Monophyly or polyphyly? Possible conflict between morphological and molecular interpretations of the wellknown genus Zoothamnium(Ciliophora,Peritrichia)

In this paper, we explore possible conflict between morphological and molecular interpretations of phylogenetic relationships within the well-known peritrichous genus Zoothamnium. On the basis of morphological evidence, for a long time this genus has been believed to be a well-defined monophyletic taxon. Nonetheless, Zoothamnium exhibits higher genetic diversity than the gross morphology of its species. Here, we used all available genetic information for the small subunit of ribosomal RNA （SSU rRNA） and internal transcribed spacer region （ITS1-5.8S-ITS2） for this genus to reconstruct phylogenies for four datasets （SSU rRNA, ITS1, ITS2, and ITS1-5.8S-ITS2） and a combined dataset （SSU rRNA＋ITSI-5.8S- ITS2） using different phylogenetic methods and with consideration of the secondary structure of the genes. Confidence in phylogenetic tree selection was assessed with the approximately unbiased test. The molecular results showed both that Zoothamnium is more likely to be polyphyletic, and morphologically similar genera Zoothamnopsis and Myoschiston were always nested among Zoothamnium species. Accordingly, as with some other groups of ciliates, to understand more fully the correct phylogeny of Zoothamnium there remains a need for additional data from both morphological and molecular studies, covering additional Zoothamnium spp. and members of closely related genera （e.g. Zoothamnopsis, Myoschiston, and Epistylis）.

Phylogenetic Reconstruction of the Family Acrypteridae (Orthoptera: Acridoidea) Based on Mitochondrial Cytochrome b Gene

Sequences from the mitochondrial cytochrome b gene （Cyt b） were determined for 25 species from the superfamily Acridoidae and the homologous sequences of 19 species of grasshoppers were downloaded from the GenBank data library. The purpose was to develop a molecular phylogeny of the Acrypteridae, and to interpret the phylogenetic position of the family within the superfamily Acridoidea. Phylogeny was reconstructed by Maximum-parsimony （MP） and Bayesian criteria using Yunnanites coriacea and Tagasta marginella as outgroups. The alignment length of the fragments was 384 bp after excluding ambiguous sites, including 167 parsimony informative sites. In the fragments, the percentages of A ＋ T and G ＋ C were 70.7% and 29.3%, respectively. The monophyly of Arcypteridae is not supported by phylogenetic trees. Within the Arcypteridae, neither Arcypterinae nor Ceracrinae is supported as a monophyletic group. The current genus Chorthippus is not a monophyletic group, and should be a polyphyletic group. The present results are significantly different from the classification scheme of Arcypteridae, which is based on morphology.

A NEW LOACH OF Schistura AND COMMENTS ON THE GENUS

Schistura heterognathos Chen,sp.nov.is described based on specimens from the Nanla River,a tri butary of the Lancangjiang River (upper Mekong River),in Yunnan Province of China.It is especially characterized by its abnormal jaws.The jaws are broad,thick and strong.The upper jaw has no dentoid process and there is a very small or no notch in the lower jaw.The dissociative margins of jaws are straight.The mouth is broad and transversal,its width approximately equals to snout length and is greater than the interorbital width.

Molecular phylogenetic analysis among species of Paridae,Remizidae and Aegithalos based on mtDNA sequences of COI and cyt b

The phylogeny of Paridae and allies has been studied intensively during past decades.However,the phylogenetic relationship among species tends to become increasingly controversial as different genetic markers emerge.In our study,the partial mitochondrial genes cytochrome b(cyt b) and cytochrome coxidase subunit Ι(COI) were obtained from 15 species that included 10 tits,4 long-tailed tits and a Chinese penduline tit. Analyses were conducted on the combined cyt b and COΙ sequences with maximum likelihood and Bayesian algorithms. Based on strong,congruent support among the different temporal partitions and models of sequence evolution,a highly resolved consensus of the relationships among Parids and their allies has been formed.The monophyly of Paridae and Remizidae is strongly supported.However,the monophyly of Paridae and Aegithalos is rejected. This agrees with previous studies using other molecular markers.Our results suggest the promotion of the subgenus Machlolophus from genus Parus to a separate genus.The phylogeny of Aegithalos is robust in the current study. However,by considering differences of both morphological and molecular characters within species,we conclude that more data are needed to define their phylogeny.Based on the patterns of taxonomic diversity and endemism,we suggest the southwestern mountain ranges of China might be the center of origin of the Aegithalos species.Divergence time estimates for the long-tailed tits range from the late Miocene to the Pleistocene(from 5.5 to 0.1 Mya)using a calibration of 2% divergence per million years. In a comparative sense,we found a congruent genetic differentiation among sympatric distribution taxa.

Phylogenetic relationships of 18 passerines based on Adenylate Kinase Intron 5 sequences

The 18 species of bird studied originally are known to belong to muscicapids, robins and sylviids of passerines, but some dis- putations are always present in their classification systems. In this experiment, phylogenetic relationships of 18 species of passerines were studied using Adenylate Kinase lntron 5 （AKS） sequences and DNA techniques. Through sequences analysis in comparison with each other, phylogenetic tree figures of 18 species of passerines were constructed using Neighbor-Joining （N J） and Maximum-Parsimony （MP） meth- ods . The results showed that sylviids should be listed as an independent family, while robins and flycatchers should be listed into Musci- capidae. Since the phylogenetic relationships between long-tailed tits and old world warblers are closer than that between long-tailed tits and parids, the long-tailed tits should be independent of paridae and be categorized into aegithalidae. Muscicapidae and Paridae are known to be two monophylitic families, but Sylviidae is not a monophyletic group. AK5 sequences had better efficacy in resolving close relationships of interspecies among intrageneric groups.

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.

Phylogenetic relationships and estimation of divergence times among Sisoridae catfishes

Nineteen taxa representing 10 genera of Sisoridae were subjected to phylogenetic analyses of sequence data for the nuclear genes Plagl2 and ADNP and the mitochondrial gene cytochrome b. The three data sets were analyzed separately and combined into a single data set to reconstruct phylogenetic relationships among Chinese sisorids. Both Chinese Sisoridae as a whole and the glyptosternoid taxa formed monophyletic groups. The genus Pseudecheneis is likely to be the earliest diverging extant genus among the Chinese Sisoridae. The four Pareuchiloglanis species included in the study formed a monophyletic group. Glaridoglanis was indicated to be earliest diverging glyptosternoid, followed by Glyptosternon maculatum and Exostoma labiatum. Our data supported the conclusion that Oreoglanis and Pseudexostoma both formed a monophyletic group. On the basis of the fossil record and the results of a molecular dating analysis, we estimated that the Sisoridae diverged in the late Miocene about 12.2 Mya. The glyptosternoid clade was indicated to have diverged, also in the late Miocene, about 10.7 Mya, and the more specialized glyptosternoid genera, such as Pareuchiloglanis, originated in the Pleistocene (within 1.9 Mya). The speciation of glyptosternoid fishes is hypothesized to be closely related with the uplift of the Qinghai-Tibet Plateau.

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.