Phylogeny and a new tribal classification of the Panicoideae s.l. (Poaceae) based on plastid and nuclear sequence data and structural data

? Premise of the study: The subfamily Panicoideae (Poaceae) encompasses nearly one-third of the diversity of grass species, including important crops such as maize and sugarcane. Previous analyses recovered strong support for a Panicoideae+Centothecoideae lineage within the diverse Panicoideae+Arundinoideae+Chloridoideae+Micrairoideae+Aristidoideae+Danthonioideae (PACMAD) clade, although support for internal relationships was inconsistent. The objectives of this research were to (1) further test the monophyly of each subfamily and previously recovered clades within the Panicoideae+Centothecoideae lineage, (2) establish phylogenetic relationships among these groups, and (3) propose a new tribal classification for this lineage based explicitly on the phylogeny. ? Methods: Maximum parsimony and Bayesian inference analyses of 37 taxa were based on previously published sequences (ndhF and rpl16 intron) and on new plastid and nuclear (rbcL and granule-bound starch synthase I) sequence data as well as structural data. ? Key results. The Panicoideae+Centothecoideae lineage and a majority of the clades identified in previous analyses continue to be robustly supported, but resolution along the backbone of the topology remains elusive. Support for the monophyly of both subfamilies was lacking although support values for some clades increased. The tribes Centotheceae and Arundinelleae were confirmed as polyphyletic. ? Conclusions: Subfamily Centothecoideae is formally submerged into the Panicoideae, and a new tribal classification for the expanded Panicoideae is proposed based explicitly on the phylogeny. This classification includes 12 tribes of which Chasmanthieae and Zeugiteae are segretated from the Centotheceae; Tristachyideae is segregated from Arundinelleae, and a new tribe, Cyperochloeae, is validated to accommodate two isolated genera. A key to the tribes is provided.     

Phylogeny of Eleusine (Poaceae: Chloridoideae) based on nuclear ITS and plastid trnT-trnF sequences

Phylogenetic relationships in the genus Eleusine (Poaceae: Chloridoideae) were investigated using nuclear ITS and plastid trnT-trnF sequences. Separate and combined data sets were analyzed using parsimony, distance, and likelihood based methods, including Bayesian. Data congruence was examined using character and topological measures. Significant data heterogeneity was detected, but there was little conflict in the topological substructure measures for triplets and quartets, and resolution and clade support increased in the combined analysis. Data incongruence may be a result of noise and insufficient information in the slower evolving trnT-trnF. Monophyly of Eleusine is strongly supported in all analyses, but basal relationships in the genus remain uncertain. There is good support for a CAIK clade (E. coracana subsp. coracana and africana, E. indica, and E. kigeziensis), with E. tristachya as its sister group. Two putative ITS homeologues (A and B loci) were identified in the allotetraploid E. coracana; the 'B' locus sequence type was not found in the remaining species. Eleusine coracana and its putative 'A' genome donor, the diploid E. indica, are confirmed close allies, but sequence data contradicts the hypothesis that E. floccifolia is its second genome donor. The 'B' genome donor remains unidentified and may be extinct.     

Phylogeny of the tribe Aveneae (Pooideae, Poaceae) inferred from plastid trnT-F and nuclear ITS sequences

New insights into evolutionary trends in the economically important oat tribe (Aveneae) are presented. Plastid trnT-F and nuclear ribosomal ITS sequences were used to reconstruct the phylogeny of the Aveneae-Poeae-Seslerieae complex (Pooideae, Poaceae) through Bayesian- and maximum parsimony-based analyses, separately and in combination. The plastid data identified a strongly supported core Aveneae lineage that separated from other former Aveneae and Poeae groups. Koeleriinae, Aveninae, and Agrostidinae emerged as the main groups of this core Aveneae, which also included other minor subgroups with uncertain relationships and a few former Poeae members. Several former Aveneae representatives were also placed in independent sublineages in Poeae. Seslerieae resolved as close allies of Poeae or Aveneae in the plastid and nuclear topologies, respectively. Because of the intermingling of some Aveneae and Seslerieae lineages in Poeae and vice versa, we propose to expand Poeae to include all the aforementioned lineages. This best reflects our current understanding of the phylogeny of these important temperate grasses and sheds light on their evolutionary history.     

Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase

Background  

Single- and low- copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa. Leymus is a polyploid genus with a diverse array of morphology, ecology and distribution in Triticeae. The genomic constitution of Leymus was assigned as NsXm, where Ns was presumed to be originated from Psathyrostachys, while Xm represented a genome of unknown origin. In addition, little is known about the evolutionary history of Leymus. Here, we investigate the phylogenetic relationship, genome donor, and evolutionary history of Leymus based on a single-copy nuclear Acc1 gene.     

Phylogeny of Siberian species of Carex sect. Vesicariae based on nuclear and plastid markers

Carex sect. Vesicariae is a group of about 30 sedge species widespread in temperate and cold regions of Eurasia and North America. In this study we performed a phylogenetic analysis of ten taxa (9 species and one subspecies) found in Siberia based on two plastid sequences (matK and atpF‐H) and the nuclear ribosomal ITS2 sequence. We also developed a novel sequence marker for the genus Carex, an intron of the nuclear hsp90 gene, which was found to be several times more variable than plastid and nuclear ribosomal sequences. Total nucleotide variation within the Vesicariae section was found to be very low, comparable to that within single other sedge species. Phylogenetic analysis supported the existence of two groups within this section: clade A (C. vesicata, C. vesicaria, both subspecies of C. saxatilis and C. pamirica) and clade B (C. rostrata, C. mollissima, C. jacutica, C. rotundata and C. membranacea). Carex rhynchophysa holds an intermediate position between these groups. The main morphological difference between these clades lies in the nature of the transition of the utricle into the beak: it is gradual in clade A and abrupt in clade B. This division is in good accordance with the results of previous allozyme studies and with current taxonomy. These results may become the basis for consideration of subsectional taxa within this section.     

Phylogeny of Celastrus L. (Celastraceae) inferred from two nuclear and three plastid markers

This is the first comprehensive molecular investigation of the genus Celastrus L. Phylogenetic relationships within the genus were assessed based on sequences of two nuclear (ETS, ITS) and three plastid (psbA-trnH, rpl16 and trnL-F) regions using the Bayesian inference and the maximum parsimony methods. Our results show that Celastrus, together with Tripterygium, formed a maximal supported clade. Within the cluster, Celastrus is composed of a basal clade and a core Celastrus clade, and the latter is consisted of six subclades. Relationships among species are more influenced by latitude than continental distribution patterns. The cauline cyme and lunate seeds are distinct characters to one of the maximal supported subclades. Their close relationship, similar geographical pattern and habitat imply that C. flagellaris may be a potential invasive species threatening C. scandens in North America. Celastrus leiocarpus, C. oblanceifolius and C. rugosus are confirmed as synonyms of C. punctatus, C. aculeatus and C. glaucophyllus, respectively. Discordance between the molecular data and previous morphology-based subgeneric classifications are noted. More works are needed to clarify the relationship between Celastrus and Tripterygium and the species within Celastrus.     

Phylogeny of Chloranthus (Chloranthaceae) based on nuclear ribosomal ITS and plastid TRNL-F sequence data

The internal transcribed spacers (ITS) of the nuclear ribosomal DNA and trnL-F region of the chloroplast DNA were sequenced for all ten species of Chloranthus and the outgroup Sarcandra (Chloranthaceae). Parsimony analyses of separate and combined data sets strongly suggest that Chloranthus is monophyletic and can be divided into two major clades: one containing C. erectus, C. spicatus, C. serratus, C. henryi, C. sessilifolius, and C. oldhamii (Clade A), and the other comprising C. angustifolius, C. fortunei, C. nervosus, and C. japonicus (Clade B). Taxonomically, these two clades correspond to Bentham and Hooker's sections Euchloranthus and Tricercandra. Within Clade A, two subclades, corresponding to Solms-Laubach's sections Triandri and Brachyuri, can be recognized. Solms-Laubach's subgenera Fruticosi and Herbacei, however, were resolved as paraphyletic, and thus the traditional division of Chloranthus on the basis of growth habit was not supported. Evidence from ITS and trnL-F sequences, in agreement with morphology, anatomy, and cytology, strongly suggest that Chloranthus consists of two groups that morphologically may be distinguished by their androecial characters. The present study also supports the hypothesis that the tripartite androecium of Chloranthus may have arisen by splitting of a single stamen with two marginal thecae.     

Phylogeny of Hystrix and related genera (Poaceae: Triticeae) based on nuclear rDNA ITS sequences

The taxonomic status of Hystrix and phylogenetic relationships among Hystrix and its related genera of Pseudoroegneria (St), Hordeum (H), Psathyrostachys (Ns), Elymus (StH), Leymus (NsXm), Thinopyrum bessarabicum (E(b)) and Lophopyrum elongatum (E(e)) were estimated from sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The type species of Hystrix, H. patula, clustered with species of Pseudoroegneria, Hordeum, Elymus, Th. bessarabicum and Lo. elongatum, while H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii were grouped with Psathyrostachys and Leymus species. The results indicate that: (i) H. patula is distantly related to other species of Hystrix, but is closely related to Elymus species; (ii) H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii have a close affinity with Psathyrostachys and Leymus species, and H. komarovii might contain the NsXm genome of Leymus; and (iii) the St, H and Ns genomes in Hystrix originate from Pseudoroegneria, Hordeum and Psathyrostachys, respectively, while the Xm in Hystrix and Leymus has a complex relationship with the E or St genomes. According to the genomic system of classification in Tiritceae, it is reasonable to treat Hystrix patula as Elymus hystrix L, and the other species of Hystrix as species of a section of Leymus, Leymus Sect. Hystrix.     

Phylogeny of Cidaroida (Echinodermata: Echinoidea) based on mitochondrial and nuclear markers

We present the first molecular phylogeny of Cidaroida, one of the most problematic groups within the echinoids. Two genes??the nuclear ribosomal gene 28?S rRNA and the mitochondrial protein-encoding gene COI??were obtained from 21 specimens representing 17 genera and 20 species, among which 13 species belong to Cidaroida. Phylogenetic analyses of the combined molecular data using parsimony and maximum likelihood optimality criteria resulted in a well-resolved phylogeny. Our results are broadly compatible (with the notable exception of Cidaris cidaris) with previous results obtained from morphological data. We find that Cidaroida represent a monophyletic group sister to the non-cidaroid Echinoidea. The family Cidaridae sensu Mortensen (1928) and Fell (1966) is paraphyletic because of the placement of Psychocidaris ohshimai as sister-group to Histocidaris elegans. Inside the Stylocidarina, we show that the two Atlantic species Stylocidaris affinis and Stylocidaris lineata constitute a well-supported clade. However, these two taxa could also represent two morphotypes within a single species showing high morphological variation.     

Phenylpropanoids from Paspalum atratum (Poaceae)

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A phylogenetic analysis of the genus Paspalum (Poaceae) based on cpDNA and morphology

With about 350 species, Paspalum is one of the richest genera within the Poaceae. Its species inhabit ecologically diverse areas along the Americas and they are largely responsible for the biodiversity of grassland ecosystems in South America. Despite its size and relevance, no phylogeny of the genus as a whole is currently available and infrageneric relationships remain uncertain. Many Paspalum species consist of sexual-diploid and apomictic-polyploid cytotypes, and several have arisen through hybridization. In this paper we explore the phylogenetic structure of Paspalum using sequence data of four non-coding cpDNA fragments from a wide array of species which were combined with morphological data for a subset of diploid taxa. Our results confirmed the general monophyly of Paspalum if P. inaequivalve is excluded and the small genus Thrasyopsis is included. Only one of the four currently recognized subgenera was monophyletic but nested within the remainder of the genus. Some informal morphological groups were found to be polyphyletic. The placement of known allopolyploid groups is generally congruent with previously stated hypotheses although some species with shared genomic formulae formed paraphyletic arrangements. Other species formed a basal grade including mostly umbrophilous or hygrophilous species. It is hypothesized that the genus may have diversified as a consequence of the expansion of C4 grass-dominated grasslands in South America.     

Phylogeny of Veronica in the Southern and Northern Hemispheres based on plastid,nuclear ribosomal and nuclear low-copy DNA

The cosmopolitan and ecologically diverse genus Veronica with approximately 450 species is the largest genus of the newly circumscribed Plantaginaceae. Previous analyses of Veronica DNA sequences were in stark contrast to traditional systematics. However, analyses did not allow many inferences regarding the relationship between major groups identified, hindering further analysis of diversification and evolutionary trends in the genus. To resolve the backbone relationships of Veronica, we added sequences from additional plastid DNA regions to existing data and analyzed matching data sets for 78 taxa and more than 5000 aligned characters from nuclear ribosomal DNA and plastid DNA regions. The results provide the best resolved and supported estimate of relationships among major groups in the Northern (Veronica s. str.) and Southern Hemisphere (hebes). We present new informal names for the five main species groups within the Southern Hemisphere sect. Hebe. Furthermore, in two instances we provide morphological and karyological characters supporting these relationships. Finally, we present the first evidence from nuclear low-copy CYCLOIDEA2-region to compare results from the plastid genome with the nuclear genome.