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PubMed2004

Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome.

Natural selection leaves its footprints on protein-coding sequences by modulating their silent and replacement evolutionary rates. In highly expressed genes in invertebrates, these footprints are seen in the higher codon usage bias and lower synonymous divergence. In mammals, the highly expressed genes have a shorter gene length in the genome and the breadth of expression is known to constrain the rate of protein evolution. Here we have examined how the rates of evolution of proteins encoded by the vertebrate genomes are modulated by the amount (intensity) of gene expression. To understand how natural selection operates on proteins that appear to have arisen in earlier and later phases of animal evolution, we have contrasted patterns of mouse proteins that have homologs in invertebrate and protist genomes (Precambrian genes) with those that do not have such detectable homologs (vertebrate-specific genes). We find that the intensity of gene expression relates inversely to the rate of protein sequence evolution on a genomic scale. The most highly expressed genes actually show the lowest total number of substitutions per polypeptide, consistent with cumulative effects of purifying selection on individual amino acid replacements. Precambrian genes exhibit a more pronounced difference in protein evolutionary rates (up to three times) between the genes with high and low expression levels as compared to the vertebrate-specific genes, which appears to be due to the narrower breadth of expression of the vertebrate-specific genes. These results provide insights into the differential relationship and effect of the increasing complexity of animal body form on evolutionary rates of proteins.

Animals↗
PubMed1981

How heritable is innate behaviour?

The relations between innateness and heritability of behaviour, environmental heterogeneity, genetic diversity of populations, and rates of evolution of behaviour are discussed on the basis of a simple quantitative model. An index I of innateness is proposed which can be related to the heritability index h2. I and h2 are positively related but the degree of correlation depends on the genetic variability of the population, the heterogeneity of the conditioning environment, and the level of spontaneous behavioural variability. The influence of innateness on rates of evolution is moderate. The frequency distributions of I and h2 are unimodal, there is no evidence for an innate-acquired dichotomy.

Animals↗
PubMed2003

Evolution of evolvability via adaptation of mutation rates.

We examine a simple form of the evolution of evolvability-the evolution of mutation rates-in a simple model system. The system is composed of many agents moving, reproducing, and dying in a two-dimensional resource-limited world. We first examine various macroscopic quantities (three types of genetic diversity, a measure of population fitness, and a measure of evolutionary activity) as a function of fixed mutation rates. The results suggest that (i) mutation rate is a control parameter that governs a transition between two qualitatively different phases of evolution, an ordered phase characterized by punctuated equilibria of diversity, and a disordered phase of characterized by noisy fluctuations around an equilibrium diversity, and (ii) the ability of evolution to create adaptive structure is maximized when the mutation rate is just below the transition between these two phases of evolution. We hypothesize that this transition occurs when the demands for evolutionary memory and evolutionary novelty are typically balanced. We next allow the mutation rate itself to evolve, and we observe that evolving mutation rates adapt to values at this transition. Furthermore, the mutation rates adapt up (or down) as the evolutionary demands for novelty (or memory) increase, thus supporting the balance hypothesis.

Adaptation, Physiological↗
PubMed1981

Evolution of the mutation rate at a heterotic locus.

A diffusion model of the modification of mutation rates at a heterotic locus in a finite population is examined. An asymptotic analysis assuming strong selection and weak linkage shows that selection can operate on mutation rates in this setting. There exists a favored mutation rate which is a function only of the equilibrium allele frequency of the heterotic locus and the population size. It is independent of the strength of selection at the heterotoxic locus. Computer simulations are also provided to show that this form of natural selection can occur.

Biological Evolution↗
PubMed2003

Conversion rate in laparoscopic cholecystectomy: evolution from 1993 and current state.

The definition of difficult laparoscopic cholecystectomy (LC) is inconsistent. The aim of this study was to analyze the factors that make LC difficult to perform and determine ways to avoid conversion, based on our series. All patients who underwent LC or open cholecystectomy (OC) between January 1993 and December 2001 in our division of general surgery were the subject matter of this study. Preliminary decisions regarding LC or OC were avoided. Our experience (1993-2001) was based on 1360 consecutive elective LC procedures in 381 male and 979 female patients. The mean age of the patients at operation was 53 years (range, 17-84). The median operating time was 55 minutes (range, 35-180). The overall conversion rate was 1.8%. Indications for conversion included surgical difficulty during the laparoscopic procedure and anesthesia issues. The conversion rate has decreased to less than 1% in recent years. There were no mortalities, and the postoperative complication rates were low. The mean hospital stay of the patients was 2.6 days. In conclusion, based on our experience, we suggest limiting OC to patients with proven contraindications to LC (i.e., Mirizzi syndrome or systemic illness incompatible with pneumoperitoneum), attempting LC in all other cases, and considering cholecystostomy and delayed LC as an alternative to conversion during difficult LC.

Adolescent↗
PubMed2005

Comparing artificial and natural selection in rate of adaptation to genetic stress in Aspergillus nidulans.

In an experimental study of adaptation to negative pleiotropic effects of a major fungicide resistance mutation in the filamentous fungus Aspergillus nidulans we have investigated the relative effectiveness of artificial selection vs. natural selection on the rate of compensatory evolution. Using mycelial growth rate as a fitness measure, artificial selection involved the weekly transfer of the fastest growing sector onto a fresh plate. Natural selection was approximated by transferring random samples of all the spores produced by the mycelium. Fungicide resistant and fungicide sensitive haploid and diploid strains were used in an evolution experiment over 10 weekly transfers, which is equivalent to 1200 cell cycles. Two different environmental conditions were applied: a constant fungicide-free environment and a weekly alternation between presence and absence of fungicide. Results show that for all strains and conditions used the transfer of a random sample of all spores leads to more rapid adaptation than the transfer of the visually 'fittest' sector. The rates of compensatory evolution in the constant and the alternating environment did not differ. Moreover, haploid strains tend to have a higher rate of adaptation than isogenic diploid strains.

Adaptation, Physiological↗
PubMed2006

There is no universal molecular clock for invertebrates, but rate variation does not scale with body size.

The existence of a universal molecular clock has been called into question by observations that substitution rates vary widely between lineages. However, increasing empirical evidence for the systematic effects of different life history traits on the rate of molecular evolution has raised hopes that rate variation may be predictable, potentially allowing the "correction" of the molecular clock. One such example is the body size trend observed in vertebrates; smaller species tend to have faster rates of molecular evolution. This effect has led to the proposal of general predictive models correcting for rate heterogeneity and has also been invoked to explain discrepancies between molecular and paleontological dates for explosive radiations in the fossil record. Yet, there have been no tests of an effect in any nonvertebrate taxa. In this study, we have tested the generality of the body size effect by surveying a wide range of invertebrate metazoan lineages. DNA sequences and body size data were collected from the literature for 330 species across five phyla. Phylogenetic comparative methods were used to investigate a relationship between average body size and substitution rate at both interspecies and interfamily comparison levels. We demonstrate significant rate variation in all phyla and most genes examined, implying a strict molecular clock cannot be assumed for the Metazoa. Furthermore, we find no evidence of any influence of body size on invertebrate substitution rates. We conclude that the vertebrate body size effect is a special case, which cannot be simply extrapolated to the rest of the animal kingdom.

Animals↗
PubMed2005

The evolution of intratetrad mating rates.

Intratetrad mating, the fusion of gametes formed in a single meiosis, has unusual consequences for genetic diversity, especially in genome regions linked to mating type loci. Here we investigate the fate of modifier alleles that alter the rate of intratetrad mating, under models of heterozygote advantage and of genetic load resulting from recurrent mutation. In both cases, intratetrad mating is favored if the recombination rate between the selected locus and mating type is less than the frequency of lethal recessive alleles at that locus in the population. Positive feedback often accelerates the invasion of modifiers to the intratetrad mating rate. Recombination rate and intratetrad mating rate exert indirect selection on one another, resulting in a cascading decline in outcrossing, even in the absence of any cost of sex. However, under recurrent mutation, alleles for obligate intratetrad mating invade only very slowly, perhaps explaining why outcrossing can persist at low frequencies in a largely intratetrad mating population.

Biological Evolution↗
PubMed1979

The evolution of the long and short repetitive DNA sequences in sea urchins.

The rates of evolution of purified long and short repetitive DNA sequences were examined by hybridisation analysis between the DNAs from several species of sea urchins. We find that the rates of nucleotide substitution are very comparable within mutually retained sequences for the two classes of repetitive DNA. The loss of hybridisable sequences between species also occurs at similar rates among both the short and long repetitive DNA sequences. Between species that separated less than 50 million years ago, hybridisable short repetitive sequences are lost all through the spectrum of reiteration frequencies. The long repeats contain a few sequences which are highly conserved within all of the species examined, and which amount to approximately 1% of the total genome. The short repetitive class, on the other hand, does not seem to contain any such highly conserved elements. The long repetitive sequences internally appear to contain short 'units' of reiteration, which may comprise families within the long repetitive class. We find no evidence to indicate that the majority of long and short repetitive sequences evolve by different mechanisms or at different rates.

Animals↗
PubMed1987

Molecular evolution of mammalian class I alcohol dehydrogenase.

Phylogenetic relationship and the rates of evolution of mammalian alcohol dehydrogenases (ADHs) have been studied by using the amino acid sequences from the human (ADH alpha, ADH beta, and ADH gamma), rat, mouse, and horse (ADH E and ADH S). With the maize ADH1 and ADH2 used as references, the patterns of the amino acid replacements in the beta-sheets, alpha-helices, and random coils in each of the catalytic and coenzyme-binding domains were analyzed separately. The phylogenetic trees based on the different sets of amino acid substitutions consistently showed that (1) multiple ADHs in human and horse have arisen after mammalian radiation, (2) the common ancestor of human ADHs alpha and beta diverged from the ancestor of ADH gamma first and the former two ADHs diverged from each other more recently, and (3) the human ADHs are more closely related to the rodent ADHs than to the horse ADHs. Furthermore, the estimated branch lengths showed that the rodent ADHs are evolving faster than the other ADHs. This difference in evolutionary rate between the two groups of organisms is explainable either in terms of the difference in the number of cell generations per year or in terms of reduction of functional constraints.

Alcohol Dehydrogenase↗
PubMed2000

Evolution of avian influenza viruses.

Although influenza viruses can infect a wide variety of birds and mammals, the natural host of the virus is wild waterfowl, shorebirds, and gulls. When other species of animals, including chickens, turkeys, swine, horses, and humans, are infected with influenza viruses, they are considered aberrant hosts. The distinction between the normal and aberrant host is important when describing virus evolution in the different host groups. The evolutionary rate of influenza virus in the natural host reservoirs is believed to be slow, while in mammals the rate is much higher. The higher rate of evolution in mammals is thought to be a result of selective pressure on the virus to adapt to an aberrant host species. Chickens and turkey influenza virus isolates have previously and incorrectly been lumped together with wild waterfowl, gull, and shorebird influenza viruses when determining rates of evolutionary change. To determine mutational and evolutionary rates of a virus in any host species, two primary assumptions must be met: first, all isolates included in the analysis must have descended from a single introduction of the virus, and second, the outbreak must continue long enough to determine a trend. For poultry, three recent outbreaks of avian influenza meet these criteria, and the sequences of the hemagglutinin and nonstructural genes were compared. Sequences from all three outbreaks were compared to an avian influenza virus consensus sequence, which at the amino acid level is highly conserved for all the internal viral proteins. The consensus sequence also provides a common point of origin to compare all influenza viruses. The evolutionary rates determined for all three outbreaks were similar to what is observed in mammals, providing strong evidence of adaptation of influenza to the new host species, chickens and turkeys.

Amino Acid Sequence↗
PubMed2004

Expected rates and modes of evolution of enhancer sequences.

The evolution of new functions takes place partially through changes in the way transcription is controlled. Transcriptional control is brought about by the interactions of transcription factors with short target motifs in the DNAs of promoters and enhancers. One way in which changes in gene expression can evolve is through the acquisition of new transcription factor targets in enhancer sequences. Since such target sites are simple, they can be produced rapidly from random DNA by mutation and selection. Here we consider a population of organisms that finds itself in an ecological situation where bringing a particular target gene under the control of a particular transcription factor would be favored by natural selection. What will be the time required for such a process, as a function of the selection for the new target, the mutation rate, and the population size? The starting sequences considered are either real enhancers from the Drosophila melanogaster genome, or randomized versions of these. We find that the time required to find binding sites is strongly dependent on the existence in the starting sequence of sites that differ from binding sites by single substitutions (presites). The process of converting presites to binding sites is driven by natural selection, and thus the time required typically reduces with the strength of selection. However, if there is a strongly distorted G:C ratio in the starting sequence, presites will typically be absent, and the finding of binding sites will be preceded by a long time period of neutral evolution, however strong is the selection favoring sites. The positions of presites largely determine where binding sites will evolve. One result of this is that any incremental selective benefits that result from the relative positioning of sites have a surprisingly small impact on the final binding-site positions.

Base Composition↗
PubMed1979

The amino acid sequence of mouse pancreatic ribonuclease. Extremely rapid evolutionary rates of the myomorph rodent ribonucleases.

The complete amino acid sequence of mouse pancreatic ribonuclease has been determined by analysis of tryptic, chymotryptic, thermolytic and CNBr peptides and by automatic sequence analysis of the intact protein. The sequence of mouse RNase differs in 20--30% of the positions from other RNase sequences. Three unique or neraly unique substitutions were found, viz. Gly-68 leads to Arg-68, Arg-85 leads to His-85 and Ser-123 leads to Thr-123. All these three residues might be involved in interactions with substrate molecules. A most parsimonious tree of the myomorph rodent RNase shows that after the divergence of rat and mouse, the ribonuclease of rat accumulated substitutions at a rate 2.5--4.3 times as high as the rates in other branches of the tree and 23 times as high as the average rate in the Bovidae ribonuclease evolution. These extreme fluctuations in substitution rate are difficult to reconcile with the hypothesis of the evolutionary clock. The high evolution rate of rat ribonuclease is thought to be caused by positive selection, leading to new functional properties of the enzyme.

Amino Acid Sequence↗
PubMed1997

Host-specific driving force in human immunodeficiency virus type 1 evolution in vivo.

To investigate the process of human immunodeficiency virus type 1 (HIV-1) evolution in vivo, a total of 179 HIV-1 V3 sequences derived from cell-free plasma were determined from serial samples in three epidemiologically linked individuals (one infected blood donor and two transfusion recipients) over a maximum period of 8 years. A systematic analysis of pairwise comparisons of intrapatient sequences, both within and between each sample time point, revealed a preponderance and accumulation of nonsynonymous rather than synonymous substitutions in the V3 loop and flanking regions as they diverged over time. This strongly argues for the dominant role that positive selection for amino acid change plays in governing the pattern and process of HIV-1 env V3 evolution in vivo and nullifies hypotheses of purely neutral or mutation-driven evolution or completely chance events. In addition, different rates of evolution of HIV-1 were observed in these three different individuals infected with the same viral strain, suggesting that the degree of positive pressure for HIV-1 amino acid change is host dependent. Finally, the observed similar rate of accumulation in divergence within and between infected individuals suggests that the process of genetic divergence in the HIV epidemic proceeds regardless of host-to-host transmission events, i.e., that transmission does not reset the evolutionary clock.

Amino Acid Sequence↗
PubMed2006

Cloning and sequence analysis of pituitary prolactin cDNA from the northern brown bandicoot (Isoodon macrourus).

The nucleotide sequence for pituitary prolactin cDNA from the marsupial bandicoot (Isoodon macrourus) was determined by reverse transcription-polymerase chain reaction and 5'/3' rapid amplification of cDNA ends. The deduced amino acid sequence showed high sequence identity with brushtail possum prolactin (95%) and all of the expected structural features of a quadruped prolactin. A prolactin gene tree was constructed and rates of evolution calculated for bandicoot, possum, opossum and several mammalian and non-mammalian prolactins. Bootstrap analysis provided strong support for marsupials as a sister group with eutherian mammals and weak support for opossum and bandicoot as an independent grouping from the brushtail possum. The rates of molecular evolution for marsupial prolactins were comparable to the slow rate seen in the majority of quadruped prolactins that have been sequenced.

Amino Acid Sequence↗
PubMed2006

How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants.

Greater phylogenetic signal is often found in parsimony-based analyses of third codon positions of protein-coding genes relative to their corresponding first and second codon positions, even for early-derived ("basal") clades. We used the Soltis et al. (2000; Bot. J. Linn. Soc. 133:381-461) data matrix of atpB and rbcL from 567 seed plants to quantify how each of six factors (observed character-state space, frequencies of observed character states, substitution probabilities among nucleotides, rate heterogeneity among sites, overall rate of evolution, and number of parsimony-informative characters) contributed to this phenomenon. Each of these six factors was estimated from the original data matrix for parsimony-informative third codon positions considered separately from first and second codon positions combined. One of the most parsimonious trees found was used as the constraint topology; branch lengths were estimated using likelihood-based distances, and characters were simulated on this tree. Differential frequencies of observed character states were found to be the most limiting of the factors simulated for all three codon positions. Differential frequencies of observed character states and differential substitution probabilities among states were relatively advantageous for first and second codon positions. In contrast, differential numbers of observed character states, differential rate heterogeneity among sites, the greater number of parsimony-informative characters, and the higher overall rate of evolution were relatively advantageous for third codon positions. The amount of possible synapomorphy was predictive of the overall success of resolution.

Base Sequence↗
PubMed1990

Evolution in Oryctes baculovirus: rate and types of genomic change.

Three cloned strains of Oryctes baculovirus were released into a previously unexposed population of the host insect, the coconut palm rhinoceros beetle, Oryctes rhinoceros. The experiment was conducted on Meemu Atoll in the Maldive Islands. Viruses were isolated from the beetle population at 1 year, 1.75 years, and 4 years after release. No changes in genotype were observed in viruses isolated after 1 and 1.75 years. After 4 years, however, three types of genomic change had occurred. A recombinant derived from two of the released strains, an isolate containing a 100-bp insert, and one example of a point mutation were found in the 22 isolates examined.

Animals↗