The neighbor-joining method: a new method for reconstructing phylogenetic trees.
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
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TL;DR: It is demonstrated that vertebrate opsin sequences fall into five fundamental subfamilies and is speculated that this is crucial for the diversity of the spectral sensitivity observed in vertebrate photoreceptors and provides the vertebrates with the molecular tools to discriminate the color of incident light.
Abstract: Vision is one of the most important senses for vertebrates. As a result, vertebrates have evolved a highly organized system of retinal photoreceptors. Light triggers an enzymatic cascade, called the phototransduction cascade, that leads to the hyperpolarization of photoreceptors. It is expected that a systematic comparison of phototransduction cascades of various vertebrates can provide insights into the diversity of vertebrate photoreceptors and into the evolution of vertebrate vision. However, only a few attempts have been made to compare each phototransduction protein participating in this cascade. Here, we determine phylogenetic trees of the vertebrate phototransduction proteins and compare them. It is demonstrated that vertebrate opsin sequences fall into five fundamental subfamilies. It is speculated that this is crucial for the diversity of the spectral sensitivity observed in vertebrate photoreceptors and provides the vertebrates with the molecular tools to discriminate the color of incident light. Other phototransduction proteins can be classified into only a few subfamilies. Cones generally share isoforms of phototransduction proteins that are different from those found in rods. The difference in sensitivity to light between rods and cones is likely due to the difference in the molecular properties of these isoforms. The phototransduction proteins seem to have co-evolved as a system. Switching the expression of these isoforms may characterize individual vertebrate photoreceptors.
59 citations
TL;DR: The likely existence of unknown CPXV hosts and their distribution may present a risk for other exotic animals but also for the general public, as was shown in this outbreak of cowpox virus in Germany.
Abstract: Background
Often described as an extremely rare zoonosis, cowpox virus (CPXV) infections are on the increase in Germany. CPXV is rodent-borne with a broad host range and contains the largest and most complete genome of all poxviruses, including parts with high homology to variola virus (smallpox). So far, most CPXV cases have occurred individually in unvaccinated animals and humans and were caused by genetically distinguishable virus strains.
Methodology/Principal Findings
Generalized CPXV infections in banded mongooses (Mungos mungo) and jaguarundis (Herpailurus yagouaroundi) at a Zoological Garden were observed with a prevalence of the affected animal group of 100% and a mortality of 30%. A subsequent serological investigation of other exotic animal species provided evidence of subclinical cases before the onset of the outbreak. Moreover, a time-delayed human cowpox virus infection caused by the identical virus strain occurred in a different geographical area indicating that handling/feeding food rats might be the common source of infection.
Conclusions/Significance
Reports on the increased zoonotic transmission of orthopoxviruses have renewed interest in understanding interactions between these viruses and their hosts. The list of animals known to be susceptible to CPXV is still growing. Thus, the likely existence of unknown CPXV hosts and their distribution may present a risk for other exotic animals but also for the general public, as was shown in this outbreak. Animal breeders and suppliers of food rats represent potential multipliers and distributors of CPXV, in the context of increasingly pan-European trading. Taking the cessation of vaccination against smallpox into account, this situation contributes to the increased incidence of CPXV infections in man, particularly in younger age groups, with more complicated courses of clinical infections.
59 citations
Cites methods from "The neighbor-joining method: a new ..."
...net) using the neighbor-joining method [27]....
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...The evolutionary history was inferred using the Neighbor-Joining method [27]....
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TL;DR: The results indicate that the hsp60 gene may be a useful alternative target for phylogenetic analysis and species identification of marine Vibrios to complement more conventional identification systems.
Abstract: The use of hsp60 gene sequences for phylogenetic study and identification of pathogenic marine vibrios was investigated. A 600-bp partial hsp60 gene was amplified by PCR and sequenced from 29 strai...
59 citations
Cites methods from "The neighbor-joining method: a new ..."
...The unrooted phylogenetic tree was constructed by the neighbor-joining distance method (Saitou and Nei 1987) using the Jukes and Cantor one-parameter model to correct for multiple, superimposed substitutions (Jukes and Cantor 1969)....
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TL;DR: Forty one strains isolated from 21 samples of various mushroom composts in Korea were analyzed by 16S rRNA gene sequencing to investigate the phylogenetic diversity of thermophilic actinomycetes and M104 and M109 were placed in distinct taxonomic positions.
Abstract: Forty one strains isolated from 21 samples of various mushroom composts in Korea were analyzed by 16S rRNA gene sequencing to investigate the phylogenetic diversity of thermophilic actinomycetes. The 25 strains of thermophilic actinomycete isolates were related to the five genera, Pseudonocardia, Saccharomonospora, Saccharopolyspora, Streptomyces, and Thermobifida, within the order Actinomycetales, and 16 strains were classified into the genus Thermoactinomyces within the family Bacillaceae. Most of 41 isolates were encompassed by two genera, Streptomyces and Thermoactinomyces, that were isolated mainly in composts prepared from waste cotton and hay, respectively. Among them, M104 and M109 were placed in distinct taxonomic positions although these strains formed phylogenetic lineages related to the genus Streptomyces and to the family Streptosporangiaceae, respectively. Therefore, a phenetic and genetic characterization of these strains will be needed to pinpoint their taxonomic position.
59 citations
Cites methods from "The neighbor-joining method: a new ..."
...Evolutionary trees for the data sets were inferred from the neighbor-joining method of Saitou and Nei [27] by using the program of MEGA [28]....
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TL;DR: The 19-mer epitope cluster was shown to have the potential for use as a vaccine candidate against dengue, and the cumulative population coverage for these epitopes as vaccine candidates was high.
Abstract: A major problem in designing vaccine for the dengue virus has been the high antigenic variability in the envelope protein of different virus strains. In this study, a computational approach was adopted to identify a multi-epitope vaccine candidate against dengue virus that may be suitable for large populations in the dengue-endemic regions. Different bioinformatics tools were exploited that helped the identification of a conserved immunological hot-spot in the dengue envelope protein. The tools also rendered the prediction of immunogenicity and population coverage to the proposed 'in silico' vaccine candidate against dengue. A peptide region, spanning 19 amino acids, was identified in the envelope protein which found to be conserved in all four types of dengue viruses. Ten proteasomal cleavage sites were identified within the 19-mer conserved peptide sequence and a total of 8 overlapping putative cytotoxic T cell (CTL) epitopes were identified. The immunogenicity of these epitopes was evaluated in terms of their binding affinities to and dissociation half-time from respective human leukocyte antigen (HLA) molecules. The HLA allele frequencies were studied among populations in the dengue endemic regions and compared with respect to HLA restriction patterns of the overlapping epitopes. The cumulative population coverage for these epitopes as vaccine candidates was high ranging from approximately 80% to 92%. Structural analysis suggested that a 9-mer epitope fitted well into the peptide-binding groove of HLA-A*0201. In conclusion, the 19-mer epitope cluster was shown to have the potential for use as a vaccine candidate against dengue.
59 citations
Cites methods from "The neighbor-joining method: a new ..."
...0) was utilized for generating MSA and neighbor-joining method was used for the construction of phylogenetic tree [18]....
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References
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Book•
01 Feb 1987
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Abstract: Recent developments of statistical methods in molecular phylogenetics are reviewed. It is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used. However, when the rate of evolution varies exlensively from branch to branch, many methods may fail to recover the true topology. Solid statistical tests for examining'the accuracy of trees obtained by neighborjoining, minimum evolution, and least-squares method are available, but the methods for likelihood and parsimony trees are yet to be refined. Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct.
15,840 citations
Additional excerpts
...Here, 2 represents a group of OTUs including all but 1 and 2, and Dlz and Dzz are the distances between 1 and 2 and 2 and 2, respectively (see Nei 1987, pp. 298-302, for an elementary exposition of this method)....
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01 Jan 1969
10,262 citations
3,734 citations
"The neighbor-joining method: a new ..." refers methods in this paper
...After the nucleotide sequences for eight OTUs were produced, nucleotide differences were counted for all pairs of sequences, and the evolutionary distance (Jukes and Cantor 1969) was computed for each pair of OTUs....
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3,454 citations
"The neighbor-joining method: a new ..." refers methods in this paper
...Our procedure of estimating branch lengths is essentially the same as that of Fitch and Margoliash ( 1967)....
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Book•
01 Jan 1963
TL;DR: The authors continued the story of psychology with added research and enhanced content from the most dynamic areas of the field, such as cognition, gender and diversity studies, neuroscience and more, while at the same time using the most effective teaching approaches and learning tools.
Abstract: This new edition continues the story of psychology with added research and enhanced content from the most dynamic areas of the field--cognition, gender and diversity studies, neuroscience and more, while at the same time using the most effective teaching approaches and learning tools
3,332 citations