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PubMed1999

Molecular phylogeny of phi29-like phages and their evolutionary relatedness to other protein-primed replicating phages and other phages hosted by gram-positive bacteria.

The phi29-like phage genus of Podoviridae family contains phages B103, BS32, GA-1, M2, Nf, phi15, phi29, and PZA that all infect Bacillus subtilis. They have very similar morphology and their genomes consist of linear double-stranded DNA of approximately 20 kb. The nucleotide sequences of individual genomes or their parts determined thus far show that these phages evolved from a common ancestor. A terminal protein (TP) that is covalently bound to the DNA 5'-end primes DNA replication of these phages. The same mechanism of DNA replication is used by the Cp-1 related phages (also members of the Podoviridae family) and by the phage PRD1 (member of the Tectoviridae family). Based on the complete or partial genomic sequence data of these phages it was possible to analyze the evolutionary relationship within the phi29-like phage genus as well as to other protein-primed replicating phages. Noncoding regions containing origins of replication were used in the analysis, as well as amino acid sequences of DNA polymerases, and with the phi29-like phages also amino acid sequences of the terminal proteins and of the gene 17 protein product, an accessory component of bacteriophage DNA replicating machinery. Included in the analysis are also results of a comparison of these phage DNAs with the prophages present in the Bacillus subtilis genome. Based on this complex analysis we define and describe in more detail the evolutionary branches of phi29-like phages, one branch consisting of phages BS32, phi15, phi29, and PZA, the second branch composed of phages B103, M2, and Nf, and the third branch having phage GA-1 as its sole member. In addition, amino acid sequences of holins, proteins involved in phage lysis were used to extend the evolutionary study to other phages infecting Gram-positive bacteria. The analysis based on the amino acid sequences of holins showed several weak points in present bacteriophage classification.

Amino Acid Sequence↗
PubMed2005

Mosaics of convergences and noise in morphological phylogenies: what's in a viverrid-like carnivoran?

Adaptive convergence in morphological characters has not been thoroughly investigated, and the processes by which phylogenetic relationships may be misled by morphological convergence remains unclear. We undertook a case study on the morphological evolution of viverrid-like feliformians (Nandinia, Cryptoprocta, Fossa, Eupleres, Prionodon) and built the largest morphological matrix concerning the suborder Feliformia to date. A total of 349 characters grouped into four anatomical partitions were used for all species of Viverridae and viverrid-like taxa plus representatives of the Felidae, Hyaenidae, Herpestidae, and one Malagasy mongoose. Recent molecular phylogenetic analyses suggest that viverrid-like morphotypes appeared independently at least three times during feliformian evolution. We thus used a synthetic molecular tree to assess morphological evolutionary patterns characterizing the viverrid-like taxa. We examined phylogenetic signal, convergence and noise in morphological characters using (a) tree-length distribution (g1), (b) partitioned Bremer support, (c) RI values and their distribution, (d) respective contributions of diagnostic synapomorphies at the nodes for each partition, (e) patterns of shared convergences among viverrid-like taxa and other feliformian lineages, (f) tree-length differences among alternative hypotheses, and (g) the successive removal of convergent character states from the original matrix. In addition, the lability of complex morphological structures was assessed by mapping them onto the synthetic molecular tree. The unconstrained morphological analysis yielded phylogenetic groupings that closely reflected traditional classification. The use of a synthetic molecular tree (constraint) combined with our thorough morphological investigations revealed the mosaics of convergences likely to have contributed to part of the historical uncertainty over viverrid classification. It also showed that complex morphological structures could be subjected to reversible evolutionary trends. The morphological matrix proved useful in characterizing several feliformian clades with diagnostic synapomorphies. These results support the removal from the traditionally held Viverridae of several viverrid-like taxa into three distinct families: Nandiniidae (Nandinia), Prionodontidae (Prionodon), and the newly defined Eupleridae (including Cryptoprocta, Fossa, Eupleres plus all "mongoose-like" Malagasy taxa). No clearly "phylogenetically misleading" data subsets could be identified, and the great majority of morphological convergences appeared to be nonadaptive. The multiple approaches used in this study revealed that the most disruptive element with regards to morphological phylogenetic reconstruction was noise, which blured the expression of phylogenetic signal. This study demonstrates the crucial need to consider independent (molecular) phylogenies in order to produce reliable evolutionary hypotheses and should promote a new approach to the definition of morphological characters in mammals. [Constrained analysis; convergence; evolutionary scenario; Feliformia; morphology; noise; phylogenetic signal; phylogeny; Viverridae.].

Anatomy, Comparative↗
PubMed1995

The marine red alga Chondrus crispus has a highly divergent beta-tubulin gene with a characteristic 5' intron: functional and evolutionary implications.

We characterized a nuclear gene and its corresponding cDNA encoding beta-tubulin (gene TubB1) of the marine red alga Chondrus crispus. The deduced TubB1 protein is the most divergent beta-tubulin so far reported with only 64 to 69% amino acid identity relative to other beta-tubulins from higher and lower eukaryotes. Our analysis reveals that TubB1 has an accelerated evolutionary rate probably due to a release of functional constraints in connexion with a specialization of microtubular structures in rhodophytes. It further indicates that isoform diversity and functional differentiation of tubulins in eukaryotic cells may be controlled by independent selective constraints. TubB1 has a short spliceosomal intron at its 5' end which seems to be a characteristic feature of nuclear protein-coding genes from rhodophytes. The splice junctions of the four known rhodophyte introns comply well with the corresponding consensus sequences of higher plants in agreement with previous suggestions from phylogenetic inference that red algae and green plants may be sister groups. The paucity and asymmetrical location of introns in rhodophyte genes can be explained by differential intron loss due to conversion of genes by homologous recombination with cDNAs corresponding to reverse transcribed mRNAs or partially spliced pre-mRNAs, respectively. The identification of an intron containing TubB1 cDNA in C. crispus confirms that pre-mRNAs can escape both splicing and degradation in the nucleus prior to transport into the cytoplasm. Differential Southern hybridizations under non-stringent conditions with homologous and heterologous probes suggest that C. crispus contains a second degenerate beta-tubulin gene (or pseudogene?) which, however, is only distantly related to TubB1 as it is to the more conserved homologues of other organisms.

Amino Acid Sequence↗
PubMed2005

Identification of a novel class of mammalian phosphoinositol-specific phospholipase C enzymes.

Phosphoinositol (PhoIns)-specific phospholipase C enzymes (PLCs) are central to the inositol lipid signaling pathways and contribute to intracellular Ca2+ release and protein kinase C activation. Five distinct classes of PhoIns-specific PLCs are known to exist in mammals, which are activated by membrane receptor-mediated events. Here we have identified a sixth class of PhoIns-specific PLC with a novel domain structure, which we have termed PLC-eta. Two putative PLC-eta enzymes were identified in humans and in mice. Sequence analysis revealed that residues implicated in substrate binding and catalysis from other PhoIns-specific PLCs are conserved in the novel enzymes. PLC-eta enzymes are most closely related to the PLC-delta class and share a close evolutionary relationship with other PLC isozymes. EST analysis and RT-PCR data suggest that PLC-eta enzymes are expressed in several cell types and, by analogy with other mammalian PhoIns-specific PLCs, are likely to be involved in signal transduction pathways.

Amino Acid Sequence↗
PubMed2004

Three-dimensional window analysis for detecting positive selection at structural regions of proteins.

Detection of natural selection operating at the amino acid sequence level is important in the study of molecular evolution. Single-site analysis and one-dimensional window analysis can be used to detect selection when the biological functions of amino acid sites are unknown. Single-site analysis is useful when selection operates more or less constantly over evolutionary time, but less so when selection operates temporarily. One-dimensional window analysis is more sensitive than single-site analysis when the functions of amino acid sites in close proximity in the linear sequence are similar, although this is not always the case. Here I present a three-dimensional window analysis method for detecting selection given the three-dimensional structure of the protein of interest. In the three-dimensional structure, the window is defined as the sphere centered on the alpha-carbon of an amino acid site. The window size is the radius of the sphere. The sites whose alpha-carbons are included in the window are grouped for the neutrality test. The window is moved within the three-dimensional structure by sequentially moving the central site along the primary amino acid sequence. To detect positive selection, it may also be useful to group the surface-exposed sites in the window separately. Three-dimensional window analysis appears not only to be more sensitive than single-site analysis and one-dimensional window analysis but also to provide similar specificity for inferring positive selection in the analyses of the hemagglutinin and neuraminidase genes of human influenza A viruses. This method, however, may fail to detect selection when it operates only on a particular site, in which case single-site analysis may be preferred, although a large number of sequences is required.

Amino Acid Substitution↗
PubMed2002

Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence.

Phylogenetic analysis of about 200 strains of Salmonella, Shigella, and Escherichia coli was carried out using the nucleotide sequence of the gene for DNA gyrase B (gyrB), which was determined by directly sequencing PCR fragments. The results establish a new phylogenetic tree for the classification of Salmonella, Shigella, and Escherichia coli in which Salmonella forms a cluster separate from but closely related to Shigella and E. coli. In comparison with 16S rRNA analysis, the gyrB sequences indicated a greater evolutionary divergence for the bacteria. Thus, in screening for the presence of bacteria, the gyrB gene might be a useful tool for differentiating between closely related species of bacteria such as Shigella spp. and E. coli. At present, 16S rRNA sequence analysis is an accurate and rapid method for identifying most unknown bacteria to the genus level because the highly conserved 16S rRNA region is easy to amplify; however, analysis of the more variable gyrB sequence region can identify unknown bacteria to the species level. In summary, we have shown that gyrB sequence analysis is a useful alternative to 16S rRNA analysis for constructing the phylogenetic relationships of bacteria, in particular for the classification of closely related bacterial species.

DNA Gyrase↗
PubMed1996

Microsatellites and PCR genomic analysis.

Microsatellites form a significant proportion of the growing family of repetitive DNA sequences, widely dispersed in the human genome. Due to their ubiquity, PCR (polymerase chain reaction) typability, Mendelian co-dominant inheritance, and extreme polymorphism, microsatellites have assumed an increasingly important role as markers in the genome. Apart from their obvious applications in genome mapping and positional cloning, these markers have been applied in fields as disparate as tumour biology, personal identification, population genetic analysis, and the construction of human evolutionary trees. Microsatellites are associated with human disease, not only as markers of risk but also directly in disease aetiopathogenesis, providing new insights into non-Mendelian inheritance; the replication, repair, and mutation of eukaryotic DNA; the regulation of gene transcription; and protein-protein interactions. These insights have resulted in novel paradigms for oncogenesis and neurological disease.

Chromosome Mapping↗
PubMed2001

Occurrence of neanderthal features in mandibles from the Atapuerca-SH site.

Analysis of variation and distribution of evolutionary novelties is meaningful in understanding evolutionary processes. The mandible, as a morphological complex, comprises a large number of derived Neanderthal features. The present study investigates whether the features usually considered as European lineage apomorphies evolved independently; the occurrence of these features is studied in the mandibles from the Sima de los Huesos (SH) site (Atapuerca, Spain). For comparative purposes, a large sample of Neanderthal mandibles as well as older fossil Homo specimens have been used for the study. Chi-square tests were employed to test for independence. The SH mandibles present a set of features that clearly show the basic architecture of the Neanderthal mandible. A highly significant association is detected in the variation of the position of the mental foramen, the lateral prominence, and the anterior marginal tubercle, as well as in the development of retromolar space. However, a much weaker association is detected in the features of the internal aspect of the mandible, with a few exceptions. Features of the external aspect of the mandible occur chronologically earlier than those observed in the internal aspect. The hypothesis that two distinct and consecutive morphological processes have driven the emergence of the European lineage throughout the Middle Pleistocene is proposed. A first transformation affects the mandible by means of backwards displacement of the structures located at the external aspect, as well as the position of the condyle. A second process would modify the features of the internal aspect of the mandible, in which the relief of the masseteric and pterygoid fossae are affected, in association with a spatial rearrangement of the corpus and ramus. Analyzed individually, some of the considered features may be questioned as Neanderthal apomorphies (Trinkaus,1993; Franciscus and Trinkaus, 995); however, the joint occurrence of many of them suggests that the complex is an evolutionary novelty.

Adolescent↗
PubMed2006

Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes.

Autonomous transposable elements, generally considered as junk and selfish, encode transposition proteins that can bind, copy, break, join or degrade nucleic acids as well as process or interact with other proteins. Such a repertoire of activities might be of interest for the host cell. There is indeed substantial evidence that mobile DNA can serve as a dynamic reservoir for new cellular functions. Transposable element genes encoding transposase, integrase, reverse transcriptase as well as structural and envelope proteins have been repeatedly recruited by their host during evolution in most eukaryotic lineages. Such domesticated sequences protect us against infections, are necessary for our reproduction, allow the replication of our chromosomes and control cell proliferation and death; others are essential for plant development. Many new candidates for domesticated sequences have been revealed by sequencing projects. Their functional analysis will uncover new aspects of evolutionary alchemy, the turning of junk into gold within genomes.

Animals↗
PubMed1993

Nucleotide sequence analysis of the 5.8S rDNA and adjacent ITS2 region of Candida albicans and related species.

We have determined the nucleotide sequence for the DNA encoding the 5.8S RNAs and downstream internal transcribed spacer (ITS2) regions for Candida albicans and the taxonomically related species C. parapsilosis, C. tropicalis, C. glabrata and C. krusei. Phylogenetic analysis of all known fungal 5.8S RNA sequences revealed a close relationship between C. tropicalis and C. parapsilosis, and to a lesser extent C. albicans within the yeast-like fungi. This group can itself be delineated from predominantly filamentous species. The more distal relationships between Candida (Torulopsis) glabrata and C. krusei support previous findings based on small (18S) ribosomal RNA sequence analysis, suggesting a greater degree of evolutionary divergence of these species from the C. albicans group. Among strains of C. albicans we observed conservation of the ITS2 region at the nucleotide level. Conservation was also observed for a more limited number of C. parapsilosis strains. Although the 3' region of the ITS spacer was species specific, sequence homology was observed in the 5' end within the albicans/parapsilosis/tropicalis group. Our findings suggest a rapid approach to species identification through the use of non-conserved regions flanked by highly conserved, functional domains.

Base Sequence↗
PubMed1994

Colocalization of nestin and vimentin/desmin in skeletal muscle cells demonstrated by three-dimensional fluorescence digital imaging microscopy.

During skeletal muscle development three intermediate filament proteins are expressed: nestin, vimentin, and desmin. Vimentin and desmin belong to the class III intermediate filaments and are closely related to each other, whereas nestin is a more distantly related, class VI, intermediate filament. It was previously observed by conventional immunocytochemistry that the intracellular patterns of nestin, desmin, and vimentin appeared indistinguishable, despite nestin's more distant evolutionary relationship. We here extend this analysis by applying three-dimensional fluorescence digital imaging microscopy to compare the intracellular distribution of nestin with that of desmin, vimentin, actin, and tubulin in G6 human fetal skeletal muscle cells. We show that in vitro differentiation of G6 cells can produce an intermediate filament expression pattern similar to that observed during myogenesis in vivo, i.e., downregulation of vimentin but not of nestin and desmin during myotube maturation. The image analysis demonstrated that the degree of overlap between nestin and desmin/vimentin was very extensive in myoblasts and in multinucleate myotubes in all regions of the cells. In contrast, nestin did not colocalize with tubulin or actin in G6 myoblasts. In particular, nestin immunoreactivity was not detected at the microtubule-organizing center, and it was only sparsely observed at the cell periphery where actin stress fibers were seen. Our data lend further support to the notion that nestin interacts very closely with the two more distantly related class III intermediate filament proteins desmin and vimentin in the entire muscle cell, before and after myotube formation. A comparison of conserved amino acid residues in the different IFs suggest that charged amino acid residues in the alpha-helical rod domain may play a role in the interaction.

Amino Acid Sequence↗
PubMed1999

Specialized conservation of surface loops of myosin: evidence that loops are involved in determining functional characteristics.

The molecular motor myosin has been the focus of considerable structure-function analysis. Of key interest are the portions of the protein that control the rate of ATP hydrolysis, the affinity for actin, and the velocity at which myosin moves actin. Two regions that have been implicated in determining these parameters are the "loop" regions at the junctions of the 25 kDa and 50 kDa domains and the 50 kDa and 20 kDa domains of the protein. However, the sequences of these regions are poorly conserved between different myosin families, suggesting that they are not constrained evolutionarily, and thus are relatively unimportant for myosin function. In order to address this apparent incongruity, we have performed an analysis of relative rates of observed evolutionary change. We found that the sequences of these loop regions appear to be actually more constrained than the sequences of the rest of the myosin molecule, when myosins are compared that are known to be kinetically or developmentally similar. This suggests that these loop regions could play an important role in myosin function and supports the idea that they are involved in modulating the specific kinetic characteristics that functionally differentiate one myosin isoform from another. Apparently "unconserved" loops may generally play a role in determining kinetic properties of enzymes, and similar analyses of relative rates of evolution may prove useful for the study of structure-function relationships in other protein families.

Amino Acid Sequence↗
PubMed1994

The evolution of virulence in parasites and pathogens: reconciliation between two competing hypotheses.

According to conventional wisdom, parasites and pathogens should evolve reduced virulence to their hosts, because more virulent parasites and pathogens are more likely to drive their hosts, and themselves, to extinction. But this view has been criticized for its reliance on group selection. According to an alternative perspective, selection will favor whatever level of virulence maximizes the rate of increase of the parasite or pathogen. This optimum virulence depends on the functional relationship between a parasite or pathogen's transmissibility and its effect on host mortality, with selection often favoring an intermediate degree of virulence. The thesis of this paper is that models in which intermediate levels of virulence are favored lead quite naturally to the further conclusion that parasites and pathogens should-up to a point-become less virulent over time, once the feedbacks between ecological and evolutionary processes are incorporated into the analysis. As a consequence of successive adaptations by the parasite or pathogen, the density of susceptible hosts is reduced, thereby altering the balance between selective forces so as to favor reduced virulence. However, the evolutionarily stable strategy that is achieved is bounded away from complete avirulence. We conclude that models in which intermediate virulence is favored do not necessarily contradict the conventional wisdom in the long run; in fact, these models provide a simple mechanistic explanation for the evolution of reduced virulence.

Animals↗
PubMed1996

Synthesis and analysis of a 640-bp pol region of novel human endogenous retroviral sequences and their evolutionary relationships.

Nucleotide sequence comparisons of the pol gene among 47 retroelements identified two very conserved regions, separated by a span of approximately 640 bp, that have not been previously reported. A set of mixed oligonucleotide primers, 5'-MOP-2 and 3'-MOP-2, homologous to these two conserved pol regions was constructed for use in detection of retroelements. When MOPs-2 were employed in PCR amplification studies, products of about 0.64 kb in size were amplified from human and mouse genomic DNAs and from HIV-1 proviral DNA, but not from negative control plasmid DNAs. The PCR products amplified with MOPs-2 from human LuC-1 teratocarcinoma cell DNA were subcloned and sequenced. Five clones of approximately 0.64 kb in size were identified, and sequence comparisons with all entries in GenBank indicated that these five clones have highest homology, in a range of 64.31 to 98.65%, with the corresponding pol region of HERV-K10 and HM-16 of the human endogenous retrovirus-K (HERV-K) family. Southern hybridizations at high stringency demonstrated that these five clones are present in all human DNAs tested. The evolutionary relationships of these clones with the equivalent pol region of other retroelements were defined by phylogenetic analyses that placed three clones into the HERV-K family and two clones into a new family of human endogenous retroelements. In addition, clone HERV-(K)73 contains the smaller PV1b pol segment that was reported to be selectively expressed in blood leukocytes of patients with polycythemia vera.

Amino Acid Sequence↗
PubMed1991

Evolution and path models in human behavioral genetics.

The evolutionary implications of the path-analysis model most often used in human behavior genetics are examined. With directional selection, a model of pure vertical environmental transmission does not respond in a fully adaptive fashion. Unless the coefficients of transmission are exactly 0.50, the population mean will not equilibrate at the selective optimum over time. If there is both genetic and vertical environmental transmission, then the population mean can equilibrate at the selective optimum. In the presence of genetic transmission, vertical environmental transmission increases population fitness and has a strong effect on the rapid movement of the mean toward the selective optimum. This raises the intriguing paradox of why empirical evidence suggests that vertical environmental transmission is usually small when it possesses such important fitness properties.

Biological Evolution↗
PubMed2001

Characterization of the MHC class I region of the Japanese pufferfish (Fugu rubripes).

A BAC map of the Japanese pufferfish (Fugu) MHC class I region was constructed using a mixture of sequence scanning and sequence-tagged site mapping methodologies. The Fugu MHC class Ia genes are linked to genes which are found within the human classical MHC class II and extended class II regions, a situation which has been found in the MHC of all teleosts mapped so far. The 300-kb contig comprises 24 MHC-related genes and is bounded by six non-MHC genes, which are thought to represent an evolutionary breakpoint within the region. Comparative analysis with both human and zebrafish MHC maps indicates two blocks of genes (KNSL2, ZNF297, DAXX, TAPBP, FLOTILLIN; and PSMB8, PSMB10, PSMB9, ABCB3, FABGL, BRD2, COL11A2, RXRB) which have remained linked over 400 million years and may represent an ancestral arrangement of the vertebrate MHC. Zebrafish and Fugu diverged between 100-200 million years ago and differences exist between these two fish species. The position and number of MHC class Ia genes is not conserved between species, there is an inversion of a block of nine genes centering on the PSMB cluster, and additional genes are present in zebrafish coding for a transport-associated protein and a beta proteasome subunit. The extent of these differences has implications for the extrapolation of fish model organism data to commercial aquaculture species. The data presented here represent the most extensive analysis of a fish MHC class Ia region described so far and clearly delimit the extent of this region in Fugu and, potentially, all teleosts.

Animals↗
PubMed2002

Analysis of a mathematical model for the growth of tumors under the action of external inhibitors.

In this paper we make rigorous analysis to a mathematical model for the growth of nonnecrotic tumors under the action of external inhibitors. By external inhibitor we mean an inhibitor that is either developed from the immune system of the body or administered by medical treatment to distinguish with that secreted by tumor itself. The model modifies a similar model proposed by H. M. Byrne and M. A. J. Chaplain. After simply establishing the well-posedness of the model, we discuss the asymptotic behavior of its solutions by rigorous analysis. The result shows that an evolutionary tumor will finally disappear, or converge to a stationary state (dormant state), or expand unboundedly, depending on which of the four disjoint regions Delta1,..., Delta4 the parameter vector (A1,A2) belongs to, how large the scaled apoptosis number;sigma is, and how large the initial radius R(0) of the tumor is. Finally, we discuss some biological implications of the result, which reveals how a tumor varies when inhibitor supply is increased and nutrient supply is reduced.

Animals↗
PubMed2001

Y chromosome compound haplotypes with the microsatellite markers DXYS265, DXYS266, and DXYS241.

Two newly developed microsatellite markers on Yp11 (DXYS265) and Yq11.21 (DXYS266) and our previously reported marker, on Yp11 (DXYS241), were typed by triplex polymerase chain reaction (PCR) in 102 Japanese, 18 white American, and 17 black American males. The DXYS265 locus revealed three alleles, the DXYS266 locus showed two alleles, while the DXYS241 locus showed five alleles. Nine different compound haplotypes were observed among the males. Of these, two haplotypes were common to all groups, while four were limited to Japanese. Pedigree analysis of 61 Japanese families revealed no mutations of these loci. The triplex PCR developed in this study, as well as the new loci, are useful for tracing paternal lineages in human migration studies and population analysis, in addition to Y chromosome evolutionary studies.

Alleles↗