Molecular phylogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov

The genus Chlamydomonas (including Chloromonas) is one of the largest green algal genera comprising more than 600 species. To initiate a comprehensive analysis of the phylogeny and systematics of the genus, we determined nuclear-encoded SSU rRNA sequences from 32 strains of Chlamydomonas, Chloromonas and Chlorogonium with emphasis on oogamous taxa and related strains, and incorporated these into global molecular phylogenetic analyses of 132 strains of Chlorophyceae. In addition, we studied the morphology and reproduction of oogamous and related strains by light microscopy. We recognize and designate 18 monophyletic lineages (clades) within the Chlorophyceae, 11 of which are confined to the CW (basal bodies displaced clockwise) subgroup. The majority of clades recognized within the Chlorophyceae do not correspond to any of the traditional classification systems, which are still largely based on the organization level. Strains assigned to Chlamydomonas and Chloromonas were found in seven different clades confirming the polyphyly of the two genera as presently conceived. To initiate the taxonomic revision of Chlamydomonas, C. reinhardtii is proposed as the conserved type of the genus. In consequence, species in clades other than the clade containing C. reinhardtii must be transferred to other genera, a process initiated in this contribution. The oogamous strains studied represent a monophyletic lineage, which is described as Oogamochlamys gen. nov. comprising three species (O. gigantea, O. zimbabwiensis and O. ettlii spec. nov.). The sister clade to Oogamochlamys consists of isogamous strains characterized by chloroplasts with incisions and is described as Lobochlamys gen. nov. with two species (L. culleus and L. segnis). Another clade is characterized by asteroid or perforated, parietal chloroplasts and contains the type species of Chloromonas (C. reticulata). Thus, the polyphyletic Chloromonas (traditionally defined as “Chlamydomonas without pyrenoids”) can be legitimized as a monophyletic genus by restriction to this clade and is here emended on the basis of chloroplast characters (the clade contains strains with or without pyrenoids thus rejecting the character “absence of pyrenoids”).     

Large-scale diversity reassessment,evolutionary history,and taxonomic revision of the green macroalgae family Udoteaceae (Bryopsidales,Chlorophyta)

Udoteaceae is a morphologically diverse family of the order Bryopsidales. Despite being very widespread geographically, this family is little known as compared with the closely related Halimedaceae or Caulerpaceae. Using the most extensive Udoteaceae collection to date and a multilocus genetic data set (tufA, rbcL, and 18S rDNA), we reassessed the species diversity of the family, as well as the phylogenetic relationships, the diagnostic morphoanatomical characters, and evolutionary history of its genera, toward a proposed taxonomic revision. Our approach included a combination of molecular and morphological criteria, including species delimitation methods, phylogenetic reconstruction, and mapping of trait evolution. We successfully delimited 62 species hypotheses, of which 29 were assigned (existing) species names and 13 represent putative new species. Our results also led us to revise the genera Udotea s.s., Rhipidosiphon s.s., and Chlorodesmis s.s., to validate the genus Rhipidodesmis, and to propose three new genera: Glaukea gen. nov., Ventalia gen. nov., and Udoteopsis gen. nov. We also identified two large species complexes, which we refer to as the “Penicillus–Rhipidosiphon–Rhipocephalus–Udotea complex” and the “Poropsis–Penicillus–Rhipidodesmis complex”. Using a time-calibrated phylogeny, we estimated the origin of the family Udoteaceae at Late Triassic (ca. 216 Ma), whereas most of the genera originated during Paleogene. Our morphological inference results indicated that the thallus of the Udoteaceae ancestor was likely entirely corticated and calcified, composed of a creeping axis with a multisiphonous stipe and a pluristromatic flabellate frond. The frond shape, cortication, and calcification are still symplesiomorphies for most extant Udoteaceae genera and represent useful diagnostic characters.     

Relationships in subtribe Diocleinae (Leguminosae; Papilionoideae) inferred from internal transcribed spacer sequences from nuclear ribosomal DNA

The complete sequences of nuclear ribosomal DNA (nrDNA) internal transcribed spacer regions (ITS/5.8S) were determined for species belonging to six genera from the subtribe Diocleinae as well as for the anomalous genera Calopogonium and Pachyrhizus. Phylogenetic trees constructed by distance matrix, maximum parsimony and maximum likelihood methods showed that Calopogonium and Pachyrhizus were outside the clade Diocleinae (Canavalia, Camptosema, Cratylia, Dioclea, Cymbosema, and Galactia). This finding supports previous morphological, phytochemical, and molecular evidence that Calopogonium and Pachyrhizus do not belong to the subtribe Diocleinae. Within the true Diocleinae clade, the clustering of genera and species were congruent with morphology-based classifications, suggesting that ITS/5.8S sequences can provide enough informative sites to allow resolution below the genus level. This is the first evidence of the phylogeny of subtribe Diocleinae based on nuclear DNA sequences.     

Molecular and morphological evidence for a new grass genus,Dupontiopsis (Poaceae tribe Poeae subtribe Poinae s.l.), endemic to alpine Japan,and implications for the reticulate origin of Dupontia and Arctophila within Poinae s.l.

Phylogenetic analyses within Poaceae tribe Poeae subtribes Puccinellinae (=Coleanthinae), Phleinae, Poinae s.l. (including Alopecurinae), and Miliinae (PPAM clade), revealed that one species formerly placed in Poa represents a new monotypic genus belonging to subtribe Poinae s.l., Dupontiopsis gen. nov., D. hayachinensis comb. nov. (based on Poa hayachinensis), endemic to wet, gravelly, serpentine, alpine habitats in northern Japan. This genus forms a strongly supported clade (DAD) with two circumarctic Poinae genera, Arctophila and Dupontia, in phylogenetic analyses of plastid and nuclear ribosomal DNA sequence data. Both morphology and DNA sequence analyses provide support for D. hayachinensis as a lineage distinct from either Arctophila or Dupontia, with moderate DNA support for a position as sister to these two genera. Dupontiopsis resembles these other monotypic genera in its several-flowered spikelets, lemmas usually 3-nerved, with frequently awned attenuate scarious apices (as in Dupontia) and calluses with a crown of hairs around the base of the lemma, but differs in its keeled lemmas, scabrous palea keels, glumes shorter than the first lemma. Our investigation suggests that the most recent shared ancestor of the DAD clade evolved from a single hybridization event, as a hexaploid, probably in western Beringia. The probable parentage of the ancestor is considered to be within the Poinae–Alopecurinae clade excluding Poa. We provide evidence for possible secondary hybridization and introgression of duodecaploid Dupontia fisheri with Puccinellia. A key to perennial genera of PPAM with hairy calluses, and a supplemental table of morphological characters in the genera accepted in PPAM are provided.     

Phylogeny,classification, and biogeography of Afrotrichloris,Apochiton, Coelachyrum,Dinebra, Eleusine,Leptochloa, Schoenefeldia,and a new genus,Schoenefeldiella (Poaceae: Chloridoideae: Cynodonteae: Eleusininae)

To investigate the evolutionary relationships among species of Afrotrichloris, Apochiton, Coelachyrum, Dinebra, Eleusine, Leptochloa, and Schoenefeldia of subtribe Eleusininae, a phylogeny based on DNA sequences from nine gene regions (ITS, rps16-trnK, rps3, rps16, rpoC2, rpl32-trnL, ndhF, ndhA, ccsA) is presented. Previous molecular phylogenies indicated that Coelachyrum was polyphyletic and Schoenefeldia was paraphyletic, with Afrotrichloris embedded within it. Apochiton burttii was embedded in the Coelachyrum clade paired with C. longiglume, Coelachyrumpoiflorum was placed outside of Coelachyrum and sister to Eleusine, and Schoenefeldia is paraphyletic, with its two species forming a grade sister to Afrotrichoris. Our molecular phylogeny supports recognition of a new genus, Schoenefeldiella, and a new combination, Schoenfeldiella transiens. In addition, we provide generic emendations for Coelachyrum, which now includes five species including a new combination proposed here, Coelachyrum burttii, and Eleusine, which now includes 11 species.     

Systematic reappraisal of species in Phoma section Paraphoma, Pyrenochaeta and Pleurophoma

Sequence data from the 18S nrDNA (SSU) and 28S nrDNA (LSU) regions of isolates of Phoma section Paraphoma were compared with those of representative isolates of the morphologically similar anamorph genera Pleurophoma and Pyrenochaeta and of the type species of Phoma sections Phoma, Pilosa and Plenodomus. Phoma section Paraphoma was found to be highly polyphyletic within the Pleosporales and only distantly related to Phoma section Phoma. The genus Paraphoma, which is based on Paraphoma radicina, is reintroduced in the Phaeosphaeriaceae with two additional taxa. The new genera Setophoma and Neosetophoma, type species Setophoma terrestris comb. nov. and Neosetophoma samarorum comb. nov., are introduced and represent species that are closely related to Paraphoma but differ based on morphological characters and molecular phylogeny. Phoma coonsii is transferred to genus Chaetosphaeronema that also belongs to the Phaeosphaeriaceae. Pyrenochaetopsis gen. nov. is introduced to accommodate the type species Pyrenochaetopsis leptospora comb. nov., as well as several other species formerly accommodated in Phoma and Pyrenochaeta. Pyrenochaetopsis is closely related to Pyrenochaeta and classified in the Cucurbitariaceae. Pleurophoma cava is transferred to genus Pyrenochaeta. The new genera elucidate the confusing taxonomy of species in genera Phoma, Pyrenochaeta and Pleurophoma and recognize monophyletic genera with distinct teleomorph affinities.     

Phylogenetic and morphological diversity of novel soil cercomonad species with a description of two new genera (Nucleocercomonas and Metabolomonas)

Cercomonads are important components of microbial food webs in soils and aquatic sediments. Here, we investigated the general morphology, behaviour, life cycle and 18S rDNA phylogeny of cercomonad cultures from a German grassland soil habitat. We describe ten new species including two new genera from 23 strains. Three Cercomonas, two Eocercomonas and three Paracercomonas species are described. Based on large phylogenetic distance and distinct morphology, we erect two novel clade B genera near the root of the cercomonad tree. Nucleocercomonas nov. gen. bears a number of characters unusual for cercomonads: Its anterior flagellum is extremely long, it mostly does not glide, and in its most frequent life stage the cell body does not attach to the substratum, but produces unattached pseudopodia. Furthermore, it has a unique nucleus with a peripheral nucleolus that attaches to the nuclear envelope opposite the basal body connection. Metabolomonas nov. gen. is extremely metabolic. It is characterized by a very high beating frequency of the anterior flagellum, fast gliding, rapid changes in shape and strong cytoplasmic streams. A new genus Brevimastigomonas is erected for the previously described species Paracercomonas anaerobica. The general morphology of cercomonad species often does not correspond with their phylogenetic position: closely related species may have a very different morphology.     

Toward Modern Classification of Eustigmatophytes,Including the Description of Neomonodaceae Fam. Nov. and Three New Genera1

The class Eustigmatophyceae includes mostly coccoid, freshwater algae, although some genera are common in terrestrial habitats and two are primarily marine. The formal classification of the class, developed decades ago, does not fit the diversity and phylogeny of the group as presently known and is in urgent need of revision. This study concerns a clade informally known as the Pseudellipsoidion group of the order Eustigmatales, which was initially known to comprise seven strains with oval to ellipsoidal cells, some bearing a stipe. We examined those strains as well as 10 new ones and obtained 18S rDNA and rbcL gene sequences. The results from phylogenetic analyses of the sequence data were integrated with morphological data of vegetative and motile cells. Monophyly of the Pseudellipsoidion group is supported in both 18S rDNA and rbcL trees. The group is formalized as the new family Neomonodaceae comprising, in addition to Pseudellipsoidion, three newly erected genera. By establishing Neomonodus gen. nov. (with type species Neomonodus ovalis comb. nov.), we finally resolve the intricate taxonomic history of a species originally described as Monodus ovalis and later moved to the genera Characiopsis and Pseudocharaciopsis. Characiopsiella gen. nov. (with the type species Characiopsiella minima comb. nov.) and Munda gen. nov. (with the type species Munda aquilonaris) are established to accommodate additional representatives of the polyphyletic genus Characiopsis. A morphological feature common to all examined Neomonodaceae is the absence of a pyrenoid in the chloroplasts, which discriminates them from other morphologically similar yet unrelated eustigmatophytes (including other Characiopsis-like species).     

Revision of the Neotropical Scleropactidae (Crustacea: Oniscidea)

The species of Scleropactidae from America are revised and redescribed. A phylogeny hypothesis based on an analysis of morphological characters is presented. The genera are redefined and the generic placement of several species is corrected. The Neotropical Scleropactidae include Colomboscia , Scleropactes , Circoniscus , Neosanfilippia , Sphaeroniscus , Richardsoniscus , Spherarmadillo , Colomboniscus , Amazoniscus and Protosphaeroniscus . The genus Chileoniscus is excluded from the Scleropactidae. Sphaerobathytropa is excluded from the Scleropactidae and its previous record from Argentina is revealed to be erroneous. Synuropus is revalidated and excluded from the Scleropactidae. The following new genera are introduced: Scleropactoides gen. nov. , Globopactes gen. nov. , Caecopactes gen. nov. , and Troglopactes gen. nov. Thirteen species are described as new: Caecopactes minimus sp. nov. , Colomboscia parva sp. nov. , Globopactes falconensis sp. nov. , Globopactes hispidus sp. nov. , Globopactes meridae sp. nov. , Scleropactes cotopaxii sp. nov. , Scleropactes ecuadoriensis sp. nov. , Scleropactes pululahua sp. nov. , Scleropactoides curvatus sp. nov. , Circoniscus hirsutus sp. nov. , Sphaeroniscus quintus sp. nov. , Spherarmadillo nebulosus sp. nov. , and Chileoniscus armadillidioides sp. nov. Identification keys to all species are provided.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 (Suppl. 1), 1–339.     

Paranepheliinae亚族(菊科,Liabeae族)的系统发育和可能的属间杂交

The nuclear ribosomal ITS region and the chloroplast trnL-trnF (trnLF) intergenic region were sequenced for 45 accessions of Paranephelius and six accessions of Pseudonoseris, the two genera of the subtribe Paranepheliinae (Liabeae, Asteraceae) distributed in the alpine regions of the Andes. This data set was used to estimate relationships between these genera and within each genus to aid in evaluating morphological variation and classification. Our results with both ITS and trnLF markers support the monophyly of subtribe Paranepheliinae, and place Pseudonoseris discolor as the first diverged taxon sister to the clade containing Paranephelius. Pseudonoseris szyszylowiczii exhibited intraspecific divergence supporting intergeneric hybridization between Pseudonoseris and Paranephelius. Within Paranephelius, genetic divergence is low and not adequate to fully resolve phylogenetic relationships at the species level, but two genetically and morphologically recognizable groups were revealed by the ITS data. Several accessions possessing multiple ITS sequences represent putative hybrids between the two groups. These putative hybrids have caused some taxonomic confusion and difficulties in establishing species boundaries in Paranephelius. The divergence time estimates based on ITS sequences indicated that the stem of subtribe Paranepheliinae dates to 13 million years ago, but the diversification of the crown clade of the extant members began in the early Pleistocene or late Pliocene, perhaps associated with the uplift of the Andes and the climatic changes of global cooling.     

New Late Cretaceous Pollen Genera and Species in the Jiaag Han Basin of Hubei

In this paper, five new pollen genera and twenty new pollen species of angiospermae from the Late Cretaceous of a certain basin in central China are described. Four new organ genera and their species include: Morinoipollenites normalis gen. et sp. nov., Morinoipollenites minor gen. et sp. nov., Morinoipollenites polyprojectus gen. et sp. nov., Morinoipollenites rhombiformis gen. et sp. nov., Jianghanpollis ringens gen. et sp. nov., Jianghanpollis, mikros gen. et sp. nov., Jianghanpollis radiatus gen. et sp. nov., Jianghanpollis sayangensis gen. et sp. nov., Jianghanpollis arciformis gen. et sp. nov., Myoporumpollonites variabilis gen. et sp. nov., Myoporumpollenites striatus gen. et sp. nov., Lythraites giganteus Yu, Guo et Mao gen. et sp. nov. Lythraites clavatus sp. nov., Lythraites dilutus sp. nov., Lythraites magnus sp. nov., Lythraites varrustriatus sp. nov., Lythraites pachyrrhachis sp. nov.; the new-form genus and its species are: Crassimarginpollenites reticulatus gen. et sp. nov., Crassimerginpollenites mirus gen. et sp. nov., Crassimarginpollenites psilatus gen. et sp. nov. The new pollen genera and their species described herein have been compared in some details with recent pollens and considered their affinity with such recent families as Dipsacaceae, Myoporaceae, Apocynaceae and Lythraceae. According to the age of the pollen-bearing strata, a preliminary discussion is made regarding to the taxonomy of the recent plants families with which our new described pollens are related. Hence, this study may provide some mieropalaeobotanical information for deciphering 'the phylogeny of these plants.     

New Genera and Species of Psychodoid Flies from the Lower Cretaceous Amber Lebanon

Until now, only two Psychodoidea were known from Lebanese amber. We describe two new genera and species of Phlebotomidae ( Mesophlebotomites hennigi gen. et sp. nov., Libanophlebotomus lutfallahi gen. et sp. nov.) and four new genera with six new species of Psychodidae ( Paleopsychoda solignaci gen. et sp. nov., Paleopsychoda jacquelinae sp. nov., Protopsychoda nadiae gen. et sp. nov., Protopsychoda hammanaensis sp. nov., Libanopsychoda abillamai gen. et sp. nov., Cretapsychoda inexpectata gen. et sp. nov.) from the Lower Cretaceous amber of Hammana/Mdeirij, Lebanon. These fossils are included in a phylogenetic analysis of the subfamilies of Psychodoidea. This superfamily was probably as diverse in the Early Cretaceous as now.