Tribal assignment of <Emphasis Type="Italic">Heldreichia</Emphasis> Boiss. (Brassicaceae): evidence from nuclear ITS and plastidic <Emphasis Type="Italic">ndh</Emphasis>F markers

Heldreichia Boiss. is a monospecific genus mainly distributed in Anatolia and the Lebanon. Although morphological variation and infrageneric phylogenetic relationships were recently studied in detail, Heldreichia remained as one of the few orphan genera that have not yet been assigned to any tribe. In the current study, we used sequence data from the nuclear ITS and chloroplast ndhF regions of Heldreichia and representatives of main Brassicaceae lineages and tribes to determine its tribal affiliation. Bayesian-based phylogenetic analyses clearly show with high support that Heldreichia is a member of the recently expanded tribe Biscutelleae. Furthermore, we characterize the tribe Biscutelleae morphologically and provide a determination key for all its genera.     

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.     

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.     

Contribution to ITS phylogeny of the Brassicaceae, with special reference to some Asian taxa

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region for 189 accessions representing 184 species in 121 genera of Brassicaceae were used to determine monophyly of tribes and genera, tribal boundaries, and component genera. Parsimony analysis and Bayesian inference suggest that the tribes Camelineae and Arabideae are polyphyletic and should be subdivided into smaller tribes. The study also supports the recent recognition of the new tribes Aphragmeae, Biscutelleae, Buniadeae, Calepineae, Conringieae, Dontostemoneae, Erysimeae, Malcolmieae, Megacarpaeeae, and Turritideae. The data argue for the placement of Borodinia in the tribe Boechereae, Litwinowia and Pseudoclausia in the Chorisporeae, Atelanthera and Streptoloma in the Euclidieae, and Megacarpaea and Pugionium in the Megacarpaeeae, and exclusion of Asperuginoides, Didymophysa, and Ptilotrichum from the Alysseae, Macropodium, Pseudoturritis, and Stevenia from the Arabideae, and Crucihimalaya, Irenepharsus, Pachycladon, and Turritis from the Camelineae. Finally, the findings support the expansion of Stevenia to include both Berteroella and Ptilotrichum, Sterigmostemum to include Oreoloma and one species of Anchonium, Crucihimalaya to include Transberingia and several species of Arabis, and Parrya to include Pseudoclausia. The data also suggest that Calymmatium and Olimarabidopsis may be congeneric.     

Revision and tribal placement of the Argentinean genus Parodiodoxa (Brassicaceae)

Parodiodoxa is a monotypic genus of Brassicaceae endemic to northwestern Argentina. It is poorly known and until now remained the only South American genus of the family that had not been assigned to a particular tribe. Sequence data from the nuclear ribosomal ITS region and the chloroplast trnL intron/trnL-F spacer region were used in this study to determine the systematic position of Parodiodoxa. For this purpose, taxa were sampled both at the tribal and generic levels. Results from tribal-level sampling support the inclusion of Parodiodoxa in the tribe Thelypodieae, whereas those at the generic level reveal a relationship to Weberbauera (W. rosulans and W. herzogii). Topologies within the Thelypodieae were poorly resolved, in agreement with previous studies. Morphological characteristics of Parodiodoxa are also discussed in relation to other genera of the tribe.     

Phylogenetic relationships of Brassicaceae in China: Insights from a non-coding chloroplast,mitochondrial, and nuclear DNA data set

Understanding of the systematics and evolution of the Brassicaceae has advanced greatly in recent years. In particular, molecular techniques offer a way to address issues of homoplasy that had limited morphology-based research. In this study, we used sequence data from chloroplast, mitochondrial, and nuclear genomes to construct the phylogeny of Brassicaceae. We adopted maximum parsimony, maximum likelihood, and Bayesian methods to illustrate the relationships of 71 species belonging to 51 genera. Results from trnS_(GCU)-trnG_(UUC), nad7 second intron, and pistillata (PI) first intron analyses supported the delimitation of Lineages I–III and agreed with previous findings from phyA, ITS, and ndhF analyses. The results indicated that Pachypterygium should be placed in the tribe Isatideae. The position of Leiospora agreed with speculation based on morphology. Furthermore, Conringia planisiliqua together with Orychophragmus violaceus can be recognized as a new tribe as proposed by previous studies. Finally, this study also supported the recently recognized new tribes Dontostemoneae and Erysimeae.     

Phylogeny and morphological evolution of tribe Menispermeae (Menispermaceae) inferred from chloroplast and nuclear sequences

The Menispermaceae family contains ca. 72 genera with 450 species that are almost entirely tropical. Its phylogeny at the tribal level has never been examined using molecular data. Here we used DNA sequences of the chloroplast matK gene and trnL-F regions, and the nuclear ITS region to study the delimitation and position of the tribe Menispermeae within the family and its subtribal monophyletic groups. Family-wide phylogenetic analyses of the chloroplast data produced two strongly supported clades. The first clade contains two subclades: Coscinieae including Arcangelisia and Anamirta, and Tinosporeae sensu lato including Fibraureae, supported by morphological characters, such as traits of the cotyledon, stylar scar and embryo. The second clade consists of the tribes Menispermeae sensu DC. and Tiliacoreae Miers. All our analyses surprisingly recognized that tribe Menispermeae is not monophyletic unless tribe Tiliacoreae is included, suggesting that characters of cotyledon and stylar scar are very important for the infrafamilial classification, and that endosperm presence vs. absence was over-emphasized in traditionally tribal division of the family. Our topologies indicate a secondary loss of endosperm. The monophyly of two subtribes of the tribe Menispermeae, Stephaniinae and Cissampelinae, is supported by the cpDNA and ITS data, as well as by morphological characters, including aperture types and shapes, and colpal membrane features of pollen grains, and sepal number of male flowers. The Cocculinae was recognized as a paraphyletic group containing the remaining genera of the tribe Menispermeae.     

Toward a global phylogeny of the Brassicaceae

The Brassicaceae is a large plant family (338 genera and 3,700 species) of major scientific and economic importance. The taxonomy of this group has been plagued by convergent evolution in nearly every morphological feature used to define tribes and genera. Phylogenetic analysis of 746 nrDNA internal transcribed spacer (ITS) sequences, representing 24 of the 25 currently recognized tribes, 146 genera, and 461 species of Brassicaceae, produced the most comprehensive, single-locus-based phylogenetic analysis of the family published to date. Novel approaches to nrDNA ITS analysis and extensive taxonomic sampling offered a test of monophyly for a large complement of the currently recognized tribes and genera of Brassicaceae. In the most comprehensive analysis, tribes Alysseae, Anchonieae plus Hesperideae, Boechereae, Cardamineae, Eutremeae, Halimolobeae, Iberideae, Noccaeeae, Physarieae, Schizopetaleae, Smelowskieae, and Thlaspideae were all monophyletic. Several broadly defined genera (e.g., Draba and Smelowskia) were supported as monophyletic, whereas others (e.g., Sisymbrium and Alyssum) were clearly polyphyletic. Analyses of ITS data identified several problematic sequences attributable to errors in sample identification or database submission. Results from parsimony ratchet and Bayesian analyses recovered little support for the backbone of the phylogeny, suggesting that many lineages of Brassicaceae have undergone rapid radiations that may ultimately be difficult to resolve with any single locus. However, the development of a preliminary supermatrix including the combination of 10 loci for 65 species provides an initial estimate of intertribal relations and suggests that broad application of such a method will provide greater understanding of relationships in the family.     

Phylogenetic relationships of subfamilies and circumscription of tribes in the family Hesperiidae (Lepidoptera: Hesperioidea)

A comprehensive tribal‐level classification for the world’s subfamilies of Hesperiidae, the skipper butterflies, is proposed for the first time. Phylogenetic relationships between tribes and subfamilies are inferred using DNA sequence data from three gene regions (cytochrome oxidase subunit I‐subunit II, elongation factor‐1α and wingless). Monophyly of the family is strongly supported, as are some of the traditionally recognized subfamilies, with the following relationships: (Coeliadinae + (“Pyrginae” + (Heteropterinae + (Trapezitinae + Hesperiinae)))). The subfamily Pyrginae of contemporary authors was recovered as a paraphyletic grade of taxa. The formerly recognized subfamily Pyrrhopyginae, although monophyletic, is downgraded to a tribe of the “Pyrginae”. The former subfamily Megathyminae is an infra‐tribal group of the Hesperiinae. The Australian endemic Euschemon rafflesia is a hesperiid, possibly related to “Pyrginae” (Eudamini). Most of the traditionally recognized groups and subgroups of genera currently employed to partition the subfamilies of the Hesperiidae are not monophyletic. We recognize eight pyrgine and six hesperiine tribes, including the new tribe Moncini. © The Willi Hennig Society 2008.     

Phylogenetic relationships of New Zealand Asteraceae inferred from ITS sequences

Forty-five sequences from members of all genera of Asteraceae indigenous to New Zealand and 50 published sequences representing the tribal diversity in the family were analyzed to assess the utility of ITS sequences to resolve phylogenetic relationships. Previous studies using chloroplast DNA sequences and morphology provided support for several clades in the Asteraceae, yet the relationships among some of these were uncertain. The results from ITS analysis were largely consistent with these earlier studies. The New Zealand species are included in at least six clades, most of these corresponding to recognized tribes. Our results have also clarified the tribal affinities of a few anomalous genera. Haastia, previously aligned with the Gnaphalieae or the Astereae, is nested in the Senecioneae. Centipeda, previously included in the Astereae or Anthemideae, emerges near the Heliantheae. The relationships of Abrotanella remain unresolved. Received August 8, 2001 Accepted November 6, 2001     

Mitogenomic phylogeny of Typhlocybinae (Hemiptera: Cicadellidae) reveals homoplasy in tribal diagnostic morphological traits

The subfamily Typhlocybinae is a ubiquitous, highly diverse group of mostly tiny, delicate leafhoppers. The tribal classification has long been controversial and phylogenetic methods have only recently begun to test the phylogenetic status and relationships of tribes. To shed light on the evolution of Typhlocybinae, we performed phylogenetic analyses based on 28 newly sequenced and 19 previously sequenced mitochondrial genomes representing all currently recognized tribes. The results support the monophyly of the subfamily and its sister‐group relationship to Mileewinae. The tribe Zyginellini is polyphyletic with some included genera derived independently within Typhlocybini. Ancestral character state reconstruction suggests that some morphological characters traditionally considered important for diagnosing tribes (presence/absence of ocelli, development of hind wing submarginal vein) are homoplastic. Divergence time estimates indicate that the subfamily arose during the Middle Cretaceous and that the extant tribes arose during the Late Cretaceous. Phylogenetic results support establishment of a new genus, Subtilissimia Yan & Yang gen. nov., with two new species, Subtilissimia fulva Yan & Yang sp. nov. and Subtilissimia pellicula Yan & Yang sp. nov.; but indicate that two previously recognized species of Farynala distinguished only by the direction of curvature of the processes of the aedeagus are synonyms, that is, Farynala dextra Yan & Yang, 2017 equals Farynala sinistra Yan & Yang, 2017 syn. nov. A key to tribes of Typhlocybinae is provided.     

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.     

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.     

Phylogenetic relationships in the Lejeuneaceae (Hepaticae) inferred using ITS sequences of nuclear ribosomal DNA

Sequences of the ITS1–5.8S–ITS2 region of nuclear ribosomal DNA were generated for 12 species from 9 genera of Lejeuneaceae and a single species of Jubulaceae (outgroup). The taxon sampling of Lejeuneaceae included representatives of the two widely recognized subfamilies, Lejeuneoideae and Ptychanthoideae. The molecular dataset was analysed independently and in combination with a morphological dataset. The nrITS dataset and the combined dataset resulted in identical topologies. The genus Bryopteris, sometimes treated as a separate family Bryopteridaceae, is nested within the Lejeuneaceae subfamily Ptychanthoideae. Lejeuneaceae subfamily Lejeuneoideae proved to be paraphyletic with the tribe Lejeuneeae sister to Ptychanthoideae, albeit without significant bootstrap support. The tribes Brachiolejeuneeae and Cheilolejeuneeae of Lejeuneoideae, established recently based on morphological evidence, are well supported in bootstrap analyses both of the ITS and the combined molecular–morphological datasets. The results support classifications of Lejeuneaceae based on morphological data and demonstrate the usefulness of the ITS region for phylogenetic studies within or among closely related genera of Lejeuneaceae.     

Nomenclature of tribes within the Urticaceae

Summary  As part of systematic studies of the genus Elatostema (Urticaceae) and its sister genera, it was apparent that different names had been applied at the tribal level for these genera. This paper proposes that the tribal name Elatostemeae be used for the genera currently delineated as belonging to tribe Lecantheae (Friis 1993). It is also proposed that the authorship of the currently recognised tribes in the Urticaceae should be attributed to Charles Gaudichaud-Beaupres as described in H. L. C. de Freycinet’s Voyage autour du monde…executé sur les corvettes de S. M. l’Uranie et la Physiciene, published in 1830.     

Phylogeny of the subfamily Larentiinae (Lepidoptera: Geometridae): integrating molecular data and traditional classifications

Larentiinae are the second largest subfamily of Geometridae, with more than 6200 described species. Despite recent advances in molecular systematics of geometrid moths, phylogenetic relationships between the numerous subgroups of Larentiinae are poorly known. In this study we present the most comprehensive attempt to date to resolve the phylogeny of Larentiinae, having sampled at least one species from all currently recognized 23 tribes. Fragments of one mitochondrial (COI) and eight nuclear (EF‐1α, WGL, GAPDH, RPS5, IDH, MDH, CAD and 28S) genes were sequenced, for a total of 6939 bp. Maximum likelihood and Bayesian analyses resulted in identical well‐resolved phylogenetic trees, which had maximum or near‐maximum support values at most nodes. Almost all conventionally recognized tribes represented by more than one genus were found to be monophyletic. Close to the root of Larentiinae, six tribes branch off the main lineage one after another, with Dyspteridini being sister to all other members of the subfamily. The rest of larentiines are divided into two very diverse lineages, comprising eight and at least ten tribes, respectively. There were just three findings incongruent with the conventional tribal subdivision of the subfamily. First, the genera Collix Guenée and Anticollix Prout formed a separate, previously unrecognized but well‐supported clade at the tribe level. Second, the Palaearctic genus Pelurga Hübner was placed apart from Larentia Treitschke and Mesoleuca Hübner, which were the other members of Larentiini in this analysis. Third, Cataclysmini appeared together with genera belonging to Xanthorhoini, leaving the latter paraphyletic. The Neotropic genus Oligopleura Herrich‐Schäffer is shown to belong to the tribe Euphyiini ( comb.n. ) according to both molecular data and male genital morphology. The results and the tribal classification of Larentiinae are discussed with reference to the principal publications since the end of the 19th Century. We conclude that the current tribal classification of Larentiinae is not controversial from the phylogenetic point of view and that its increasing complexity has merely reflected the accumulation of information, mainly through different methods of biosystematic study having become available for researchers. Our results indicate that diurnal lifestyle, accompanied by conspicuous coloration, has evolved independently in several subgroups of Larentiinae.     

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.