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PubMed1971

Polymorphisms in continental and island populations of Drosophila willistoni.

A comparative study of genic allozyme and chromosomal polymorphisms in four continental (South American) and six oceanic island (West Indies) populations of Drosophila willistoni has been made. The pattern of genic polymorphism is closely similar in all populations. Although regional and local differences in gene frequencies are found, generally the same alleles occur at high, intermediate, and low frequencies in all populations. An average individual is heterozygous at 18.4 and 16.2% of its loci in the continental and island populations, respectively. By contrast, chromosomal polymorphism is sharply reduced on the islands compared to most continental populations, and some chromosomal inversions are more frequent on some islands than on others. The observations are not compatible with the hypothesis that most of the gene variants are adaptively neutral. Balancing natural selection is responsible for most of the genic polymorphism in natural populations of D. willistoni.

Alleles↗
PubMed1974

Genetic differentiation within and between species of the Drosophila willistoni group.

We describe allelic variation at 28 loci in six Caribbean populations of four sympatric species of Drosophila. Within any one species the allelic frequencies are very similar from population to population, although there is evidence of local as well as regional genetic differentiation. The genetic distance is greater between populations from different islands than between populations of the same island. When the allelic frequencies are compared between different species, a remarkable pattern appears. In any pair of species nearly half of the loci have essentially identical allelic frequencies, while nearly the other half of the loci have different alleles and in different frequencies. The loci with nearly identical allelic frequencies are different when different pairs of species are compared. The patterns of allelic variation within and between species are inconsistent with the hypothesis that the variation is adaptively neutral. Migration or mutation cannot explain the patterns of genetic variation, either. Balancing natural selection is the main process maintaining protein polymorphisms in natural populations.

Acid Phosphatase↗
PubMed2000

Twenty-five strategies for improving the design, implementation and analysis of health services research related to alcohol and other drug abuse treatment.

While some aspects of addiction can be studied in laboratory or controlled settings, the study of long-term recovery management and the health services that support it requires going out into the community and dealing with populations and systems that are much more diverse and less under our control. This in turn raises many methodological challenges for the health service researchers studying alcohol and other drug abuse treatment. This paper identifies some of these challenges related to the design, measurement, implementation and effectiveness of health services research. It then recommends 25 strategies (and key primers) for addressing them: (1) identifying in advance all stakeholders and issues; (2) developing conceptual models of intervention and context; (3) identifying the population to whom the conclusions will be generalized; (4) matching the research design to the question; (5) conducting randomized experiments only when appropriate and necessary; (6) balancing methodological and treatment concerns; (7) prioritizing analysis plans and increasing design sensitivity, (8) combining qualitative and quantitative methods; (9) identifying the four basic types of measures needed; (10) identifying and using standardized measures; (11) carefully balancing measurement selection and modification; (12) developing and evaluating modified and new measures when necessary; (13) identifying and tracking major clinical subgroups; (14) measuring and analyzing the actual pattern of services received; (15) incorporating implementation checks into the design; (16) incorporating baseline measures into the intervention; (17) monitoring implementation and dosage as a form of quality assurance; (18) developing procedures early to facilitate tracking and follow-up of study participants; (19) using more appropriate representations of the actual experiment; (20) using appropriate and sensitive standard deviation terms; (21) partialing out variance due to design or known sources prior to estimating experimental effect sizes; (22) using dimensional, interval and ratio measures to increase sensitivity to change; (23) using path or structural equation models; (24) integrating qualitative and quantitative analysis into reporting; and (25) using quasi-experiments, economic or organizational studies to answer other likely policy questions. Most of these strategies have been tried and tested in this and other areas, but are not widely used. Improving the state of the art of health services research and bridging the gap between research and practice do not depend upon using the most advanced methods, but rather upon using the most appropriate methods.

Alcoholism↗
PubMed2003

Determinant of HIV-1 mutational escape from cytotoxic T lymphocytes.

CD8+ class I-restricted cytotoxic T lymphocytes (CTLs) usually incompletely suppress HIV-1 in vivo, and while analogous partial suppression induces antiretroviral drug-resistance mutations, epitope escape mutations are inconsistently observed. However, escape mutation depends on the net balance of selective pressure and mutational fitness costs, which are poorly understood and difficult to study in vivo. Here we used a controlled in vitro system to evaluate the ability of HIV-1 to escape from CTL clones, finding that virus replicating under selective pressure rapidly can develop phenotypic resistance associated with genotypic changes. Escape varied between clones recognizing the same Gag epitope or different Gag and RT epitopes, indicating the influence of the T cell receptor on pressure and fitness costs. Gag and RT escape mutations were monoclonal intra-epitope substitutions, indicating limitation by fitness constraints in structural proteins. In contrast, escape from Nef-specific CTL was more rapid and consistent, marked by a polyclonal mixture of epitope point mutations and upstream frameshifts. We conclude that incomplete viral suppression by CTL can result in rapid emergence of immune escape, but the likelihood is strongly determined by factors influencing the fitness costs of the particular epitope targeted and the ability of responding CTL to recognize specific epitope variants.

Amino Acid Sequence↗
PubMed2003

ACTN3 genotype is associated with human elite athletic performance.

There is increasing evidence for strong genetic influences on athletic performance and for an evolutionary "trade-off" between performance traits for speed and endurance activities. We have recently demonstrated that the skeletal-muscle actin-binding protein alpha-actinin-3 is absent in 18% of healthy white individuals because of homozygosity for a common stop-codon polymorphism in the ACTN3 gene, R577X. alpha-Actinin-3 is specifically expressed in fast-twitch myofibers responsible for generating force at high velocity. The absence of a disease phenotype secondary to alpha-actinin-3 deficiency is likely due to compensation by the homologous protein, alpha-actinin-2. However, the high degree of evolutionary conservation of ACTN3 suggests function(s) independent of ACTN2. Here, we demonstrate highly significant associations between ACTN3 genotype and athletic performance. Both male and female elite sprint athletes have significantly higher frequencies of the 577R allele than do controls. This suggests that the presence of alpha-actinin-3 has a beneficial effect on the function of skeletal muscle in generating forceful contractions at high velocity, and provides an evolutionary advantage because of increased sprint performance. There is also a genotype effect in female sprint and endurance athletes, with higher than expected numbers of 577RX heterozygotes among sprint athletes and lower than expected numbers among endurance athletes. The lack of a similar effect in males suggests that the ACTN3 genotype affects athletic performance differently in males and females. The differential effects in sprint and endurance athletes suggests that the R577X polymorphism may have been maintained in the human population by balancing natural selection.

Actinin↗
PubMed2025

Adaptive laboratory evolution of Saccharomyces cerevisiae CEN.PK 113-7D to enhance ethanol tolerance.

Saccharomyces cerevisiae is a widely used yeast for industrial production of ethanol. However, elevated ethanol, temperature, and osmotic stress adversely affect fermentation efficiency. In this study, adaptive laboratory evolution for S. cerevisiae CEN.PK 113-7D on higher concentrations of ethanol was performed. After 144 days, the maximum specific growth rate (&#xb5;max) increased from 0.0240 to 0.1150 h-1 for the strain evolved on 9% v/v ethanol, and from 0.0002 to 0.0530 h-1 for the strain evolved on 11% v/v ethanol, and the specific glucose uptake rate increased by 30%. The strain evolved on 11% ethanol produced 94.5&#xa0;g/L ethanol in a fermentation as compared to 78.5&#xa0;g/L production by a non-evolved strain. By whole-genome sequencing of the evolved clones, we identified multiple coding mutations in genes involved in processes such as stress response, cell growth regulation, pentose phosphate pathway, lipid synthesis, and redox balance. The selected mutations in RKI1, CYC2, ANR2, RGA2, RGA1, LPX1, and LRE1 genes were validated by introducing them in the nonevolved yeast, showing 1.7-5-fold growth improvement at 9% ethanol (P&#xa0;<&#xa0;0.05). Notably, RGA2, RGA1 and LPX 1 carried an identical missense mutation across three independent clones. The RKI1I208V mutant showed the highest ethanol tolerance, while CYC2N342A achieved the highest ethanol production.

Ethanol↗
PubMed1994

A pleiotropic nonadditive model of variation in quantitative traits.

A model of mutation-selection-drift balance incorporating pleiotropic and dominance effects of new mutations on quantitative traits and fitness is investigated and used to predict the amount and nature of genetic variation maintained in segregating populations. The model is based on recent information on the joint distribution of mutant effects on bristle traits and fitness in Drosophila melanogaster from experiments on the accumulation of spontaneous and P element-induced mutations. These experiments suggest a leptokurtic distribution of effects with an intermediate correlation between effects on the trait and fitness. Mutants of large effect tend to be partially recessive while those with smaller effect are on average additive, but apparently with very variable gene action. The model is parameterized with two different sets of information derived from P element insertion and spontaneous mutation data, though the latter are not fully known. They differ in the number of mutations per generation which is assumed to affect the trait. Predictions of the variance maintained for bristle number assuming parameters derived from effects of P element insertions, in which the proportion of mutations with an effect on the trait is small, fit reasonably well with experimental observations. The equilibrium genetic variance is nearly independent of the degree of dominance of new mutations. Heritabilities of between 0.4 and 0.6 are predicted with population sizes from 10(4) to 10(6), and most of the variance for the metric trait in segregating population is due to a small proportion of mutations (about 1% of the total number) with neutral or nearly neutral effects on fitness and intermediate effects on the trait (0.1-0.5 sigma P).(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1995

Spontaneous mutation rate of modifiers of metabolism in Drosophila.

A rigorous test of our understanding of evolutionary quantitative genetics would be to predict accurately the equilibrium distribution of a character from empirical estimates of the relevant parameters in a mutation-selection-drift balance model. An aspect of this problem that is amenable to experimental analysis is the distribution of the effects of new mutations. This study quantifies the divergence among 200 lines of Drosophila melanogaster as they accumulated mutations on the second chromosome and estimates the rate of increase of variation and covariation in metabolic characters. Amounts of stored triacylglycerol and glycogen and the activities of a series of 12 metabolic enzymes were assayed in a subset of lines at generations 0, 11, 22, 33 and 44. Analyses of the rate of increase in the among-line variance in each trait allowed estimation of Vm/Ve, the ratio of among-line variance added per generation to the environmental variance. Values of Vm/Ve for the second chromosome ranged from 0.0004 to 0.0289 per generation. Six of the 16 characters showed significant departure from a normal distribution, and several lines exhibited large changes in more than one character. The covariance of pairs of traits also was partitioned into a within-line component (environmental covariance, Cov(e)) and an among-line component (mutational covariance, Covm). Both variances and covariance among lines increased over time, as assessed by linear regression, whereas environmental covariance showed no such trend. Results indicate that the quantitative genetic parameters describing the variation in metabolic traits are similar to those of other continuous characters.

Analysis of Variance↗
PubMed1996

Estimation of deleterious-mutation parameters in natural populations.

The rate and average effects of spontaneous deleterious mutations are important determinants of the evolution of breeding systems and of the vulnerability of small populations to extinction. Nevertheless, few attempts have been made to estimate the properties of such mutations, and those studies that have been performed have been extremely labor intensive, relying on long-term, laboratory mutation-accumulation experiments. We present an alternative to the latter approach. For populations in which the genetic variance for fitness is a consequence of selection-mutation balance, the mean fitness and genetic variance of fitness in outbred generations can be expressed as simple functions of the genomic mutation rate, average homozygous effect and average dominance coefficient of new mutations. Using empirical estimates for the mean and genetic variance of fitness, these expressions can then be solved to obtain joint estimates of the deleterious-mutation parameters. We employ computer simulations to evaluate the degree of bias of the estimators and present some general recommendations on the application of the technique. Our procedures provide some hope for obtaining estimates of the properties of deleterious mutations from a wide phylogenetic range of species as well as a mechanism for testing the validity of alternative models for the maintenance of genetic variance for fitness.

Gene Deletion↗
PubMed1997

Sex chromosome meiotic drive in stalk-eyed flies.

Meiotically driven sex chromosomes can quickly spread to fixation and cause population extinction unless balanced by selection or suppressed by genetic modifiers. We report results of genetic analyses that demonstrate that extreme female-biased sex ratios in two sister species of stalk-eyed flies, Cyrtodiopsis dalmanni and C. whitei, are due to a meiotic drive element on the X chromosome (Xd). Relatively high frequencies of Xd in C. dalmanni and C. whitei (13-17% and 29%, respectively) cause female-biased sex ratios in natural populations of both species. Sex ratio distortion is associated with spermatid degeneration in male carriers of Xd. Variation in sex ratios is caused by Y-linked and autosomal factors that decrease the intensity of meiotic drive. Y-linked polymorphism for resistance to drive exists in C. dalmanni in which a resistant Y chromosome reduces the intensity and reverses the direction of meiotic drive. When paired with Xd, modifying Y chromosomes (Ym) cause the transmission of predominantly Y-bearing sperm, and on average, production of 63% male progeny. The absence of sex ratio distortion in closely related monomorphic outgroup species suggests that this meiotic drive system may predate the origin of C. whitei and C. dalmanni. We discuss factors likely to be involved in the persistence of these sex-linked polymorphisms and consider the impact of Xd on the operational sex ratio and the intensity of sexual selection in these extremely sexually dimorphic flies.

Animals↗
PubMed1972

Enzyme variability in the Drosophila willistoni group. IV. Genic variation in natural populations of Drosophila willistoni.

We describe allelic variation at 28 gene loci in natural populations of D. willistoni. Seventy samples were studied from localities extending from Mexico and Florida, through Central America, the West Indies, and tropical South America, down to South Brazil. At least several hundred, and often several thousand, genomes were sampled for each locus. We have discovered a great deal of genetic variation. On the average, 58% loci are polymorphic in a given population. (A locus is considered polymorphic when the frequency of the most common allele is no greater than 0.95). An individual fly is heterozygous, on the average, at 18.4% loci.-Concerning the pattern of the variation, the most remarkable finding is the similarity of the configuration of allelic frequencies from locality to locality throughout the distribution of the species. Our observations support the conclusion that balancing natural selection is the major factor responsible for the considerable genetic variation observed in D. willistoni.

Alleles↗
PubMed2006

Evolutionary insights into the high worldwide prevalence of MBL2 deficiency alleles.

Human mannose-binding lectin (MBL) is a member of the collectin protein family that binds a broad range of microorganisms and activates the lectin-complement pathway of innate immunity. Common alleles of MBL2 disrupt the MBL protein or modulate the amount of protein produced, resulting in MBL deficiency. The clinical manifestations of MBL deficiency have been extensively studied but the actual role of this lectin in immunity to infection remains a matter of strong debate. MBL is commonly thought to play a key role in protective immunity, because MBL deficiency has been associated with an increase in susceptibility to infectious diseases. However, the high worldwide prevalence of multiple MBL2 deficiency or low-producing alleles suggests the converse that MBL deficiency confers protection. To explore the underlying forces accounting for the high worldwide prevalence of MBL2 deficiency alleles, we characterized genetic diversity in and around the MBL2 genomic region in 1166 chromosomes from 24 worldwide populations. Our results clearly demonstrate that the patterns of MBL2 variation are compatible with neutral evolution, as opposed to negative, positive or balanced natural selection. The high worldwide frequencies of MBL2 alleles associated with the production of little or no protein therefore result exclusively from human migration and genetic drift. The evolutionary neutrality of MBL2 strongly supports the notion that MBL2 variation does not have strong effects on population fitness, suggesting, therefore, that this lectin is largely redundant in host human defences.

Alleles↗
PubMed2006

Crab scars reveal survival advantage of left-handed snails.

Biological asymmetries are important elements of the structure and function of many living organisms. Using the Plio-Pleistocene fossil record of crab predation on morphologically similar pairs of right- and left-handed snail species, we show here for the first time, contrary to traditional wisdom, that rare left-handed coiling promotes survival from attacks by right-handed crabs. This frequency-dependent result influences the balance of selection processes that maintain left-handedness at the species level and parallels some social interactions in human cultures, such as sports that involve dual contests between opponents of opposite handedness.

Adaptation, Physiological↗
PubMed2003

Are reproductive skew models evolutionarily stable?

Reproductive skew theory has become a popular way to phrase problems and test hypotheses of social evolution. The diversity of reproductive skew models probably stems from the ease of generating new variations. However, I show that the logical basis of skew models, that is, the way in which group formation is modelled, makes use of hidden assumptions that may be problematical as they are unlikely to be fulfilled in all social systems. I illustrate these problems by re-analysing the basic concessive skew model with staying incentives. First, the model assumes that dispersal is an all-or-nothing response: all subordinates disperse as soon as concessions drop below a certain value. This leads to a discontinuous 'cliff-edge' shape of dominant fitness, and it is not clear that selection will balance a population at such an edge. Second, it is assumed that subordinates have perfect knowledge of their benefits if they stay in the group. I examine the effects of relaxing these two assumptions. Relaxing the first one strengthens reproductive skew theory, but relaxing the latter makes evolutionary stability disappear. In cases where subordinates cannot accurately measure benefits provided by the individual dominant with which they live, so that their behaviour instead evolves as a response to population-wide average benefits, the logic of reproductive skew models does not apply. This warns against too indiscriminate an application of reproductive skew theory to problems in social evolution: for example, transactional models of extra-pair paternity assume perfect knowledge of paternity, which is unlikely to hold true in nature. It is recommended that models specify the mechanisms by which individuals can adjust their behaviour to that of others, and pay attention to changes that occur in evolutionary versus behavioural time.

Animals↗
PubMed2025

Inbreeding load in finite populations from dominant and overdominant mutations.

Inbreeding depression is a widespread phenomenon that reflects the burden of deleterious effects hidden in heterozygosis in non-inbred populations but exposed in homozygosis in inbred individuals, known as inbreeding load (B). This load can be due to partially or fully recessive deleterious mutations (dominance model) or to heterozygote advantage (overdominance model, where both homozygotes are deleterious relative to the heterozygote). There are many studies addressing the changes in inbreeding load in finite populations assuming the dominance model. However, the contribution of overdominance to inbreeding depression has been focused on infinite-size populations. We carried out computer simulations to investigate the joint impact of dominant and pure overdominant mutations on inbreeding load, both for self-fertilizing populations and for panmictic populations suffering from a drastic bottleneck. We found that the overdominant inbreeding load can be substantially reduced by drift even for symmetrical overdominance, at least when considering mutations of small effect. For panmictic bottlenecked populations, the reduction in inbreeding load under dominance and overdominance loci cannot be easily distinguished. However, while purging depletes inbreeding load from dominant loci, slowing inbreeding depression and leading to partial fitness recovery, for overdominant loci fitness declines monotonically.

Inbreeding↗
PubMed2005

Genetics of individual differences in bitter taste perception: lessons from the PTC gene.

The ability or inability to taste the compound phenylthiocarbamide (PTC) is a classic inherited trait in humans and has been the subject of genetic and anthropological studies for over 70 years. This trait has also been shown to correlate with a number of dietary preferences and thus may have important implications for human health. The recent identification of the gene that underlies this phenotype has produced several surprising findings. This gene is a member of the T2R family of bitter taste receptor genes. It exists in seven different allelic forms, although only two of these, designated the major taster and major non-taster forms, exist at high frequency outside sub-Saharan Africa. The non-taster allele resides on a small chromosomal region identical by descent, indicating that non-tasters are descended from an ancient founder individual, and consistent with an origin of the non-taster allele preceding the emergence of modern humans out of Africa. The two major forms differ from each other at three amino acid positions, and both alleles have been maintained at high frequency by balancing natural selection, suggesting that the non-taster allele serves some function. We hypothesize that this function is to serve as a receptor for another, as yet unidentified toxic bitter substance. At least some of the remaining five haplotypes appear to confer intermediate sensitivity to PTC, suggesting future detailed studies of the relationships between receptor structure and taste function.

Alleles↗
PubMed1999

The pharmacological basis and pathophysiological significance of the heart rate-lowering property of diltiazem.

The calcium channel blocker diltiazem lowers heart rate in man and this property probably contributes to its clinical effectiveness in ischaemic heart disease and hypertension. This review examines the pharmacological basis of diltiazem's heart rate-lowering activity and considers its pathophysiological significance. The points discussed include the potent direct inhibitory effect of diltiazem on the sinus node and the frequency-dependence of this action. In addition, the well-balanced tissue selectivity profile of diltiazem and its ability to modulate cardiac reflex responsiveness contribute by counteracting the potential for reflex tachycardia.

Calcium Channel Blockers↗