Results 1 - 10
of
7,284
Biological identifications through DNA barcodes
- Proc. Biol. Sci
, 2003
"... Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon ‘barcodes’. In this study, we establish that ..."
Abstract
-
Cited by 335 (3 self)
- Add to MetaCart
(Show Context)
Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon ‘barcodes’. In this study, we establish that the mitochondrial gene, cytochrome c oxidase I (COI), can serve as the core of a global bioidentification system for animals. We show firstly that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analyzed taxa to the appropriate phylum or order. We subsequently demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100 % successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problems of species identification. Its assembly will also generate important new insights concerning the diversification of life and the rules of molecular evolution. 2
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building
- Mol Biol Evol
, 2010
"... We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous ..."
Abstract
-
Cited by 319 (0 self)
- Add to MetaCart
(Show Context)
We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees. In relation to the wide present offer of tools and algorithms for phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at
An enhanced MITOMAP with a global mtDNA mutational phylogeny
- Nucleic Acids Res
, 2007
"... The MITOMAP ..."
(Show Context)
Iterative cluster analysis of protein interaction data
- Bioinformatics
, 2005
"... Motivation: Generation of fast tools of hierarchical clustering to be applied when distances among elements of a set are con-strained, causing frequent distance ties, as happens in protein interaction data. Results: We present in this work the program UVCLUSTER, that iteratively explores distance da ..."
Abstract
-
Cited by 63 (1 self)
- Add to MetaCart
(Show Context)
Motivation: Generation of fast tools of hierarchical clustering to be applied when distances among elements of a set are con-strained, causing frequent distance ties, as happens in protein interaction data. Results: We present in this work the program UVCLUSTER, that iteratively explores distance datasets using hierarch-ical clustering. Once the user selects a group of proteins, UVCLUSTER converts the set of primary distances among them (i.e. the minimum number of steps, or interactions, required to connect two proteins) into secondary distances that measure the strength of the connection between each pair of proteins when the interactions for all the proteins in the group are considered. We show that this novel strategy has advantages over conventional clustering methods to explore protein–protein interaction data. UVCLUSTER easily incorpor-ates the information of the largest available interaction data-sets to generate comprehensive primary distance tables. The versatility, simplicity of use and high speed of UVCLUSTER on standard personal computers suggest that it can be a benchmark analytical tool for interactome data analysis.
The causes of phylogenetic conflict in a classic Drosophila species
"... Bifurcating phylogenies are frequently used to describe the evolutionary history of groups of related spec-ies. However, simple bifurcating models may poorly represent the evolutionary history of species that have been exchanging genes. Here, we show that the history of three well-known closely rela ..."
Abstract
-
Cited by 52 (0 self)
- Add to MetaCart
(Show Context)
Bifurcating phylogenies are frequently used to describe the evolutionary history of groups of related spec-ies. However, simple bifurcating models may poorly represent the evolutionary history of species that have been exchanging genes. Here, we show that the history of three well-known closely related species, Droso-phila pseudoobscura, D. persimilis and D. p. bogotana, is not well represented by a bifurcating phylogenetic tree. The phylogenetic relationships among these species vary widely between different genomic regions. Much of this phylogenetic variation can be explained by the potential of different genomic regions to introgress between species, as measured in laboratory studies. We argue that the utility of multiple markers in species-level phylogenetic studies can be greatly enhanced by knowledge of genomic location and, in the case of hybridizing species, by knowledge of the functional or linkage relationships among the markers and regions of the genome that reduce hybrid fitness.
Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing
- J. Clin. Microbiol
, 2003
"... A multilocus sequence typing (MLST) scheme has been developed for the unambiguous characterization of encapsulated and noncapsulated Haemophilus influenzae isolates. The sequences of internal fragments of seven housekeeping genes were determined for 131 isolates, comprising a diverse set of 104 sero ..."
Abstract
-
Cited by 47 (3 self)
- Add to MetaCart
(Show Context)
A multilocus sequence typing (MLST) scheme has been developed for the unambiguous characterization of encapsulated and noncapsulated Haemophilus influenzae isolates. The sequences of internal fragments of seven housekeeping genes were determined for 131 isolates, comprising a diverse set of 104 serotype a, b, c, d, e, and f isolates and 27 noncapsulated isolates. Many of the encapsulated isolates had previously been characterized by multilocus enzyme electrophoresis (MLEE), and the validity of the MLST scheme was established by the very similar clustering of isolates obtained by these methods. Isolates of serotypes c, d, e, and f formed monophyletic groups on a dendrogram constructed from the differences in the allelic profiles of the isolates, whereas there were highly divergent lineages of both serotype a and b isolates. Noncapsulated isolates were distinct from encapsulated isolates and, with one exception, were within two highly divergent clusters. The
Phylogeny of the genus Flavivirus
- J. Virol
, 1998
"... This article cites 35 articles, 13 of which can be accessed free at: ..."
Abstract
-
Cited by 46 (1 self)
- Add to MetaCart
(Show Context)
This article cites 35 articles, 13 of which can be accessed free at:
Recombination in the genesis and evolution of hepatitis B virus genotypes
- J Virol
"... These include: This article cites 49 articles, 31 of which can be accessed free at: ..."
Abstract
-
Cited by 45 (3 self)
- Add to MetaCart
(Show Context)
These include: This article cites 49 articles, 31 of which can be accessed free at:
WB: An emerging recombinant human enterovirus 71 responsible for the 2008 outbreak of hand foot and mouth disease in Fuyang city of China. Virology journal 2010
- Li Q, Dong XP, Zhang J, Zhao YP, Wan JF, Feng ZJ, Sun JL, Wang SW, Li DX, Xu
"... Hand, foot and mouth disease (HFMD), a common contagious disease that usually affects children, is normally mild but can have life-threatening manifestations. It can be caused by enteroviruses, particularly Coxsackieviruses and human enterovirus 71 (HEV71) with highly variable clinical manifestation ..."
Abstract
-
Cited by 45 (6 self)
- Add to MetaCart
(Show Context)
Hand, foot and mouth disease (HFMD), a common contagious disease that usually affects children, is normally mild but can have life-threatening manifestations. It can be caused by enteroviruses, particularly Coxsackieviruses and human enterovirus 71 (HEV71) with highly variable clinical manifestations. In the spring of 2008, a large, unprecedented HFMD outbreak in Fuyang city of Anhui province in the central part of southeastern China resulted in a high aggregation of fatal cases. In this study, epidemiologic and clinical investigations, laboratory testing, and genetic analyses were performed to identify the causal pathogen of the outbreak. Of the 6,049 cases reported between 1 March and 9 May of 2008, 3023 (50%) were hospitalized, 353 (5.8%) were severe and 22 (0.36%) were fatal. HEV71 was confirmed as the etiological pathogen of the outbreak. Phylogenetic analyses of entire VP1 capsid protein sequence of 45 Fuyang HEV71 isolates showed that they belong to C4a cluster of the C4 subgenotype. In addition, genetic recombinations were found in the 3D region (RNA-dependent RNA polymerase, a major component of the viral replication complex of the genome) between the Fuyang HEV71 strain and Coxsackievirus A16 (CV-A16), resulting in a recombination virus. In conclusion, an emerging recombinant HEV71 was responsible for the HFMD outbreak in Fuyang City of China, 2008.
