Leaf anatomy as an additional taxonomy tool for 18 taxa of Matricaria L. and Tripleurospermum Sch. Bip. (Anthemideae-Asteraceae) in Turkey

This study concerns the evaluation of leaf anatomical characteristics of the closely related genera Matricaria (4 taxa) and Tripleurospermum (14 endemic taxa, 15 accessions) in Turkey using cluster analysis (CA) and principal component analysis (PCA). All taxa have the same basic leaf structure composed of lower and upper epidermis including anomocytic or anomocytic-anisocytic stomata, parenchymatic mesophyll, and vascular bundle. Statistically significant differences based on ploidy level have been found without generic delimitation. The differences mainly concern stomatal length and the relative size of the vascular bundle. These anatomical characters can be used to distinguish diploid from polyploid taxa of the genera.     

Taxonomic Reference Libraries for Environmental Barcoding: A Best Practice Example from Diatom Research

DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 unialgal diatom strains from Berlin waters have been established and cultured to obtain morphological and molecular data. The strains were sequenced for 18S V4 rDNA (the pre-Barcode for protists) as well as rbcL data, and identified by microscopy. LM and for some strains also SEM pictures were taken and physical vouchers deposited at the BGBM. 37 freshwater taxa from 15 naviculoid diatom genera were identified. Four taxa from the genera Amphora, Mayamaea, Planothidium and Stauroneis are described here as new. Names, molecular, morphological and habitat data as well as additional images of living cells are also available electronically in the AlgaTerra Information System. All reference sequences (or reference barcodes) presented here are linked to voucher specimens in order to provide a complete chain of evidence back to the formal taxonomic literature.     

Fossil representatives of the family Greenideidae (Hemiptera, Aphidoidea) from the Miocene of Europe

Four new aphid species (Hemiptera, Aphidoidea, Greenideidae) are described on the basis of imprints in oil-shales from the Miocene of Europe (Rubielos de Mora, Spain; Vishnevaya Balka ?Stavropol?, Russia): Eutrichosiphum europaeum nov. sp., Greenidea hispanica nov. sp., Greenideoida (Pentatrichosiphum) turolensis nov. sp. and Mollitrichosiphum rubusensis nov. sp. All the taxa are placed within recent genera of the subfamily Greenideinae. Miocene representatives of this subfamily have been found in the south of Europe. Later changes of climatic conditions limited its geographic range to south-eastern Asia, where it is now represented by over 130 species of seven genera.     

Zygomorphy evolved from disymmetry in Fumarioideae (Papaveraceae,Ranunculales): new evidence from an expanded molecular phylogenetic framework

Background and Aims Fumarioideae (20 genera, 593 species) is a clade of Papaveraceae (Ranunculales) characterized by flowers that are either disymmetric (i.e. two perpendicular planes of bilateral symmetry) or zygomorphic (i.e. one plane of bilateral symmetry). In contrast, the other subfamily of Papaveraceae, Papaveroideae (23 genera, 230 species), has actinomorphic flowers (i.e. more than two planes of symmetry). Understanding of the evolution of floral symmetry in this clade has so far been limited by the lack of a reliable phylogenetic framework. Pteridophyllum (one species) shares similarities with Fumarioideae but has actinomorphic flowers, and the relationships among Pteridophyllum, Papaveroideae and Fumarioideae have remained unclear. This study reassesses the evolution of floral symmetry in Papaveraceae based on new molecular phylogenetic analyses of the family.Methods Maximum likelihood, Bayesian and maximum parsimony phylogenetic analyses of Papaveraceae were conducted using six plastid markers and one nuclear marker, sampling Pteridophyllum, 18 (90 %) genera and 73 species of Fumarioideae, 11 (48 %) genera and 11 species of Papaveroideae, and a wide selection of outgroup taxa. Floral characters recorded from the literature were then optimized onto phylogenetic trees to reconstruct ancestral states using parsimony, maximum likelihood and reversible-jump Bayesian approaches.Key Results Pteridophyllum is not nested in Fumarioideae. Fumarioideae are monophyletic and Hypecoum (18 species) is the sister group of the remaining genera. Relationships within the core Fumarioideae are well resolved and supported. Dactylicapnos and all zygomorphic genera form a well-supported clade nested among disymmetric taxa.Conclusions Disymmetry of the corolla is a synapomorphy of Fumarioideae and is strongly correlated with changes in the androecium and differentiation of middle and inner tepal shape (basal spurs on middle tepals). Zygomorphy subsequently evolved from disymmetry either once (with a reversal in Dactylicapnos) or twice (Capnoides, other zygomorphic Fumarioideae) and appears to be correlated with the loss of one nectar spur.     

Systematic biostratigraphy: A solution to problematic classification systems in biostratigraphy

Systematic biostratigraphy is based on the exclusive use of monophyletic marker taxa. Non-monophyletic, or artificial, marker taxa have been shown to change biostratigraphic correlations, a situation that can be rectified by using systematics to ensure that marker taxa are monophyletic or natural. Both hypothetical and real examples demonstrate the validity of the methodology. The foraminiferal genera Praemurica and Parvularugoglobigerina are examples of non-monophyletic marker taxa. Cladistic results permit the reclassification of both genera, and a revision of foraminiferal biostratigraphy. Systematic biostratigraphy ensures the use of monophyletic marker taxa, preventing artificial classifications from hindering biostratigraphic correlations and producing more accurate, and stable, biostratigraphic zonations.     

Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities

Cystic fibrosis (CF) patients suffer from chronic bacterial lung infections that lead to death in the majority of cases. The need to maintain lung function in these patients means that characterising these infections is vital. Increasingly, culture-independent analyses are expanding the number of bacterial species associated with CF respiratory samples; however, the potential significance of these species is not known. Here, we applied ecological statistical tools to such culture-independent data, in a novel manner, to partition taxa within the metacommunity into core and satellite species. Sputa and clinical data were obtained from 14 clinically stable adult CF patients. Fourteen rRNA gene libraries were constructed with 35 genera and 82 taxa, identified in 2139 bacterial clones. Shannon–Wiener and taxa-richness analyses confirmed no undersampling of bacterial diversity. By decomposing the distribution using the ratio of variance to the mean taxon abundance, we partitioned objectively the species abundance distribution into core and satellite species. The satellite group comprised 67 bacterial taxa from 33 genera and the core group, 15 taxa from 7 genera (including Pseudomonas (1 taxon), Streptococcus (2), Neisseria (2), Catonella (1), Porphyromonas (1), Prevotella (5) and Veillonella (3)], the last four being anaerobes). The core group was dominated by Pseudomonas aeruginosa. Other recognised CF pathogens were rare. Mantel and partial Mantel tests assessed which clinical factors influenced the composition observed. CF transmembrane conductance regulator genotype and antibiotic treatment correlated with all core taxa. Lung function correlated with richness. The clinical significance of these core and satellite species findings in the CF lung is discussed.     

First palynological data from the Jurassic South Xiangshan Formation (Nanjing area,China)

The outcrops of the Xiangshan Group have been studied since the beginning of the twentieth century, yielding a rich macroflora (the Xiangshan Flora), mainly from the lower part of the Xiangshan Group (South Xiangshan Formation). Nevertheless, no palynological data have been published so far from the South Xiangshan Formation. The present study provides the first palynostratigraphic data of the South Xiangshan Formation. More than 50 fossil taxa from 30 fossil genera have been identified, allowing for a more accurate dating. The most characteristic taxa are Polycingulatisporites triangularis, Quadraeculina anellaeformis, Manumia delcourtii, Ischyosporites variegatus, Callialasporites turbatus, C. trilobatus, C. minus, and Sestrosporites pseudoalveolatus, suggesting a late Toarcian-late Aalenian age for the South Xiangshan Formation. These results are consistent with previous studies suggesting a middle-late Early Jurassic age for this formation; consequently, the most probable age for the South Xiangshan Formation is late Toarcian (late Early Jurassic).     

Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo,Tibet Autonomous Region

The soil bacterial communities have been widely investigated. However, there has been little study of the bacteria in Qinghai-Tibet Plateau, especially about the culturable bacteria in highland barley cultivation soil. Here, a total of 830 individual strains were obtained at 4°C and 25°C from a highland barley cultivation soil in Qamdo, Tibet Autonomous Region, using fifteen kinds of media. Seventy-seven species were obtained, which belonged to 42 genera and four phyla; the predominant phylum was Actinobacteria (68.82%), followed by Proteobacteria (15.59%), Firmicutes (14.29%), and Bacteroidetes (1.30%). The predominant genus was Streptomyces (22.08%, 17 species), followed by Bacillus (6.49%, five species), Micromonospora (5.19%, four species), Microbacterium (5.19%, four species), and Kribbella (3.90%, three species). The most diverse isolates belonged to a high G+C Gram-positive group; in particular, the Streptomyces genus is a dominant genus in the high G+C Gram-positive group. There were 62 species and 33 genera bacteria isolated at 25°C (80.52%), 23 species, and 18 genera bacteria isolated at 4°C (29.87%). Meanwhile, only eight species and six genera bacteria could be isolated at 25°C and 4°C. Of the 77 species, six isolates related to six genera might be novel taxa. The results showed abundant bacterial species diversity in the soil sample from the Qamdo, Tibet Autonomous Region.     

New hybodont shark assemblage from the Early Cretaceous of the Basque-Cantabrian Basin

Hybodont remains from the Early Cretaceous of the Basque-Cantabrian Basin (Cantabric Range) in the North of Spain are described for the first time. This assemblage represents a highly diversified shark fauna adapted to different feeding habits. Isolated remains of six hybodont genera, namely Hybodus, Egertonodus, Planohybodus, Lonchidion, Parvodus, and Lissodus, have been recovered and described from the freshwater Vega de Pas Formation in the locality of Vega de Pas (Cantabria, Northern Spain). Most of these taxa are known from the English Wealden, making the shark fauna of the Vega de Pas 1 site the most similar assemblage to English Wealden shark fauna among any other site known in Europe.     

New records of Protura (Entognatha,Arthropoda) from Romania,with an identification key to the Romanian species

The Romanian Protura were studied based on 175 specimens collected from Romania, along with bibliographic data. The main publication on the Romanian proturans was written by M.A. Ionescu (1951), who described 13 species mainly from soil and forest litter from 15 collecting points. The current paper represents the first study at a national level. Faunal data on Protura were obtained from 22 sites, mostly from forests of the Romanian Carpathians and also from a peri-urban area of Bucharest, which had not been studied before. As a result, the Romanian Protura fauna now consists of 27 known taxa in 6 genera and 4 families. Of the 27 taxa, 15 species are new records for Romanian fauna. An identification key to the Romanian Protura species is provided.     

A model for determining ex situ conservation priorities in big genera is provided by analysis of the subgenera of <Emphasis Type="Italic">Rhododendron</Emphasis> (Ericaceae)

The large size and complex taxonomy of big genera complicates decision making for conservation. We propose that Rhododendron, comprising some 1215 taxa, divided into nine subgenera and many sections, can be used as a model for other big genera. Although Red List assessments placed 715 taxa in a threat category, or listed them as Data Deficient, and moreover Target 8 of the Global Strategy for Plant Conservation requires 75 % of Red List taxa to be held in ex situ collections by 2020, to date there have been few studies of Rhododendron ex situ collections or conservation priorities. Utilising the subgenus structure of Rhododendron as a framework for examining conservation priorities, we analysed the Red List and determined that subgenera Vireya and Hymenanthes have the most acute conservation issues. Examination of taxa in cultivation shows that 844 of 1215 taxa (70 %) are in cultivation, with subgenera varying from 45 to 100 %. Of the 715 Red List taxa, 400 (56 %) are in cultivation, with subgenera varying from 28 to 72 %. Subgenera Vireya and Azaleastrum have the poorest representation in cultivation and should have precedence for ex situ conservation. As no subgenus reaches the requirement for Target 8, further planning is needed for ex situ conservation of Rhododendron. After combining the two analyses, we propose the priorities for ex situ conservation should be ordered (i) Vireya, (ii) Azaleastrum and (iii) Hymenanthes. Finally, we propose five conservation actions for Rhododendron, and summarise our approach as a model for conservation of other big genera.     

Systématique du groupe « Palaeochelys sensu lato – Mauremys » (Chelonii,Testudinoidea) du Tertiaire d’Europe occidentale : principaux résultats

Among fossil chelonians from the Tertiary of Western Europe, freshwater Testudinoidea (sensu Hirayama, 1985, Gaffney et Meylan, 1988) are abundant, and more particularly the “Palaeochelys sensu lato—Mauremys” group. This group has never been studied as a whole. Taxa of this group were before referred to extinct genera such as Ocadia, Clemmys, Emys or to the fossil genera Palaeochelys, Borkenia and Palaeoemys. These taxa are redefined, new taxa are described and a hypothesis of phylogenetic relationships is given.     

A checklist of algal species found in the East Siberian Sea in May 1987

Summary A checklist of microalgae found in sea-ice in the East Siberian Sea in May 1987 has been compiled. A total of 122 taxa have been identified, consisting of 101 taxa in 18 genera of pennate diatoms, 14 taxa in 8 genera of centric diatoms, 4 taxa in 3 genera of dinoflagellates (including Ebria sp.), and 2 taxa in 1 genus of chrysophytes (silicoflagellates); choanoflagellates (Craspedomonadales) were found in one sample.     

454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants

Activated sludge (AS) contains highly complex microbial communities. In this study, PCR-based 454 pyrosequencing was applied to investigate the bacterial communities of AS samples from 14 sewage treatment plants of Asia (mainland China, Hong Kong, and Singapore), and North America (Canada and the United States). A total of 259 K effective sequences of 16S rRNA gene V4 region were obtained from these AS samples. These sequences revealed huge amount of operational taxonomic units (OTUs) in AS, that is, 1183–3567 OTUs in a sludge sample, at 3% cutoff level and sequencing depth of 16 489 sequences. Clear geographical differences among the AS samples from Asia and North America were revealed by (1) cluster analyses based on abundances of OTUs or the genus/family/order assigned by Ribosomal Database Project (RDP) and (2) the principal coordinate analyses based on OTUs abundances, RDP taxa abundances and UniFrac of OTUs and their distances. In addition to certain unique bacterial populations in each AS sample, some genera were dominant, and core populations shared by multiple samples, including two commonly reported genera of Zoogloea and Dechloromonas, three genera not frequently reported (i.e., Prosthecobacter, Caldilinea and Tricoccus) and three genera not well described so far (i.e., Gp4 and Gp6 in Acidobacteria and Subdivision3 genera incertae sedis of Verrucomicrobia). Pyrosequencing analyses of multiple AS samples in this study also revealed the minority populations that are hard to be explored by traditional molecular methods and showed that a large proportion of sequences could not be assigned to taxonomic affiliations even at the phylum/class levels.     

Taxonomic study of the tetrahedral, pentagonal and hexagonal spongy spumellarian Radiolaria from the middle Carnian (Late Triassic) of the Köseyahya nappe (Elbistan, SE Turkey) and other Triassic localities

This article is a taxonomic study of all spongy radiolarian taxa with five to six coplanar and four tetrahedrally disposed spines or spongy arms occurring in the middle Carnian from the Köseyahya section, near the town of Elbistan, SE Turkey. This fauna is characteristic of the Tetraporobrachia haeckeli radiolarian Zone, and comes from an 8 m thick succession of clayey–cherty limestones occurring at the lower part of the section. In addition, a few species from the Middle and Upper Triassic from other areas have been also included in this study to improve some generic diagnoses and to better understand the diversity and evolutionary trends of some genera, subfamilies and families. The taxonomy at the generic and suprageneric levels is based primarily on the types of microsphere. This new approach allowed new taxonomic arrangements of genera and suprageneric units, and suggested new and unexpected phylogenetic relationships among these radiolarians and between them and younger radiolarians. The authors discuss and describe 42 species, of which 36 are new, and 12 genera of which three are new (Charlottalum, Pentaspongodisculus, and Trimiducaella). The genera Pseudohagiastrum Pessagno, Natraglia Pessagno, Cantalum Pessagno and others are reinterpreted. All the genera studied, except Charlottalum, are assigned to three subfamilies, of which two (Pseudohagiastrinae and Trimiducinae) are new, and to two families (Angulobracchiidae and Relindellidae). The genus Charlottalum is described to replace the genus Cantalum, which has been erroneously used until present for Late Triassic pantanelliids with four tetrahedrally disposed three-bladed spines.     

Phylogenetic consideration of two scuticociliate genera, Philasterides and Boveria (Protozoa, Ciliophora) based on 18 S rRNA gene sequences

Many scuticociliates are facultative parasites of aquatic organisms and are among the most problematic ciliate taxa regarding their systematic relationships. The main reason is that most species, especially taxa in the order Thigmotrichida have similar morphology and have not been studied yet using molecular methods. In the present work, two scuticociliate genera, represented by two rare parasitic species, Philasterides armatalis (order Philasterida) and Boveria subcylindrica (order Thigmotrichida), were studied, and phylogenetic trees concerning these two genera were constructed based on their 18 S rRNA gene sequences. The results indicate that: 1) Philasterides forms a sister group with Philaster, supporting the classification that these two genera belong to the family Philasteridae; 2) it is confirmed that the nominal species, Philasterides dicentrarchi Dragesco et al., 1995 should be a junior synonym of Miamiensis avidus as revealed by both previous investigations and the data revealed in the present work; and 3) the poorly known form B. subcylindrica, the only member in the order Thigmotrichida, of which molecular data are available so far, always clusters with Cyclidium glaucoma, a highly specialized scuticociliate, indicating a sister relationship between the orders Thigmotrichida and Pleuronematida.     

Fossil woods from the Lower Coal-bearing Formation of the Janggi Group (Early Miocene) in the Pohang Basin,Korea

Fourteen species of fossil wood belonging to eleven genera and seven families were identified from 38 well preserved specimens collected from the Lower Coal-bearing Formation of Janggi Group at Donghae-myeon, Pohang City, Gyeongsangbuk-do Prefecture, Korea. Seven new taxa were found and described; they are Carya koreana Jeong et Kim, Betula janggiensis Jeong et Kim, Carpinus donghaensis Jeong et Kim, Ostrya geumgwangensis Jeong et Kim, Stewartia pseudo-camellioxylon Jeong et Kim, Acer minokamoensis Jeong, Kim et Suzuki and Acer pohangensis Jeong et Kim. The most abundant taxa are Betulaceae, Aceraceae, Ulmaceae, and Wataria. Except Wataria of which the habitat preference has not been confirmed, these taxa are major elements of cool-temperate vegetation and are similar to the Aniai-type flora of Japan. Previous studies of fossil plants from the Geumgwangdong Shale (leaves and seeds), the Upper Coal-bearing Formation (fossil woods) and the Yeonil Group (leaves and seeds) and this study, show that the climate of the Pohang Basin changed from cool-temperate to warm-temperate and subtropical during the Miocene.     

Occurrence of physical dormancy in seeds of Australian Sapindaceae: a survey of 14 species in nine genera

Background and Aims

Sapindaceae is one of 16 angiosperm families whose seeds have physical dormancy (PY). However, the extent and nature of PY within this family is poorly known. The primary aims of this study were: (1) to evaluate seed characteristics and determine presence (or not) of PY within nine genera of Australian Sapindaceae; and (2) to compare the frequency of PY across the phylogenetic tree within Australian Sapindaceae.

Methods

Viability, imbibition and seed characteristics were assessed for 14 taxa from nine genera of Sapindaceae. For five species of Dodonaea, optimal conditions for germination and dormancy break were evaluated. An in situ burial experiment was performed on D. hackettiana seeds to identify the factor(s) responsible for overcoming PY. Classes of dormancy and of non-dormancy for 26 genera of Sapindaceae were mapped onto a phylogenetic tree for the family.

Key Results

Mean seed viability across all taxa was 69·7 %. Embryos were fully developed and folded (seven genera) or bent (two genera); no endosperm was present. Seeds of all five Dodonaea spp. and of Distichostemon hispidulus had PY. Hot-water treatment released PY in these six species. Optimal germination temperature for seeds of the four Dodonaea spp. that germinated was 15–20 °C. Following 5 months burial in soil, 36·4 % of D. hackettiana seeds had lost PY and germinated by the beginning of the winter wet season (May). Laboratory and field data indicate that dormancy was broken by warm, moist temperatures (≥50 °C) during summer.

Conclusions

PY occurs infrequently in genera of Sapindaceae native to Australia. Seeds of Dodonaea and Distichostemon had PY, whereas those of the other seven genera did not. Seeds of these two genera and of Diplopeltis (a previous study) are the only three of the 20 native Australian genera of Sapindaceae for which germination has been studied that have PY; all three belong to subfamily Dodonaeoideae.Key words: Dodonaea spp., physical dormancy, Sapindaceae, seed ecology, seed germination     

Pelecyogyra (Mollusca) from the Early Ordovician of the Montagne Noire,France

A new occurrence of the onychochilid mollusc Pelecyogyra is reported from the late Floian Landeyran Formation (Apatokephalus incisus Biozone) in the Montagne Noire, southern France, where it is associated with the two tergomyans Carcassonnella courtessolei and Thoralispira laevis, and a mollusc indet. With a low cap-shaped shell. The Montagne Noire specimens compare morphologically with Pelecyogyra fezouataensis from the late Tremadocian Fezouata Formation (Araneograptus murrayi Biozone) in Morocco and are tentatively referred to this species. Each occurrence of Pelecyogyra is from one or two localities only, but separated in time. They differ further in the deeper facies, association with Carcassonnella and Thoralispira, and non-gregarious occurrence in Montagne Noire compared to the shallower facies, lack of other molluscs and gregarious occurrence in the Fezouata Formation. In the Lower Ordovician, Pelecyogyra, Carcassonnella courtessolei, the rare C. vizcainoi and Thoralispira laevis are taxa that occur only in Montage Noire and the Anti-Atlas, while Lesueurilla prima also occurs in the Prague basin of the Czech Republic. Contrary to other faunal elements, like echinoderms and trilobites, these genera seem to have a wide environmental tolerance and are long ranging taxa. The main occurrence of the three key taxa Carcassonnella, Thoralispira and Lesueurilla in the Montagne Noire is in the lower part of the La Maurerie Formation (Taihungshania miqueli acme Zone), while the same taxa appear just slightly later in Morocco (?Cymatograptus protobalticus Biozone). Migration to the Anti-Atlas during the early Floian seems to have been possible during a period of general faunal exchange. Pelecyogyra may either have migrated from the Anti-Atlas to Montagne Noire during the same interval or possibly during the late Floian as indicated by shared faunal elements between these two regions at that time.