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Results for “phylogenetic comparative analysis”

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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↗

PubMed1992

Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants.

Sequences obtained in the 5' non-coding region (5'NCR) of hepatitis C virus (HCV) were obtained from Scottish blood donors and compared with previously published HCV sequences. Phylogenetic analysis revealed the existence of three distinct groups of sequences; two of these corresponded to the recently described HCV types 1 and 2 variants, while viral sequences detected in around a third of the blood donors formed a separate phylogenetic group that probably represents infection with a novel virus species. Nucleotide sequences of this latter group differed from all previously published 5'NCR sequence variants by at least 9%. This new virus type also differed considerably from previously published variants in other regions of the viral genome (core, NS-3 and NS-5), with corrected nucleotide distances of 15, 43 and 49% respectively from the prototype HCV-1 sequence. Formal phylogenetic analysis of each of the coding regions confirmed that HCV type 1 variants could be clearly differentiated into regional variants (Far East and U.S.A./European), in contrast to the clearly overlapping geographical distributions of the main HCV types in U.K. blood donors. We discuss the evidence for and against the hypothesis that the three main phylogenetic groups identified in this study represent separate species of HCV.

Amino Acid Sequence↗

PubMed1996

[Analysis of hepatitis C virus (HCV) genotypes in hepatocellular carcinoma].

Chronic hepatitis C virus (HCV) infection has been clearly established as a major risk factor in the development of hepatocellular carcinoma. In the present study we have attempted to identify the HCV genotypes associated with hepatocellular carcinoma in patients from the USA and Japan. RNAs from tumorous and non-tumorous tissues from 11 HCV seropositive Japanese patients, and plasma from 4 American patients were analysed by reverse transcription-polymerase chain reaction (RT-PCR) methods employing primers specific for the 5'UTR, the NS5 and E2/NS1 regions. Amplified products were cloned and compared by nucleotide sequencing and phylogenetic analysis. The 5'UTR region could be successfully amplified and sequenced from all samples, and phylogenetic analysis of the nucleotide sequences demonstrated with the exception of two of Japanese viruses were closely related to HCV type 1. Type 2 was detected in these two cases. In addition, two of the Japanese patients who were found to have cholangiocarcinoma were also found to be infected with type 1. HCV amplification of the NS5 was successful in 7 of the Japanese and 1 USA sample and clearly demonstrated that genotype 1b was predominant. Amplification of the E2/NS1 regions proved to be extremely difficult and was unsuccessful in all HCC patients despite the fact that these regions could be consistently amplified in samples from patients with both acute and chronic HCV infection. These findings might suggest that with long term persistent HCV infection, there may be marked heterogeneity in both the structural and non-structural regions of the virus, and/or possibly that the viral genomes may be defective.

Aged↗

PubMed2004

Phylogeny of the Falconidae (Aves): a comparison of the efficacy of morphological, mitochondrial, and nuclear data.

We sequenced 2800+ bp of the RAG-1 exon for representatives of all the currently recognized genera in the avian family Falconidae. A phylogenetic analysis of these data was compared to prior analyses of mitochondrial (cytochrome-b) and morphological (syringeal) data. The nuclear RAG-1 sequences produced results that were in agreement with the morphological results, but differed from the mitochondrial results with regard to monophyly of the genus Micrastur. A reanalysis of the cytochrome-b (cyt-b) data suggested that this result was due to heterogeneity in base composition. Comparisons of data quality and quantity across the three data sets indicate that the nuclear DNA sequences and the morphological data have similar consistency and retention indices as well as noise distributions that are superior to those of cyt-b. However, the RAG-1 data identify more nodes with high bootstrap support indices than do either morphology or mitochondrial sequences. In the final assessment, RAG-1 sequences were superior in phylogenetic utility both to syringeal morphology (because of sheer number of characters) and to cyt-b sequences (because of reduced noise and homogeneity of base composition, but in spite of having many fewer characters).

Animals↗

PubMed2006

Mitochondrial chromosome structure: an insight from analysis of complete yeast genomes.

Recent progress in the analysis of protein components of the mitochondrial nucleoid and replisome of baker's yeast, Saccharomyces cerevisiae, opens a unique opportunity for understanding the molecular principles of mitochondrial inheritance. In this work we identified homologs of proteins involved in the mitochondrial DNA packaging and replication in the complete genome sequence of the petite-negative yeast Kluyveromyces lactis. Comparative analysis of their counterparts from phylogenetically diverse yeast species revealed conserved as well as diverged features of the organellar chromosome structure and its replication strategy. Moreover, it provides a basis for subsequent functional studies of the structure and dynamics of the mitochondrial nucleoids.

Amino Acid Sequence↗

PubMed2003

Ancient introgression of Lepus timidus mtDNA into L. granatensis and L. europaeus in the Iberian Peninsula.

A 587 bp fragment of cytochrome b sequences from 90 individuals of 15 hare (Lepus) species and two outgroups were phylogenetically analysed and compared to an analysis derived from 474 bp sequences of the nuclear transferrin gene. Mountain hare (Lepus timidus) type mtDNA was observed in L. granatensis and L. europaeus from the Iberian Peninsula, far away from the extant distributional range of L. timidus. In addition to these two hare species, other hare species may also contain mtDNA from L. timidus. This species may have introgressed with other species of Lepus that occur within its present range, or where fossils indicate its historical presence during glacial periods. L. timidus mtDNA is common in the northern part of the L. granatensis range. Finally, we reassessed the phylogenetic relationships of the five European hare species based on both mitochondrial and nuclear DNA sequences.

Animals↗

PubMed2001

Amycolatopsis albidoflavus sp. nov.

The generic position of an actinomycete strain, 'Pseudonocardia sp.' IMSNU 22139, was investigated by the phylogenetic analysis of 16S rDNA sequence. Comparative studies of 16S rDNA sequences indicated that this organism consistently formed a distinct clade within the radiation of the genus Amycolatopsis of the family Pseudonocardiaceae. This organism was also found to have chemotaxonomic properties consistent with those of the genus Amycolatopsis, which were represented by a type IV cell wall (meso-diaminopimelic acid, arabinose and galactose), a major menaquinone of MK-9(H4), a predominant fatty acid of 14-methylpentadecanoic acid, phosphatidylmethylethanolamine as a diagnostic phospholipid (a phospholipid type PII pattern) and DNA base composition of 68.5 mol% G+C. On the basis of physiological properties, cellular fatty acid profiles and its unique phylogenetic position, this organism is readily differentiated from all of the validly described species of the genus Amycolatopsis, and the name Amycolatopsis albidoflavus sp. nov. is proposed for it. The type strain is IMSNU 22139T (= KCTC 9471T = ATCC 53205T).

Actinomycetales↗

PubMed1997

Genomic organization and evolution of alternative exons in a Drosophila calcium channel gene.

The genomic organization of a gene coding for an alpha 1 subunit of a voltage-gated calcium channel of Drosophila melanogaster (Dmca IA) was determined. Thirty-four exons, distributed over 45 kb of genomic sequence, have been identified and mapped, including exons in three regions involved in alternative splicing and new sites potentially involved in RNA editing. The comparison of the intron/exon boundaries of this channel with a mammalian counterpart shows that the genomic structure of these two genes has remained fairly similar during evolution, with more than half of the Drosophila intron positions being perfectly conserved compared to the human channel. Phylogenetic analysis of the mutually exclusive alternative exons revealed that they have diverged considerably. It is suggested that this divergence, rather than reflecting evolutionary age, is the likely result of accelerated rates of evolution following duplication.

Amino Acid Sequence↗

PubMed2003

Methods of horizontal gene transfer determination using phylogenetic data.

A new approach for comparative analysis of multiple trees reconstructed for representative protein families is proposed. This approach is based on the hypothesis of gene duplication, gene loss and horizontal gene transfer and makes use of stochastic methods and optimization. We present a species tree of 40 prokaryotic organisms obtained by our algorithm on the basis of 132 clusters of orthologous groups of proteins (COGs) from the GenBank of the National Center for Biotechnology Information (USA). We also present a computer technology intended to determine horizontally transferred genes. Some application results of the technology, based on comparative analysis of protein and species trees, are given.

Bacteria↗

PubMedDate not supplied

RpoA: a useful gene for phylogenetic analysis in diatoms.

The aim of this study was to compare the usefulness of two chloroplast-encoded genes (rpoA and rbcL) and the nuclear-encoded small subunit (SSU) ribosomal RNA for reconstructing phylogenetic relationships among diatoms at lower taxonomic levels. To this end, the rpoA and rbcL genes for selected centric and pennate diatoms were sequenced. The new rpoA and rbcL sequences, and an existing nuclear-encoded SSU rRNA data set, were subjected to weighted/unweighted parsimony, maximum likelihood, minimum evolution, and Bayesian analyses. All of the tree-building methods employed showed, based on the support values, that the rpoA gene was the most useful, relative to the rbcL and SSU rRNA genes, in determining phylogenetic relationships among the sampled diatoms. The support values for the relationships among the pennate lineages were, in many instances, greater in the rpoA trees than in the SSU rRNA trees. These results suggest that rpoA might be of value in determining phylogenetic relationships among pennate lineages.

Base Sequence↗

PubMed1994

Variability at the carpometacarpal and midcarpal joints involving the fourth metacarpal, hamate, and lunate in catarrhini.

Intraspecies variability is investigated in two regions of the wrist, for the purpose of determining whether patterns may be discerned in the variability that may be compared in the functional and phylogenetic analysis of living and fossil catarrhines. In the midcarpal joint region, two lunatohamate configuration patterns are found, and at the fourth carpometacarpal joint four types of configuration are identified. These two sites previously were reported to show almost continuous variability in humans, thus precluding comparison with other species. The different types of configuration in our study are delineated on the basis of their relation to differences in joint function. At the lunatohamate site there is a strong tendency in each species examined for one type to dominate in frequency. At the fourth carpometacarpal joint there is a tendency for one type or for two related types to predominate in each species. The chimpanzee sample exhibits the least variability of all species studied in joint configuration at the two sites. Australopithecus afarensis has a combination of joint types in these regions likely to be found today in only a small percentage of living Hominoidea. We conclude that patterns may be discerned at some joints in what was formerly considered to be a continuum of variation. Since these patterns (joint types) differ in their relative frequencies among living species, the frequency differences may be useful as a guide to the reconstruction of phylogenetic relationships and of potential wrist functions in fossil species.

Animals↗

PubMed2000

Heterogeneity found in the cagA gene of Helicobacter pylori from Japanese and non-Japanese isolates.

We analyzed cagA genes from Helicobacter pylori strains isolated from Japanese and non-Japanese individuals for differences that could be associated with variations in virulence. The cagA genes from Japanese isolates (n = 12) and non-Japanese American Type Culture Collection (ATCC) strains (n = 4) were sequenced and compared with three published sequences. Phylogenetic analysis resolved two distinct clusters with a genetic distance of 0.1602. Similarity plot analysis of the amino acid sequences identified two highly variable regions of which each was unique to the Japanese and non-Japanese isolates, respectively. Furthermore, nucleic acid sequence analysis revealed that the multiple repeated sequences present in cagA may have been generated by homologous recombination and/or misaligned replication to promote variation in the cagA gene products. Our data indicate that alleic variations in the H. pylori genome exist between isolates from Japanese and non-Japanese subjects and that distinct H. pylori populations may be circulating in different geographical regions. Phylogenetic analysis did not reveal any association of a specific CagA type with a particular disease. Although extensive alterations were found in the cagA gene, none of the isolates contained a prematurely terminated CagA protein. The cagA gene may be advantageous to H. pylori, possibly by aiding its escape from host immune recognition by antigen modulation. Thus, this ability to elude the host immune system may contribute to an increased risk for gastric disease.

Algorithms↗

PubMed2006

Expression of endothelin receptors in frog, chicken, mouse and human pigment cells.

Several reports have shown the participation of vasoactive endothelins (ETs) in the regulation of vertebrate pigment cells. In the present study, we identified ET receptors in pigment cells of vertebrate species by RT-PCR assays, and compared the differential expression of the various subtypes in each species by quantitative PCR. RT-PCR was performed with specific primers for ETC, ETA(X) or ETA in Xenopus laevis melanophores, ETA or ETB(2) in chicken melanocytes, ETA or ETB in murine (B-16, S-91 or Melan-A) or human (SK-Mel 23 or SK-Mel 28) melanoma cells, and the products obtained were confirmed by cloning and sequencing. The results showed the presence of ETA(X), but not ETA mRNA, and confirmed the expression of ETC in X. laevis melanophores. ETA and ETB(2) mRNAs were also demonstrated in chicken melanocytes. ETA and ETB receptor were identified in S-91, B16 and Melan-A murine cells. In human melanoma cells, SK-Mel 23 and SK-Mel 28, we confirmed the presence of ETB mRNA, and also found ETA mRNA. The comparison between the two subtypes present in the pigment cell of each species and among species demonstrated that the expression of ETAs in chicken, mouse, and human melanocytes is negligible, as is the expression of ETA(X) in Xenopus melanophores. The relative expression, as determined by quantitative PCR, was as follows: chicken ETB>SK-Mel 23 ETB>S91 ETB>>>Xenopus ETC, suggesting that the endothelin system plays a major role in avian and mammalian pigment cell regulation, as compared to lower vertebrates. The phylogenetic analysis revealed that subtype A receptors were probably the most primitive ET receptors, directly deriving from the ancestral type; all the other receptors, B subtypes and C, originated from diverse derivative molecules.

Animals↗

PubMed2026

Genomic and phenotypic characterization of mcr-9 carrying Enterobacter oligotrophicus recovered from bovine mastitis.

Bovine mastitis (BM) is a leading cause of economic loss in the dairy industry, driven by decreased milk yields, involuntary culling, and substantial veterinary costs. A single Gram-negative isolate recovered from BM was characterized in this study. For this, antimicrobial susceptibility testing (AST) was performed using the Neg-Urine-Combo 98 panel. Whole-genome sequencing (WGS) was employed to identify antimicrobial resistance genes (ARG), virulence factors (VF) genes, plasmid replicons and prophage sequences. Comparative genomic analysis was performed through phylogenetic analysis. The BM isolate was phenotypically identified as Citrobacter rodentium, however, WGS analysis reclassified the isolate as Enterobacter oligotrophicus. Phenotypic AST revealed a resistance profile of 12%, with the isolate exhibiting resistance to β-lactams antimicrobials, specifically amoxicillin-clavulanate, ampicillin and the cephalosporin-cefoxitin. Conversely, susceptibility was demonstrated for the remaining tested antimicrobials. Genomic profiling identified 31 ARG, 10 VF genes and 6 prophage sequences within the E. oligotrophicus genome. This study provides the first evidence of E. oligotrophicus as a causative agent of BM, expanding the known spectrum of pathogens affecting the dairy industry by delivering the second complete genome of E. oligotrophicus available globally. The identification of 31 ARG, 10 VF, and 6 prophage sequences underscore the potential pathogenic risk and environmental resilience of this isolate. These findings highlight the critical role of WGS-based surveillance in identifying non-conventional mastitis pathogens and underscore the need for targeted mitigation strategies in veterinary medicine.

Animals↗

PubMed2006

Evolutionarily distinct residues in the uncoupling protein UCP1 are essential for its characteristic basal proton conductance.

The uncoupling proteins (UCPs) are mitochondrial transporters that modulate the efficiency of oxidative phosphorylation. Members of this family have been described in many phyla within the animal and plant kingdoms, as well as in fungi. The mammalian uncoupling protein UCP1 is activated by fatty acids and inhibited by nucleotides. In the absence of both regulators, UCP1 presents a high ohmic proton conductance that is a unique property of this carrier. The increasing number of protein sequences available has enabled us to apply a sequence analysis approach to investigate transporter function. We reconstructed a robust phylogeny of UCPs and used comparative sequence analysis to search for phylogenetically shared derived sequence features that may confer distinct properties on UCP1. We assessed the functional relevance of shared derived UCP1 residues by substituting them with their counterparts in UCP2, and expressing the protein chimeras in yeast. We found that substitution of both Glu134 and Met140 abolishes the basal proton permeability of UCP1 while preserving fatty acid activation and its nucleotide inhibition.

Amino Acid Sequence↗

PubMed2000

A cytochrome P4501B gene from a fish, Pleuronectes platessa.

Tetrapod cytochrome P4501 family (CYP1A1, CYP1A2 and CYP1B1) enzymes are most active in hydroxylating a variety of environmental contaminants including polyaromatic hydrocarbons (PAH), planar polychlorinated biphenyls and arylamines and thus play a pivotal role in the toxicology of these compounds. Mammalian CYP1A1 and CYP1A2 genes appear to have diverged after the evolutionary emergence of mammals, whereas fish species apparently possess only one CYP1A family gene, and fish CYP1A enzymes exhibit properties of both of the mammalian isoforms. We have isolated a further CYP1 family gene from a marine flatfish (plaice; Pleuronectes platessa), which, on the basis of exon organisation and sequence similarity, can be assigned as a piscine CYP1B. Its deduced amino acid sequence shows the closest (54%) identity to mammalian CYP1B1 proteins and, on the basis of molecular modeling studies, shows a high degree of positional and structural conservation of the substrate contacting amino acid residues in its putative active site when compared to other CYP1 enzymes. Phylogenetic analysis of fish and mammalian CYP1 family sequences indicates that the plaice CYP1B and mammalian CYP1B1 genes share a common ancestry. Plaice CYP1B has a more restricted tissue expression profile than the previously isolated plaice CYP1A, only being detectable, by Northern blotting, in gill tissue. In contrast to CYP1A, which shows extensive PAH-dependent induction in a variety of tissues, plaice CYP1B appears unresponsive to treatment with a prototypical PAH-type inducer, beta-naphthoflavone (BNF).

Amino Acid Sequence↗