Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes

The phylogeny of Celastraceae tribe Euonymeae (∼230 species in eight genera in both the Old and New Worlds) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. Tribe Euonymeae has been defined as those genera of Celastraceae with generally opposite leaves, isomerous carpels, loculicidally dehiscent capsules, and arillate seeds (except Microtropis). Euonymus is the most diverse (129 species) and widely cultivated genus in the tribe. We infer that tribe Euonymeae consists of at least six separate lineages within Celastraceae and that a revised natural classification of the family is needed. Microtropis and Quetzalia are inferred to be distinct sister groups that together are sister to Zinowiewia. The endangered Monimopetalum chinense is an isolated and early derived lineage of Celastraceae that represents an important component of phylogenetic diversity within the family. Hedraianthera is sister to Brassiantha, and we describe a second species (Brassiantha hedraiantheroides A.J. Ford) that represents the first reported occurrence of this genus in Australia. Euonymus globularis, from eastern Australia, is sister to Menepetalum, which is endemic to New Caledonia, and we erect a new genus (Dinghoua R.H. Archer) for it. The Madagascan species of Euonymus are sister to Pleurostylia and recognized as a distinct genus (Astrocassine ined.). Glyptopetalum, Torralbasia, and Xylonymus are all closely related to Euonymus sensu stricto and are questionably distinct from it. Current intrageneric classifications of Euonymus are not completely natural and require revision.     

Fruit and Seed Anatomy of Chenopodium and Related Genera (Chenopodioideae,Chenopodiaceae/Amaranthaceae): Implications for Evolution and Taxonomy

A comparative carpological study of 96 species of all clades formerly considered as the tribe Chenopodieae has been conducted for the first time. The results show important differences in the anatomical structure of the pericarp and seed coat between representatives of terminal clades including Chenopodium s.str.+Chenopodiastrum and the recently recognized genera Blitum, Oxybasis and Dysphania. Within Chenopodium the most significant changes in fruit and seed structure are found in members of C. sect. Skottsbergia. The genera Rhagodia and Einadia differ insignificantly from Chenopodium. The evolution of heterospermy in Chenopodium is discussed. Almost all representatives of the tribe Dysphanieae are clearly separated from other Chenopodioideae on the basis of a diverse set of characteristics, including the small dimensions of the fruits (especially in Australian taxa), their subglobose shape (excl. Teloxys and Suckleya), and peculiarities of the pericarp indumentum. The set of fruit and seed characters evolved within the subfamily Chenopodioideae is described. A recent phylogenetic hypothesis is employed to examine the evolution of three (out of a total of 21) characters, namely seed color, testa-cell protoplast characteristics and embryo orientation.     

The phylogeny and taxonomy of genera Cystoderma and Cystodermella (Agaricales) based on nuclear ITS and LSU sequences

Species delimitation in Cystoderma and Cystodermella was evaluated based on ITS and LSU rDNA sequences as well as morphological data. Two species of Cystoderma are synonymised with C. carcharias and three species with C. jasonis, distinguishing the synonymised taxa as varieties of these accepted species. Analyses of partial LSU rDNA sequences revealed Cystoderma and Cystodermella as distinct monophyletic genera, with Ripartitella representing a well-supported sister group of the latter. Phaeolepiota aurea represents either an unsupported sister group or member of Cystoderma in the phylogenies based on LSU and ITS sequences rDNA data, respectively. The tribe Cystodermateae sensu Singer did not appear monophyletic according to analyses of LSU sequences. On the basis of these data, the phylogenetic relationships among most of the analyzed genera could not be resolved unequivocally.     

Phylogenetic relationships in Peniocereus (Cactaceae) inferred from plastid DNA sequence data

The phylogenetic relationships of Peniocereus (Cactaceae) species were studied using parsimony analyses of DNA sequence data. The plastid rpl16 and trnL-F regions were sequenced for 98 taxa including 17 species of Peniocereus, representatives from all genera of tribe Pachycereeae, four genera of tribe Hylocereeae, as well as from three additional outgroup genera of tribes Calymmantheae, Notocacteae, and Trichocereeae. Phylogenetic analyses support neither the monophyly of Peniocereus as currently circumscribed, nor the monophyly of tribe Pachycereeae since species of Peniocereus subgenus Pseudoacanthocereus are embedded within tribe Hylocereeae. Furthermore, these results show that the eight species of Peniocereus subgenus Peniocereus (Peniocereus sensu stricto) form a well-supported clade within subtribe Pachycereinae; P. serpentinus is also a member of this subtribe, but is sister to Bergerocactus. Moreover, Nyctocereus should be resurrected as a monotypic genus. Species of Peniocereus subgenus Pseudoacanthocereus are positioned among species of Acanthocereus within tribe Hylocereeae, indicating that they may be better classified within that genus. A number of morphological and anatomical characters, especially related to the presence or absence of dimorphic branches, are discussed to support these relationships.     

Is the mega-diverse genus Ocyptamus (Diptera, Syrphidae) monophyletic? Evidence from molecular characters including the secondary structure of 28S rRNA

Phylogenetic relationships between two New World Syrphinae taxa (Diptera, Syrphidae), i.e. the highly diverse genus Ocyptamus and the large genus Toxomerus, were analysed based on molecular characters. The monophyly of both taxa was tested and the taxonomic status of included subgenera and species groups was examined. Toxomerus constitutes the monogeneric tribe Toxomerini with more than 140 described species, while Ocyptamus (tribe Syrphini) is a very diverse genus (over 300 spp.) with multiple recognised subgenera and species groups. Sequence data from three gene regions were used: the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S and 18S ribosomal RNA genes. The secondary structure of two expansion segments (D2, D3) of the ribosomal 28S RNA gene is presented for the family Syrphidae and used for the first time in a multiple sequence alignment. Molecular data were analysed using parsimony, maximum likelihood and Bayesian inference. Toxomerus was always recovered as monophyletic within Ocyptamus, and relationships to other New World taxa such as Salpingogaster (Eosalpingogaster) were well-supported. Only the subgenera and species groups of Ocyptamus were consistently recovered as monophyletic lineages, thus the apparent non-monophyly of Ocyptamus demands reclassification of this clade.     

Phylogeny of Isatis (Brassicaceae) and allied genera based on ITS sequences of nuclear ribosomal DNA and morphological characters

Systematics of the genus Isatis (Brassicaceae) is difficult and controversial, and previous studies were based solely on morphological characters. Sequence variation of the internal transcribed spacer (ITS) regions and the 5.8S gene of nuclear ribosomal DNA (nrDNA) were analyzed using parsimony and Bayesian methods. Twenty-eight taxa of Isatis and related genera of the tribe Isatideae were sampled, including 20 Isatis species representing almost all major morphological lineages, all three species of Pachypterygium, two of nine species of Sameraria, and monospecific Boreava, Myagrum, and Tauscheria. Two well-supported clades were resolved in the ITS tree, and they demonstrate the artificiality of the present delimitation of the tribe. One clade includes I. emarginata, I. minima, I. trachycarpa, P. brevipes, P. multicaule, P. stocksii, and T. lasiocarpa. The second clade includes I. buschiana, the polymorphic I. cappadocica with five subspecies, I. gaubae, I. kotschyana, I. leuconeura, I. pachycarpa, I. takhtajanii, I. tinctoria, and S. armena. Pachypterygium is polyphyletic and, together with Boreava, Sameraria, and Tauscheria, all are nested within Isatis. This study is a continuation of our recent systematic survey based on seed-coat microsculpturing ( Moazzeni et al., 2007. Flora 202, 447–454) and reveals that fruit characters mapped onto the molecular tree show considerable convergence. The reliance on fruit characters alone in the delimitation of genera may well lead to erroneous phylogenetic results and thus to incorrect taxonomic conclusions.     

A two-gene phylogeny shows the lichen genus Niebla (Lecanorales) is endemic to the New World and does not occur in Macaronesia nor in the Mediterranean basin

The generic segregates of the widespread fruticose genus Ramalina (mostly based on empirical data on morphology, cortex anatomy and secondary metabolites) are studied using maximum parsimony, maximum likelihood and Bayesian analyses of nuclear LSU and ITS sequences. The species examined include the three species aggregates within Niebla from the western coasts of North America, all species except one assumed to belong to the same genus from Macaronesia and the Mediterranean basin, the type species of Dievernia and Ramalina, and representatives of the genus Fistulariella. The genus Niebla is strongly supported when restricted to species from the New World, and all species referred to it from Macaronesia and the Mediterranean basin belong to Ramalina (R. bourgeana, R. crispatula, R. cupularis, R. hamulosa, R. portosantana, R. rosacea, R. subwebbiana and R. webbii). No support is found for the genera Dievernia and Fistulariella. The internal topology of the large genus Ramalina is unresolved and needs further studies.     

Hebeloma species associated with Cistus

The genus Hebeloma has a number of species highly specific to Cistus and others that occur with several host genera. This paper discusses the species of Hebeloma that appear to be ectomycorrhizal with Cistus, judging from their occurrence when Cistus is the only available host. The previously unknown species H. plesiocistum spec. nov. is described. We also provide a key to the known Hebeloma associates of Cistus. Molecular analyses based on ITS sequence data further illustrate the distinctness of the newly described species and difficulties in the species delimitation with view to H. erumpens. Specific associations with Cistus may have evolved more than once within the genus Hebeloma.     

Molecular systematics and phytochemistry of Rehmannia (Scrophulariaceae)

The relationships between the six known species of Rehmannia were investigated. With regard to the content of iridoid glucosides, caffeoyl phenylethanoid glycosides (CPGs) and ionone glucosides, no conclusions could be drawn. Phylogenetic analysis of DNA sequence data (ITS region, trnL-F region and rps16 intron) reveal a well-resolved topology in which Rehmannia glutinosa and Rehmannia solanifolia and Rehmannia piasezkii and Rehmannia elata are well-supported species pairs. Rehmannia chingii is sister to the rest of the genus, which is congruent with its distribution distant to the other species of the genus.     

Phylogeny of the Celastreae (Celastraceae) and the relationships of Catha edulis (qat) inferred from morphological characters and nuclear and plastid genes

The phylogeny of Celastraceae tribe Celastreae, which includes about 350 species of trees and shrubs in 15 genera, was inferred in a simultaneous analysis of morphological characters together with nuclear (ITS and 26S rDNA) and plastid (matK, trnL-F) genes. A strong correlation was found between the geography of the species sampled and their inferred relationships. Species of Maytenus and Gymnosporia from different regions were resolved as polyphyletic groups. Maytenus was resolved in three lineages (New World, African, and Austral-Pacific), while Gymnosporia was resolved in two lineages (New World and Old World). Putterlickia was resolved as nested within the Old World Gymnosporia. Catha edulis (qat, khat) was resolved as sister to the clade of Allocassine, Cassine, Lauridia, and Maurocenia. Gymnosporia cassinoides, which is reportedly chewed as a stimulant in the Canary Islands, was resolved as a derived member of Gymnosporia and is more closely related to Lydenburgia and Putterlickia than it is to Catha. Therefore, all eight of these genera are candidates for containing cathinone- and/or cathine-related alkaloids.     

Molecular phylogeny and biogeography of the narrow endemic Coelonema and affinitive Draba (Brassicaceae) based on two DNA regions

To clarify the relationship between two genera, Draba and the narrow genus Coelonema, endemic to the QilianMountains of the northeastern Qinghai-Tibet Plateau, phylogenetic analyses were conducted using nuclear ribosomal DNA ITS, and the chloroplast DNA trnL, from Coelonema draboides and 30 species of Draba representing eight sections, including 25 species of Chinese Draba, seven of which were endemic to the study region. The results unambiguously support several previously published proposals to unite Coelonema with Draba and accommodate C. draboides in the latter genus on the basis of morphological re-examination. Our molecular data presented here also provide evidence that these two genera should be combined as a monophyletic group with high support. In addition, it is estimated that Draba may have originated about 1.36–2.71 Mya, with C. draboides diverging from Draba about 0.15–0.31 Mya, based on the molecular calibration of ITS datasets. The assumed speciation and rapid expansion of these two genera is likely to have occurred in the eastern edge of the QilianMountains area according to molecular phylogeny and estimated divergence times, which correspond well with the known geological and paleobotanical histories of the Qinghai-Tibet Plateau.     

Phylogenetic relationships in European Ceriporiopsis species inferred from nuclear and mitochondrial ribosomal DNA sequences

The aim of this work was to clarify taxonomy and examine evolutionary relationships within European Ceriporiopsis species using a combined analysis of the large subunit (nLSU) nuclear rRNA and small subunit (mtSSU) mitochondrial rRNA gene sequences. Data from the ITS region were applied to enhance the view of the phylogenetic relationships among different species. The studied samples grouped into four complex clades, suggesting that the genus Ceriporiopsis is polyphyletic. The generic type Ceriporiopsis gilvescens formed a separate group together with Ceriporiopsis guidella and Phlebia spp. in the phlebioid clade. In this clade, the closely related species Ceriporiopsis resinascens and Ceriporiopsis pseudogilvescens grouped together with Ceriporiopsis aneirina. C. resinascens and C. pseudogilvescens have identical LSU and SSU sequences but differ in ITS. Ceriporiopsis pannocincta also fell in the phlebioid clade, but showed closer proximity to Gloeoporus dichrous than to C. gilvescens or C. aneirina–C. pseudogilvescens–C. resinascens group. Another clade was composed of a Ceriporiopsis balaenae–Ceriporiopsis consobrina group and was found to be closely related to Antrodiella and Frantisekia, with the overall clade highly reminiscent of the residual polyporoid clade. The monotypic genus Pouzaroporia, erected in the past for Ceriporiopsis subrufa due to its remarkable morphological differences, also fell within the residual polyporoid clade. Ceriporiopsis subvermispora held an isolated position from the other species of the genus. Therefore, the previously proposed name Gelatoporia subvermispora has been adopted for this species. Physisporinus rivulosus appeared unrelated to two other European Physisporinus species. Moreover, Ceriporiopsis (=Skeletocutis) jelicii grouped in a separate clade, distinct from Ceriporiopsis species. Finally, the ITS data demonstrated the proximity of some Ceriporiopsis species (Ceriporiopsis portcrosensis and Ceriporiopsis subsphaerospora) to Skeletocutis amorpha.     

Analysis of DNA sequences of six chloroplast and nuclear genes suggests incongruence, introgression, and incomplete lineage sorting in the evolution of Lespedeza (Fabaceae)

The genus Lespedeza (Fabaceae) consists of 40 species disjunctively distributed in East Asia and eastern North America. Phylogenetic relationships of all Lespedeza species and closely related genera were reconstructed using maximum parsimony, maximum likelihood, and Bayesian analyses of sequence data from five chloroplast (rpl16, rpl32-trnL, rps16-trnQ, trnL-F, and trnK/matK) and one nuclear (ITS) DNA regions. All analyses yielded consistent relationships among major lineages. Our results suggested that Campylotropis, Kummerowia, and Lespedeza are monophyletic, respectively. Lespedeza is resolved as sister to Kummerowia and these two together are further sister to Campylotropis. Neither of the two subgenera, subgen. Lespedeza and subgen. Macrolespedeza, in Lespedeza based on morphological characters, is recovered as monophyletic. Within Lespedeza, the North American clade is retrieved as sister to the Asian clade. The nuclear and chloroplast markers showed incongruent phylogenetic signals at shallow-level phylogeny, which may point to either introgression or incomplete lineage sorting in Lespedeza. The divergence times within Lespedeza and among related genera were estimated using Bayesian approach with BEAST. It is assumed that following the divergence between Kummerowia and Lespedeza in Asia in the late Miocene, the ancestor of Lespedeza diverged into the North American and the Asian lineages. The North American ancestor quickly migrated to North America through the Bering land bridge in the late Miocene. The North American and Asian lineages started to diversify almost simultaneously in the late Miocene but resulted in biased numbers of species in two continents.     

Phylogenetic position of the genus Ferula (Apiaceae) and its placement in tribe Scandiceae as inferred from nrDNA ITS sequence variation

Recent molecular systematic investigations suggested that Ferula, an umbellifer genus of about 170 species, is polyphyletic, with its members placed in the apioid superclade and within tribe Scandiceae. We analyzed ITS sequence variation from 134 accessions of Apiaceae, including 83 accessions (74 species) of Ferula to ascertain the phylogenetic position of the genus within the family. Phylogenetic analyses of these data using maximum parsimony, Bayesian, and neighbor-joining methods support the monophyly of Ferula upon the addition of Dorema and Leutea (as Ferula sensu lato) and its placement in tribe Scandiceae. Ferula sensu is closely allied with other major lineages of Scandiceae, corresponding to subtribes Scandicinae, Daucinae, and Torilidinae. Therefore, we recognize the Ferula clade as subtribe Ferulinae. Another addition to tribe Scandiceae is a clade composed of genera Glaucosciadium and Mozaffariania. The three accessions of Ferula misplaced in the apioid superclade represent a species of Silaum.     

Evolutionary lineages of nickel hyperaccumulation and systematics in European Alysseae (Brassicaceae): evidence from nrDNA sequence data

Background and Aims

Nickel (Ni) hyperaccumulation is a rare form of physiological specialization shared by a small number of angiosperms growing on ultramafic soils. The evolutionary patterns of this feature among European members of tribe Alysseae (Brassicaceae) are investigated using a phylogenetic approach to assess relationships among Ni hyperaccumulators at the genus, species and below-species level.

Methods

Internal transcribed spacer (ITS) sequences were generated for multiple accessions of Alysseae. Phylogenetic trees were obtained for the genera of the tribe and Alyssum sect. Odontarrhena. All accessions and additional herbarium material were tested for Ni hyperaccumulation with the dimethylglyoxime colorimetric method.

Key Results

Molecular data strongly support the poorly known hyperaccumulator endemic Leptoplax (Peltaria) emarginata as sister to hyperaccumulator species of Bornmuellera within Alysseae. This is contrary to current assumptions of affinity between L. emarginata and the non-hyperaccumulator Peltaria in Thlaspideae. The lineage Bornmuellera–Leptoplax is, in turn, sister to the two non-hyperaccumulator Mediterranean endemics Ptilotrichum rupestre and P. cyclocarpum. Low ITS sequence variation was found within the monophyletic Alyssum sect. Odontarrhena and especially in A. murale sensu lato. Nickel hyperaccumulation was not monophyletic in any of three main clades retrieved, each consisting of hyperaccumulators and non-hyperaccumulators of different geographical origin.

Conclusions

Nickel hyperaccumulation in Alysseae has a double origin, but it did not evolve in Thlaspideae. In Bornmuellera–Leptoplax it represents an early synapomorphy inherited from an ancestor shared with the calcicolous, sister clade of Mediterranean Ptilotrichum. In Alyssum sect. Odontarrhena it has multiple origins even within the three European clades recognized. Lack of geographical cohesion suggests that accumulation ability has been lost or gained over the different serpentine areas of south Europe through independent events of microevolutionary adaptation and selection. Genetic continuity and strong phenotypic plasticity in the A. murale complex call for a reduction of the number of Ni hyperaccumulator taxa formally recognized.     

Evolutionary history of frogfishes (Teleostei: Lophiiformes: Antennariidae): a molecular approach

Fishes of the family Antennariidae (order Lophiiformes) are primarily shallow-water benthic forms found in nearly all tropical and subtropical oceans and seas of the world, with some taxa extending into temperate waters. Despite an earlier attempt based on morphology, no previous hypothesis of intergeneric relationships of the Antennariidae exists. To resolve phylogenetic relationships within the Antennariidae, and to test the validity of species groups within Antennarius, DNA sequences from the mitochondrial 16S and cytochrome oxidase c subunit 1 (COI) genes, and nuclear recombination activating gene 2 (RAG2), for 25 described and four undescribed antennariid species, representing 10 of 12 known genera and one undescribed genus, were unambiguously aligned and analyzed using Bayesian and maximum likelihood methods. The markers were partitioned and analyzed for substitution saturation and only the third codon position of COI (COI-3) was found to have reached saturation. However, analysis of both datasets, one with the saturated data and one without, differed only slightly. All molecular analyses recovered two major clades, one comprised of Fowlerichthys, Antennarius, Histrio, and Antennatus; and another containing Rhycherus, Antennariidae gen. et sp. nov., Kuiterichthys, Phyllophryne, Echinophryne, Tathicarpus, Lophiocharon, and Histiophryne. Evidence is presented to illustrate a correlation between phylogeny, geographic distribution, and reproductive life history. The results of these analyses provide the first hypothesis of evolutionary relationships within the Antennariidae.     

Boselaphines (Artiodactyla, Ruminantia, Bovidae) from the Middle Siwaliks of Hasnot, Pakistan

In this paper, boselaphine material from several localities in the area of the Hasnot Pakistan, is described, identified, and discussed. Four species that belong to three different genera of the tribe Boselaphini have been found: Selenoportax vexillarius, S. lydekkeri, Pachyportax latidens and Eotragus sp. Eotragus sp. is reported for the first time from the Hasnot and consequently from other Upper Middle Siwalik sediments of Pakistan and equivalent strata of the world, extending the range of the genus from the Lower to the Middle Siwaliks. Reviewing the Siwaliks’ Selenoportax species, S. dhokpathanensis Akhtar and S. tatrotensis Akhtar are synonymized with S. lydekkeri and S. vexillarius, respectively.     

A molecular phylogeny and classification of Leptochloa (Poaceae: Chloridoideae: Chlorideae) sensu lato and related genera

Background and Aims

Leptochloa (including Diplachne) sensu lato (s.l.) comprises a diverse assemblage of C₄ (NAD-ME and PCK) grasses with approx. 32 annual or perennial species. Evolutionary relationships and a modern classification of Leptochloa spp. based on the study of molecular characters have only been superficially investigated in four species. The goals of this study were to reconstruct the evolutionary history of Leptochloa s.l. with molecular data and broad taxon sampling.

Methods

A phylogenetic analysis was conducted of 130 species (mostly Chloridoideae), of which 22 are placed in Leptochloa, using five plastid (rpL32-trn-L, ndhA intron, rps16 intron, rps16-trnK and ccsA) and the nuclear ITS 1 and 2 (ribosomal internal transcribed spacer regions) to infer evolutionary relationships and revise the classification.

Key results

Leptochloa s.l. is polyphyletic and strong support was found for five lineages. Embedded within the Leptochloa sensu stricto (s.s.) clade are two Trichloris spp. and embedded in Dinebra are Drake-brockmania and 19 Leptochloa spp.

Conclusions

The molecular results support the dissolution of Leptochloa s.l. into the following five genera: Dinebra with 23 species, Diplachne with two species, Disakisperma with three species, Leptochloa s.s. with five species and a new genus, Trigonochloa, with two species.     

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.