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At least 451 records · Page 25Linked to original sources
PubMed1998

The phylogenetic potential of entire 26S rDNA sequences in plants.

18S ribosomal RNA genes are the most widely used nuclear sequences for phylogeny reconstruction at higher taxonomic levels in plants. However, due to a conservative rate of evolution, 18S rDNA alone sometimes provides too few phylogenetically informative characters to resolve relationships adequately. Previous studies using partial sequences have suggested the potential of 26S or large-subunit (LSU) rDNA for phylogeny retrieval at taxonomic levels comparable to those investigated with 18S rDNA. Here we explore the patterns of molecular evolution of entire 26S rDNA sequences and their impact on phylogeny retrieval. We present a protocol for PCR amplification and sequencing of entire (approximately 3.4 kb) 26S rDNA sequences as single amplicons, as well as primers that can be used for amplification and sequencing. These primers proved useful in angiosperms and Gnetales and likely have broader applicability. With these protocols and primers, entire 26S rDNA sequences were generated for a diverse array of 15 seed plants, including basal eudicots, monocots, and higher eudicots, plus two representatives of Gnetales. Comparisons of sequence dissimilarity indicate that expansion segments (or divergence domains) evolve 6.4 to 10.2 times as fast as conserved core regions of 26S rDNA sequences in plants. Additional comparisons indicate that 26S rDNA evolves 1.6 to 2.2 times as fast as and provides 3.3 times as many phylogenetically informative characters as 18S rDNA; compared to the chloroplast gene rbcL, 26S rDNA evolves at 0.44 to 1.0 times its rate and provides 2.0 times as many phylogenetically informative characters. Expansion segment sequences analyzed here evolve 1.2 to 3.0 times faster than rbcL, providing 1.5 times the number of informative characters. Plant expansion segments have a pattern of evolution distinct from that found in animals, exhibiting less cryptic sequence simplicity, a lower frequency of insertion and deletion, and greater phylogenetic potential.

Base Composition↗
PubMed2000

c-mos variation in songbirds: molecular evolution, phylogenetic implications, and comparisons with mitochondrial differentiation.

Nucleotide sequences from the c-mos proto-oncogene have previously been used to reconstruct the phylogenetic relationships between distantly related vertebrate taxa. To explore c-mos variation at shallower levels of avian divergence, we compared c-mos sequences from representative passerine taxa that span a range of evolutionary differentiation, from basal passerine lineages to closely allied genera. Phylogenetic reconstructions based on these c-mos sequences recovered topologies congruent with previous DNA-DNA hybridization-based reconstructions, with many nodes receiving high support, as indicated by bootstrap and reliability values. One exception was the relationship of Acanthisitta to the remaining passerines, where the c-mos-based searches indicated a three-way polytomy involving the Acanthisitta lineage and the suboscine and oscine passerine clades. We also compared levels of c-mos and mitochondrial differentiation across eight oscine passerine taxa and found that c-mos nucleotide substitutions accumulate at a rate similar to that of transversion substitutions in mitochondrial protein-coding genes. These comparisons suggest that nuclear-encoded loci such as c-mos provide a temporal window of phylogenetic resolution that overlaps the temporal range where mitochondrial protein-coding sequences have their greatest utility and that c-mos substitutions and mtDNA transversions can serve as complementary, informative, and independent phylogenetic markers for the study of avian relationships.

Animals↗
PubMed2000

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.

The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.

Amino Acid Sequence↗
PubMed2000

Likelihood analysis of phylogenetic networks using directed graphical models.

A method for computing the likelihood of a set of sequences assuming a phylogenetic network as an evolutionary hypothesis is presented. The approach applies directed graphical models to sequence evolution on networks and is a natural generalization of earlier work by Felsenstein on evolutionary trees, including it as a special case. The likelihood computation involves several steps. First, the phylogenetic network is rooted to form a directed acyclic graph (DAG). Then, applying standard models for nucleotide/amino acid substitution, the DAG is converted into a Bayesian network from which the joint probability distribution involving all nodes of the network can be directly read. The joint probability is explicitly dependent on branch lengths and on recombination parameters (prior probability of a parent sequence). The likelihood of the data assuming no knowledge of hidden nodes is obtained by marginalization, i.e., by summing over all combinations of unknown states. As the number of terms increases exponentially with the number of hidden nodes, a Markov chain Monte Carlo procedure (Gibbs sampling) is used to accurately approximate the likelihood by summing over the most important states only. Investigating a human T-cell lymphotropic virus (HTLV) data set and optimizing both branch lengths and recombination parameters, we find that the likelihood of a corresponding phylogenetic network outperforms a set of competing evolutionary trees. In general, except for the case of a tree, the likelihood of a network will be dependent on the choice of the root, even if a reversible model of substitution is applied. Thus, the method also provides a way in which to root a phylogenetic network by choosing a node that produces a most likely network.

Computer Graphics↗
PubMed2000

Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences.

Two spurious nodes were found in phylogenetic analyses of vertebrate rhodopsin sequences in comparison with well-established vertebrate relationships. These spurious reconstructions were well supported in bootstrap analyses and occurred independently of the method of phylogenetic analysis used (parsimony, distance, or likelihood). Use of this data set of vertebrate rhodopsin sequences allowed us to exploit established vertebrate relationships, as well as the considerable amount known about the molecular evolution of this gene, in order to identify important factors contributing to the spurious reconstructions. Simulation studies using parametric bootstrapping indicate that it is unlikely that the spurious nodes in the parsimony analyses are due to long branches or other topological effects. Rather, they appear to be due to base compositional bias at third positions, codon bias, and convergent evolution at nucleotide positions encoding the hydrophobic residues isoleucine, leucine, and valine. LogDet distance methods, as well as maximum-likelihood methods which allow for nonstationary changes in base composition, reduce but do not entirely eliminate support for the spurious resolutions. Inclusion of five additional rhodopsin sequences in the phylogenetic analyses largely corrected one of the spurious reconstructions while leaving the other unaffected. The additional sequences not only were more proximal to the corrected node, but were also found to have intermediate levels of base composition and codon bias as compared with neighboring sequences on the tree. This study shows that the spurious reconstructions can be corrected either by excluding third positions, as well as those encoding the amino acids Ile, Val, and Leu (which may not be ideal, as these sites can contain useful phylogenetic signal for other parts of the tree), or by the addition of sequences that reduce problems associated with convergent evolution.

Animals↗
PubMed1993

Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis.

Using sequence data from the 28S ribosomal RNA (rRNA) genes of selected vertebrates, we investigated the effects that constraints imposed by secondary structure have on the phylogenetic analysis of rRNA sequence data. Our analysis indicates that characters from both base-pairing regions (stems) and non-base-pairing regions (loops) contain phylogenetic information, as judged by the level of support of the phylogenetic results compared with a well-established tree based on both morphological and molecular data. The best results (the greatest level of support of well-accepted nodes) were obtained when the complete data set was used. However, some previously supported nodes were resolved using either the stem or loop bases alone. Stem bases sustain a greater number of compensatory mutations than would be expected at random, but the number is < 40% of that expected under a hypothesis of perfect compensation to maintain secondary structure. Therefore, we suggest that in phylogenetic analyses, the weighting of stem characters be reduced by no more than 20%, relative to that of loop characters. In contrast to previous suggestions, we do not recommend weighting of stem positions by one-half, compared with that of loop positions, because this overcompensates for the constraints that selection imposes on the secondary structure of rRNA.

Animal Population Groups↗
PubMed1994

Phylogenetic relationship of the kingdoms Animalia, Plantae, and Fungi, inferred from 23 different protein species.

The phylogenetic relationship among the kingdoms Animalia, Plantae, and Fungi remains uncertain, because of lack of solid fossil evidence. In spite of the extensive molecular phylogenetic analyses since the early report, this problem is a longstanding controversy; the proposed phylogenetic relationships differ for different authors, depending on the molecules and methods that they use. To settle this problem, we have accumulated 23 different protein species from the three kingdoms and have inferred the phylogenetic trees by three different methods--the maximum-likelihood method, the neighbor-joining method, and the maximum-parsimony method--for each data set. Although inferred tree topologies differ for different protein species and methods used, both the maximum-likelihood analysis based on the difference (delta l) between the total log-likelihood of a tree and that of the maximum-likelihood tree and bootstrap probability (P) of 23 proteins consisting of 10,051 amino acid sites in total have shown that a tree ((A,F),P), in which Plantae (P) is an outgroup to an Animalia (A)-Fungi (F) clade, is the maximum-likelihood tree; the delta l (= 0.0) and P (94%) of ((A,F),P) are significantly larger than those of ((A,P),F) (delta l = -54.4 +/- 36.3; and P = 6%) and ((F,P),A) (delta l = -141.1 +/- 30.9; and P = 0%).(ABSTRACT TRUNCATED AT 250 WORDS)

Animal Population Groups↗
PubMed1995

Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents.

We analyze sequences from two mitochondrial genes, cytochrome b (cyt b) and 12S rRNA (12S), for a group of sigmodontine rodents among which phylogenetic relationships are well understood based on concordance of morphological, chromosomal, allozyme, and other DNA data sets. Because these two genes are physically linked on the nonrecombining mitochondrial genome, they necessarily share the same history. Phylogenetic analysis of the cyt b gene recovers the well-corroborated relationships, generally with strong support. None of the methods that we employed, including variously weighted parsimony, neighbor joining on both single-rate and gamma-corrected distances, and maximum likelihood, were able to recover these relationships for the 12S gene. Parsimony analyses of the 12S data resulted in a relatively strongly supported placement of Peromyscus eremicus that conflicts with that suggested by cyt b and all other data. There is extreme among-site rate variation in the 12S sequences and moderate levels in the cyt b sequences. This highly skewed distribution of rates in the 12S gene makes phylogenetic analyses of these sequences particularly susceptible to the misleading effects of nonindependence and other nonrandom noise, suggesting that phylogenetic analyses of data sets that contain a great deal of among-site rate variation be interpreted with caution.

Animals↗
PubMed2000

Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences.

Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.

Agaricales↗
PubMed1993

Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes.

OBJECTIVE: To determine the extent of genetic variation among internationally collected HIV-1 isolates, to analyse phylogenetic relationships and the geographic distribution of different variants. DESIGN: Phylogenetic comparison of 70 HIV-1 isolates collected in 15 countries on four continents. METHODS: To sequence the complete gag genome of HIV-1 isolates, build multiple sequence alignments and construct phylogenetic trees using distance matrix methods and maximum parsimony algorithms. RESULTS: Phylogenetic tree analysis identified seven distinct genotypes. The seven genotypes were evident by both distance matrix methods and maximum parsimony analysis, and were strongly supported by bootstrap resampling of the data. The intra-genotypic gag distances averaged 7%, whereas the inter-genotypic distances averaged 14%. The geographic distribution of variants was complex. Some genotypes have apparently migrated to several continents and many areas harbor a mixture of genotypes. Related variants may cluster in certain areas, particularly isolates from a single city collected over a short time. CONCLUSIONS: The genetic variation among HIV-1 isolates is more extensive than previously appreciated. At least seven distinct HIV-1 genotypes can be identified. Diversification, migration and establishment of local, temporal 'blooms' of particular variants may all occur concomitantly.

Africa↗
PubMed1996

Phylogenetic analysis of the env gene of HIV-1 isolates taking into account individual nucleotide substitution rates.

OBJECTIVE: To estimate the relative substitution rate of the individual positions in an alignment of HIV-1 env sequences coding for areas V3, V4, V5, and the beginning of gp41, and to study phylogenetic relationships between HIV-1 strains taking into account these substitution rate estimates. DESIGN: Phylogenetic comparison of 145 HIV-1 strains classified in HIV-1 group M, subtypes A-H and isolated from patients of 24 different geographical origins. METHODS: A new method recently developed for measuring the substitution rates of the individual nucleotides in a sequence alignment was applied to an alignment of env gene sequences. From the resulting substitution rate distribution, an equation was derived that describes the relationship between dissimilarity and evolutionary distance better than equations previously available. Phylogenetic trees were then constructed from matrices of distances computed using this new equation. RESULTS: 'Substitution rate calibration' offers detailed information on the relative substitution rate or variability of the nucleotides in the env gene. A large phylogenetic tree of 145 env gene sequences constructed by neighbour-joining and taking into account the substitution rate spectrum for this gene, clearly shows the existence of the eight subtypes A-H, all supported at a bootstrap level of 90% or higher. Intersubtype distances were between 0.25 and 0.38, which is considerably higher than those found in trees not considering differences in substitution rates among different alignment positions. CONCLUSIONS: Evolutionary distances are seriously underestimated when individual substitution rates are not considered in the estimation evolutionary distances. Furthermore, due to the more accurate estimation of evolutionary distances, naturally occurring HIV-1 intersubtype recombinants could be recognized more easily.

Base Sequence↗
PubMed2003

The causes of phylogenetic conflict in a classic Drosophila species group.

Bifurcating phylogenies are frequently used to describe the evolutionary history of groups of related species. 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, Drosophila 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.

Animals↗
PubMed1994

Phylogenetic pattern and the quantification of organismal biodiversity.

Biodiversity can be explored at a number of different levels and in principle may be separately quantified at each. Phylogenetic pattern has the potential to quantify and estimate biodiversity at the finest scale, that is, variation among species in features or attributes. This scale is an important one for conservation, as it should form the basis for prioritizing conservation efforts at the species level. Further, recent published objections to differentially weighting species are answered by defining option value at this feature-level. Unfortunately, there has been no consensus on exactly how phylogeny can be used to value species, possibly because proper consideration of the link between pattern and underlying features generally has been unresolved. 'Phylogenetic diversity' (PD) represents just one of several approaches that do consider diversity at the feature-level explicitly. These alternative approaches are discussed in the context of a general framework for using pattern to quantify diversity at a level below that of the original objects. The pattern framework highlights that estimation of biodiversity at a lower level using pattern will require decisions about the nature of the units of diversity, the kind of pattern to be used, the model relating unit items to pattern, and finally how this implies a pattern-based measure reflecting biodiversity. An alternative published model for relating features to a particular form of phylogenetic pattern is considered, and shown to make unwarranted assumptions. A possible alternative definition of the underlying units of diversity is examined, which may represent a different form of option value, also quantifiable using phylogeny. A possible alternative pattern to a phylogenetic tree for the prediction of feature diversity is also discussed. The appeal of these alternative approaches depends on the goals of conservation; in addition, justification for prioritizing or weighting requires that any practical approach avoid arbitrary, unwarranted, assumptions.

Animals↗
PubMed1993

Phylogenetic relationships between some members of the genera Deleya, Halomonas, and Halovibrio.

The genera Halomonas and Deleya, which constitute the family Halomonadaceae, are difficult to differentiate on the basis of phenotypic and chemotaxonomic attributes. DNA-rRNA hybridization studies have indicated that some Halomonas spp. have the same level of relationship to the type species of the genus Deleya as some Deleya spp. A phylogenetic analysis of the 16S rRNA sequences of seven members of the Halomonadaceae indicated that the members of the genera Halomonas and Deleya do not form separate monophyletic subgroups, confirming the lack of any phylogenetic support for retention of these taxa as separate genera. A phylogenetic analysis of the 16S rRNA sequence of Halovibrio variabilis confirmed that this species belongs in the Halomonadaceae. All of the members of the Halomonadaceae examined and Halovibrio variabilis possess a cytosine residue at position 486 (Escherichia coli numbering), which is an extremely rare attribute among the prokaryotes and has been reported in only one other species, Listonella anguillarum. Several other signature characteristics which define this group in the gamma subclass of the Proteobacteria are identified. The Jukes-Cantor distances between members of the family Halomonadaceae, including Halovibrio variabilis, range from 0.086 to 0.000 (the levels of similarity between the 16S rRNA sequences range from 92.6 to 100%). The members of the genera Halomonas, Deleya, and Halovibrio form a monophyletic group and share common chemotaxonomic and phenotypic characteristics. Subgroups containing members of the genera Halomonas, Deleya, and Halovibrio cannot be resolved on the basis of phylogenetic, chemotaxonomic, or phenotypic data. Our data indicate that the members of the genera Halomonas, Deleya, and Halovibrio should be united in a single genus.

Biological Evolution↗
PubMed1997

Phylogenetic diversity of the deinococci as determined by 16S ribosomal DNA sequence comparison.

16S ribosomal DNA (rDNA) sequences were determined for the five species of the genus Deinococcus (Deinococcus erythromyxa, Deinococcus proteolyticus, Deinococcus radiodurans, Deinococcus radiophilus, and Deinococcus radiopugnans) and the single species of the genus. Deinobacter (Deinobacter grandis). With the exception of Deinococcus erythromyxa, the deinococci form a coherent phylogenetic cluster which is related to the Thermus-Meiothermus lineage. An analysis of the 16S rDNA sequence of Deinococcus erythromyxa revealed that this organism is an actinomycete and a member of the genus Kocuria. Deinobacter grandis falls within the radiation of the genus Deinococcus and phylogenetically can be considered a member of this genus. The results of the phylogenetic analyses are consistent with chemotaxonomic data. On the basis of our data, Deinobacter grandis is transferred to the genus Deinococcus as Deinococcus grandis comb. nov., the description of the genus Deinococcus is emended accordingly, and Deinococcus erythromyxa is transferred to the genus Kocuria as Kocuria erythromyxa comb. nov. The description of the family Deinococcaceae is emended to include organisms with rod-shaped cells, and a set of 16S rDNA signature nucleotides is designated for this group. On the basis of the distinct phylogenetic position of the Deinococcus lineage and a set of 16S rDNA signature nucleotides, the order Deinococcales ord. nov. is described.

DNA, Bacterial↗
PubMed1998

Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes.

Phylogenetic analysis of 20 Pseudomonas strains (Pseudomonas putida, Pseudomonas fluorescens and Pseudomonas chlororaphis) was conducted by using the nucleotide sequences of the genes for 16S RNA, DNA gyrase B subunit (gyrB) and RNA polymerase delta 70 factor (rpoD), which have been determined by the direct sequencing of PCR-amplified fragments. On the basis of gyrB and rpoD sequences, these strains were split into two major clusters: one including the type strain of P. putida and all biovar A strains and the other including all P. putida biovar B strains, P. fluorescens stains and the P. chlororaphis strain. In the phylogenetic tree reconstructed from the 16S rRNA sequences included variable regions, P. Putida biovar A and B strains were not separated into two independent clusters, whereas in the phylogenetic tree reconstructed from the 16S rRNA sequences excluding the variable region sequences, these strains were separated into P. putida biovar A and biovar B clusters. The pairwise distances estimated from the variable regions of 16S rRNA correlated poorly with the synonymous distances estimated from the gyrB and rpoD genes. On the other hand, a highly significant correlation was observed between the pairwise distances estimated from the non-variable regions of 16S rRNA and the synonymous distances from gyrB and rpoD genes. Consequently, only the 16S rRNA sequences in the non-variable regions should be used for the phylogenetic analysis. The gyrB and rpoD analyses showed the necessity for the reclassification of P. putida biovar B strains.

Base Sequence↗
PubMed1999

RFLP of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidizing bacteria: a phylogenetic approach.

It has been established that 16S rRNA gene-based phylogeny gives a low resolution between members of the chemoautotrophic ammonia-oxidizing bacteria (AOB) belonging to the beta-subclass of the Proteobacteria. In this study, 12 isolates of AOB were ribotyped, and the sequences of the 16S-23S rDNA intergenic spacer region (ISR) were determined and used in a phylogenetic study. 16S and 23S rDNA ribotyping revealed that the AOB studied contain only one rrn operon per genome, in contrast to most bacteria, which have 5-10 copies of the rRNA genes per genome. It is likely that the presence of only one set of rRNA genes is related to the slow growth of the AOB. The 16S and 23S rRNA genes of the AOB were shown to be arranged in the classical way: a 16S rRNA gene, an ISR and a 23S rRNA gene. Despite the close phylogenetic relationship among the AOB, the relative location of the rRNA genes in the genome appears to vary considerably. The size of the ISR was approximately 400 bp in the Nitrosomonas isolates and 645-694 bp in the Nitrosospira isolates, suggesting a species-specific size difference in the ISR. The ISR contained two potential tRNA genes in the 5' end in all isolates studied. The similarity values between the ISR sequences of the AOB are low (42.9-96.2%) compared with the 16S rDNA sequence similarity values, and therefore the ISR sequences are valuable as a complementary phylogenetic tool in combination with 16S rRNA gene sequences. The phylogenetic analysis of the AOB based on ISR sequences confirms the 16S rRNA gene-based phylogeny but has the benefit of giving a higher resolution.

Ammonia↗
PubMed1999

Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization.

The phylogenetic relationships of 49 Acinetobacter strains, 46 of which have previously been classified into 18 genomic species by DNA-DNA hybridization studies, were investigated using the nucleotide sequence of gyrB, the structural gene for the DNA gyrase B subunit. The phylogenetic tree showed linkages between genomic species 1 (Acinetobacter calcoaceticus), 2 (Acinetobacter baumannii), 3 and TU13; genomic species 6, BJ15, BJ16 and BJ17; genomic species 5, BJ13 (synonym of TU14) and BJ14; genomic species 7 (Acinetobacter johnsonii), 10 and 11; and genomic species 8 and 9. The phylogenetic grouping of Acinetobacter strains based on gyrB genes was almost congruent with that based on DNA-DNA hybridization studies. Consequently, gyrB sequence comparison can be used to resolve the taxonomic positions of bacterial strains at the level of genomic species. However, minor discrepancies existed in the grouping of strains of genomic species 8, 9 and BJ17. The phylogenetic tree for these strains was reconstructed from the sequence of rpoD, the structural gene for the RNA polymerase sigma 70 factor. The latter tree was 100% congruent with the grouping based on DNA-DNA hybridization. The reliability of DNA-DNA hybridization may be superior to that of sequence comparison of a single protein-encoding gene in resolving closely related organisms since the former method measures the homologies between the nucleotide sequences of total genomic DNAs. Three strains that have not been characterized previously by DNA-DNA hybridization seem to belong to two new genomic species, one including strain ATCC 33308 and the other including strains ATCC 31012 and MBIC 1332.

Acinetobacter↗