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PubMed1999

Phylogenetic status of Anaerobacter polyendosporus, an anaerobic, polysporogenic bacterium.

The almost complete sequence of the 16S rRNA gene of the Gram-positive polysporogenic bacterium Anaerobacter polyendosporus was determined. This allowed phylogenetic analysis of A. polyendosporus by comparing sequences of the 16S rRNA gene of this bacterium to similar genes of other Gram-positive bacteria. It was shown that this polysporogenic bacterium belongs to the Clostridium cluster I, subcluster A. Phylogenetically, A. polyendosporus is distantly related to another polysporogenic, but non-cultivatable, bacterium, 'Metabacterium polyspora' and can be satisfactorily clustered within the saccharolytic clostridia with a low DNA G+C content grouped in subcluster A. A. polyendosporus was most closely related to Clostridium intestinale (94.8% identity of 16S rRNA genes) and Clostridium fallax (93.1%). Like other members of the Clostridium cluster I, subcluster A, A. polyendosporus possesses such common phenotypic features as a Gram-positive cell wall structure, anaerobiosis, derivation of energy from carbohydrate fermentation yielding butyric acid among other organic acids and the capacity for endogenous spore-formation. However, the scale of evolutionary change in the 16S rRNA gene between A. polyendosporus and phylogenetically related Clostridium species does not correspond to the profound changes in the phenotype of A. polyendosporus. Distinctive phenotypic features of the latter are large cell size, polysporogenesis (up to seven spores per cell), alternative modes of development and an unusual membrane ultrastructure.

Anaerobiosis↗
PubMed2005

Comparative sequence analysis of the hexon gene in the entire spectrum of human adenovirus serotypes: phylogenetic, taxonomic, and clinical implications.

The adenovirus (AdV) hexon constitutes the major virus capsid protein. The epitopes located on the hexon protein are targets of neutralizing antibodies in vivo, serve in the recognition by cytotoxic T cells, and provide the basis for the classification of adenoviruses into the 51 serotypes known to date. We have sequenced the entire hexon gene from human serotypes with incomplete or no sequence information available (n = 34) and performed a comparative analysis of all sequences. The overall sequence divergence between the 51 human serotypes ranged from 0.7 to 25.4% at the protein level. The sequence information has been exploited to assess the phylogeny of the adenovirus family, and protein distances between the six AdV species (A to F) and among individual serotypes within each species were calculated. The analysis revealed that the differences among serotypes within individual species range from 0.3 to 5.4% in the conserved regions (765 amino acids [aa]) and from 1.5 to 59.6% in the variable regions (154 to 221 aa). Serotypes of different species showed an expectedly greater divergence both in the conserved (5.9 to 12.3%) and variable (49.0 to 74.7%) regions. Construction of a phylogenetic tree revealed three major clades comprising the species B+D+E, A+F, and C, respectively. For serotypes 50 and 51, the original assignment to species B and D, respectively, is not in accordance with the hexon DNA and protein sequence data, which placed serotype 50 within species D and serotype 51 within species B. Moreover, the hexon gene of serotype 16, a member of species B, was identified as the product of recombination between sequences of species B and E. In addition to providing a basis for improved molecular diagnostics and classification, the elucidation of the complete hexon gene sequence in all AdV serotypes yields information on putative epitopes for virus recognition, which may have important implications for future treatment strategies permitting efficient targeting of any AdV serotype.

Adenovirus Infections, Human↗
PubMed1998

Phylogenetic heterogeneity of the genus Williopsis as revealed by 18S rRNA gene sequences.

A phylogenetic investigation of the ascomycetous yeast genus Williopsis was performed by using 18S rRNA gene sequence analysis. Comparative sequence analysis revealed the genus to be phylogenetically heterogeneous. The five varieties of Williopsis saturnus [var. mrakii, var. sargentensis, var. saturnus (type), var. suaveolens and var. subsufficiens] were found to have identical 18S rRNA gene sequences and formed a distinct group, quite separate from all other Williopsis and non-Williopsis species examined. Williopsis mucosa was found to be the closet phylogenetic relative to the Williopsis saturnus group, however a sequence divergence of approximately 2.3% suggests this species may belong to a separate genus. The recently described species Williopsis salicorniae was found to exhibit a relatively close association with Ogataea minuta (identical to Pichia minuta), the type species of the genus Ogataea. The remaining two members of the genus, Williopsis californica and Williopsis pratensis, were found to form distinct lineages, displaying no specific association with any other Williopsis or non-Williopsis species. Based on comparative analysis of 18S rRNA genes it is apparent that the genus Williopsis as presently constituted is not monophyletic, and that the five currently recognized species form separate sublines each potentially worthy of separate generic status. The genus Williopsis should be restricted to the type species Williopsis saturnus and its five varieties. Despite the five varieties of Williopsis saturnus being genealogically indistinguishable at the 18S rRNA gene level, sequence analysis of the Internal transcribed spacer (ITS) region revealed that the five varieties could be differentiated on both their ITS1 and their ITS2 sequences, providing further evidence of the value of ITS sequences for discrimination of yeasts at the subspecies level.

Base Sequence↗
PubMed2001

[Evolution of Lycopodiaceae from results of sequencing spacer sequences of chloroplast rRNA genes].

Nucleotide sequences of a chloroplast rDNA region including 8 bp from the 3' end of 23S rDNA-ITS2-4.5S rDNA-ITS3-5S rDNA-ITS4 (approximately 800 bp) were determined in 25 species of Lycopodiaceae and two species of the genus Isoetes. The rate of molecular evolution of spacers significantly varied in different Lycopsida taxa. A phylogenetic analysis by the neighbor-joining (NJ) method revealed that the family Lycopodiaceae is monophyletic. The topology of phylogenetic trees suggests the isolation of four or probably five genera in family Lycopodiaceae. For these genera, synapomorphic indels were detected. The obtained data were compared with the results of phylogenetic analysis of Lycopsida with regard to other sequences. The relationships of taxa within the family Lycopodiaceae is discussed.

Chloroplasts↗
PubMed2003

Deriving phylogenetic trees from the similarity analysis of metabolic pathways.

MOTIVATION: Comparative analysis of metabolic pathways in different genomes can give insights into the understanding of evolutionary and organizational relationships among species. This type of analysis allows one to measure the evolution of complete processes (with different functional roles) rather than the individual elements of a conventional analysis. We present a new technique for the phylogenetic analysis of metabolic pathways based on the topology of the underlying graphs. A distance measure between graphs is defined using the similarity between nodes of the graphs and the structural relationship between them. This distance measure is applied to the enzyme-enzyme relational graphs derived from metabolic pathways. Using this approach, pathways and group of pathways of different organisms are compared to each other and the resulting distance matrix is used to obtain a phylogenetic tree. RESULTS: We apply the method to the Citric Acid Cycle and the Glycolysis pathways of different groups of organisms, as well as to the Carbohydrate metabolic networks. Phylogenetic trees obtained from the experiments were close to existing phylogenies and revealed interesting relationships among organisms.

Algorithms↗
PubMed2003

Rabies emergence among foxes in Turkey.

Sixteen rabies isolates recently collected from mainland Turkey and two isolates held within a British archive were used to form a representative cohort from a range of vectors, and were analyzed to identify potential causes for an increase of rabies within the fox (Vulpes vulpes) population in Turkey. Each isolate was characterized by sequence analysis of the nucleoprotein gene and compared phylogenetically to the cohort, to isolates from neighboring countries and to isolates from continental Europe and Russia. From this analysis the isolates could be divided into three groups associated with geographic location. This included a western group, an eastern group, and one isolate that did not group with any other Turkish isolate. This observation was also found using the heteroduplex mobility assay as an alternative method for typing rabies virus isolates. Further comparison with isolates from neighboring countries suggests that this isolate was related to viruses present in Georgia and could represent a recent import to Turkey from that country. Within the two larger groups, sequence data were obtained from both infected dogs and foxes suggesting that there has been transmission of virus between these two species. The direction of transmission could not be identified by the phylogenetic analysis, although absence of rabies within the fox population in previous years suggests that this could represent a recent spillover from the domestic dog to the fox.

Animals↗
PubMedDate not supplied

["Phylogenetic presumptions"--can jurisprudence terms promote comparative biology?].

The paper presents the results of a critical analysis of the "phylogenetic presumptions" conception by means of its comparison with the hypothetic-deductive method of the phylogeny reconstruction within the framework of the evolutionary systematics. Rasnitsyn (1988, 2002) suggested this conception by analogy with the presumption of innocence in jurisprudence, where it has only moral grounds. Premises of all twelve the "phylogenetic presumptions" are known for a long time as the criteria of character homology and polarity or as the criteria of relationship between organisms. Many of them are inductive generalizations based on a large body of data and therefore are currently accepted by most of taxonomists as criteria or corresponding rules, but not as presumptions with the imperative "it is true until the contrary is proved". The application of the juristic term "presumption" in phylogenetics introduces neither methodical profits, nor anything to gain a better insight of problems of the phylogenetic reconstruction. Moreover, it gives ill effects as, by analogy with a judicially charged person and his legal defense, it allows a researcher not to prove or substantiate his statements on characters and relationships. Some of Rasnitsyn's presumptions correspond to criteria, which have been recognized as invalid ones on the reason of their non-operationality (presumption "apomorphic state corresponds more effective adaptation") or insufficient ontological grounds (presumptions "are more complex structure is apomorphic", "the most parsimonious cladogram is preferable", and "one should considered every to be inherited").

Biology↗
PubMed1994

Tracing paternal ancestry in mice, using the Y-linked, sex-determining locus, Sry.

The molecular evolution of mammalian Y-linked DNA sequences is of special interest because of their unique mode of inheritance: most Y-linked sequences are clonally inherited from father to son. Here we investigate the use of Y-linked sequences for phylogenetic inference. We describe a comparative analysis of a 515-bp region from the male sex-determining locus, Sry, in 22 murine rodents (subfamily Murinae, family Muridae), including representatives from nine species of Mus, and from two additional murine genera--Mastomys and Hylomyscus. Percent sequence divergence was < 0.01% for comparisons between populations within a species and was 0.19%-8.16% for comparisons between species. Our phylogenetic analysis of 12 murine taxa resulted in a single most-parsimonius tree that is highly concordant with phylogenies based on mitochondrial DNA and allozymes. A total evidence tree based on the combined data from Sry, mitochondrial DNA, and allozymes supports (1) the monophyly of the subgenus Mus, (2) its division into a Palearctic group (M. musculus, M. domesticus, M. spicilegus, M. Macedonicus, and M. spretus) and an Oriental group (M. cookii++, M. cervicolor, and M. caroli), and (3) sister-group relationships between M. spicilegus and M. macedonicus and between M. cookii and M. cervicolor. We argue that Y-chromosome DNA sequences represent a valuable new source of characters for phylogenetic inference.

Animals↗
PubMed1998

Carnimonas nigrificans gen. nov., sp. nov., a bacterial causative agent for black spot formation on cured meat products.

Nine different strains, CTCBS1T or CTCBS9, were identified to be the causative agents of black spots on the surface of raw cured meat products. The formation of black spots under aerobic conditions is reproducible upon reinoculation of meat products with any of these strains, indicating that they are the causative agent. The strains were Gram-negative, catalase-positive and obligately aerobic rods. The G+C content of DNA of strain CTCBS1T is 56.0 +/- 0.3 mol%. The content of non-polar main fatty acids were 16:0, 16:1, 18:1 and 19:0 cyc. Its phylogenetic position was elucidated by comparative sequence analysis of the 16S rRNA gene. Overall sequence similarity to other bacteria does not exceed 93.3%. Isolate CTCBS1T clustered phylogenetically within the gamma-subclass of the Proteobacteria and is closely related to members of Halomonas (90:5-91.9%) and to Zymobacter palmae (93.3%). A genetic homogeneity of the nine strains was demonstrated by M13 random amplified polymorphic DNA-PCR, whereas differentiation from other genera, e.g. Zymobacter and Pseudomonas, could easily be achieved by their chemotaxonomic characteristics. Taxonomic data revealed the status of a separate genus for which the name Carnimonas gen. nov., sp., nov. is proposed. Despite chemotaxonomic and physiological similarities, the new genus is at present not a member of the family Halomonadacease because of the lack of two out of 15 descriptive 16S rRNA signature sequences. The first member of the new genus is Carnimonas nigrificans. The use of a specific, 16S rRNA-targeted oligonucleotide primer allowed the identification of all nine strains of C. nigrificans in a PCR assay. Toxicological studies showed no pathogenic potential for C. nigrificans strain CTCBS1T (CECT 4437T).

Animals↗
PubMed2000

Neurobiological constraints and fly systematics: how different types of neural characters can contribute to a higher level dipteran phylogeny.

Much uncertainty still exists regarding higher level phylogenetic relationships in the insect order Diptera, and the need for independent analyses is apparent. In this paper, I present a parsimony analysis that is based on details of the nervous system of flies. Because neural characters have received little attention in modern phylogenetic analyses and the stability of neural traits has been debated, special emphasis is given to testing the robustness of the analysis itself and to evaluating how neurobiological constraints (such as levels of neural processing) influence the phylogenetic information content. The phylogenetic study is based on 14 species in three nematoceran and nine brachyceran families. All characters used in the analysis are based on anatomical details of the neural organization of the fly visual system. For the most part they relate to uniquely identifiable neurons, which are cells or cell types that can be confidently recognized as homologues among different species and thus compared. Parsimony analysis results in a phylogenetic hypothesis that favors specific previously suggested phylogenetic relationships and suggests alternatives regarding other placements. For example, several heterodactylan families (Bombyliidae, Asilidae, and Dolichopodidae) are supported in their placement as suggested by Sinclair et al. (1993), but Tipulidae and Syrphidae are placed differently. Tipulidae are placed at a derived rather than ancestral position within the Nematocera, and Syrphidae are placed within the Schizophora. The analysis suggests that neural characters generally maintain phylogenetic information well. However, by "forcing" neural characters onto conventional phylogenetic analyses it becomes apparent that not all neural centers maintain such information equally well. For example, neurons of the second-order visual neuropil, the medulla, contain stronger phylogenetic "signal" than do characters of the deeper visual center, the lobula plate. These differences may relate to different functional constraints in the two neuropils.

Animals↗
PubMed1997

A phylogenetic analysis of the genus Saccharomyces based on 18S rRNA gene sequences: description of Saccharomyces kunashirensis sp. nov. and Saccharomyces martiniae sp. nov.

A phylogenetic investigation of the ascomycetous yeast genus Saccharomyces was performed by using 18S rRNA gene sequence analysis. Comparative sequence analysis showed that the genus is phylogenetically very heterogeneous. Saccharomyces species were found to be phylogenetically interdispersed with members of other ascomycetous genera (e.g., the genera Kluyveromyces, Torulaspora, and Zygosaccharomyces). The four species of the Saccharomyces sensu stricto complex (viz., Saccharomyces bayanus, Saccharomyces cerevisiae, Saccharomyces paradoxus, and Saccharomyces pastorianus) were found to be phylogenetically closely related to one another, displaying exceptionally high levels of sequence similarity (> or = 99.9%). These four species formed a natural group that was quite separate from the other Saccharomyces and non-Saccharomyces species examined. Saccharomyces exiguus and its anamorph, Candida holmii, were found to be genealogically almost identical and, along with Saccharomyces barnettii, formed a stable group closely related to, but nevertheless distinct from, Kluyveromyces africanus, Kluyveromyces lodderae, Saccharomyces rosinii, Saccharomyces spencerorum, and Saccharomyces sp. strain CBS 7662T (T = type strain). Saccharomyces spencerorum and Kluyveromyces lodderae displayed a particularly close genealogical affinity with each other, as did Saccharomyces castellii and Saccharomyces dairensis. Similarly, Saccharomyces servazzii, Saccharomyces unisporus, and Saccharomyces sp. strain CBS 6904 were found to be genotypically highly related and to form a phylogenetically distinct lineage. The recently reinstated species Saccharomyces transvaalensis was found to form a distinct lineage and displayed no specific association with any other Saccharomyces or non-Saccharomyces species. Saccharomyces kluyveri formed a very loose association with a group which included Kluyveromyces thermotolerans, Kluyveromyces waltii, Zygosaccharomyces cidri, and Zygosaccharomyces fermentati. Saccharomyces spp. strain CBS 6334T, on the other hand, displayed no specific association with any of the other Saccharomyces spp. studied, although a neighbor-joining analysis did reveal that this strain exhibited a loose phylogenetic affinity with Kluyveromyces polysporus and Kluyveromyces yarrowii. On the basis of the phylogenetic findings, two new Saccharomyces species, Saccharomyces kunashirensis (with type strain CBS 7662) and Saccharomyces martiniae (with type strain CBS 6334), are described.

DNA, Fungal↗
PubMed2006

Cross-sectional geometry of the dentary in bats.

Bats exhibit remarkable diversity in dietary habits, with species specializing on insects, fruit, nectar, vertebrates and blood. Studies of larger mammals have shown that structural differences in dentary cross-sectional properties exist among species with different diets. Unfortunately, few of these studies have considered the role of phylogeny in shaping these apparent form-function associations. Here we ask whether a relationship exists between diet and dentary structure in bats when phylogenetic history is factored into the analysis. To answer this question, we compared results from phylogenetic generalized least squares (PGLS) and traditional (nonphylogenetic) regression analyses of dentary cross-sectional shape in frugivorous, nectarivorous, and insectivorous bats (253 individuals representing 72 species). Cross-sectional moments of inertia of the dentary between M(1) and M(2) were computed from bone densitometry scans of skeletal specimens. Traditional regressions of cross-sectional parameters against dentary length detected significant departures from isometry among frugivores. In contrast, PGLS analyses indicated that cross-sectional variables for each dietary group scaled with isometry. Thus, the allometric patterns illuminated by traditional statistics are linked to the phylogenetic structure of the sample. Identical patterns of significant differences in slopes and intercepts between frugivores and nectarivores emerged from both traditional and PGLS analyses. As predicted, the cross-sectional shape of the dentary in frugivores is consistent with increased resistance to torsion and bending, while that of nectarivores suggested a less resistant dentary. Although traditional and PGLS analyses yielded some similar results, the phylogenetic structure of a sample can drive apparent patterns of scaling and should be considered in comparative functional analyses.

Animals↗
PubMed2006

Genetic variation in the zebrafish.

Although zebrafish was introduced as a laboratory model organism several decades ago and now serves as a primary model for developmental biology, there is only limited data on its genetic variation. An establishment of a dense polymorphism map becomes a requirement for effective linkage analysis and cloning approaches in zebrafish. By comparing ESTs to whole-genome shotgun data, we predicted >50,000 high-quality candidate SNPs covering the zebrafish genome with average resolution of 41 kbp. We experimentally validated approximately 65% of a randomly sampled subset by genotyping 16 samples from seven commonly used zebrafish strains. The analysis reveals very high nucleotide diversity between zebrafish isolates. Even with the limited number of samples that we genotyped, zebrafish isolates revealed considerable interstrain variation, ranging from 7% (inbred) to 37% (wild-derived) of polymorphic sites being heterozygous. The increased proportion of polymorphic over monomorphic sites results in five times more frequent observation of a three allelic variant compared with human or mouse. Phylogenetic analysis shows that comparisons between even the least divergent strains used in our analysis may provide one informative marker approximately every 500 nucleotides. Furthermore, the number of haplotypes per locus is relatively large, reflecting independent establishment of the different lines from wild isolates. Finally, our results suggest the presence of prominent C-to-U and A-to-I RNA editing events in zebrafish. Overall, the levels and organization of genetic variation between and within commonly used zebrafish strains are markedly different from other laboratory model organisms, which may affect experimental design and interpretation.

Animals↗
PubMed1997

Sequence analysis of the VP6 gene in group A turkey and chicken rotaviruses.

cDNAs corresponding to the VP6 gene of the turkey rotavirus strains Ty-1 and Ty-3, and the chicken rotavirus strain Ch-1, were cloned and sequenced. The nucleotide and deduced amino acid sequence homology in the coding region of the VP6 gene in avian rotaviruses ranged from 78.1 to 93.9% and 86.1 to 98.7%, respectively. Both sequences of VP6 from avian rotaviruses exhibited a low degree of sequence homology (67.8-70.7% and 69.8-74.6%, respectively) compared with mammalian rotaviruses. Phylogenetic tree analysis showed that all avian rotaviruses were included in a single cluster and have separated early or from mammalian rotaviruses during evolution. The chicken rotavirus strain Ch-1 was a distant relative of other avian rotaviruses.

Amino Acid Sequence↗
PubMed2003

The first non-LTR retrotransposon characterised in the cephalochordate amphioxus, BfCR1, shows similarities to CR1-like elements.

BfCR1 is the first non-long terminal repeat retrotransposon to be characterised in the amphioxus genome. Sequence alignment of the predicted translation product reveals that BfCR1 belongs to the CR1-like retroposon class, a family widely distributed in vertebrate and invertebrate lineages. Structural analysis shows conservation of the specific motifs of the ORF2-CR1 elements: the N-terminal endonuclease, the reverse transcriptase and the C-terminal domains. The BfCR1 element possesses an atypical 3' terminus consisting of the tandem repeat (AAG)6. We gathered evidence supporting the mobility of this element and report an estimated 15 copies of BfCR1, mostly truncated, per haploid genome, a remarkably low number when compared to that of vertebrates. Phylogenetic analysis, including the amphioxus element, seems to indicate that (i) CR1-like retroposons cluster in a monophyletic group and (ii) the CR1-like family was already present in the chordate ancestor. Our data provide further support for the horizontal transmission of CR1-like elements during early vertebrate evolution.

Amino Acid Sequence↗
PubMed1998

Molecular evolution of Mycoplasma capricolum subsp. capripneumoniae strains, based on polymorphisms in the 16S rRNA genes.

Mycoplasma capricolum subsp. capripneumoniae belongs to the so-called Mycoplasma mycoides cluster and is the causal agent of contagious caprine pleuropneumonia (CCPP). All members of the M. mycoides cluster have two rRNA operons. The sequences of the 16S rRNA genes of both rRNA operons from 20 strains of M. capricolum subsp. capripneumoniae of different geographical origins in Africa and Asia were determined. Nucleotide differences which were present in only one of the two operons (polymorphisms) were detected in 24 positions. The polymorphisms were not randomly distributed in the 16S rRNA genes, and some of them were found in regions of low evolutionary variability. Interestingly, 11 polymorphisms were found in all the M. capricolum subsp. capripneumoniae strains, thus defining a putative ancestor. A sequence length difference between the 16S rRNA genes in a poly(A) region and 12 additional polymorphisms were found in only one or some of the strains. A phylogenetic tree was constructed by comparative analysis of the polymorphisms, and this tree revealed two distinct lines of descent. The nucleotide substitution rate of strains within line II was up to 50% higher than within line I. A tree was also constructed from individual operonal 16S rRNA sequences, and the sequences of the two operons were found to form two distinct clades. The topologies of both clades were strikingly similar, which supports the use of 16S rRNA sequence data from homologous operons for phylogenetic studies. The strain-specific polymorphism patterns of the 16S rRNA genes of M. capricolum subsp. capripneumoniae may be used as epidemiological markers for CCPP.

Africa↗
PubMed2002

An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference.

The objective of this study was to obtain a quantitative assessment of the monophyly of morning glory taxa, specifically the genus Ipomoea and the tribe Argyreieae. Previous systematic studies of morning glories intimated the paraphyly of Ipomoea by suggesting that the genera within the tribe Argyreieae are derived from within Ipomoea; however, no quantitative estimates of statistical support were developed to address these questions. We applied a Bayesian analysis to provide quantitative estimates of monophyly in an investigation of morning glory relationships using DNA sequence data. We also explored various approaches for examining convergence of the Markov chain Monte Carlo (MCMC) simulation of the Bayesian analysis by running 18 separate analyses varying in length. We found convergence of the important components of the phylogenetic model (the tree with the maximum posterior probability, branch lengths, the parameter values from the DNA substitution model, and the posterior probabilities for clade support) for these data after one million generations of the MCMC simulations. In the process, we identified a run where the parameter values obtained were often outside the range of values obtained from the other runs, suggesting an aberrant result. In addition, we compared the Bayesian method of phylogenetic analysis to maximum likelihood and maximum parsimony. The results from the Bayesian analysis and the maximum likelihood analysis were similar for topology, branch lengths, and parameters of the DNA substitution model. Topologies also were similar in the comparison between the Bayesian analysis and maximum parsimony, although the posterior probabilities and the bootstrap proportions exhibited some striking differences. In a Bayesian analysis of three data sets (ITS sequences, waxy sequences, and ITS + waxy sequences) no supoort for the monophyly of the genus Ipomoea, or for the tribe Argyreieae, was observed, with the estimate of the probability of the monophyly of these taxa being less than 3.4 x 10(-7).

Bayes Theorem↗