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PubMed1998

Analysis of genetic information of an insect picorna-like virus, infectious flacherie virus of silkworm: evidence for evolutionary relationships among insect, mammalian and plant picorna(-like) viruses.

We synthesized the cDNAs of an insect picornavirus, infectious flacherie virus of silkworm (IFV), genomic RNA and inserted it into a bacterial plasmid (pUC119). The 9,650 nucleotides (nts) sequence except for the poly(A) tail was obtained from the cloned cDNAs, and the sequence integrity was confirmed by primer extension and direct RNA sequencing. The sequence has a large open reading frame (ORF) of 9,255 nts (3,085 codons) flanked by the short 5' non-coding region (156 nts) and by the rather long 3' non-coding (239 nts). The structural proteins VP3, 4, 1 and 2 were located at the N-terminus of the polyprotein in this order and were preceded by a tentative small peptide. Computer analysis identified the sequences similar to the consensus sequences of 2C (helicase?), 3C (protease), and 3D (RNA polymerase) conserved among mammalian and plant picorna(-like) viruses. In addition, the predicted genome organization of IFV was quite similar to those of picornaviruses. Further analyses of the characteristics of the genome structure and a tentative phylogenetic tree constructed on the basis of the amino acid sequence similarity emphasized the evolutionary relationships among the insect and plant viruses.

Adenoviridae↗
PubMed1998

Molecular characterization of Coxiella burnetii isolates.

Restriction fragment length polymorphism (RFLP) was used for the differentiation of 80 Coxiella burnetii isolates derived from animals and humans in Europe, USA, Africa and Asia. After NotI restriction of total C. burnetii DNA and pulsed field gel electrophoresis (PFGE) 20 different restriction patterns were distinguished. The index of discrimination for this typing system was 0.86. Comparison and phylogenetic analysis of the different RFLP patterns revealed evolutionary relationships among groups that corresponded to the geographical origin of the isolates. This finding was confirmed by genetic mapping. No correlation between restriction group and virulence of isolates was detected.

Animals↗
PubMed2025

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories.

Tumor evolution is driven by various mutational processes, ranging from single-nucleotide variants (SNVs) to large structural variants (SVs) to dynamic shifts in DNA methylation. Current short-read sequencing methods struggle to accurately capture the full spectrum of these genomic and epigenomic alterations due to inherent technical limitations. To overcome that, here we introduce an approach for long-read sequencing of single-cell derived subclones, and use it to profile 23 subclones of a mouse melanoma cell line, characterized with distinct growth phenotypes and treatment responses. We develop a computational framework for harmonization and joint analysis of different variant types in the evolutionary context. Uniquely, our framework enables detection of recurrent amplifications of putative driver genes, generated by independent SVs across different lineages, suggesting parallel evolution. In addition, our approach revealed gradual and lineage-specific methylation changes associated with aggressive clonal phenotypes. We also show our set of phylogeny-constrained variant calls along with openly released sequencing data can be a valuable resource for the development of new computational methods.

Journal Article↗
PubMed2003

Evolution of bacterial and archaeal multicomponent monooxygenases.

We report the results of a comparative analysis of the sequences of multicomponent monooxygenases, a family of enzymes of great interest for bioremediation of contaminated soil. We show that their function, in terms of substrate specificity, can be deduced from their subunit organization and composition, that rearrangements of subunits as well as recruitments of new ones can be used to explain their different properties and functionalities, and that the observed pattern can be rationalized invoking a number of evolutionary events, including horizontal gene transfer. Our analysis highlights the plasticity and modularity of this family of enzymes, which might very well be the reason underlying the extremely rapid emergence of new bacterial strains able to grow on contaminated soils.

Archaea↗
PubMed2001

The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number.

Extensive cDNA analysis demonstrated that all human and mouse protocadherin-beta genes are one-exon genes. The protein sequences of these genes are highly conserved, especially the three most membrane-proximal extracellular domains. Phylogenetic analysis suggested that this unique gene family evolved by duplication of one single protocadherin-beta gene to 15 copies. The final difference in the number of protocadherin-beta genes in man (#19) and mouse (#22) is probably caused by duplications later in evolution. The complex relationship between human and mouse genes and the lack of pseudogenes in the mouse protocadherin-beta gene cluster suggest a species-specific evolutionary pressure for maintenance of numerous protocadherin-beta genes.

Amino Acid Sequence↗
PubMed2005

Mutational risk in highly repetitive exon ORF15 of the RPGR multidisease gene is not associated with haplotype background.

Exon ORF15 is an alternative exon in the retinitis pigmentosa GTPase regulator (RPGR) gene containing a highly repetitive, purine-rich internal region. It constitutes a mutational hot spot giving rise to a group of heterogeneous X-linked retinal disorders. We sought to determine whether non-pathogenic substitutions and sequence length variations in the repetitive sequence have an influence on the risk of pathogenic exon ORF15 mutations. The type and distribution of exon ORF15 polymorphisms were assessed by genotyping 107 healthy German males using standard procedures. Polymorphisms were grouped into haplotypes and their frequencies determined in normal controls and previously analyzed patients with X-linked retinitis pigmentosa (XLRP). In the control group we identified 6 complex variants of the most common, ancestral exon ORF15 allele corresponding to the GenBank reference sequence (accession no. AF286472). Exon ORF15 mutations in XLRP patients were associated with the ancestral allele in 75% of affected cases. Four of the most recent founder haplotypes termed H3, H4, H6 and H7 were not identified in the patient samples. Our analysis and review of polymorphism data from the published literature suggests the presence of common exon ORF15 haplotypes in the European population. While the mutational risk in the RPGR gene appears not to be altered by the haplotype background, exon ORF15 haplotype analysis may be useful for tracing the evolutionary history of RP3-associated diseases.

Exons↗
PubMed1995

Use of spectral analysis to test hypotheses on the origin of pinnipeds.

The evolutionary origin of the pinnipeds (seals, sea lions, and walruses) is still uncertain. Most authors support a hypothesis of a monophyletic origin of the pinnipeds from a caniform carnivore. A minority view suggests a diphyletic origin with true seals being related to the mustelids (otters and ferrets). The phylogenetic relationships of the walrus to other pinniped and carnivore families are also still particularly problematic. Here we examined the relative support for mono- and diphyletic hypotheses using DNA sequence data from the mitochondrial small subunit (12S) rRNA and cytochrome b genes. We first analyzed a small group of taxa representing the three pinniped families (Phocidae, Otariidae, and Odobenidae) and caniform carnivore families thought to be related to them. We inferred phylogenetic reconstructions from DNA sequence data using standard parsimony and neighbor-joining algorithms for phylogenetic inference as well as a new method called spectral analysis (Hendy and Penny) in which phylogenetic information is displayed independently of any selected tree. We identified and compensated for potential sources of error known to lead to selection of incorrect phylogenetic trees. These include sampling error, unequal evolutionary rates on lineages, unequal nucleotide composition among lineages, unequal rates of change at different sites, and inappropriate tree selection criteria. To correct for these errors, we performed additional transformations of the observed substitution patterns in the sequence data, applied more stringent structural constraints to the analyses, and included several additional taxa to help resolve long, unbranched lineages in the tree. We find that there is strong support for a monophyletic origin of the pinnipeds from within the caniform carnivores, close to the bear/raccoon/panda radiation. Evidence for a diphyletic origin was very weak and can be partially attributed to unequal nucleotide compositions among the taxa analyzed. Subsequently, there is slightly more evidence for grouping the walrus with the eared seals versus the true seals. A more conservative interpretation, however, is that the walrus is an early, but not the first, independent divergence from the common pinniped ancestor.

Algorithms↗
PubMed1995

The evolutionary relationships of two families of cottoid fishes of Lake Baikal (east Siberia) as suggested by analysis of mitochondrial DNA.

Fragments of mtDNA genes Cyt B, ATPase 6, and ATPase 8 of six cottoid fishes species of Lake Baikal (East Siberia) were amplified and sequenced. In addition mtDNAs of the same fish were subjected to restriction analysis. The data obtained were used to construct phylogenetic trees. The topology of the ATPase tree differs from those of the Res (restriction) and Cyt B trees. Clustering of species within the trees confirms the viewpoint of Taliev (1955, Baicalian Sculpins (Cottoidei)) according to which Baikalian cottoids originate from two ancestral forms. The times of branching obtained do not confirm the existing viewpoint according to which the two golomyankas (Comephorus baicalensis and Comephorus dybowskii) are pre-Baikal (Myocene) relicts: these two species may have originated 1.2-1.8 million years ago in Baikal, and they seem to represent an example of rapid morphological evolution which resulted in the formation of a new family.

Animals↗
PubMed1992

The evolutionary history of the sinica-group of macaque monkeys as revealed by mtDNA restriction site analysis.

We estimated the phylogenetic relationships of mitochondrial DNA haplotypes within the sinica-group of macaques, which includes Macaca sinica, M. radiata, M. thibetana, M. assamensis, and possibly M. arctoides. Some effort was made to detect intraspecific variation by sampling individuals from different parts of the species' range or from different matrilines. In the case of M. assamensis, individuals were sampled from both subspecies (M. assamensis assamensis and M. assamensis pelops). Total genomic DNA was extracted from blood samples and cut with a battery of 16 restriction endonucleases. A total of 97 restriction sites were mapped for these enzymes in the sinica-group and M. nemestrina, which was used as an outgroup. Phylogenetic trees constructed by both the maximum parsimony method and the neighbor-joining method were highly congruent. A bootstrap analysis of the maximum parsimony tree indicated a high degree of confidence to the association of particular haplotypes within the 80% majority rule consensus tree. An exhaustive search of all possible trees also supported this topology, although one haplotype had to be eliminated from this analysis to save computer time. The results were also unaffected by weighting the character state changes in favor of site gains over site losses. The mtDNA phylogeny produced here differs from trees based on morphology and allozymes in three ways: M. sinica and M. radiata sit in two different branches of the tree; the two subspecies of M. assamensis are separated from one another; and M. arctoides consistently fell outside the rest of the sinica-group.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2001

Evolutionary conservation of the folding nucleus.

Here, we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein (AcP) folding nucleus residues are significantly more conserved than the rest of the protein. Two aspects of our study are especially important: (i) grouping of amino acid residues into classes according to their physical-chemical properties and (ii) proper normalization of amino acid probabilities that reflects the fact that evolutionary pressure to conserve some amino acid types may itself affect concentration of various amino acid types in protein families. Neglect of any of those two factors may make physical and biological "signals" from conservation profiles disappear.

Conserved Sequence↗
PubMed1996

Analysis of molecular variance (AMOVA) of Y-chromosome-specific microsatellites in two closely related human populations.

The analysis of seven Y-chromosome-specific microsatellite loci revealed a high level of polymorphism in two closely related human populations (Dutch, n = 89, and German, n = 70). Four of these loci were found to generate at least 77 different haplotypes, only 15 of which were shared by the two populations. These results demonstrate that highly informative PCR-based DNA typing of the Y chromosome is now feasible. Assuming a stepwise mutation model, a network comprising all minimum spanning evolutionary trees connecting the haplotypes was constructed. Analysis of molecular variance based upon this network indicated that the within-population heterogeneity with respect to haplotype descent was significantly smaller than the between-population heterogeneity, suggesting that males were more closely related to males from their own population as opposed to males from the other population. These findings suggest that Y-chromosomal microsatellites might be very useful not only for forensic purposes but also in association studies of multifactorial traits, allowing the characterization of the level of genetic distinctiveness of supposedly inbred or isolated populations and discrimination even between closely related populations.

Analysis of Variance↗
PubMed1989

Interactive analysis of phylogeny and character evolution using the computer program MacClade.

Computer programs for phylogenetic analysis have been important tools in systematics and evolutionary biology, but most have been designed primarily for the reconstruction of phylogenetic trees and not the interpretation of patterns of character evolution. Described here is the computer program MacClade, designed for interactive analysis of character evolution and phylogeny. For a given tree and a matrix of character data, MacClade displays its reconstruction of character evolution by shading the branches of the tree to indicate ancestral states. Trees can be manipulated for instance by picking up and moving branches. Assumptions underlying the reconstruction of character evolution can be varied extensively. With these manipulations and MacClade's graphical feedback, one can explore the relationships among phylogenetic trees, character data, assumptions and interpretations of character evolution. MacClade has extensive facilities for editing data, displaying various summaries of character evolution in charts and diagrams, and printing.

Animals↗
PubMed1989

Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree.

How many primary lineages of life exist and what are their evolutionary relationships? These are fundamental but highly controversial issues. Woese and co-workers propose that archaebacteria, eubacteria and eukaryotes are the three primary lines of descent and their relationships can be represented by Fig. 1a (the 'archaebacterial tree') if one neglects the root of the tree. In contrast, Lake claims that archaebacteria are paraphyletic, and he groups eocytes (extremely thermophilic, sulphur-dependent bacteria) with eukaryotes, and halobacteria with eubacteria (the 'eocyte tree', Fig. 1b). Lake's view has gained considerable support as a result of an analysis of small subunit ribosomal RNA sequence data by a new approach, the evolutionary parsimony method. Here we report that analysis of small subunit data by the neighbour-joining and maximum parasimony methods favours the archaebacterial tree and that computer simulations using either the archaebacterial or the eocyte tree as a model tree show that the probability of recovering the model tree is very high (greater than 90 per cent) for both the neighbour-joining and maximum parsimony methods but is relatively low for the evolutionary parsimony method. Moreover, analysis of large subunit rRNA sequences by all three methods strongly favours the archaebacterial tree.

Archaea↗
PubMed2004

Comparative genomics: the evolutionary history of the Bcl-2 family.

The Bcl-2 family is a huge family composed of various members, occurring in all animals, which are key regulators of apoptosis, the cell death program critical for cell survival and development, tissue homeostasis, and protection against pathogens. The members of the Bcl-2 family can be divided into pro-apoptotic and anti-apoptotic proteins. A delicate balance between these members exists in each cell and the regulations of these two groups of proteins determines whether the cell survives or undergoes apoptosis. Bcl-2 family proteins are characterized by distinct domains. All members possess at least one of the four motifs known as Bcl-2 homology domains (BH1 to BH4). Most pro-survival members which can inhibit apoptosis facing a wide variety of cytotoxic insults, contain at least BH1 and BH2 domains; those most similar to Bcl-2 have all four BH domains. All the pro-apoptosis family members possess BH3 domain which is the central domain. For the first time, a global phylogenetic analysis of all Bcl-2 family members is presented here. We have analyzed the genes known so far that have a different composition of the functional domains BH1, BH2, BH3 and BH4. The analyses were performed both on complete sequences (124 sites analyzed) and on single domains. We present the results obtained using both approaches. We have also analyzed the amino acid profile and the degree of conservation of the BH3 domains of pro- and anti-apoptotic proteins. The results of our phylogenetic analyses show that a clear-cut clustering into pro- and anti-apoptotic products, reproducible with different evolutionary methods, could also be obtained by analyzing restricted areas such as the BH1 and BH2 domains. It is noteworthy that even when the analysis is performed only on the BH3 domain, we have two clear-cut clusters. The evolutionary analysis of gene family members is a valuable tool to predict their functions and guide experimental assays to validate predictions. Once the functions of all the components are known, it will be possible to study the process in a holistic way.

Amino Acid Sequence↗
PubMed2006

Detection and identification of avian, duck, and goose reoviruses by RT-PCR: goose and duck reoviruses are part of the same genogroup in the genus Orthoreovirus.

A reverse transcription-polymerase chain reaction (RT-PCR) procedure for the detection of avian, duck, and goose reovirus (ARV, DRV, and GRV) RNA from cell culture supernatant and clinical samples was established. Based on multiple sequence alignment, a pair of degenerate primers was selected and synthesized. The amplified, cloned, and sequenced 598-base-pair products from the sigmaA-encoding gene fragment from 16 isolates (ranging over 30 years) indicated that the primer regions were well conserved. The sensitivity of this method was determined to be 10(-2) PFU. The specificity of the RT-PCR method was determined by testing specimens containing avian influenza A viruses, Newcastle disease virus, and infectious bronchitis virus, all of which yielded negative results with no discernible background. The efficiency of the system for detection of ARV, DRV, and GRV directly in 71/83 clinical samples was confirmed. The nucleotide sequence analysis indicated that DRV and GRV isolated from China in different locales and years were closely related, showing 97.4-100% homology to each other, but with only 86.7-88.5% identity to DRV 89026. The nucleotide and amino acid sequence identities in the amplified sigmaA-encoding gene were 74.2-78.4% and 86.9-92.0%, respectively, between duck/goose and chicken species. Phylogenetic analysis indicated that GRV and DRV aggregated into the same specified genogroup within subgroup II of the genus Orthoreovirus and are more closely related to ARV than to Nelson Bay virus. Overall, this study developed a sensitive and specific technique for the identification ARV, DRV, and GRV, and sequencing analysis has enhanced our understanding of the evolutionary relationship between ARV, DRV, and GRV.

Animals↗
PubMed1987

An analysis of the interrelationship of nuclear and plasma triiodothyronine in the sea lamprey, lake trout, and rat: evolutionary considerations.

We have studied the interrelationship of plasma and hepatic nuclear T3 in two lower vertebrates, lake trout and sea lamprey. Specific nuclear T3-binding sites were observed in liver of both species. Binding affinities for T3 and several analogs in lamprey and trout were similar to those in rat liver. The findings of identical sedimentation coefficients, Stokes radii, and mol wt suggest a high degree of homology of the receptor molecule among these species. In lamprey ammocoete, both total (approximately 26 nM) and free (approximately 0.12 nM) T3 concentrations were 7- to 36-fold higher than in the trout or rat. The concentration of free T4 was 4 times greater than that in rat plasma despite somewhat lower total T4 levels. This resulted from a 6 times lesser binding of T4 by ammocoete plasma. Total and free T3 and T4 levels fell sharply during transformation to the adult form. In trout, a 27 times greater concentration of free T3 in hepatic nuclei than in cytosol, previously documented for rat liver, gave evidence of the early evolution of an active transport process between these compartments. Analysis of [125I]T3 interchange in trout indicated the existence of two kinetically distinct compartments within the liver, an outer compartment in rapid equilibrium with plasma, and a slowly equilibrating compartment decaying with a t1/2 of 3.7 h. T3 associated with the nuclear receptor appeared to be in equilibrium with the slower hepatic compartment. Despite the apparent resemblance of T3 receptors in these species to those in the rat, administration of T3 (200 micrograms/100 g BW for 4 days) to trout caused no increase in hepatic oxygen consumption or the activities of malic enzyme or alpha-glycerophosphate dehydrogenase. Further, such treatment produced no consistent changes in hepatic mRNA activity profiles analyzed by two-dimensional electrophoresis of in vitro translational products. As suggested by the high free T3 concentration in the larval lamprey ammocoete, T3 in early vertebrates may have a primarily developmental function, manifested over a restricted time frame.

Animals↗
PubMed2003

Common evolutionary origin of mitochondrial and rickettsial respiratory chains.

Comprehensive phylogenetic analysis of the subunits of respiratory chain was carried out using a variety of mitochondrial and bacterial sequences including those from all unfinished alpha-proteobacterial genomes known to date. Maximum likelihood, neighbor-joining, and maximum parsimony consensus trees, based on four proton-translocating complexes, placed mitochondria as a sister group to the order Rickettsiales of obligate endosymbiotic bacteria to the exclusion of free-living alpha-proteobacteria. Thus, phylogenetic relationship of most eukaryotic respiratory enzymes conforms to canonical pattern of mitochondrial ancestry, prior established in analyses of ribosomal RNAs, which are encoded by residual mitochondrial genomes. These data suggest that mitochondria may have derived from a reduced intracellular bacterium and that respiration may be the only evolutionary novelty brought into eukaryotes by mitochondrial endosymbiont.

Alphaproteobacteria↗
PubMed2001

Flagellin gene sequence variation in the genus Pseudomonas.

Flagellin gene (fliC) sequences from 18 strains of Pseudomonas sensu stricto representing 8 different species, and 9 representative fliC sequences from other members of the gamma sub-division of proteobacteria, were compared. Analysis was performed on N-terminal, C-terminal and whole fliC sequences. The fliC analyses confirmed the inferred relationship between P. mendocina, P. oleovorans and P. aeruginosa based on 16S rRNA sequence comparisons. In addition, the analyses indicated that P. putida PRS2000 was closely related to P. fluorescens SBW25 and P. fluorescens NCIMB 9046T, but suggested that P. putida PaW8 and P. putida PRS2000 were more closely related to other Pseudomonas spp. than they were to each other. There were a number of inconsistencies in inferred evolutionary relationships between strains, depending on the analysis performed. In particular, whole flagellin gene comparisons often differed from those obtained using N- and C-terminal sequences. However, there were also inconsistencies between the terminal region analyses, suggesting that phylogenetic relationships inferred on the basis of fliC sequence should be treated with caution. Although the central domain of fliC is highly variable between Pseudomonas strains, there was evidence of sequence similarities between the central domains of different Pseudomonas fliC sequences. This indicates the possibility of recombination in the central domain of fliC genes within Pseudomonas species, and between these genes and those from other bacteria.

DNA, Bacterial↗