Molecular phylogeny of tribe Atraphaxideae(Polygonaceae)evidenced from five cpDNA genes

Traditionally, Atraphaxis, Calligonum, Pteropyrum and Parapteropyrum are included in the tribe Atraphxideae. Recently, sequence data has revealed that this tribe is not monophyletic. The structure of the tribe was examined by adding more taxa and sequences to clarify the congruence between morphology and molecular phylogeny, the systematic placements of four genera in Polygonaceae, as well as the infra-generic relationships of Atraphaxis and Calligonum within Atraphaxideae. Five chloroplast genes, atpB-rbcL, psbA-trnH, trnL-tmF, psbK-psbl, and rbcL of Atraphaxis, Calligonum, Pteropyrum, and Parapteropyrum were sequenced. The non-monophyly of Atraphaxideae was confirmed. Atraphaxis and Calligonum, respectively, formed a monophyletic group that was well supported. Calligonum is closely related to Pteropyrum; Atraphaxis is sister to Polygonum s. str. and Parapteropyrum is allied with Fagopyrum. Although the morphology suggested the four genera should form a tribe, the molecular data indicated Atraphaxideae was not one monophyletic group. The clades identified within Atraphaxis corresponded well with the current sectional classification based on morphological features. As for Cal- ligonum, Medusa was identified as a non-monophyletic section.

Multiple lines of evidence supports the two varieties of Halenia elliptica(Gentianaceae)as two species

Delimiting species requires multiple sources of evidence.Here,we delimited two varieties of Halenia elliptica(Gentianaceae)using several lines of evidence,including morphological traits and mating system in a sympatric population,phylogenetic relationships based on nrITS and cpDNA(rpl16)data,and complete chloroplast genome sequences.Comparative analysis of 21 morphological traits clearly separates the two varieties of H.elliptica.Examination of the flowering process and pollination treatments indicate that H.elliptica var.grandiflora produces seeds via outcrossing,whereas H.elliptica var.elliptica produces seeds via mixed mating.Furthermore,hand-pollinated hybridization of the two varieties produced no seeds.Observations of pollinators showed that when bees began a pollination bout on H.elliptica var.grandiflora they preferred to continue pollinating this variety;however,when they began a pollination bout on H.elliptica var.elliptica,they showed no preference for either variety.Phylogenetic analysis confirmed the monophyly of H.elliptica,which was further divided into two monophyletic clades corresponding to the two varieties.A large number of variants from the chloroplast genomes reflected remarkable genetic dissimilarities between the two varieties of H.elliptica.We recommend that the two varieties of H.elliptica should be revised as two species(H.elliptica and H.grandiflora).Our findings indicate that H.elliptica varieties may have split into two separate species due to a shift in mating system,changes in flowering phenology and/or post-pollination reproductive isolation.

LVTree Viewer:An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics

We describe an interactive viewer for the All-Species Living Tree（LVTree）. The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16 S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner.In view of the fact that the present prokaryotic systematics is largely based on 16 S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla（Proteobacteria and Firmicutes） to monophyletic clusters.

Phylogeny of higher taxa of hexapoda according to 12sRNA sequences

The phylogenetic relationship of Hexapoda has been debated for a long time, which will be resolved mainly depending on the settlement of monophyly, affinities and interrelationships among Protura, Collembola and Diplura. Mitochondrial 12sRNA gene about 355 bp fragments from one proturan species, two collembolan species, two dipluran species and one oribatid species were sequenced. The Ki-mura 2-parameter distances were calculated and a series of molecular phylogenetic trees were reconstructed by using the N-J method, from which the following points were drawn: (i) Protura and Collembola compose a monophyletic group representing absent-cerci; (ii) Diplura is not a monophyletic group, in which Campodeoid with filiform cerci belongs to a clade and Japygoid with pincer cerci and Ectognatha compose another clade, that is, Insecta s. str. stemmed from Japygoid. So it would be suggested that the phylogenetic relationship of Hexapoda is [Parainsecta (Collembola + Protura) +Campodeoid +Insecta (Japygoid +

A revised generic classification of the jelly lichens, Collemataceae

Phylogenetic studies have shown the need for a revised circumscription of generic boundaries in the jelly lichens(Collemataceae).Using a four-marker dataset from a recently published phylogeny of Collemataceae,we tested the monophyly of ten morphologically well-characterized groups.To achieve this,we performed Bayesian and maximum likelihood analyses.The monophyly of the ten morphological groups was confirmed.In order to reconcile molecular and morphological data into a formal classification,we here propose new generic delimitations in Collemataceae.Collema and Leptogium are re-circumscribed and six old generic names are resurrected to accommodate the Collema Crispum-group(Blennothallia),the Collema Tenax-group(Enchylium),the Collema Cristatum-group(Lathagrium),the Collema Occultatum-group(Rostania),the former small Leptogium species(Scytinium),and Leptogium diffractum(Pseudoleptogium).In addition,two new genera are described to accommodate Collema multipartitum(Callome)and the Collema Italicum-group(Paracollema).The presence/absence of a eucortex,which was earlier used as the cardinal character to define genera in the family,is still useful,but only in combination with other traits such as thallus habit(size),lobe size,ascospore characteristics,thallus anatomical structure,and habitat preference.A key to the genera is provided.Lectotypes are designated for Collema marginale Hoffm.,Synechoblastus nigrescens(Huds.)Trevis.,Eucollema(Cromb.)Horw.,Collema section Enchylium Ach.,Collema section Lathagrium Ach.,Collema sect.Mallotium Ach.,Collema section Scytinium Ach.,Collemodium Nyl.ex Lamy,and Homodium Nyl.ex Olivier.

On monospecific genera in prokaryotic taxonomy

A monospecific genus contains a single species ever since it was proposed.Though formally more than half of the known prokaryotic genera are monospecific,we pick up those which actually raise taxonomic problems by violating monophyly of the taxon within which it resides.Taking monophyly as a guiding principle,our arguments are based on simultaneous support from 16S rRNA sequence analysis and whole-genome phylogeny of prokaryotes,as provided by the LVTree Viewer and CVTree Web Server,respectively.The main purpose of this study consists in calling attention to this specific way of global taxonomic analysis.Therefore,we refrain from making formal emendations for the time being.