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Complete Sequences (complete + sequence)
Selected AbstractsComplete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putidaENVIRONMENTAL MICROBIOLOGY, Issue 12 2002Alicia Greated Summary The TOL plasmid pWW0 (117 kb) is the best studied catabolic plasmid and the archetype of the IncP-9 plasmid incompatibility group from Pseudomonas. It carries the degradative (xyl) genes for toluenes and xylenes within catabolic transposons Tn4651 and Tn4653. Analysis of the complete pWW0 nucleotide sequence revealed 148 putative open reading frames. Of these, 77 showed similarity to published sequences in the available databases predicting functions for: plasmid replication, stable maintenance and transfer; phenotypic determinants; gene regulation and expression; and transposition. All identifiable transposition functions lay within the boundaries of the 70 kb transposon Tn4653, leaving a 46 kb sector containing all the IncP-9 core functions. The replicon and stable inheritance region was very similar to the mini-replicon from IncP-9 antibiotic resistance plasmid pM3, with their Rep proteins forming a novel group of initiation proteins. pWW0 transfer functions exist as two blocks encoding putative DNA processing and mating pair formation genes, with organizational and sequence similarity to IncW plasmids. In addition to the known Tn4651 and IS1246 elements, two additional transposable elements were identified as well as several putative transposition functions, which are probably genetic remnants from previous transposition events. Genes likely to be responsible for known resistance to ultraviolet light and free radicals were identified. Other putative phenotypic functions identified included resistance to mercury and other metal ions, as well as to quaternary ammonium compounds. The complexity and size of pWW0 is largely the result of the mosaic organization of the transposable elements that it carries, rather than the backbone functions of IncP-9 plasmids. [source] Complete sequences of small acid-soluble proteins from Bacillus globigiiJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 10 2004Jeffrey R. Whiteaker Abstract Three abundant small acid-soluble proteins (SASPs) from spores of Bacillus globigii were sequenced using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with post-source decay and nanoelectrospray collision-induced dissociation tandem mass spectrometry. The proteins were extracted from spores with 1 M HCl. Scanning electron micrographs of spores before and after acid extraction show that the spores retain their overall structure but have a shriveled texture following the acid treatment. Extracted SASPs were purified by high-performance liquid chromatography and molecular masses of the SASPs were identified at 7068 (SASP-1), 7332 (SASP-2), and 8889 (,-SASP). De novo peptide sequencing was used to determine the protein sequences. The correct ordering of peptide sequences was aided by mapping overlapping enzymatic digests and by comparison with homologous SASPs from Bacillus stearothermophilus. B. globigii is used in many field tests as a surrogate for B. anthracis. Thus complete SASP sequences from B. globigii will facilitate the development of methods for rapid identification of bacteria based on mass spectrometry and the examination of taxonomic relationships between Bacillus species. Copyright © 2004 John Wiley & Sons, Ltd. [source] Prioritizing regions of candidate genes for efficient mutation screening,HUMAN MUTATION, Issue 2 2006Terry A. Braun Abstract The availability of the complete sequence of the human genome has dramatically facilitated the search for disease-causing sequence variations. In fact, the rate-limiting step has shifted from the discovery and characterization of candidate genes to the actual screening of human populations and the subsequent interpretation of observed variations. In this study we tested the hypothesis that some segments of candidate genes are more likely than others to contain disease-causing variations and that these segments can be predicted bioinformatically. A bioinformatic technique, prioritization of annotated regions (PAR), was developed to predict the likelihood that a specific coding region of a gene will harbor a disease-causing mutation based on conserved protein functional domains and protein secondary structures. This method was evaluated by using it to analyze 710 genes that collectively harbor 4,498 previously identified mutations. Nearly 50% of the genes were recognized as disease-associated after screening only 9% of the complete coding sequence. The PAR technique identified 90% of the genes as containing at least one mutation, with less than 40% of the screening resources that traditional approaches would require. These results suggest that prioritization strategies such as PAR can accelerate disease-gene identification through more efficient use of screening resources. Hum Mutat 27(2), 195,200, 2006. © 2006 Wiley-Liss, Inc. [source] New model for the formation and function of sagittocysts: Symsagittifera corsicae n. sp. (Acoela)INVERTEBRATE BIOLOGY, Issue 2 2002Robert Gschwentner Abstract. This study is focused on the formation and function of sagittocysts, which are secretions typical of members of the acoel family Sagittiferidae. The needle-shaped sagittocysts are produced in specialized gland cells (sagittocytes) whose distal necks are often surrounded by muscle mantles. Contraction of the muscle mantle ejects the sagittocyst. We establish a model for the development of sagittocytes and muscle mantles out of the stem cell pool of the new acoel species Symsagittifera corsicae. We used various techniques, especially interference and phase-contrast microscopy of living specimens as well as labeling of the body-wall musculature, for species characterization. In addition to the morphological features, we provide the third complete sequence of the 18S rDNA gene in the family Sagittiferidae. [source] Zircon sensitive high mass-resolution ion microprobe U,Pb and fission-track ages for gabbros and sheeted dykes of the Taitao ophiolite, Southern Chile, and their tectonic implicationsISLAND ARC, Issue 1 2006Ryo Anma Abstract The Late Miocene,Pliocene Taitao ophiolite is composed of a complete sequence of classic oceanic lithosphere and is exposed approximately 50 km southeast of the Chile triple junction, where the Chile Ridge subducts beneath the South American Plate. Gabbros and ultramafic rocks are folded into a complex pattern, but only evidence for block rotation has been reported in the overriding sheeted dyke complex. In the present study, sensitive high mass-resolution ion microprobe U,Pb and fission-track dating methods were applied to zircon crystals separated from gabbros and sheeted dykes. Two sets of radiometric ages of gabbros range between 5.9 ± 0.4 and 5.6 ± 0.1 Ma. These ages coincide within their error ranges and imply rapid intrusion and cooling of gabbros. The U,Pb age of a dacite dyke intruded into the sheeted dyke complex was determined to be 5.2 ± 0.2 Ma. These data indicate that the magmas of the Taitao ophiolite were formed during the 6 Ma Chile Ridge collision event and emplaced in a shorter period than previously thought. A short segment of the Chile Mid-oceanic Ridge must have been emplaced during the 6 Ma event. [source] Conserved regions from Plasmodium falciparum MSP11 specifically interact with host cells and have a potential role during merozoite invasion of red blood cellsJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 4 2010Ana Zuleima Obando-Martinez Abstract Despite significant global efforts, a completely effective vaccine against Plasmodium falciparum, the species responsible for the most serious form of malaria, has not been yet obtained. One of the most promising approaches consists in combining chemically synthesized minimal subunits of parasite proteins involved in host cell invasion, which has led to the identification of peptides with high binding activity (named HABPs) to hepatocyte and red blood cell (RBC) surface receptors in a large number of sporozoite and merozoite proteins, respectively. Among these proteins is the merozoite surface protein 11 (MSP11), which shares important structural and immunological features with the antimalarial vaccine candidates MSP1, MSP3, and MSP6. In this study, 20-mer-long synthetic peptides spanning the complete sequence of MSP11 were assessed for their ability to bind specifically to RBCs. Two HABPs with high ability to inhibit invasion of RBCs in vitro were identified (namely HABPs 33595 and 33606). HABP-RBC bindings were characterized by means of saturation assays and Hill analysis, finding cooperative interactions of high affinity for both HABPs (nH of 1.5 and 1.2, Kd of 800 and 600,nM for HABPs 33595 and 33606, respectively). The nature of the possible RBC receptors for MSP11 HABPs was studied in binding assays to enzyme-treated RBCs and cross-linking assays, finding that both HABPs use mainly a sialic acid-dependent receptor. An analysis of the immunological, structural and polymorphic characteristics of MSP11 HABPs supports including these peptides in further studies with the aim of designing a fully effective protection-inducing vaccine against malaria. J. Cell. Biochem. 110: 882,892, 2010. © 2010 Wiley-Liss, Inc. [source] Hepatitis in Albanian children: Molecular analysis of hepatitis A virus isolatesJOURNAL OF MEDICAL VIROLOGY, Issue 4 2004Rosanna Gabrieli Abstract Hepatitis A is a common disease in developing countries and Albania has a high prevalence of this disease associated to young age. In spite of the occurrence of a unique serotype there are different genotypes classified from I to VII. Genotype characterisation of HAV isolates circulating in Albania has been undertaken, as well as the study of the occurrence of antigenic variants in the proteins VP3 and VP1. To evaluate the genetic variability of the Albanian hepatitis A virus (HAV) isolates, samples were collected from 12 different cities, and the VP1/2A junction amplified and sequenced. These sequences were aligned and a phylogenetic analysis performed. Additionally, the amino half sequence of the protein VP3 and the complete sequence of the VP1 was determined. Anti-HAV IgM were present in 66.2% of all the sera. Fifty HAV isolates were amplified and the analysis revealed that all the isolates were sub-genotype IA with only limited mutations. When the deduced amino acid sequences were obtained, the alignment showed only two amino acids substitutions at positions 22 and 34 of the 2A protein. A higher genomic stability of the VP1/2A region, in contrast with what occurs in other parts of the world could be observed, indicating high endemicity of HAV in Albania. In addition, two potential antigenic variants were detected. The first at position 46 of VP3 in seven isolates and the second at position 23 of VP1 in six isolates. J. Med. Virol. 72:533,537, 2004. © 2004 Wiley-Liss, Inc. [source] Factors determining the performance of triple quadrupole, quadrupole ion trap and sector field mass spectrometer in electrospray ionization mass spectrometry.RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 13 2001The sequence coverage by fragment ions resulting from collision-induced dissociation in a triple stage quadrupole (TSQ) and a quadrupole ion trap (QIT) mass spectrometer of 10,20-mer oligonucleotides was investigated. While (a-B) and w ion series were the most abundant on both instruments, additional ion series of sequence relevance were preferably formed in the TSQ. Thus, a total number of 83 fragment ions were used to deduce the complete sequence of a 10-mer oligonucleotide of mixed sequence from a tandem mass spectrum recorded on the TSQ. The complete sequence was also encoded in the 28 fragments that were obtained from the QIT under comparable fragmentation conditions. Spectrum complexity increased considerably at the cost of signal-to-noise ratio upon fragmentation of a 20-mer oligonucleotide in the TSQ, whereas spectrum interpretation with longer oligonucleotides was significantly more straightforward in spectra recorded on the QIT. The extent of fragmentation had to be optimized by appropriate setting of collision energy and choice of precursor ion charge state in order to obtain full sequence coverage by fragments for de novo sequencing. Moreover, full sequence information was also dependent on base sequence because of the low tendency of backbone cleavage at thymidines. Tandem mass spectrometry on the QIT yielded redundant information that was successfully utilized to deduce the complete sequence of 20-mer oligonucleotides with high confidence. Copyright © 2001 John Wiley & Sons, Ltd. [source] Molecular phylogeny and evolution of the Asian lineage of vole genus Microtus (Rodentia: Arvicolinae) inferred from mitochondrial cytochrome b sequenceBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2010ANNA A. BANNIKOVA To examine phylogenetic relationships within the Asian lineage of voles (Microtus) belonging to subgenus Alexandromys, the mitochondrial cytochrome b gene (cytb) was sequenced for its representatives, and the results were compared with the cytogenetic, morphological, and paleontological data. In all the trees inferred from maximum likelihood, parsimony, and Bayesian phylogenetic analyses, the Asian clade is subdivided into highly supported Alexandromys s.s. and moderately supported Pallasiinus lineages. Four subclades are recovered within Alexandromys: (1) Microtus maximowiczii and Microtus sachalinensis; (2) Microtus miiddendorffii s.l., Microtus mongolicus and Microtus gromovi; (3) Microtus fortis; and (4) Microtus limnophilus. Thus, M. limnophilus demonstrates clear affinities to Alexandromys s.s. but not to Microtus oeconomus (subgenus Pallasiinus), which was always regarded as its sibling species. The results obtained indicate M. mongolicus as a member of Alexandromys but not of the Microtus arvalis group, thus being concordant with the cytogenetic data. The mitochondrial data support the species status of M. gromovi; moreover, its placement as a part of a trichotomy with M. miiddendorffii s.l. and M. mongolicus contradicts the traditional affiliation of M. gromovi with M. maximowiczii. The divergence rate of cytb third position transversions in Microtus is estimated at approximately 8% per Myr, which corresponds to approximately 30% per Myr for all substitution types at all codon positions. The maximum likelihood distance based on complete sequence showed a tendency for a progressive underestimation of divergence and time for older splits. According to our molecular clock analysis employing nonlinear estimation methods, the split between Alexandromys and Pallasiinus and basal radiation within Alexandromys date back to approximately 1.2 Mya and 800 Kya, respectively. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 595,613. [source] Phylogeny and Systematic Position of Opiliones: A Combined Analysis of Chelicerate Relationships Using Morphological and Molecular Data,CLADISTICS, Issue 1 2002Gonzalo Giribet The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones. [source] Developmental expression and comparative genomic analysis of Xenopus cardiac myosin heavy chain genesDEVELOPMENTAL DYNAMICS, Issue 4 2005Robert J. Garriock Abstract Myosin heavy chains (MHC) are cytoskeletal motor proteins essential to the process of muscle contraction. We have determined the complete sequences of the Xenopus cardiac MHC genes, ,-MHC and ventricular MHC (vMHC), and have characterized their developmental expression profiles. Whereas ,-MHC is expressed from the earliest stages of cardiac differentiation, vMHC transcripts are not detected until the heart has undergone chamber formation. Early expression of vMHC appears to mark the cardiac conduction system, but expression expands to include the ventricle and outflow tract myocardium during subsequent development. Sequence comparisons, transgenic expression analysis, and comparative genomic studies indicate that Xenopus ,-MHC is the true orthologue of the mammalian ,-MHC gene. On the other hand, we show that the Xenopus vMHC gene is most closely related to chicken ventricular MHC (vMHC1) not the mammalian ,-MHC. Comparative genomic analysis has allowed the detection of a mammalian MHC gene (MyH15) that appears to be the orthologue of vMHC, but evidence suggests that this gene is no longer active. Developmental Dynamics 233:1287,1293, 2005. © 2005 Wiley-Liss, Inc. [source] Conservation and dispersion of sequence and function in fungal TRK potassium transporters: focus on Candida albicansFEMS YEAST RESEARCH, Issue 2 2009Manuel Miranda Abstract TRK proteins , essential potassium (K+) transporters in fungi and bacteria, as well as in plants , are generally absent from animal cells, which makes them potential targets for selective drug action. Indeed, in the human pathogen Candida albicans, the single TRK isoform (CaTrk1p) has recently been demonstrated to be required for activity of histidine-rich salivary antimicrobial peptides (histatins). Background for a detailed molecular investigation of TRK-protein design and function is provided here in sequence analysis and quantitative functional comparison of CaTrk1p with its better-known homologues from Saccharomyces cerevisiae. Among C. albicans strains (ATCC 10261, SC5314, WO-1), the DNA sequence is essentially devoid of single nucleotide polymorphisms in regions coding for evolutionarily conserved segments of the protein, meaning the four intramembranal [membrane,pore,membrane (MPM)] segments thought to be involved directly with the conduction of K+ ions. Among 48 fungal (ascomycete) TRK homologues now described by complete sequences, clades (but not the detailed order within clades) appear conserved for all four MPM segments, independently assessed. The primary function of TRK proteins, ,active' transport of K+ ions, is quantitatively conserved between C. albicans and S. cerevisiae. However, the secondary function, chloride efflux channeling, is present but poorly conserved between the two species, being highly variant with respect to activation velocity, amplitude, flickering (channel-like) behavior, pH dependence, and inhibitor sensitivity. [source] Late Quaternary landscape history and geoarchaeology of two drainages on Black Mesa, northeastern Arizona, USAGEOARCHAEOLOGY: AN INTERNATIONAL JOURNAL, Issue 1 2005Eric T. Karlstrom Two approximately 5- to 6-km drainage segments on Black Mesa preserve unusually complete sequences of late Quaternary alluvium and soils. Radiocarbon- and tree-ring-dated alluvial and soil stratigraphy suggests entrenched paleoarroyos were beginning to aggrade at about >24,260, 11,070, 9660, 8800, 7060, 3500, 2140, and 1870 14C yr B.P. Using the quantity of sediment removal from post-A.D. 1900 arroyos as analogue, at least 77,200% of total valley alluvium has been removed and replaced by younger sediments during an estimated 11 late Pleistocene and Holocene erosion epicycles. Given that most (59%) of the 150 recorded prehistoric sites in the two study areas occur on valley floors where only about 3% of surface alluvium predates Lolomai phase Basketmaker II occupation (,1900,1600 yr B.P.), it may be inferred that pre-Lolomai phase Basketmaker II sites which may have been located along washes have been removed or buried by fluvial erosion. Identification of five buried hearths in alluvial sections, including White Dog and Lolomai phase Basketmaker II sites (dating about 3500 and 1870 14C yr B.P., respectively) and one possible Early Archaic site, supports this conclusion. © 2005 Wiley Periodicals, Inc. [source] Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeetsJOURNAL OF BIOGEOGRAPHY, Issue 9 2009Camila C. Ribas Abstract Aim, We present a molecular phylogenetic analysis of Brotogeris (Psittacidae) using several distinct and complementary approaches: we test the monophyly of the genus, delineate the basal taxa within it, uncover their phylogenetic relationships, and finally, based on these results, we perform temporal and spatial comparative analyses to help elucidate the historical biogeography of the Neotropical region. Location, Neotropical lowlands, including dry and humid forests. Methods, Phylogenetic relationships within Brotogeris were investigated using the complete sequences of the mitochondrial genes cyt b and ND2, and partial sequences of the nuclear intron 7 of the gene for Beta Fibrinogen for all eight species and 12 of the 17 taxa recognized within the genus (total of 63 individuals). In order to delinetae the basal taxa within the genus we used both molecular and plumage variation, the latter being based on the examination of 597 skin specimens. Dates of divergence and confidence intervals were estimated using penalized likelihood. Spatial and temporal comparative analyses were performed including several closely related parrot genera. Results,Brotogeris was found to be a monophyletic genus, sister to Myiopsitta. The phylogenetic analyses recovered eight well-supported clades representing the recognized biological species. Although some described subspecies are diagnosably distinct based on morphology, there was generally little intraspecific mtDNA variation. The Amazonian species had different phylogenetic affinities and did not group in a monophyletic clade. Brotogeris diversification took place during the last 6 Myr, the same time-frame as previously found for Pionus and Pyrilia. Main conclusions, The biogeographical history of Brotogeris implies a dynamic history for South American biomes since the Pliocene. It corroborates the idea that the geological evolution of Amazonia has been important in shaping its biodiversity, argues against the idea that the region has been environmentally stable during the Quaternary, and suggests dynamic interactions between wet and dry forest habitats in South America, with representatives of the Amazonian biota having several independent close relationships with taxa endemic to other biomes. [source] Proteomic identification of biomarkers related to Helicobacter pylori -associated gastroduodenal disease: Challenges and opportunitiesJOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 11 2008Ming-Shiang Wu Abstract Helicobacter pylori colonize the stomach of over half the world's population. While 80,90% H. pylori -infected individuals have clinically asymptomatic gastritis, 10,15% develop peptic ulcer, and 1,2% gastric malignancies. These variable clinical outcomes have led to an interest in prognostic indicators. The current disease paradigm suggests that host genetics and bacterial virulence both play important roles in modulating the final outcome of H. pylori infection. Elucidation of the interaction between host and bacterium is essential to clarify pathogenesis and to develop new strategies for prevention and treatment. Proteomic technology is a powerful tool for simultaneously monitoring proteins and protein variation on a large scale in biological samples. It has provided an unprecedented opportunity to survey a cell's translational landscape comprehensively, and the results may allow in-depth analyses of host and pathogen interactions. Using this high-throughput platform and taking advantage of complete sequences for both the H. pylori and the human genome in available databases, we have identified several crucial proteins that have pathogenic and prognostic potential. Among them, antibodies to AhpC and GroEs of H. pylori could be utilized for identification of patients who are at high risk of disease complications after H. pylori infection. Evolving proteomic technologies, together with appropriate clinical phenotyping and genotype information should enhance understanding of disease pathogenesis and lead to more precise prediction of variable disease outcomes. It will also facilitate development of biomarkers for diagnosis, treatment, and prevention of H. pylori infection. [source] The Aulacostephanidae (Ammonoidea) of the Oxfordian/Kimmeridgian boundary beds (Upper Jurassic) of southern EnglandPALAEONTOLOGY, Issue 1 2010JOHN K. WRIGHT Abstract:, Four areas in southern England centred on Swindon and Westbury (Wiltshire), Bourton (north Dorset) and the Dorset coast near Weymouth (south Dorset) have yielded well-preserved late Oxfordian and early Kimmeridgian (Upper Jurassic) ammonites in abundance. These ammonites belong principally to the aulacostephanid genera Ringsteadia and Pictonia, and their microconch equivalents Microbiplices and Prorasenia. Systematic descriptions of these genera are included herein. Within the zonal and subzonal sequence of the English Oxfordian/Kimmeridgian Stage boundary beds, the established subdivision of the Late Oxfordian Pseudocordata Zone into Pseudoyo, Pseudocordata and Evoluta Subzones is confirmed. In the Early Kimmeridgian Baylei Zone, however, the evidence is that the sequence throughout much of southern England is incomplete compared with more complete sequences such as that at Staffin in the Isle of Skye, with the presence of only one faunal biohorizon, the densicostata horizon. [source] Identification of a Second rRNA Gene Unit in the Perkinsus andrewsi GenomeTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2004WOLF T. PECHER ABSTRACT. Perkinsus species are parasitic protozoa of mollusks, currently classified within the Perkinsozoa, a recently established phylum that is basal to the Apicomplexa and Dinozoa. Ribosomal RNA (rRNA) genes and their intergenic spacers have been used to support the taxonomy of Perkinsus species, the description of new species, and to develop molecular probes for their detection and identification. We previously described ultrastructure, behavior in culture, and partial sequence of the rRNA locus of a Perkinsus species isolated from the baltic clam Macoma balthica. The rRNA genes and intergenic spacers of this Perkinsus isolate differed from those described in the currently accepted species to a degree that led to its designation as a new species, Perkinsus andrewsi. In this study, we identify an additional rRNA gene unit (rRNA-B) in the P. andrewsi holotype, and report the complete sequences of both rRNA gene units. Except for the 5. 8S, all regions of the rRNA-B gene unit exhibited sequence differences from that initially described (rRNA-A). Each rRNA gene unit is arranged in a "head-to-tail" tandem repeat. This is the first report demonstrating two distinct rRNA units in a Perkinsus species. [source] Northern and Southern expansions of Atlantic brown trout (Salmo trutta) populations during the PleistoceneBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009MARTÍ CORTEY The phylogeography of Atlantic brown trout (Salmo trutta) was analysed using mitochondrial DNA control region complete sequences of 774 individuals from 57 locations. Additionally, the available haplotype information from 100 published populations was incorporated in the analysis. Combined information from nested clade analysis, haplotype trees, mismatch distributions, and coalescent simulations was used to characterize population groups in the Atlantic basin. A major clade involved haplotypes assigned to the Atlantic (AT) lineage, but another major clade should be considered as a distinct endemic lineage restricted to the Iberian Peninsula. The phylogeography of the Atlantic populations showed the mixed distribution of several Atlantic clades in glaciated areas of Northern Europe, whereas diverged haplotypes dominated the coastal Iberian rivers. Populations inhabiting the Atlantic rivers of southern France apparently contributed to postglacial colonization of northern basins, but also comprised the source of southern expansions during the Pleistocene. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 904,917. [source] Phylogeny, biogeography and the stepwise evolutionary colonization of intertidal habitat in the Liparocephalini based on morphological and molecular characters (Coleoptera: Staphylinidae: Aleocharinae)CLADISTICS, Issue 4 2010Kee-Jeong Ahn A phylogenetic analysis of the tribe Liparocephalini Fenyes is presented based on morphological and molecular characters. The data set comprised 50 adult morphological characters, partial COI (907 bp), COII (366 bp) and 12S rDNA (325,355 bp), and nearly complete sequences of 18S rDNA (1768,1902 bp) for 21 species. Eighteen species of liparocephaline beetles from all eight genera and three outgroups, are included. The sequences were analysed separately and simultaneously with morphological characters by direct optimization in the program POY4 and by partitioned Bayesian analysis for the combined data. The direct optimization (DO) tree for the combined data under equal weighting, which also shows a minimum incongruence length difference value, resulted in a monophyletic Liparocephalini with the following patterns of phylogenetic relationships (outgroup ((Baeostethus, Ianmoorea) (Paramblopusa ((Amblopusa, Halorhadinus) (Liparocephalus, Diaulota))))). A sensitivity analysis using 16 different parameter sets for the combined data shows the monophyly of the liparocephalines and all its genera under all parameter sets. Bayesian analysis resulted in topological differences in comparison with the DO tree under equal weighting only in the position of the genus Paramblopusa and clade (Amblopusa + Halorhadinus), which were reversed. Historical biogeography and the stepwise evolutionary colonization of intertidal habitat in the Liparocephalini are discussed. Based on the biogeographical analyses, we hypothesize that the ancestor of the Liparocephalini occurred along the Panthallassan Ocean, the direct antecedent of the Pacific Ocean, followed by repeated dispersals to the Nearctic from the Palearctic. We also hypothesize that ancestors of the Liparocephalini appear to have arisen in the littoral zone of beaches and then colonized rocky reef areas in the low tidal zone later through high- to mid-tide zones. ,© The Willi Hennig Society 2009. [source] Phylogeny of Nerillidae (Polychaeta, Annelida) as inferred from combined 18S rDNA and morphological dataCLADISTICS, Issue 2 2005Katrine Worsaae A phylogeny of the meiofaunal polychaete family Nerillidae based on morphological, molecular and combined data is presented here. The data sets comprise nearly complete sequences of 18S rDNA and 40 morphological characters of 17 taxa. Sequences were analyzed simultaneously with the morphological data by direct optimization in the program POY, with a variety of parameter sets (costs of gaps: transversions: transitions). Three outgroups were selected from the major polychaete group Aciculata and one from Scolecida. The 13 nerillid species from 11 genera were monophyletic in all analyses with very high support, and three new apomorphies for Nerillidae are identified. The topology of the ingroup varied according to the various parameter settings. Reducing the number of outgroups to one decreased the variance among the phylogenetic hypotheses. The congruence among these was tested and a parameter set, with equal weights (222) and extension gap weighted 1, yielded minimum incongruence (ILD). Several terminal clades of the combined analysis were highly supported, as well as the position of Leptonerilla prospera as sister terminal to the other nerillids. The evolution of morphological characters such as segment numbers, chaetae, appendages and ciliation are traced and discussed. A regressive pathway within Nerillidae is indicated for several characters, however, generally implying several convergent losses. Numerous genera are shown to require revision. © The Willi Hennig Society 2005. [source] | |||||||||||||||||||