Showing papers on "Genus published in 2008"
TL;DR: The small-subunit rRNA sequences of 51 species of Bacillus were determined by reverse transcription to elucidate the phylogenetic structure of the genus Bacillus and revealed five phylogenetically distinct clusters as mentioned in this paper.
Abstract: The small-subunit rRNA sequences of 51 species of Bacillus were determined by reverse transcription to elucidate the phylogenetic structure of the genus. Comparative analysis of the sequence data revealed five phylogenetically distinct clusters. Group 1 (Bacillus sensu stricto) included B. subtilis the type species of the genus and 27 other species. Group 2 consisted of B. sphaericus and five other bacilli and Sporosarcina ureae clustered within the confines of this group. Group 3 consisted of a phylogenetically coherent group of 10 species whereas groups 4 and 5 comprised two and three species respectively. It is evident that the genus Bacillus in genetically extremely heterogeneous and requires extensive taxonomic revision. The rRNA structures defined in the present study will provide a firm basis for the division of Bacillus into several phylogenetically distinct genera.
674 citations
TL;DR: Multilocus sequence analysis (MLSA) of partial nucleotide sequences of the genes gyrB, rpoB, atpD and infB can be used for classification, identification and phylogenetic analyses of Pantoea strains.
305 citations
TL;DR: DNA barcodes can be used to identify cryptic species of skipper butterflies previously detected by classic taxonomic methods and to provide first clues to the existence of yet other cryptic species, and this complex likely includes still more species, whose exposure may require barcoding.
Abstract: DNA barcodes can be used to identify cryptic species of skipper butterflies previously detected by classic taxonomic methods and to provide first clues to the existence of yet other cryptic species. A striking case is the common geographically and ecologically widespread neotropical skipper butterfly Perichares philetes (Lepidoptera, Hesperiidae), described in 1775, which barcoding splits into a complex of four species in Area de Conservacion Guanacaste (ACG) in northwestern Costa Rica. Three of the species are new, and all four are described. Caterpillars, pupae, and foodplants offer better distinguishing characters than do adults, whose differences are mostly average, subtle, and blurred by intraspecific variation. The caterpillars of two species are generalist grass-eaters; of the other two, specialist palm-eaters, each of which feeds on different genera. But all of these cryptic species are more specialized in their diet than was the morphospecies that held them. The four ACG taxa discovered to date belong to a panneotropical complex of at least eight species. This complex likely includes still more species, whose exposure may require barcoding. Barcoding ACG hesperiid morphospecies has increased their number by nearly 10%, an unexpectedly high figure for such relatively well known insects.
231 citations
Journal Article•
TL;DR: The present review discusses the taxonomic revision of Phoma and its teleomorphs, with a special focus on its molecular biology and papers published in the post-Boerema era.
Abstract: Species of the coelomycetous genus Phoma are ubiquitously present in the environment, and occupy numerous ecological niches. More than 220 species are currently recognised, but the actual number of taxa within this genus is probably much higher, as only a fraction of the thousands of species described in literature have been verified in vitro. For as long as the genus exists, identification has posed problems to taxonomists due to the asexual nature of most species, the high morphological variability in vivo, and the vague generic circumscription according to the Saccardoan system. In recent years the genus was revised in a series of papers by Gerhard Boerema and co-workers, using culturing techniques and morphological data. This resulted in an extensive handbook, the ?Phoma Identification Manual? which was published in 2004. The present review discusses the taxonomic revision of Phoma and its teleomorphs, with a special focus on its molecular biology and papers published in the post-Boerema era.
186 citations
TL;DR: The systematic morphology of species within the HyalommA (Euhyalomma) marginatum Koch complex of ticks is illustrated and their relationships within this assemblage are discussed.
Abstract: The systematic morphology of species within the Hyalomma (Euhyalomma) marginatum Koch complex of ticks is illustrated and their relationships within this assemblage are discussed. Traditionally this group comprises the extremely polymorphic species Hyalomma (Euhyalomma) marginatum Koch, 1844 subdivided into four subspecies, namely H. (E.) marginatum marginatum Koch, 1844; H (E.) marginatum rufipes Koch, 1844; H (E.) marginatum isaaci Sharif, 1928 and/H. (E.) marginatum turanicum Pomerantzev, 1946. A fifth member of the association, namely H (E.) glabrum Delpy, 1949, has recently been re-instated as a full species. The taxonomic rank of the first mentioned four ticks is herein raised to species level. Details on the repositories of type specimens, synonyms, descriptions, variability, hosts, geographic distribution, and disease relationships of these four ticks are provided, and all their developmental stages are illustrated.
186 citations
TL;DR: The results of this study show the need for molecular tools within this morphologically cryptic group of weevils and provide a scaffold based on which genus assignment can be tested.
Abstract: A phylogeny is presented for the western Palaearctic representatives of the weevil subfamily Cryptorhynchinae using a combination of phenotypic and genotypic characters. This phylogeny is the first for the extremely species-rich Cryptorhynchinae to use molecular data (mitochondrial CO1 and 16S as well as nuclear ribosomal 28S). The results of this study show the need for molecular tools within this morphologically cryptic group of weevils and provide a scaffold based on which genus assignment can be tested. The present study mostly corroborates the current subdivision into genera (but many of the subgeneric groups are questioned). Three new genera are described: Montanacalles gen. nov. (type species: Kyklioacalles nevadaensis Stuben, 2001), Coloracalles gen. nov. (type species: Acalles humerosus Fairmaire, 1862) and Elliptacalles gen. nov. (type species: Acalles longus Desbrochers, 1892). Relevant external characters and the male genitalia of all discussed taxa are illustrated. Three species are transferred to different genera: Kyklioacalles aubei (Boheman, 1837) (formerly: Acalles), Ruteria major (Solari A. & F., 1907) and Ruteria minosi (Bahr & Bayer, 2005) (both formerly Echinodera).
182 citations
TL;DR: The major evolutionary diversifications within the Neotropical tribe Miconieae have been obscured by convergence in stamen morphology, leading to many arbitrary generic and sectional circumscriptions.
Abstract: Phylogenetic relationships within Miconia and other genera in the Neotropical tribe Miconieae were investigated using a maximum parsimony analysis of nuclear internal transcribed spacer and ndhF nucleotide sequences. Included were all sections in Miconia (212 species, ∼20% of the genus) and 12 of the 15 remaining genera assigned to the tribe (an additional 239 species). Given the tribe’s reputation for problematic generic distinctions, it was not surprising that most traditionally recognized taxonomic groups—both genera and sections—were shown to be polyphyletic or paraphyletic. Nevertheless, Miconia is composed of several distinct monophyletic groups, with a large majority of the species belonging to only four clades. Some of these groups represent parts of sections proposed in the last revision of the genus, but most of the diversification seems to have occurred in geographical areas that are more restricted than would have been predicted by the distribution of these sections. Moreover, parallel evoluti...
178 citations
TL;DR: This treatise is intended to serve as a basic working tool--providing easy identifications to genus and species of adult strongylid nematodes of equids.
177 citations
TL;DR: Four novel species were discovered, originating from soft drinks, alkylbenzene-polluted soil, and infected patients, and Membership of the both carrionii and bantiana clades might be indicative of potential virulence to humans.
170 citations
TL;DR: The history, medicinal uses, chemical composition, and cultivation of Cordyceps spp.
Abstract: This review looks in depth at the history and medicinal value of the Cordyceps spe- cies, especially C. sinensis. The C. sinensis medicinal species, with a long history of use, has only been found growing from the head of one type of subterranean caterpillar, at high altitudes, in the Qinghai-Tibetan plateau. Because of this highly specifi c growth environment and restricted geographical distribution, C. sinensis has a long reputation of being the single-most expensive raw material used in Oriental Medicine. Due to environmental and ecological factors, the annual harvest has been steadily declining, while at the same time the worldwide demand has been increasing. This situation has driven Cordyceps spp. prices into an ever-increasing spiral over the last few years, driving research to deter- mine ways of cultivating it to make it a more affordable material for commercial trade. Part of the goal of this research has been to understand the complex biological niche such an organism fi lls. This is a mushroom that is only found in cohabitation with the larvae of an insect, and it is this unique growth parameter that has made it challenging to produce Cordyceps spp. in artifi cial cultivation. Further complicating this cultivation issue is the rarefi ed atmosphere, mineral-rich soil, and low temperature in which Cordyceps naturally grows, resulting in a unique profi le of secondary metabolites possessing interesting biological potential for medical exploitation, but which are not readily reproduced in normal laboratory cultivation. In this article, we attempt to unravel many of the mysteries of Cordyceps spp., detailing the history, medicinal uses, chemical composition, and cultivation of Cordyceps spp., with special attention to C. sinensis, the world's most costly medicinal mushroom.
TL;DR: Cyanobacterial species currently classified within the cyanobacterial genus Microcoleus were determined to fall into two distinct clades in a 16S rDNA phylogeny, one containing taxa within the Oscillatoriaceae, the other containing taxas within the Phormidiaceae, and the new genus Coleofasciculus is proposed.
Abstract: Species currently classified within the cyanobacterial genus Microcoleus were determined to fall into two distinct clades in a 16S rDNA phylogeny, one containing taxa within the Oscillatoriaceae, the other containing taxa within the Phormidiaceae. The two lineages were confirmed in an analysis of the 16S-23S internal transcribed spacer (ITS) region sequences and secondary structures. The type species for Microcoleus is M. vaginatus Gomont, and this taxon belongs in the Oscillatoriaceae. Consequently, Microcoleus taxa in the Phormidiaceae must be placed in separate genera, and we propose the new genus Coleofasciculus to contain marine taxa currently placed in Microcoleus. The type species for Coleofasciculus is the well-studied and widespread marine mat-forming species Microcoleus chthonoplastes (Mert.) Zanardini ex Gomont. Other characters separating the two families include type of cell division and thylakoid structure.
TL;DR: Fungal strains isolated from rocks and lichens collected in the Antarctic ice-free area of the Victoria Land, one of the coldest and driest habitats on earth, were found in two phylogenetically isolated positions within the subclass Dothideomycetidae, and are reported as new genera and species.
TL;DR: A new model system for the integration of development, evolution, and ecology, the lizard genus Anolis, a diverse group of lizards whose ecology and evolution is well understood, and whose genome has recently been sequenced is introduced.
Abstract: Vertebrate developmental biologists typi- cally rely on a limited number of model organisms to understand the evolutionary bases of morphological change. Unfortunately, a typical model system for squa- mates (lizards and snakes) has not yet been developed leaving many fundamental questions about morphologi- cal evolution unaddressed. New model systems would ideally include clades, rather than single species, that are amenable to both laboratory studies of development and field-based analyses of ecology and evolution. Com- bining an understanding of development with an under- standing of ecology and evolution within and between closely related species has the potential to create a seam- less understanding of how genetic variation underlies eco- logically and evolutionarily relevant variation within pop- ulations and between species. Here we briefly introduce a new model system for the integration of development, evolution, and ecology, the lizard genus Anolis, a diverse group of lizards whose ecology and evolution is well understood, and whose genome has recently been se- quenced. We present a developmental staging series for Anolis lizards that can act as a baseline for later com- parative and experimental studies within this genus. J.
TL;DR: To address biogeographic questions on the origin of the genus, both New and Old World species were included in these analyses, and the results suggest that Pheidole is New World in origin with a possible single introduction into the Old World.
TL;DR: Ricefishes, known best by the model organism, the medaka, Oryzias latipes Temminck & Schlegel, 1846, comprise the family Adrianichthyidae, which ranges broadly throughout fresh and brackish waters of Central, South and Southeast Asia and the Indo-Malay-Philippines Archipelago as far east as Timor.
TL;DR: The three root parasites, Nuytsia, Atkinsonia, and Gaiadendron, are supported as successive sister taxa to the remaining genera, resulting in a monophyletic group of aerial parasites.
Abstract: Loranthaceae (73 genera and ca. 900 species) comprise mostly aerial hemiparasitic plants. Three monotypic genera considered relicts are root parasites. The family is diverse in tropical areas, but representatives are also found in temperate habitats. Previous classifications were based on floral and inflorescence morphology, karyological information, and biogeography. The family has been divided into three tribes: Nuytsiae, Elytrantheae (subtribes Elytranthinae and Gaiadendrinae), and Lorantheae (subtribes Loranthinae and Psittacanthinae). Nuytsiae and Elytrantheae are characterized by a base chromosome number of x = 12, whereas subtribes Loranthinae (x = 9) and Psittacanthinae (x = 8) numbers are derived via aneuploid reduction. To elucidate the phylogeny of the family, we analyzed sequences from five genes (nuclear small and large subunit rDNA and the chloroplast genes rbcL, matK, and trnL-F) representing most genera using parsimony, likelihood, and Bayesian inference. The three root parasites, Nuytsia, Atkinsonia, and Gaiadendron, are supported as successive sister taxa to the remaining genera, resulting in a monophyletic group of aerial parasites. Three major clades are resolved each corresponding to a subtribe. However, two South American genera (Tristerix and Notanthera) and the New Zealand genus Tupeia, which were previously classified in subtribe Elytranthinae, are weakly supported as part of a clade representing the South American subtribe Psittacanthinae.
Dissertation•
08 Jul 2008
TL;DR: A comparative review of 58 Lepraria species and 2 varieties is provided together with species descriptions and a key to discuss some previously published but unnamed taxa by different authors.
Abstract: A comparative review of 58 Lepraria species and 2 varieties is provided together with species descriptions and a key. Lecanora leuckertiana is transferred to Lepraria. The following taxa are included: Lepraria achariana, L. adhaerens, L. alpina var. alpina, L. alpina var. zeorinica, L. atlantica, L. atrotomentosa, L. aurescens, L. bergensis, L. borealis, L. caesiella, L. caesioalba var. caesioalba, L. caesioalba var. groenlandica, L. celata, L. coriensis, L. crassissima, L. diffusa, L. eburnea, L. ecorticata, L. elobata, L. friabilis, L. gelida, L. goughensis, L. granulata, L. humida, L. impossibilis, L. incana, L. isidiata, L. jackii, L. lanata, L. lecanorica, L. leprolomopsis, L. leuckertiana, L. lobata, L. lobificans, L. membranacea, L. multiacida, L. neglecta, L. neojackii, L. nigrocincta, L. nivalis, L. normandinoides, L. nylanderiana, L. obtusatica, L. pallida, L. pulchra, L. rigidula, L. salazinica, L. santamonicae, L. santosii, L. sipmaniana, L. squamatica, L. straminea, L. sylvicola, L. texta, L. toensbergiana, L. toilenae, L. umbricola, L. usnica, L. vouauxii, L. xerophila. Additionally some previously published but unnamed taxa by different authors are discussed.
TL;DR: Clutch-size among New World passerine birds was analysed with respect to four variables: body-mass, geographic latitude, the frequency of nest predation, and the structure of the nest.
Abstract: Variation in clutch-size among New World passerine birds was analysed with respect to four variables: body-mass, geographic latitude, the frequency of nest predation, and the structure of the nest. Data were analysed separately by averaging traits at three taxonomic levels: species, genus, and subfamily. Allometric scaling with body-mass did not account for significant variation in clutch-size regardless of the taxonomic level of analysis. Latitudinal effects on clutch-size were highly significant at all taxonomic levels. For species building small-pensile nests and open-cup nests, nest predation had a significant partial effect on clutch-size, with latitude held constant. When nest predation and latitude were held constant, clutch-size was significantly different among species building small-pensile nests, open-cup nests, and domed nests. These results suggest that New World passerine clutch-size is related to at least three variables: latitudinal effects, nest predation, and nest structure.
30 Dec 2008-Species diversity : an international journal for taxonomy, systematics, speciation, biogeography, and life history research of animals
TL;DR: It is concluded that both vicariance between biogeographic provinces, and ecological mechanisms of speciation within provinces contribute to species richness in the genus Haemulon.
TL;DR: An analysis of nrITS sequence data for a sample of 63 species of Leandra shows that Seed appendages in Leandra have evolved independently at least four times and are better correlated with the phylogeny than traditional characters, such as petal morphology.
TL;DR: The relationships between all known Hordeum species except H. guatemalense were inferred from the electrophoresis of the six enzyme systems Got, 6-Pgd, Mdh, Idh, a-and B-amylases, and most of the polyploid cytotypes in the genus seemed to have originated as alloploids.
Abstract: The relationships between all known Hordeum species except H. guatemalense were inferred from the electrophoresis of the six enzyme systems Got, 6-Pgd, Mdh, Idh, a-and B-amylases. A total of eleven loci were scored for in these systems. Maximum likelihood clusters and Wagner networks calculated from the electrophoretic data divided the genus into three groups, viz. the “H. vulgare group”, the “H. marinum group” and the “H. pubiflorum group”. Only one of these groups was recognized in the morphological sectioning of the genus. Most of the polyploid cytotypes in the genus seemed to have originated as alloploids. Phylogenetic links between diploid and polyploid taxa are suggested from the enzyme phenotypes. An evolutionary theory for the genus Hordeum is proposed, with two centres of differentiation, in South-West Asia and South America, respectively.
TL;DR: It was observed that trichomes can be successfully used for the delimitation of genera within the Compositae (Asteraceae) family, and foliar anatomical characters that justify the separation of Vernonia amygdalina and Vernonia cinerea into separate tribes are highlighted.
Abstract: A comparative study of the leaf epidermis of twelve species in the Compositae (Asteraceae) family was undertaken in order to document characters that are important in the taxonomy of the family. It was observed that trichomes can be successfully used for the delimitation of genera within the family. Within each species however, there are varied assortment of trichomes with occasional transitions among them. Launaea taraxacifolia was unique in being the only species without any trichome. Stellate trichome type and K-shaped or tetraradiate trichomes were observed in Tridax procumbens only. The genus Vernonia can be delimited from the other genera by the possession of T - shaped trichomes which are absent in the other genera, while amoeboid-shaped trichomes can be found in the genus Chromolaena only. Within the same genus, the species can also be delimited on the basis of possession of unique trichome types, for example in the genera Vernonia and Emilia. Cuticular striations occur in only two species out of the twelve studied, on the abaxial surface of V. amygdalina and on both surfaces of Bidens pilosa. Four stomatal types were recorded for the family, anomocytic, brachyparacytic, anisocytic and diacytic. Stomatal type was observed to delimit not only at generic level, but also at specific or species level. Ageratum conyzoides and Synedrella nodiflora are the only two species with occasional diacytic stomatal types. Results of the statistical correlation analysis for stomatal size and stomatal index at the 0.05 and 0.01 levels revealed high positive correlation for species in the same tribe, as well as for species in different tribes affirming close interrelationship and overlap of the values of stomatal indices and sizes within the family. Foliar anatomical characters that justify the separation of Vernonia amygdalina and Vernonia cinerea into separate tribes are highlighted.
TL;DR: This is the first study to establish that the DNA barcode successfully assigns different morphologies of brown algae to known species as well as other single-gene molecular markers currently used.
Abstract: The intertidal brown algal genus Fucus (Phaeophyceae) consists of individuals with a generally dichotomously branched habit Morphological variability within species, combined with morphological si
TL;DR: The use of space, diet composition, parasite infections and parasite infections were investigated and three species and one genus of helminths, e.g. the humans pathogen parasite, Baylisascads procyonis, were identified.
Abstract: Preliminary results on the ecology of raccoon in Poland are presented. The use of space (by radiotelemetry), diet composition and parasite infections (both by scat analysis) were investigated. The home-range size of the raccoon in western Poland averaged 1 km2 in suburban areas (n = 5 individuals), 10 km2 in the Warta Mouth National Park wetland area (n = 5), and 60 km2 for a single individual studied inhabiting woodlands. Space use patterns in relation to habitat type were also studied. About 44% of the biomass consumed by raccoons were mammals, 41% other vertebrates, 12% invertebrates, 2% plant material and only 1% eggs. Three species and one genus of helminths, e.g. the humans pathogen parasite, Baylisascads procyonis, were identified.
TL;DR: Results indicate that Notholithocarpus does not possess true ‘flower cupules,’ which define Lithocarpu sensu stricto, but like the oaks, the single flower per cupule is derived through the abortion of lateral flowers within each cupule.
Abstract: We investigated the phylogenetic relationships and taxonomic status of the castaneoid component (Lithocarpus and Chrysolepis) of the family Fagaceae that is endemic to the California Floristic Province (CA-FP). Over 7800 basepairs of nuclear and chloroplast DNA were analyzed in 17 taxa representing the breadth of phylogenetic diversity in the family. The genus Lithocarpus, as currently defined, is clearly polyphyletic due to the inclusion of L. densiflorus. Here, we designate this taxon as a new genus, Notholithocarpus, which can be recognized morphologically by its relatively small, subprolate pollen. Notholithocarpus is more closely related to Quercus, Castanea, and Castanopsis; Chrysolepis was resolved as the sister group to Lithocarpus sensu stricto. These results indicate that Notholithocarpus does not possess true ‘flower cupules,’ which define Lithocarpus sensu stricto, but like the oaks, the single flower per cupule is derived through the abortion of lateral flowers within each cupule. Fu...
TL;DR: This study investigated the species boundaries between the sibling species pair A. ocellaris and A. percula and three closely related species of the subgenus Phalerebus by phylogenetic analysis of mitochondrial cytochrome b and control region sequences.
TL;DR: It is concluded that evolution within the genus Phylloscopus has taken place mainly through the development of different feeding strategies, to suit the structural properties of different niches, without altering the range of size of the prey.
Abstract: SUMMARY
The paper describes variation among species of the genus Phylloscopus in weight, relative wing-, tail-, tarsus-, and bill-length, tail/wing ratio and degree of roundness of the wing, wing formula, emargination, and plumage colour. This variation is compared with differences in niche preference within the genus, and relationships between niche, feeding strategies, and morphology are suggested. It is concluded that evolution within the genus has taken place mainly through the development of different feeding strategies, to suit the structural properties of different niches, without altering the range of size of the prey. The genus Sylvia is treated briefly in order to provide comparison, and other genera of Sylviinae are discussed where parallel adaptation seems likely.
TL;DR: This study is the first comprehensive phylogenetic treatment of the chiefly subterranean group in 160 years of its taxonomic history, providing a framework for future studies on niphargid systematics, the evolution of endemism and cryptic diversity in subterranean environments, the mechanisms leading to exceptional morphological heterogeneity, historical biogeography, and applied ecological issues.
Abstract: Niphargus is the largest genus of freshwater amphipods. Its systematics from the species to the family level has always been problematic. This study is the first comprehensive phylogenetic treatment of the chiefly subterranean group in 160 years of its taxonomic history. It includes 103 niphargid species plus outgroups, representing about one-third of all nominal species. The samples originated mainly from type localities or adjacent sites and covered most of the morphological variability of the genus. Character sampling included nuclear 28S and mitochondrial 12S rDNA sequences, and 122 morphological characters. Quantitative morphological traits were coded using two alternative methods. The first one searches for gaps in the variability range of each character, while the second one uses absolute differences between the standardized raw data as weights. Different data sets yielded alternative topologies. All data support the monophyly of Niphargidae, while Niphargopsis— another niphargid genus — was consistently nested within Niphargus, loosing justification for its separate status. We predict a similar fate for all or most of the remaining six small niphargid genera, which were not yet scrutinized phylogenetically. Different topologies agreed in species composition of five large, well-supported clades, although the hierarchic relationships between them remain unresolved. These clades reject all previously proposed taxonomic subdivisions of Niphargus, implying a high degree of morphological homoplasy that renders any morphology-based groups questionable. The clade members are distributed within well-established zoogeographical regions that do not exceed 1300 km across the longest diagonal. These results provide a framework for future studies on niphargid systematics, the evolution of endemism and cryptic diversity in subterranean environments, the mechanisms leading to exceptional morphological heterogeneity, historical biogeography, and applied ecological issues.