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PubMed1999

A simple method for estimating the intensity of purifying selection in protein-coding genes.

We propose a method by which the intensity of purifying selection on a functional protein-coding gene is estimated by using three aligned homologous sequences: a processed pseudogene (psi), a functional paralog from the same species (g), and a functional ortholog from a different species (o). For each such trio, we calculate the numbers of nucleotide substitutions along the branches leading to psi and g, i.e., K psi and K(g). If we assume that the mutation rates are the same in the genes and the pseudogenes and that mutations occurring in a pseudogene do not affect the fitness of the organism, we can show that the fraction of mutations that are selectively neutral, fg, is equal to the ratio K(g)/K psi. Since advantageous mutations occur only very rarely, such that they do not contribute significantly to the rate of molecular evolution, the fraction of deleterious mutations that are subject to purifying selection is 1-fg. Therefore, the K(g)/K psi ratio can be used directly to estimate the intensity of purifying selection, thereby isolating its effects on the rate of evolution from those of mutation. We compared the selection intensities of 12 orthologous protein-coding pairs from humans and murids. As expected, the fraction of mutations that are subject to purifying selection is strongest in the second codon position and weakest in the third. Interestingly, the mean fractions of effectively neutral mutations in the third codon position were only 41% and 42% for murids and humans, respectively, indicating that many synonymous mutations are subject to selective constraint. In several orthologous genes, we found that the intensity of purifying selection is very different between murid and human orthologous genes. There was no statistically significant difference in overall intensity of purifying selection between humans and murids. Thus, purifying selection does not seem to be an important factor contributing to the observed differences in the rates of evolution between these two taxa.

Animals↗
PubMed1983

Birds, behavior, and anatomical evolution.

Study of more than 200 species suggests that the anatomical differences among birds are as big as those among other vertebrates of comparable taxonomic rank. The result is notable because, for more than 100 years, many biologists have believed that birds are more uniform anatomically than other classes of vertebrates. Furthermore, assessment of biochemical and geological evidence suggests that the time scale for bird evolution could be quite short. Hence, birds may share with placental mammals the distinction of having had a high rate of anatomical evolution, compared to that in lower vertebrates. The rate appears to have been very high in songbirds and higher primates and extremely high in the genus Homo. In an attempt to explain such contrasts in rates of anatomical evolution, we advance the hypothesis that in higher vertebrates, behavior, rather than environmental change, is the major driving force for evolution at the organismal level. This hypothesis predicts accelerated anatomical evolution in species composed of numerous mobile individuals with the dual capacity for behavioral innovation and social propagation of new habits. Consistent with this hypothesis, we demonstrate a correlation between relative brain size and rate of anatomical evolution in land vertebrates.

Animals↗
PubMed2003

"Decoking" of a "coked" zeolite catalyst in a glow discharge.

"Decoking" of a "coked" zeolite catalyst in a glow discharge in oxygen is investigated. The "decoking" process involves reactions of atomic oxygen (O atoms) with "coke" and yields gases such as CO, CO(2) as well as other gaseous products that could be easily pumped out. Three different modes of discharge were investigated including a static mode, a flowing-gas mode, and a periodic-purge mode where the oxygen and other gaseous products of the discharge were replaced by fresh O(2)gas after short but regular intervals of time. In some cases, additional heating was also used to provide base temperatures of the order of 100 degrees C to facilitate penetration of oxygen atoms into the inner layers and cages of the zeolite catalyst. This paper presents some results of spectroscopic analytical techniques used to monitor the atomization of oxygen, oxidation of "coke", and to confirm the process of "decoking". More specifically, radiation emission on the 3 s (5)S- 3p (5)P transitions of O around 777.2-777.5 nm were selected for monitoring the atomization of O(2). On the other hand, X-ray photo-electron spectroscopy (XPS) was used to determine the amount of residual carbon and extent of "decoking". Furthermore, evolution of CO and CO(2) gases as a function of time was systematically monitored in real time. For CO, the 451.1 nm band head belonging to the B(1) Sigma - A(1) Pi bands of the Angstrom system of the CO spectrum was used, while for CO(2), the band head at 353.4 nm belonging to the CO(2)(+) spectrum was used. The rates of evolution of CO and CO(2) were related to the rate of "decoking" of the catalyst. It is noted that in the periodic-purge mode, about 63% of the total yield of CO from a given sample of the catalyst appears in the first 3-min exposure to discharge whereas it takes up to 15 min to remove nearly 94% of the removable carbon under our experimental conditions.

Journal Article↗
PubMed1988

The gamma-crystallin gene families: sequence and evolutionary patterns.

The gamma-crystallin proteins consist of two topologically equivalent domains, each built up out of two similar motifs. They are encoded by a gene family, which already contained five members before the divergence of rodents and primates. A further gene duplication took place in each lineage. To analyze the pattern of evolution within this gene family, the coding sequences of six human genes, six rat genes, and four mouse genes were compared. Between species, a uniform rate of evolution of all regions of the protein is seen. The ratio of synonymous to nonsynonymous substitution in the human/rat or human/mouse comparison is much lower than the ratio when rat and mouse are compared indicating that the gamma-crystallin proteins are better conserved in the rodent lineage. Within species, the regions encoding the two external motifs I and III of the protein show a greater extent of nonsynonymous substitution than the regions encoding the two internal protein motifs II and IV. The low extent of synonymous substitution between the second exons (encoding motifs I and II) of the rat gamma-crystallin genes suggests the frequent occurrence of gene conversion. In contrast, a high extent of synonymous substitution is found in exon 3 (encoding motifs III and IV) of the rat genes. The same phenomenon is seen within the human gene family. The frequencies of occurrence of the various dinucleotides deviate less from those predicted from the frequencies of occurrence of each individual nucleotide in the second exons than in the third exons. The sequences of the third exons are significantly depleted in CpG, ApA, and GpT and enriched in CpT and GpA.

Animals↗
PubMedDate not supplied

Dynamics and function of intron sequences of the wingless gene during the evolution of the Drosophila genus.

To understand the function and evolution of genes with complex patterns of expression, such as the Drosophila wingless gene, it is essential to know how their transcription is regulated. However, extracting the relevant regulatory information from a genome is still a complex task. We used a combination of comparative genomics and functional approaches to identify putative regulatory sequences in two introns (1 and 3) of the wingless gene and to infer their evolution. Comparison of the sequences obtained from several Drosophila species revealed colinear and well-conserved sequence blocks in both introns. Drosophila willistoni showed a rate of evolution, in both introns, faster than expected from its phylogenetic position. Intron 3 appeared to be composed of two separate modules, one of them lost in the willistoni group. We tested whether sequence conservation in noncoding regions is a reliable indicator of regulatory function and, if this function is conserved, by analyzing D. melanogaster transgenic reporter lines harboring intron 3 sequences from D. melanogaster (Sophophora subgenus) and the species from the Drosophila subgenus presenting the most divergent sequence, D. americana. The analysis indicated that intron 3 contains pupal enhancers conserved during the evolution of the genus, despite the fact that only 30% of the D. melanogaster intron 3 sequences lie in conserved blocks. Additional analysis of D. melanogaster transgenic reporter lines harboring intron 3 sequences from D. willistoni revealed the absence of an abdomen-specific expression pattern, probably due to the above-mentioned loss of a regulatory module in this species.

Animals↗
PubMed1996

Phylogenetic analysis in molecular evolutionary genetics.

Recent developments of statistical methods in molecular phylogenetics are reviewed. It is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used. However, when the rate of evolution varies extensively from branch to branch, many methods may fail to recover the true topology. Solid statistical tests for examining the accuracy of trees obtained by neighbor joining, minimum evolution, and least-squares method are available, but the methods for likelihood and parsimony trees are yet to be refined. Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct.

DNA↗
PubMed1990

Evolution of the autosomal chorion cluster in Drosophila. IV. The Hawaiian Drosophila: rapid protein evolution and constancy in the rate of DNA divergence.

Autosomal chorion genes s18, s15, and s19 are shown to diverge at extremely rapid rates in closely related taxa of Hawaiian Drosophila. Their nucleotide divergence rates are at least as fast as those of intergenic regions that are known to evolve more extensively between distantly related species. Their amino acid divergence rates are the fastest known to date. There are two nucleotide replacement substitutions for every synonymous one. The molecular basis for observed length and substitution mutations is analyzed. Length mutations are strongly associated with direct repeats in general, and with tandem repeats in particular, whereas the rate for an average transition is twice that for an average transversion. The DNA sequence of the cluster was used to construct a phylogenetic tree for five taxa of the Hawaiian picture-winged species group of Drosophila. Assignment of observed base substitutions occurring in various branches of the tree reveals an excess of would-be homoplasies in a centrally localized 1.8-kb segment containing the s15 gene. This observation may be a reflection of ancestral excess polymorphisms in the segment. The chorion cluster appears to evolve at a constant rate regardless of whether the central 1.8-kb segment is included or not in the analysis. Assuming that the time of divergence of Drosophila grimshawi and the planitibia subgroup coincides with the emergence of the island of Kauai, the overall rate of base substitution in the cluster is estimated to be 0.8% million years, whereas synonymous sites are substituted at a rate of 1.2% million years.

Amino Acid Sequence↗
PubMed1994

Regulation and evolution of the single alpha-tubulin gene of the ciliate Tetrahymena thermophila.

The single alpha-tubulin gene of Tetrahymena thermophila was isolated from a genomic library and shown to encode a single protein. Comparisons of the rates of evolution of this gene with other alpha-tubulin sequences revealed that it belongs to a group of more evolutionarily constrained alpha-tubulin proteins in animals, plants, and protozoans versus the group of more rapidly evolving fungal and variant animal alpha-tubulins. The single alpha-tubulin of Tetrahymena must be used in a variety of microtubule structures, and we suggest that equivalently conserved alpha-tubulins in other organisms are evolutionarily constrained because they, too, are multifunctional. Reduced constraints on fungal tubulins are consistent with their simpler microtubule systems. The animal variant alpha-tubulins may also have diverged because of fewer functional requirements or they could be examples of specialized tubulins. To analyze the role of tubulin gene expression in regulation of the complex microtubule system of Tetrahymena, alpha-tubulin mRNA amounts were examined in a number of cell states. Message levels increased in growing versus starved cells and also during early stages of conjugation. These changes were correlated with increases in transcription rates. Additionally, alpha-tubulin mRNA levels oscillate in a cell cycle dependent fashion caused by changes in both transcription and decay rates. Therefore, as in other organisms, Tetrahymena adjusts alpha-tubulin message amounts via message decay. However the complex control of alpha-tubulin mRNA during the Tetrahymena life cycle involves regulation of both decay and transcription rates.

Amino Acid Sequence↗
PubMed1997

Melatonin protects mice infected with Venezuelan equine encephalomyelitis virus.

We investigated whether the administration of melatonin (MLT) reduces the death rate and evolution of the disease in mice infected with Venezuelan equine encephalomyelitis (VEE) virus. Our results show that, MLT protects mice infected with the virus. The mortality rate was reduced from 100% to 16% merely by increasing the dose from 0 to 1000 micrograms/MLT per kg body weight MLT significantly postponed the onset of the disease and death by several days. In surviving mice very high titres of VEE virus IgM antibodies were found seven weeks after virus inoculation. MLT significantly reduced VEE virus levels in blood and brain of infected mice and increased the survival rate when the length of pretreatment was augmented from 3 to 7 or 10 days before virus inoculation. Serum levels of interleukin-2 were not affected by MLT administration. In control mice receiving MLT as well as in infected mice treated or non-treated with MLT, interferon gamma levels in sera were increased. Interleukin-4 concentrations were found to be elevated in sera of non-infected mice receiving MLT, but did not differ from controls in infected mice treated or non-treated with the hormone. MLT reduced the degree of cell destruction produced by VEE virus in culture plates of chicken embryo fibroblasts. The protective effect of MLT warrants further investigation of the possibility of using this hormone for the treatment of humans and equines infected with VEE virus.

Animals↗
PubMed1986

DNA structural variability as a factor in gene expression and evolution.

Redundant DNA can buffer sequence dependent structural deviations from an ideal double helix. Buffering serves a mechanistic function by reducing extraneous conformational effects which could interfere with readout or which would impose energetic constraints on evolution. It also serves an evolutionary function by allowing for gradual variations in conformation-dependent regulation of gene expression. Such gradualism is critical for the rate of evolution. The buffer structure concept provides a new interpretation for repetitive DNA and for exons and introns.

Base Sequence↗
PubMed1980

The random character of protein evolution and its effects on the reliability of phylogenetic information deduced from amino acid sequences and compositions.

Because evolution occurs by random events, the actual number of substitutions that occur in any period is not exactly equal to the number expected from the mean rate of substitution, but is statistically distributed about it. In consequence, even if rates of evolution are constant in different lineages, 'trees' deduced from descendant protein sequences contain random errors. When there are fewer than about eight differences between the sequences of the most distantly related pair from a set of proteins, this random effect is very large. It can then render trivial the statistical disadvantage inherent in using a crude measure of protein difference, such as amino acid composition or immunological cross-reactivity, in preference to a measure based the sequences of the most distantly related pair from a set of proteins, this random effect is very large. It can then render trivial the statistical disadvantage inherent in using a crude measure of protein difference, such as amino acid composition or immunological cross-reactivity, in preference to a measure based the sequences of the most distantly related pair from a set of proteins, this random effect is very large. It can then render trivial the statistical disadvantage inherent in using a crude measure of protein difference, such as amino acid composition or immunological cross-reactivity, in preference to a measure based on amino acid sequence. In some cases, such as classification of mammals on the basis of cytochrome c structure, it appears to make little difference to the reliability of the results whether the sequences of the protein concerned are known or not. It may also be possible to obtain more reliable phylogenetic information from composition measurements on several kinds of protein than one could obtain from sequence measurements on a single kind of protein.

Amino Acid Sequence↗
PubMed2003

Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation.

We have performed a large-scale analysis of amino acid sequence evolution after gene duplication by comparing evolution after gene duplication with evolution after speciation in over 1,800 phylogenetic trees constructed from manually curated alignments of protein domains downloaded from the PFAM database. The site-specific rate of evolution is significantly altered by gene duplication. A significant increase in the proportion of amino acid substitutions at constrained (slowly evolving) sites after duplication was observed. An increase in the proportion of replacements at normally constrained amino acid sites could result from relaxation of purifying selective pressure. However, the proportion of amino acid replacements involving radical changes in amino acid properties after duplication does not appear to be significantly increased by relaxed selective pressure. The increased proportion of replacements at constrained sites was observed over a relatively large range of protein change (up to 25% amino acid replacements per site). These findings have implications for our understanding of the nature of evolution after duplication and may help to shed light on the evolution of novel protein functions through gene duplication.

Algorithms↗
PubMed2001

Lateral plate evolution in the threespine stickleback: getting nowhere fast.

Gasterosteus aculeatus is a small Holarctic fish with marine, anadromous, and freshwater populations. Marine and anadromous populations apparently have changed little in the past 10 million years and exhibit limited geographical variation. In contrast, freshwater isolates have been founded repeatedly by marine and anadromous populations, and post-glacial isolates have undergone extraordinary adaptive radiation. Stickleback traits that have diversified during post-glacial radiation, including the 'lateral plates' (LP), can evolve substantially within decades after colonization of fresh water or when the environment (particularly predation regime) changes. Although highly divergent freshwater isolates of G. aculeatus have existed for at least 10 million years, they have rarely experienced sustained evolutionary divergence leading to formation of widespread, phenotypically distinct species. The paradox of rapid LP evolution without sustained divergence has resulted from selective extinction of highly divergent populations, because they are specialized for conditions in small, isolated habitats that tend to dry up within limited periods. Biological species of G. aculeatus may also evolve within decades, and are also prone to extinction because they are endemic to and specialized for small, ephemeral habitats. The high rate of evolution observed in contemporary threespine stickleback populations may not be unique to this species complex and has important implications for use of post-glacial populations in comparative studies, speciation rate, and discrimination of sympatric and allopatric speciation.

Animals↗
PubMed1987

DNA-DNA hybridization evidence of the rapid rate of muroid rodent DNA evolution.

Single-copy nuclear DNAs (scnDNAs) of eight species of arvicoline and six species of murine rodents were compared using DNA-DNA hybridization. The branching pattern derived from the DNA comparisons is congruent with the fossil evidence and supported by comparative biochemical, chromosomal, and morphological studies. The recently improved fossil record for these lineages provides seven approximate divergence dates, which were used to calibrate the DNA-hybridization data. The average rate of scnDNA divergence was estimated as 2.5%/Myr. This is approximately 10 times the rate in the hominoid primates. These results agree with previous reports of accelerated DNA evolution in muroid rodents and extend the DNA-DNA hybridization data set of Brownell.

Animals↗
PubMed1999

Crossover accelerates evolution in GAs with a Babel-like fitness landscape: mathematical analyses.

The effectiveness of crossover in accelerating evolution in genetic algorithms (GAs) is studied with a haploid finite population of bit sequences. A Babel-like fitness landscape is assumed. There is a single bit sequence (schema) that is significantly more advantageous than all the others. We study the time until domination of the advantageous schema (Τ&subd;). Evolution proceeds with appearance, spread, and domination of the advantageous schema. The most important process determining Τ&subd; is the appearance (creation) of the advantageous schema. Crossover helps this creation process and enhances the rate of evolution. To study this effect, we first establish an analytical method to estimate Τ&subd; with or without crossover. Then, we conduct a numerical analysis using the frequency vector representation of the population with the recurrence relations formulated after GA operations. Finally, we carry out direct computer simulations with simple GAs operating on a population of binary strings directly prepared in the computer memory to examine the performance of the two analytical methods. It is shown that Τ&subd; is reduced greatly by crossover with a mildly high rate when the mutation rate is adjusted to a moderate value and that an advantageous schema has a fairly larger order (the number of bits). From these observations, we can determine implementation criteria for GAs, which are useful when we are applying GAs to engineering problems having a conspicuously discontinuous fitness landscape.

Algorithms↗
PubMed1990

A gene for cytochrome c oxidase subunit III (COXIII) in broad bean mitochondrial DNA: structural features and sequence evolution.

A nucleotide sequence of broad bean mitochondrial DNA (mtDNA) that contains the coxIII gene is presented, and compared to corresponding sequences of Oenothera and corn mtDNAs. Upstream from the broad bean coxIII gene are three potential secondary structures: a single stem and loop (hairpin) that is conserved in the Oenothera and corn sequences; a second single stem and loop; and a double stem and loop. The rate of evolution of the coxIII gene has been slower in plants than in mammals. Constraints on the fixation of at least some kinds of mutations in silent (synonymous) third position nucleotides, as well as of mutations that cause amino acid replacements, seem to have contributed to this slower rate.

Amino Acid Sequence↗
PubMed1982

Novel features of animal mtDNA evolution as shown by sequences of two rat cytochrome oxidase subunit II genes.

The sequence of the region of the mitochondrial genome that encodes cytochrome oxidase subunit II (COII) has been determined for each of two closely related rat species, Rattus norvegicus and R. rattus. Comparison of the two sequences shows that 94.4% of the nucleotide substitutions are silent. The occurrence of this high proportion of silent substitutions leads us to propose that the rapid evolution of mtDNA relative to nuclear DNA is due only to silent changes and that amino acid-altering substitutions accumulate in nuclear and mtDNA at comparable rates. Other novel features of the nucleotide substitution pattern in the rat COII gene are a high transition/transversion ratio (8.0:1) and a strong bias toward C in equilibrium T transitions in the light strand. Comparison of the R. norvegicus COII sequence with the bovine and human sequences show that there may be selective constraints on some silent positions within the gene and that its rate of evolution may be different in different mammalian lineages.

Animals↗