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PubMed1970

Village and tribal genetic distances among American Indians, and the possible implications for human evolution.

Pair-wise genetic distances based on six genetic systems (Rh, MNSs, Kidd, Duffy, Diego, and haptoglobins) are presented for seven villages of Makiritare Indians, seven villages of Yanomama Indians, and 12 Indian tribes of Central and South America. It is shown that the mean genetic distance between Indian villages is 85-90 per cent of the distance between tribes. Since in the past, the initial event in the formation of a new tribe was probably the breaking away of one or several related villages from an established tribe, it is clear that this initial event could have profound consequences for subsequent tribal gene frequencies. By the criterion of changes in gene frequency in polymorphic genetic systems, the maximal rate of evolution in the American Indian has been approximately 100 times more rapid than the mean rate suggested by calculations based on amino acid substitutions in certain polypeptides of a variety of organisms. The above-mentioned findings could account in part for this 100-fold difference. Some other factors which might diminish the apparent difference between the results of these two types of calculations are mentioned.

Acculturation↗
PubMed1991

Glycinebetaine enhances and stabilizes the evolution of oxygen and the synthesis of ATP by cyanobacterial thylakoid membranes.

Glycinebetaine (betaine), an osmoregulant in halophilic plants, stabilized the evolution of oxygen and the synthesis of ATP by thylakoid membranes from the cyanobacterium Synechocystis PCC6803 when it was present during the preparation and incubation of the thylakoid membranes. Moreover, betaine enhanced the evolution of oxygen and the synthesis of ATP when present during assays. When betaine at 1.0 M was present during the preparation of thylakoid membranes and during the measurement of activity, the rate of evolution of oxygen was equivalent to that of intact cells.

2,6-Dichloroindophenol↗
PubMed2005

Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila.

Natural selection influences synonymous mutations and synonymous codon usage in many eukaryotes to improve the efficiency of translation in highly expressed genes. Recent studies of gene composition in eukaryotes have shown that codon usage also varies independently of expression levels, both among genes and at the intragenic level. Here, we investigate rates of evolution (Ks) and intensity of selection (gamma(s)) on synonymous mutations in two groups of genes that differ greatly in the length of their exons, but with equivalent levels of gene expression and rates of crossing-over in Drosophila melanogaster. We estimate gamma(s) using patterns of divergence and polymorphism in 50 Drosophila genes (100 kb of coding sequence) to take into account possible variation in mutation trends across the genome, among genes or among codons. We show that genes with long exons exhibit higher Ks and reduced gamma(s) compared to genes with short exons. We also show that Ks and gamma(s) vary significantly across long exons, with higher Ks and reduced gamma(s) in the central region compared to flanking regions of the same exons, hence indicating that the difference between genes with short and long exons can be mostly attributed to the central region of these long exons. Although amino acid composition can also play a significant role when estimating Ks and gamma(s), our analyses show that the differences in Ks and gamma(s) between genes with short and long exons and across long exons cannot be explained by differences in protein composition. All these results are consistent with the Interference Selection (IS) model that proposes that the Hill-Robertson (HR) effect caused by many weakly selected mutations has detectable evolutionary consequences at the intragenic level in genomes with recombination. Under the IS model, exon size and exon-intron structure influence the effectiveness of selection, with long exons showing reduced effectiveness of selection when compared to small exons and the central region of long exons showing reduced intensity of selection compared to flanking coding regions. Finally, our results further stress the need to consider selection on synonymous mutations and its variation--among and across genes and exons--in studies of protein evolution.

Animals↗
PubMed1998

Molecular evolution of snake toxins: is the functional diversity of snake toxins associated with a mechanism of accelerated evolution?

Recent studies revealed that animal toxins with unrelated biological functions often possess a similar architecture. To tentatively understand the evolutionary mechanisms that may govern this principle of functional prodigality associated with a structural economy, two complementary approaches were considered. One of them consisted of investigating the rates of mutations that occur in cDNAs and/or genes that encode a variety of toxins with the same fold. This approach was largely adopted with phospholipases A2 from Viperidae and to a lesser extent with three-fingered toxins from Elapidae and Hydrophiidae. Another approach consisted of investigating how a given fold can accommodate distinct functional topographies. Thus, a number of topologies by which three-fingered toxins exert distinct functions were investigated either by making chemical modifications and/or mutational analyses or by studying the three-dimensional structure of toxin-target complexes. This review shows that, although the two approaches are different, they commonly indicate that most if not all the surface of a snake toxin fold undergoes natural engineering, which may be associated with an accelerated rate of evolution. The biochemical process by which this phenomenon occurs remains unknown.

Amino Acid Sequence↗
PubMed2000

Models of experimental evolution: the role of genetic chance and selective necessity.

We present a theoretical framework within which to analyze the results of experimental evolution. Rapidly evolving organisms such as viruses, bacteria, and protozoa can be induced to adapt to laboratory conditions on very short human time scales. Artificial adaptive radiation is characterized by a list of common observations; we offer a framework in which many of these repeated questions and patterns can be characterized analytically. We allow for stochasticity by including rare mutations and bottleneck effects, demonstrating how these increase variability in the evolutionary trajectory. When the product Np, the population size times the per locus error rate, is small, the rate of evolution is limited by the chance occurrence of beneficial mutations; when Np is large and selective pressure is strong, the rate-limiting step is the waiting time while existing beneficial mutations sweep through the population. We derive the rate of divergence (substitution rate) and rate of fitness increase for the case when Np is large and illustrate our approach with an application to an experimental data set. A minimal assumption of independent additive fitness contributions provides a good fit to the experimental evolution of the bacteriophage phiX174.

Animals↗
PubMed2000

Gene conversion among chemokine receptors.

It has been proposed that proteins which are involved in host defence and susceptibility undergo accelerated evolution. Chemokine receptors have roles as pro-inflammatory agents acting in response to infection, and in addition are receptors for entry of viruses and other pathogens into cells. Consistent with this, their rate of evolution is higher than that for other members of the seven-transmembrane domain receptor family. The pattern of evolution of the chemokine receptors was examined in detail. Both chromosomal clusters of chemokine receptors (CC and CXC) showed evidence of a number of gene conversions. These are likely to have resulted in protein sequence changes, which could possibly alter function. 45% of a control group of clustered genes also showed evidence of conversion. Thus, the fixation of a gene conversion is not in itself sufficiently unusual in tandemly repeated genes and cannot be taken as strong evidence of a selection for a novel function. However, the degree of amino acid difference between the chemokine receptors CCR1 and CCR3 was greater than that for any of the control genes. Such changes could have functional implications for inter-species differences in chemokine receptor interactions with pathogens.

Amino Acid Sequence↗
PubMed2003

Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects.

Population-genetic studies have been remarkably productive and successful in the last decade following the invention of PCR technology and the introduction of mitochondrial and microsatellite DNA markers. While mitochondrial DNA has proven powerful for genealogical and evolutionary studies of animal populations, and microsatellite sequences are the most revealing DNA markers available so far for inferring population structure and dynamics, they both have important and unavoidable limitations. To obtain a fuller picture of the history and evolutionary potential of populations, genealogical data from nuclear loci are essential, and the inclusion of other nuclear markers, i.e. single copy nuclear polymorphic (scnp) sequences, is clearly needed. Four major uncertainties for nuclear DNA analyses of populations have been facing us, i.e. the availability of scnp markers for carrying out such analysis, technical laboratory hurdles for resolving haplotypes, difficulty in data analysis because of recombination, low divergence levels and intraspecific multifurcation evolution, and the utility of scnp markers for addressing population-genetic questions. In this review, we discuss the availability of highly polymorphic single copy DNA in the nuclear genome, describe patterns and rate of evolution of nuclear sequences, summarize past empirical and theoretical efforts to recover and analyse data from scnp markers, and examine the difficulties, challenges and opportunities faced in such studies. We show that although challenges still exist, the above-mentioned obstacles are now being removed. Recent advances in technology and increases in statistical power provide the prospect of nuclear DNA analyses becoming routine practice, allowing allele-discriminating characterization of scnp loci and microsatellite loci. This certainly will increase our ability to address more complex questions, and thereby the sophistication of genetic analyses of populations.

Animals↗
PubMedDate not supplied

[Microfertilization techniques: con].

The actually used microfertilization procedures are exposed according to potential indications: flagellar immotility, previous unexplained failure of IVF, and oligo-asthenoteratozoospermia. Results of two prospective randomized studies are presented in case of severe asthenozoospermia associated with at least one previous failure of IVF. Evaluation of fertilization rates confirms that ZD does not improve IVF prognosis whereas SUZI could be used to enhance IVF results. Authors focused on major methodological criticisms raising about most of published series, on relatively low evolutive pregnancy rate (5.7%) and on the need of randomized prospective studies for judge real interest of assisted fertilization.

Female↗
PubMed1997

Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes.

A comparative analysis of the transfer RNA genes in the genomes of the major kingdoms of eukaryotes and prokaryotes leads to the general conclusion that the rate of evolution of organelle tRNA genes is typically equal to of greater than that of their nuclear counterparts. Situations where this is not the case, most notably in vascular plants, are attributable to an elevated mutation rate in the nuclear genome. Through a comparison of rates of mutation with rates of nucleotide substitution, it is shown that there is a reduction in the efficiency of selection on new mutations in organelle genes. Numerous lines of evidence, including observed reductions in stem duplex stability and changes in loop sizes, suggest that the excess changes observed in the organelle genes are mildly deleterious. Uniparental inheritance of organelles causes a reduction in the efficiency of selection through the joint effects of an increase in linkage disequilibrium and a decrease in effective population size. These results provide molecular support for the idea that asexually propagating genomes are subject to long-term, gradual fitness loss and raise questions about the role of organelle mutations in the long-term survival of major phylogenetic lineages.

Animal Population Groups↗
PubMed2006

The asymmetric ATPase cycle of the thermosome: elucidation of the binding, hydrolysis and product-release steps.

Using a combination of intrinsic fluorescence to report ATP-induced rearrangements, quenched-flow to measure ATP hydrolysis "on-enzyme" and optical methods to probe the kinetics of product release, we have begun to dissect the process of energy transduction in the thermosome, a type II chaperonin from Thermoplasma acidophilum. Stoichiometric measurements of ATP binding reveal the tight association of eight nucleotide molecules per hexa-decamer, implying the filling of only one ring owing to strong negative cooperativity. After binding, we show that these eight ATP molecules are hydrolysed over the next 50 s, after which hydrolysis slows down markedly during the establishment of the steady state in the ATPase reaction, demonstrating that the kinetic system is off-rate limited. Looking in more detail, this rapid first-turnover can be dissected into two phases; the first occurring with a half-time of 0.8 s, the second with a half-time of 14 s, possibly reflecting the differential behaviour of the four alpha and four beta subunits in a single thermosome ring. To investigate the post-hydrolytic events, we used two heat-stable enzyme-linked optical assays to measure the rate of evolution of ADP and of phosphate from the thermosome active site. Neither product showed a rapid dissociation phase prior to the establishment of the steady state, showing that both are released slowly at a rate that limits the cycle. These data highlight the importance of the highly populated thermosome/ADP/Pi complex in the molecular mechanism.

Adenosine Diphosphate↗
PubMed2006

First principles study of neutral and anionic (medium-size) aluminum nitride clusters: AlnNn, n=7-16.

We report the results of a theoretical study of AlnNn (n=7-16) clusters that is based on density functional theory. We will focus on the evolution of structural and electronic properties with the cluster size in the stoichiometric AlN clusters considered. The results reveal that the structural and electronic properties tend to evolve toward their respective bulk limits. The rate of evolution is, however, slow due to the hollow globular shape exhibited by the clusters, which introduces large surface effects that dominate the properties studied. We will also discuss the changes induced upon addition of an extra electron to the respective neutral clusters.

Journal Article↗
PubMed1996

[Retrospective study of 136 cases of epidermoid carcinoma of the base of the tongue treated at the Alexis Vautrin Centre 1978-1992].

Out of 332 epidermoid carcinomas of the base of the tongue treated in Centre Alexis Vautrin from 1978 to 1992, 136 received. a treatment with a curative intent. The median age was 58 years, the median follow-up was 57 months. We numbered 55 T1-T2 and 81 N0 or N1. From the therapeutic point of view, the patients were classified into three groups: in group 1 (45 cases), they were treated by external irradiation only (median dose: 71 Gy); in group 2 (72 cases), they were treated by external irradiation and brachytherapy (the mean dose delivered by external irradiation was 50 Gy, and by brachytherapy, the mean dose was 30 Gy with a mean dose rate of 55 cGy/h); in group 3 (19 cases), they were treated by a radiosurgical association, the surgical resection was always mutilating and completed by an external irradiation (55 Gy), 8 patients received an associated barrier brachytherapy. Thirty-nine patients presented a local failure, 50 a locoregional evolution. The rate of local control at 5 years was 19% for group 1, 39% for group 2 and 32% for group 3. The calculation of the equivalent biologic dose in group 1 allows to separate this population into two subgroups whose survival rates are significantly different (at 3 years: 26% and 6%, P = 0.02) and shows the influence of fractionation and treatment time. The actuarial survival at 3 years is 19% for group 1, 55% for group 2 and 45% for group 3, the survival without evolution is 33% for group 1, 66% for group 2 and 72% for group 3. For the whole series, we numbered 18 complications of grade equal or superior to 2 (healing in more than 3 months, or sequelae or death) out of which four bone complication and 14 tissular complications that occurred in a mean delay of 9 months. Because of technical modifications, there have been no grade complications for implantations performed from 1989. The prognosis remains poor for cancers of the base of the tongue. The rates of survival are still low when they are treated by external irradiation only. There seems to exist a slight advantage in favour of the radio-brachytherapy association compared to the radiosurgical association with a lower rate of sequelae and mutilations.

Actuarial Analysis↗
PubMed1981

Globin evolution was apparently very rapid in early vertebrates: a reasonable case against the rate-constancy hypothesis.

Kimura mistook ambiguous maximum parsimony codons for wrong codons. The maximum parsimony method performed well as judged by the two classes of serine codons (which can not be connected by silent mutations) on comparing the parsimony codons for serines in human, rabbit, and mouse alpha hemoglobin chains to actual codons determined by nucleotide sequencing. In genealogical reconstructions involving 247 eucaryotic globins, the maximum parsimony distances separating the contemporary sequences show that Kimura's Poisson and Dayhoff's PAM estimates of rate of globin evolution miss most of the superimposed replacements and are therefore seriously in error. Nor is Kimura's constant rate assumption and his belief in a single origin of myoglobin supported. Lamprey myoglobin appears to be most like lamprey hemoglobin, while gnathostome myoglobin seems closest to gnathostome hemoglobin. It was found that the three types of gnathostome globins (Mb, alpha Hb, beta Hb) evolved between the shark-boney vertebrate and bird-mammal ancestors at a much faster rate than from the latter ancestor to the present. The data indicate that rates were exceedingly fast during the origin of these globin chains because a high proportion of substitutions were adaptive. It was concluded that wherever strong stabilizing selection acts on a protein, somewhere in the past positive Darwinian selection must have spread the amino acid substitutions now being preserved.

Animals↗
PubMed1996

Population evolution on a multiplicative single-peak fitness landscape.

A theory for evolution of either gene sequences or molecular sequences must take into account that a population consists of a finite number of individuals with related sequences. Such a population will not behave in the deterministic way expected for an infinite population, nor will it behave as in adaptive walk models, where the whole of the population is represented by a single sequence. Here we study a model for evolution of population in a fitness landscape with a single fitness peak. This landscape is simple enough for finite size population effects to be studied in detail. Each of the N individuals in the population is represented by a sequence of L genes which may either be advantageous or disadvantageous. The fitness of an individual with k disadvantageous genes is Wk = (1-s)k, where s determines the strength of selection. In the limit L-->infinity, the model reduces to the problem of Muller's Ratchet: the population moves away from the fitness peak at a constant rate due to the accumulation of disadvantageous mutations. For finite length sequences, a population placed initially at the fitness peak will evolve away from the peak until a balance is reached between mutation and selection. From then on the population will wander through a spherical shell in sequence space at a constant mean Hamming distance from the optimum sequence. We give an approximate theory for the way depends on N, L, s, and the mutation rate u. This is found to agree well with numerical simulation. Selection is less effective on small populations, so increases as N decreases. Our simulations also show that the mean overlap between gene sequences separated by a time of t generations is of the form Q(t) = Q infinity + (Q0-Q infinity)exp(-2ut), which means that the rate of evolution within the spherical shell is independent of the selection strength. We give a simplified model which can be solved exactly for which Q(t) has precisely this form. We then consider the limit L-->infinity keeping U = uL constant. We suppose that each mutation may be favourable with probability p, or unfavourable with probability 1-p. We show that for p less than a critical value pc, the population decreases in fitness for all values of U, whereas for pc < p < 1/2, the population increases in fitness for small U and decreases in fitness for large U. In this case there is an optimum non-zero value of U at which the fitness increases most rapidly, and natural selection will favour species with non-zero mutation rates.

Animals↗
PubMed1999

Bacterial evolution: Jittery genomes.

Recent studies of long-term experimental populations of bacteria have revealed the actual progression of evolutionary change and how rates of phenotypic evolution can be decoupled from rates of genomic evolution.

Biological Evolution↗
PubMed1993

Dental evidence for the peopling of the New World: some methodological considerations.

Turner (1985b) and Greenberg et al. (1986) proposed that New World populations originated in northern Asia and entered the Americas in three migratory waves: Macro-Indian, Aleut-Eskimo, and Na-Dene. Biological support for this model comes from Turner's unweighted pair group (UPGMA) cluster analysis of discrete dental traits in world populations. Unfortunately, UPGMA analysis often creates suspect clusters and may not be valid as a method for displaying evolutionary relationships because it assumes that rates of evolution are equal among all populations. To test whether Turner's results are an artifact of his analytical method, I analyzed his published data (Turner 1985b) using two alternative techniques that do not assume homogeneous rates of change: a Wagner distance algorithm employing the Fitch-Margoliash criterion for goodness of fit and a maximum parsimony analysis using segment-coded dental trait frequencies. Both alternative methods produce trees that are similar to the UPGMA analysis results, supporting Turner's original results and basic conclusions. Comparisons of tree topology demonstrate that there is strong congruence between trees produced by all three methods, although the placement of certain populations, such as Na-Dene, depends on the method of analysis employed.

Algorithms↗
PubMed1998

A different tempo of mitochondrial DNA evolution in birds and their parasitic lice.

A phylogeny for the lice (Insecta: Phthiraptera: genus Dennyus) parasitic on swiftlets (Aves: Collocalliinae) was constructed based on mitochondrial cytochrome b DNA sequences. This phylogeny is congruent with previous phenetic analyses of morphometric data for the lice. Comparison with a previously obtained phylogeny for the hosts indicates some degree of cospeciation. These cospeciation events are used to compare relative rates of evolution in the birds and their lice for the same segment of the cytochrome b gene. Cytochrome b is evolving two to three times more rapidly in lice than in birds, and louse cytochrome b is highly divergent compared to that of most other insects. Although generation time has been suggested as an explanation for the disparity in evolutionary rates between lice and their hosts, we suggest that the small effective population sizes of lice coupled with founder events occurring during transmission to new host individuals may be an important factor.

Amino Acid Sequence↗
PubMedDate not supplied

[Temporal evolution of blood pressure and heart rate reaction to various stressors in coronary and non-coronary subjects (author's transl)].

The temporal evolution of systolic and diastolic blood pressure and heart rate in reaction to several stresses is measured in a group of 21 post myocardial infarction and 21 non coronary subjects. Heart rate modifications depend essentially upon the nature of stress: catheterization induces tachycardia while a stressing film induces bradycardia. These observations can be connected to environmental intake or rejection. During catheterization stress, the systolic blood pressure is high in both groups but returns to its normal values as soon as the intervention ends. In response to anxiety films, it persists higher in coronary patients than in normal subjects, who do not seem to react to this kind of stress. These results arise the question of either a longer recuperation, or a different reactivity to symbolic stressors (films).

Anxiety↗