionescumia, Carpochena, and Falkmisa) was also supported. The exceptions were the genera Kasyfia, Tollsia, and Agapalsa, whose monophyly was not confirmed by our results. The distribution of the sequences of species of these genera indicated a paraphyletic origin of Kasyfia and Tollsia and a polyphyletic origin of Agapalsa.     

Molecular Phylogenetic Studies of Brassica,Rorippa,Arabidopsis and Allied Genera Based on the Internal Transcribed Spacer Region of 18S–25S rDNA

The phylogenetic relationships of nine genera in four tribes of the family Brassicaceae were estimated from the sequences of the internal transcribed spacer region (ITS) of the 18S–25S nuclear ribosomal DNA. The entire ITS region of 16 accessions belonging to 10 species of seven genera was sequenced. Eight published sequences of Brassicaceae were also used. A total of 27 sequences were included in this study; four of them were found to be pseudogenes. Both the neighbor-joining and the parsimony trees suggest that the nine genera can be divided into three groups: (1) Arabidopsis,Cardaminopsis,Capsella, and Lepidium; (2) Rorippa and Cardamine; and (3) Brassica, Sinapis, and Raphanus. In contradiction to the proposal that Cardaminopsis and Arabidopsis be put into an expanded tribe Arabideae, our data show that these two genera are more closely related to Capsella and Lepidium (tribe Lepidieae) than to Rorippa and Cardamine (tribe Arabideae). Further, our data show that within the tribe Brassiceae, Raphanus is more closely related to B. nigra than to the B. oleracea/B. rapa clade. This result is in agreement with the nuclear data obtained in several studies, but is in conflict with the RFLP data of mitochondrial and chloroplast DNA. As pointed out by previous authors, it is possible that Raphanus is a hybrid between the B. nigra and B. oleracea/B. rapa lineages with the latter as the maternal parent.     

The tropical African legume Scorodophloeus clade includes two undescribed Hymenostegia segregate genera and Micklethwaitia,a rare,monospecific genus from Mozambique

Legume subfamily Caesalpinioideae accommodates approximately 2250 species in 171 genera which traditionally are placed in four tribes: Caesalpinieae, Cassieae, Cercideae and Detarieae. The monophyletic tribe Detarieae includes the Amherstieae subclade which contains about 55 genera. Our knowledge of the relationships among those genera is good in some cases but for many other genera phylogenetic relationships have been unclear. The non-monophyletic nature of at least two amherstioid genera, Cynometra and Hymenostegia has also complicated the picture. During the course of a multi-disciplinary study of Hymenostegia sensu lato, which includes phylogenetic analyses based on matK and trnL data, we have recovered the “Scorodophloeus clade”, an exclusively tropical African clade of four genera which includes the eponymous genus Scorodophloeus, two undescribed generic segregates of Hymenostegia sensu lato, and the previously unsampled rare monospecific genus Micklethwaitia from Mozambique. Zenkerella is suggested as a possible sister genus to the Scorodophloeus clade. A distribution map is presented of the seven species that belong to the Scorodophloeus clade.     

Reduction of pseudotaenidia to taenidia (Apiaceae)

Two previously monotypic genera,Taenidia andPseudotaenidia, are combined to form a single genusTaenidia, with two species. The difference in the fruits that has caused these otherwise very similar taxa to be referred to different tribes of the Apiaceae is considered to be of only specific importance in this instance.     

G-banding homologies of some Australian rodents

G-banding comparisons of 26 species in 10 genera of three tribes of Australian rodents show that at least one representative of each of the three tribes has autosomal complements that are indistinguishable on G-banding, implying unusually high conservation of karyotypes. Three genera (Pseudomys, Notomys, and Mastacomys) are distinguished karyotypically by a reciprocal translocation, one genus (Uromys) by a tandem fusion, and one genus (Zyzomys) by a radically altered karyotype. The only other rearrangements identified from G-banding are pericentric inversions, all 12 of which involve breaks in the proximal area.     

Phylogeny and classification of Rosaceae

Phylogenetic relationships among 88 genera of Rosaceae were investigated using nucleotide sequence data from six nuclear (18S, gbssi1, gbssi2, ITS, pgip, and ppo) and four chloroplast (matK, ndhF, rbcL, and trnL-trnF) regions, separately and in various combinations, with parsimony and likelihood-based Bayesian approaches. The results were used to examine evolution of non-molecular characters and to develop a new phylogenetically based infrafamilial classification. As in previous molecular phylogenetic analyses of the family, we found strong support for monophyly of groups corresponding closely to many previously recognized tribes and subfamilies, but no previous classification was entirely supported, and relationships among the strongly supported clades were weakly resolved and/or conflicted between some data sets. We recognize three subfamilies in Rosaceae: Rosoideae, including Filipendula, Rubus, Rosa, and three tribes; Dryadoideae, comprising the four actinorhizal genera; and Spiraeoideae, comprising Lyonothamnus and seven tribes. All genera previously assigned to Amygdaloideae and Maloideae are included in Spiraeoideae. Three supertribes, one in Rosoideae and two in Spiraeoideae, are recognized.     

The leaf flavonoids of the orchidaceae

In a leaf survey of 142 species from 75 genera of the Orchidaceae, flavone C-glycosides (in 53%) and flavonols (in 37 %) were found to be the most common constituents. However, since these compounds are not found uniformly and their distribution shows a strong correlation with plant geography, it is not possible to represent the Orchidaceae by a single flavonoid profile. Thus, flavone C-glycosides are most common in tropical and subtropical species of the Epidendroid and Vandoid tribes (in 63%) and flavonol glycosides are more characteristic of temperate species of the Neottioid tribes (in 78%). By contrast 6-hydroxyflavones (in 6 species), luteolin (in 2 species) and tricin as the 5-glucoside (in 1 species) are all rare. Three new glycosides were characterised: scutellarein 6-methyl ether 7-rutinoside from Oncidium excavatum and O. sphacelatum, pectolinarigenin 7-glucoside from 0. excavatutn and Eria javanica, and luteolin 3′,4′-diglucoside from Listera ovata. The xanthones, mangiferin and isomangiferin were found in Mormolyca ringens, Maxillaria aff. luteo-alba and 5 Polystachya species and a mangiferin sulphate tentatively identified in P. nyanzensis. Other unusual phenolic constituents include 6,7-methylenedioxy- and 6,7-dimethoxycoumarins from Dendrobium densiflorum and D. farmeri, formed by the rearrangement during the extraction process from the corresponding O-glucosyloxycinnamic acids. The origin and relationship of the Orchidaceae to other monocot groups are discussed in the light of the flavonoid evidence.     

Dissecting the major American snake radiation: A molecular phylogeny of the Dipsadidae Bonaparte (Serpentes,Caenophidia)

The Dipsadidae contains more than 700 extant species belonging to 92 genera and is the largest family of American snakes. In this work, we built a data set including two mitochondrial genes (12S and 16S rRNA) for 125 dipsadid taxa belonging to 59 genera, in order to gain further insights on the phylogenetic relationships of this large group at the subfamilial and generic levels. Among dipsadines, the monotypic genus Nothopsis is the sister-group to Leptodeira. Among xenodontines, the monophyly of seven previously recognized tribes (Alsophiini, Elapomorphini, Hydropsini, Philodryadini, Pseudoboini, Tachymenini and Xenodontini) is confirmed. Among Xenodontini, the genus Liophis is paraphyletic with respect to Erythrolamprus and Umbrivaga and workers should be aware of the inadequacy of the current taxonomy. Finally, the following genera could not confidently be allocated to the above tribes: Caaeteboia, Echinantera and Taeniophallus, Tropidodryas, Manolepis and Pseudalsophis, Xenopholis, Psomophis, Hydrodynastes, Conophis and Crisantophis.     

Closing the gaps: phylogenetic relationships in the Brassicaceae based on DNA sequence data of nuclear ribosomal ITS region

Sequence data from the nuclear encoded ribosomal internal transcribed spacer (ITS) region were used to determine monophyly of tribes, tribal limits, and tribal relationships of 96 so far unassigned or tentatively assigned genera (represented by 101 taxa/accessions) within the Brassicaceae. Maximum-parsimony and maximum-likelihood analyses of 185 ITS Brassicaceae sequences, which also included representatives of each of the 34 currently recognized tribes, supported the separate phylogenetic distinctness of these tribes and permitted the tribal assignment of all but 12 of the unassigned genera into tribal clades. The data support the recognition of eight new, well-resolved, uni- or oligogeneric tribes recognized herein as the Alyssopsideae [96% bootstrap support (BS); including the central and southwestern Asian Alyssopsis and Calymmatium], Asteae (100% BS; including the Mexican Asta), Eudemeae (97% BS; South American Brayopsis, Eudema, and Xerodraba), Kernereae (96% BS; European Kernera and Rhizobotrya), Notothlaspideae (100% BS; New Zealandic Notothlaspi), Oreophytoneae (100% BS; eastern African Oreophyton and southern European Murbeckiella), and Yinshanieae (100% BS; Chinese Yinshania), as well as the moderately supported Microlepidieae (75% BS; Australian Microlepidium and Carinavalva). Furthermore, the results fully support the recent findings that the tribes Schizopetaleae and Thelypodieae ought to be recognized as two distinct tribes instead of a single tribe, as well as provide some support for the re-establishment of the tribe Cremolobeae, bringing the total number to 44 tribes in the family. Nearly 92% (308) of the 336 genera in the family have been assigned to a tribe. The earlier-published Anastaticeae is taken here to replace the Malcolmieae.     

Polyphyly and two emerging lineages in the rust genera Puccinia and Uromyces

The phylogenetic validity of Puccinia and Uromyces, Pucciniaceae, and closely related genera was evaluated using nucLSU rDNA sequences. Using a wide range of rust species with different life cycles and with different host specificities, Puccinia and Uromyces were shown to be highly polyphyletic and to also include representatives of the genera Aecidium, Cumminsiella, Dietelia, Endophyllum, Miyagia, and Uredo. Furthermore, the structure of the phylogenetic data did not reflect previous sub-generic delimitations based on teliospore pedicel structure, but rather suggests that at least two major lineages have evolved within Puccinia/Uromyces: Rusts with telial states on Poaceae were exclusively found in one of these groupings and those with telial states on Cyperaceae resided in the other lineage. This might suggest that the two lineages evolved in close association with these host groups in different biomes.     

Notes on calycophyllous Rubiaceae. Part I. Morphological comparisons of the genera Chimarrhis,Bathysa, and Calycophyllum,with new combinations and a new species,Chimarrhis gentryana

A comparison of some genera of the Condaminecae (Rubiaceae) with a few taxa of closely related tribes (Rondeletieae, Calycophylleae, and Cinchoneae) revealed that some species ofChimarrhis (Condamineeae s. 1.),Bathysa (Rondeletieae), andCalycophyllum (Calycophylleae) are often misassigned to genera. The taxonomic significance of calycophylls is discussed; the generic boundaries ofChimarrhis, Bathysa, andCalycophyllum are reevaluated; and their similarities and differences are discussed. As a result, a new calycophyllous species ofChimarrhis from the Amazon,C. gentryana, is described, two of its species are transferred toBathysa (B. Bathysoides, B. perijaënsis), and one species ofBathysa (B. difformis) is reduced to synonymy underChimarrhis (C. turbinata).