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Taxonomic Ranks (taxonomic + rank)
Selected AbstractsAppropriate probe search method to specify groups in higher taxonomic ranksJOURNAL OF BASIC MICROBIOLOGY, Issue 1 2009Masahiro Nakano Abstract A new method for procedures using a computer to find out useful candidates for probes discriminating a certain group in higher ranks of bacteria is presented. In order to make the search of the probes systematic, two indices are proposed, i.e., Coincidence Ratio Inside Group (CRIG) and Coincidence Number Outside Group (CNOG), which indicate the rate of matching of probes inside or outside group respectively. Using two indices, allowance grades indicating usefulness of arbitrary sequence as a probe are defined from 9 (5 in species) to 0. Its application to the 16S rRNA gene of 2206 bacterial species selected from the Ribosomal Database Project (RDP-II) (J.R. Cole et al., Nucleic Acids Res. 31: 442,443, 2003) is shown. Small nucleotide sequences of the length L (L = 15, 19, 23) were searched from about 550 bases. As a result of computer calculations, appropriate probes are found in all taxonomic ranks, in addition, it is found that 95% of genera can be identified uniquely. The method is useful for DNA chips or targeted PCR which can select a desirable bacteria set in any taxonomic rank. The method is in principle deterministic, and widely applied to any type of nucleotide sequences. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] A mitochondrial phylogeography of Brachidontes variabilis (Bivalvia: Mytilidae) reveals three cryptic speciesJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2007M. Sirna Terranova Abstract This study examined genetic variation across the range of Brachidontes variabilis to produce a molecular phylogeography. Neighbour joining (NJ), minimum evolution (ME) and maximum parsimony (MP) trees based on partial mitochondrial DNA sequences of 16S-rDNA and cytochrome oxidase (COI) genes revealed three monophyletic clades: (1) Brachidontes pharaonis s.l. from the Mediterranean Sea and the Red Sea; (2) B. variabilis from the Indian Ocean; (3) B. variabilis from the western Pacific Ocean. Although the three clades have never been differentiated by malacologists employing conventional morphological keys, they should be ascribed to the taxonomic rank of species. The nucleotide divergences between Brachidontes lineages (between 10.3% and 23.2%) were substantially higher than the divergence between congeneric Mytilus species (2.3,6.7%) and corresponded to interspecific divergences found in other bivalvia, indicating that they should be considered three different species. Analysis of the 16S-rDNA sequences revealed heteroplasmy, indicating dual uniparental inheritance (DUI) of mtDNA in the species of Brachidontes collected in the Indian Ocean, but not in the species in the Pacific nor in the species in the Red Sea and the Mediterranean Sea. When we employed the conventional estimate of the rate of mitochondrial sequence divergence (2% per million years), the divergence times for the three monophyletic lineages were 6,11 Myr for the Indian Ocean and Pacific Ocean Brachidontes sp. and 6.5,9 Myr for the Red Sea and Indian Ocean Brachidontes sp. Thus, these species diverged from one another during the Miocene (23.8,5.3 Myr). We infer that a common ancestor of the three Brachidontes species probably had an Indo-Pacific distribution and that vicariance events, linked to Pleistocene glaciations first and then to the opening of the Red Sea, produced three monophyletic lineages. Riassunto Lo studio filogeografico è stato condotto su tutto l'areale di Brachidontes variabilis (Krauss, 1848) attraverso l'analisi di sequenze mitocondriali (16S-rDNA e COI) che hanno separato i campioni in tre cladi monofiletici. Diversi algoritmi (NJ, ME e MP) hanno elaborato alberi con la stessa topologia, in cui è possibile riconoscere: (1) Brachidontes pharaonis s.l. dell'area Mar Mediterraneo , Mar Rosso; (2) Brachidontes variabilis dell' Oceano Indiano; (3) Brachidontesvariabilis dell'Oceano Pacifico. Il loro grado di divergenza è sufficientemente alto da potere ascrivere al rango di specie i singoli cladi, nonostante non siano stati ancora individuati i caratteri tassonomici distintivi, a causa della grande variazione morfologica. La divergenza nucleotidica tra le tre linee di Brachidontes era compresa tra 10.3% e 23.2%, in un range di valori superiori a quelli trovati nel confronto tra specie congeneriche di Mytilus sp (2.3,6.7%). Utilizzando il tasso evolutivo, che convenzionalmente viene applicato ai valori di divergenza genetica di geni mitocondriali (2% per milioni di anni), si sono ricavati tempi di divergenza corrispondenti a 6,11 milioni di anni tra Oceano Indiano e Pacifico, e a 6.5,9 milioni di anni tra Mar Rosso e Oceano Indiano. Le tre linee evolutive sembrano essersi separate durante il Miocene. Probabilmente un comune antenato con distribuzione Indo-Pacifica può essere andato incontro a processi di vicarianza e/o di dispersione legati alle glaciazioni pleistoceniche prima e all'apertura del Mar Rosso dopo. [source] Cranial allometry, phylogeography, and systematics of large-bodied papionins (primates: Cercopithecinae) inferred from geometric morphometric analysis of landmark dataTHE ANATOMICAL RECORD : ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY, Issue 2 2003Stephen R. Frost Abstract The cranial morphology of the African Old World monkeys Mandrillus, Papio, and Theropithecus (i.e., baboons) has been the subject of a number of studies investigating their systematic relationships, patterns of scaling, and growth. In this study, we use landmark-based geometric morphometrics and multivariate analysis to assess the effects of size, sex, taxonomy, and geographic location on cranial shape. Forty-five landmarks were digitized in three dimensions on 452 baboon crania and subjected to generalized Procrustes analysis (GPA), which standardizes geometric size but leaves scaling-based shape differences in the data. The resulting shape coordinates were submitted to regression analysis, principal components analysis (PCA), partial least-squares (PLS) analysis, and various clustering techniques. Scaling (shape differences correlated with size) was the largest single factor explaining cranial shape variation. For instance, most (but not all) of the shape differences between the sexes were explained by size dimorphism. However, central tendencies of shape clearly varied by taxon (both specific and subspecific) even after variations in size and sex were adjusted out. Within Papio, about 60% of the size- and sex-adjusted shape variations were explained by the geographic coordinates of the specimen's provenance, revealing a stepped cline in cranial morphology, with the greatest separation between northern and southern populations. Based on evidence from genetic studies, and the presence of at least two major hybrid/interbreeding zones, we interpret the phylogeographic pattern of cranial variation as indicating that these populations are best ranked as subspecies of a single species, rather than as two or more distinct biological species. This objective approach can be applied to other vertebrate species or species groups to help determine the taxonomic rank of problematic taxa. Anat Rec Part A 275A:1048,1072, 2003. © 2003 Wiley-Liss, Inc. [source] Appropriate probe search method to specify groups in higher taxonomic ranksJOURNAL OF BASIC MICROBIOLOGY, Issue 1 2009Masahiro Nakano Abstract A new method for procedures using a computer to find out useful candidates for probes discriminating a certain group in higher ranks of bacteria is presented. In order to make the search of the probes systematic, two indices are proposed, i.e., Coincidence Ratio Inside Group (CRIG) and Coincidence Number Outside Group (CNOG), which indicate the rate of matching of probes inside or outside group respectively. Using two indices, allowance grades indicating usefulness of arbitrary sequence as a probe are defined from 9 (5 in species) to 0. Its application to the 16S rRNA gene of 2206 bacterial species selected from the Ribosomal Database Project (RDP-II) (J.R. Cole et al., Nucleic Acids Res. 31: 442,443, 2003) is shown. Small nucleotide sequences of the length L (L = 15, 19, 23) were searched from about 550 bases. As a result of computer calculations, appropriate probes are found in all taxonomic ranks, in addition, it is found that 95% of genera can be identified uniquely. The method is useful for DNA chips or targeted PCR which can select a desirable bacteria set in any taxonomic rank. The method is in principle deterministic, and widely applied to any type of nucleotide sequences. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Invertebrates and the Restoration of a Forest Ecosystem: 30 Years of Research following Bauxite Mining in Western AustraliaRESTORATION ECOLOGY, Issue 2007Jonathan D. Majer Abstract Restoration needs to consider more than just soils and plants. The role of terrestrial invertebrates in the restoration of Alcoa's bauxite mines in the Jarrah (Eucalyptus marginata) forest of Western Australia has been the subject of over 20 individual studies. Projects range from arthropods in soil and leaf litter, to the understorey vegetation, and the tree canopy. Moreover, projects span a range of trophic groups, including decomposers (e.g., springtails and termites), predators (e.g., ants and spiders), and herbivores (e.g., true bugs and ants preying on seeds). Elucidation of recolonization trajectories uses both space-for-time substitutions and long-term regular sampling. Importantly, many studies are at species level rather than coarser taxonomic ranks. This paper provides an historical account and an integrated review of this research. The role of ants as seed predators and as indicators of ecosystem health is described. Successional data for other groups, when measured by species richness (ants, spiders, and hemipterans) and composition (ants and spiders), show their reassembly trajectories tracking toward unmined reference areas. Hemipteran species composition tracks the vegetation reassembly trajectory but not toward unmined reference areas. Studies also have revealed optimal sampling methods for surveying invertebrates and their rich biodiversity in southwestern Australia. In restored mine pits burnt to reduce fuel loads, the response of spiders to this additional disturbance was retrogression/alteration of the post-mining trajectory. Finally, attention is drawn to research areas receiving limited scrutiny to date, such as the contribution of terrestrial invertebrates to ecosystem function and taxonomic groups not yet studied. [source] A phylogenetic classification of the land plants to accompany APG IIIBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2009MARK W. CHASE A formal classification of the land plants that is compatible with the APG III classification is proposed. Previous classifications inflated taxonomic ranks, particularly of the angiosperms. If the major clades of green algae are recognized as classes, then all land plants, the embryophytes, should be included in a single class, here recognized as Equisitopsida. Accordingly, the 16 major clades of land plants, including the angiosperms, should all be recognized as subclasses, the angiosperms as Magnoliidae. Major clades within the angiosperms are then recognized as superorders. This classification still uses a few informal categories (e.g. eudicots, lamiids, etc.) within the angiosperms because this is convenient. Two new names are established: Amborellanae and Austrobaileyanae. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161, 122,127. [source] | ||||||||||