Genomics of Parallel Experimental Evolution in Drosophila.

What are the genomic foundations of adaptation in sexual populations? We address this question using fitness-character and whole-genome sequence data from 30 Drosophila laboratory populations. These 30 populations are part of a nearly 40-year laboratory radiation featuring 3 selection regimes, each shared by 10 populations for up to 837 generations, with moderately large effective population sizes. Each of 3 sets of the 10 populations that shared a selection regime consists of 5 populations that have long been maintained under that selection regime, paired with 5 populations that had only recently been subjected to that selection regime. We find a high degree of evolutionary parallelism in fitness phenotypes when most-recent selection regimes are shared, as in previous studies from our laboratory. We also find genomic parallelism with respect to the frequencies of single-nucleotide polymorphisms, transposable elements, insertions, and structural variants, which was expected. Entirely unexpected was a high degree of parallelism for linkage disequilibrium. The evolutionary genetic changes among these sexual populations are rapid and genomically extensive. This pattern may be due to segregating functional genetic variation that is abundantly maintained genome-wide by selection, variation that responds immediately to changes of selection regime.

Tracking changes in chromosomal arrangements and their genetic content during adaptation.

There is considerable evidence for an adaptive role of inversions, but how their genetic content evolves and affects the subsequent evolution of chromosomal polymorphism remains controversial. Here, we track how life-history traits, chromosomal arrangements and 22 microsatellites, within and outside inversions, change in three replicated populations of Drosophila subobscura for 30 generations of laboratory evolution since founding from the wild. The dynamics of fitness-related traits indicated adaptation to the new environment concomitant with directional evolution of chromosomal polymorphism. Evidence of selective changes in frequency of inversions was obtained for seven of 23 chromosomal arrangements, corroborating a role for inversions in adaptation. The evolution of linkage disequilibrium between some microsatellites and chromosomes suggested that adaptive changes in arrangements involved changes in their genetic content. Several microsatellite alleles increased in frequency more than expected by drift in targeted inversions in all replicate populations. In particular, there were signs of selection in the O3+4 arrangement favouring a combination of alleles in two loci linked to the inversion and changing along with it, although the lack of linkage disequilibrium between these loci precludes epistatic selection. Seven other alleles increased in frequency within inversions more than expected by drift, but were not in linkage disequilibrium with them. Possibly these alleles were hitchhiking along with alleles under selection that were not specific to those inversions. Overall, the selection detected on the genetic content of inversions, despite limited coverage of the genome, suggests that genetic changes within inversions play an important role in adaptation.

From nature to the laboratory: the impact of founder effects on adaptation.

Most founding events entail a reduction in population size, which in turn leads to genetic drift effects that can deplete alleles. Besides reducing neutral genetic variability, founder effects can in principle shift additive genetic variance for phenotypes that underlie fitness. This could then lead to different rates of adaptation among populations that have undergone a population size bottleneck as well as an environmental change, even when these populations have a common evolutionary history. Thus, theory suggests that there should be an association between observable genetic variability for both neutral markers and phenotypes related to fitness. Here, we test this scenario by monitoring the early evolutionary dynamics of six laboratory foundations derived from founders taken from the same source natural population of Drosophila subobscura. Each foundation was in turn three-fold replicated. During their first few generations, these six foundations showed an abrupt increase in their genetic differentiation, within and between foundations. The eighteen populations that were monitored also differed in their patterns of phenotypic adaptation according to their immediately ancestral founding sample. Differences in early genetic variability and in effective population size were found to predict differences in the rate of adaptation during the first 21 generations of laboratory evolution. We show that evolution in a novel environment is strongly contingent not only on the initial composition of a newly founded population but also on the stochastic changes that occur during the first generations of colonization. Such effects make laboratory populations poor guides to the evolutionary genetic properties of their ancestral wild populations.

What determines quality of life in inclusion body myositis?

BACKGROUND: Quality of life (QoL) assessment allows healthcare professionals to appreciate the patient perspective of their disease. This can help us make a better choice from among the various ways we currently measure the severity of a muscle disease such as inclusion body myositis (IBM). However, we cannot assume that QoL in IBM is just related to disease severity as psychosocial factors may play an important role in determining QoL. METHODS: Sixty subjects with IBM had assessments of disease severity and concurrent assessment of mood and QoL using the Short-Form 36 (SF-36). RESULTS: There were significant reductions in Physical functioning, Role physical, General health and Social functioning domains of the SF-36. Functional disability was more indicative of the broader effects of IBM on SF-36 than was the muscle strength sum score. Mood was relatively independent of disease severity and had a different profile of effects on SF-36 domains. Up to 14% of the effect of functional disability on some aspects of QoL was mediated through mood. CONCLUSIONS: The functional disability caused by IBM reduces QoL, but psychosocial factors such as mood affect QoL directly and by influencing the degree to which disease severity reduces QoL. Further study should follow the effects of IBM on QoL over time and look at the influence of other psychosocial factors. Such studies may point to psychosocial interventions that may help improve QoL in IBM even if the disease itself cannot be treated.

Italian validation of INQoL, a quality of life questionnaire for adults with muscle diseases.

BACKGROUND AND PURPOSE: A quality of life (QoL) questionnaire for neuromuscular diseases was recently constructed and validated in the United Kingdom in a sample of adult patients with a variety of muscle disorders. Preliminary results suggested it could be a more relevant and practical measure of QoL in muscle diseases than generic health measures of QoL. The purpose of our work was: (i) To validate INQoL in Italy on a larger sample of adult patients with muscle diseases (ii) to compare INQoL to SF-36. METHODS: We have translated into Italian and applied language adaptations to the original UK INQoL version. We studied 1092 patients with different muscle disorders and performed (i) test-retest reliability (n = 80); (ii) psychometric (n = 345), known-group (n = 1092), external criterion (n = 70), and concurrent validity with SF-36 (n = 183). RESULTS: We have translated and formally validated the Italian version of INQoL confirming and extending results obtained in the United Kingdom. In addition to good results in terms of reliability, known-group and criterion validity, a comparison with the SF-36 scales showed a stronger association between INQoL total index and SF-36 physical (r = -0.72) than mental (r = -0.38) summary health indexes. When considering comparable domains of INQoL and SF-36 with respect to an objective measure of muscle strength assessment (MMRC), regression analysis showed a stronger correlation using INQoL rather than SF-36 scores. CONCLUSIONS: INQoL is recommended to assess QoL in muscle diseases because of its ability to capture physical limitations that are specifically relevant to the muscle condition.

Molecular biological mechanisms of speciation.

Growing recognition that much of the evolutionary history of eukaryotic genomes reflects the operation of turnover processes involving repetitive DNA sequences has led to the recent formulation of models describing speciation as a consequence of such turnover. These models are of three general kinds: those attributing hybrid infertility to the process of transposition, those attributing hybrid infertility to mispairing between chromosomes of divergent repetitive DNA composition, and those assuming that change in repetitive DNA's can reset coordinated gene regulation. These models are discussed with respect to the kinds of evidence needed for their corroboration and to their significance for questions related to macroevolutionary punctuated equilibria and genetic revolutions.

Increasing atmospheric carbon dioxide: tree ring evidence for growth enhancement in natural vegetation.

A response of plant growth to increased atmospheric carbon dioxide, which has been anticipated from laboratory data, may now have been detected in the annual rings of subalpine conifers growing in the western United States. Experimental evidence shows that carbon dioxide can be an important limiting factor in the growth of plants in this high-altitude environment. The greatly increased tree growth rates observed since the mid-l9th century exceed those expected from climatic trends but are consistent in magnitude with global trends in carbon dioxide, especially in recent decades. If correctly interpreted, these findings have important implications for climate studies involving tree ring observations and for models of the global carbon dioxide budget.

Genetic analysis of mechanisms of aging.

A wide range of genetic models with postponed aging are now available, from selected mice and Drosophilia to mutant Caenorhabditis elegans and Saccharomyces cerevisiae. These systems allow efficient testing of alternative mechanistic hypotheses for aging. Genetic analysis is forging stronger connections between particular alleles and susceptibility to particular 'diseases of aging'; for example, two different genes for Alzheimer disease have been identified.

Treatment for periodic paralysis.

BACKGROUND: Primary periodic paralyses are rare inherited muscle diseases characterised by episodes of flaccid weakness affecting one or more limbs, lasting several hours to several days, caused by mutations in skeletal muscle channel genes. OBJECTIVES: The objective of this review was to systematically review treatment of periodic paralyses. SEARCH STRATEGY: We searched the Cochrane Neuromuscular Disease Group Trials Register, MEDLINE (from January 1966 to July 2007), and EMBASE (from January 1980 to July 2007) and any other available international medical library sources from the University of Milan for randomised trials. SELECTION CRITERIA: We included randomised (including cross-over studies) and quasi-randomised trials in participants with primary periodic paralyses, in which any form of treatment, including physical therapy and alternative therapies, was compared to placebo or another treatment. DATA COLLECTION AND ANALYSIS: Our primary outcome measure was the change in attack severity or frequency by eight weeks from the start of treatment. Our secondary outcome measures were: change in muscle strength and mass; change in Quality of Life, using Short Form 36 (SF36) or similar; preference of treatment strategy; adverse effects at eight weeks. MAIN RESULTS: Three studies met our inclusion criteria. In one study dichlorphenamide (DCP) vs placebo was tested in two groups of participants: 42 with hypokalemic periodic paralysis (HypoPP) and 31 with hyperkalemic periodic paralysis (HyperPP), based on clinical criteria. Thirty-four of 42 participants with hypokalemic periodic paralysis completed both treatment phases. For the 34 participants having attack rate data for both treatment phases, the mean improvement in attack rate (P = 0.02) and severity-weighted attack rate (P = 0.01) on DCP relative to placebo were statistically significant. Fifteen preferred DCP, three placebo and six their baseline medication. Twenty-four of 31 participants with hyperkalemic periodic paralysis completed both treatment phases: for the 16 participants who had attack rate data for both treatment phases, the mean improvement in attack rate (P = 0.006) and in severity-weighted attack rate (P = 0.02) on DCP relative to placebo were significant. Fifteen preferred DCP, one placebo and five their baseline medication. Acetazolamide proved to improve muscle strength in eight participants with HypoPP in one other study and pinacidil, a potassium channel opener, also improved muscle strength in 2/4 participants with HypoPP in a third study. AUTHORS' CONCLUSIONS: The largest included study that met our inclusion criteria suggested that DCP was effective in the prevention of episodic weakness in both hypokalemic and hyperkalemic periodic paralyses. The other two studies provide some evidence that either acetazolamide or pinacidil may improve muscle strength. However we still lack sufficient evidence to provide full guidelines for the treatment of people with periodic paralysis.

Genetics of life history in Drosophila melanogaster. I. Sib analysis of adult females.

A sib analysis of adult life-history characters was performed on about twelve hundred females from a laboratory Drosophila melanogaster population that had been sampled from nature and cultured so as to preserve its genetic variability. The following results were found. There was no detectable trend with age in additive or dominance genetic variances for age-specific fecundity. Environmental variance for age-specific fecundity increased with age. The genetic variance for fecundity characters was primarily additive. The genetic variance for longevity was primarily dominance variance. There were negative genetic correlations between early fecundity and lifespan, as well as between mean egg-laying rate and longevity.

Genetics of life history in Drosophila melanogaster. II. Exploratory selection experiments.

two types of small-scale selection experiments were performed. (1) Artificial selection experiments were performed on age-specific female fecundity. Selection for early fecundity over three generations produced a statistically detectable direct response. There was no detectable indirect response in other life-history characters. Selection for late fecundity over three generations did not produce any detectable direct response. Indirect responses were detected: early egg-laying decreased and longevity increased. (2) Natural selection for late-age fitness components increased late fecundity, female longevity, and the duration of female reproduction, while early fecundity and mean egg-laying rate decreased.

Quantitative genetics of postponed aging in Drosophila melanogaster. I. Analysis of outbred populations.

Selection has been used to create replicated outbred stocks of Drosophila melanogaster with increased longevity, increased later fecundity, and increased levels of physiological performance at later ages. The present study analyzed the quantitative transmission patterns of such stocks, employing extensive replication in numbers of stocks, individuals, and assayed characters. The populations used derived from five lines with postponed aging and five control lines, all created in 1980 from the same founding base population. The following characters were studied: early 24-hr fecundity, early ovary weight, early female starvation resistance, early male starvation resistance, female longevity and male longevity. Numerous crosses were performed to test for non-Mendelian inheritance, average dominance, maternal effects, sex-linkage and between-line heterogeneity. There was only slight evidence for any of these phenomena arising reproducibly in the characters studied. These findings suggest the value of this set of stocks for studies of the physiological basis of postponed aging.

Quantitative genetics of postponed aging in Drosophila melanogaster. II. Analysis of selected lines.

Quantitative genetic analyses of Drosophila melanogaster stocks with postponed aging have suffered from the problem of a lack of certainty concerning patterns of allelic differentiation. The present experiments were designed to alleviate this difficulty by selecting for enhanced levels of characters known to be related to postponed aging. Selection successfully increased the degree of differentiation of postponed aging stocks with respect to starvation resistance and fecundity, but persistent additive genetic variance suggested that selection did not result in fixation of alleles. The artificially selected stocks were subjected to crosses to test for patterns of dominance and maternal effects. There was little evidence for these effects in the inheritance of the characters underlying postponed aging, even with the increased differentiation of the selected stocks.

Perspective: reverse evolution.

For some time, the reversibility of evolution was primarily discussed in terms of comparative patterns. Only recently has this problem been studied using experimental evolution over shorter evolutionary time frames. This has raised questions of definition, experimental procedure, and the hypotheses being tested. Experimental evolution has provided evidence for multiple population genetic mechanisms in reverse evolution, including pleiotropy and mutation accumulation. It has also pointed to genetic factors that might prevent reverse evolution, such as a lack of genetic variability, epistasis, and differential genotype-by-environment interactions. The main focus of this perspective is on laboratory studies and their relevance to the genetics of reverse evolution. We discuss reverse evolution experiments with Drosophila, bacterial, and viral populations. Field studies of the reverse evolution of melanism in the peppered moth are also reviewed.

Sustained myoglobinuria: the presenting manifestation of dermatomyositis.

We describe two patients with sustained myoglobinuria that did not resolve with supportive treatment. After we established a diagnosis of dermatomyositis and started treatment with corticosteroids, there was rapid resolution of the myoglobinuria. Well-documented cases of inflammatory myopathy causing myoglobinuria are rare, but their prompt recognition has important therapeutic implications.

Neurophysiologic analysis of neuromuscular symptoms in UK Gulf War veterans: a controlled study.

BACKGROUND: UK veterans who were deployed to the Gulf in 1990 to 1991 reported higher prevalence of neuromuscular symptoms. OBJECTIVE: To investigate whether these Gulf War-related symptoms were associated with objective evidence of neuromuscular dysfunction. METHODS: Forty-nine Gulf War veterans with more than four neuromuscular symptoms (Gulf-ill), 26 Gulf-well veterans, 13 symptomatic Bosnian veterans (Bosnia-ill), and 22 symptomatic veterans who were not deployed to the Gulf (Era-ill) underwent detailed neurophysiologic assessment: nerve conduction studies, quantitative sensory and autonomic testing, and concentric needle and single-fiber electromyography (EMG). RESULTS: Nerve conduction studies detected carpal tunnel syndrome in two Gulf-ill, two Gulf-well, one Bosnia-ill, and three Era-ill veterans. Ulnar neuropathy was detected in one Gulf-ill and two Era-ill veterans. However, results of detailed nerve conduction studies of the Gulf-ill veterans were comparable with results observed in the other three groups. Quantitative sensory and autonomic assessments also failed to show any specific abnormalities in the Gulf-ill group. Similarly, quantitative assessment of concentric needle and single-fiber EMG detected no chronic denervation or myopathic changes or any abnormalities of neuromuscular transmission in the Gulf-ill veterans. CONCLUSION: Gulf War-related neuromuscular symptoms are not associated with specific impairments of peripheral nerves, neuromuscular junctions, or skeletal muscles.

A prospective natural history study of inclusion body myositis: implications for clinical trials.

Eleven patients with untreated inclusion body myositis (IBM) were prospectively studied during a 6-month period that included muscle strength, lean body mass, and muscle mass measurements. There was an overall quantifiable mean decline in percent of predicted normal muscle strength of 4% from baseline in a 6-month period, but one third of patients showed no change or slight improvements in strength. Short-term treatment trials in IBM will require large numbers of patients to detect slowing, arrest, or even slight improvement in muscle strength.

Excretion of iodine-123-hippuran, technetium-99m-red blood cells, and technetium-99m-macroaggregated albumin into breast milk.

The amount of radioactivity excreted in breast milk following three different nuclear medicine procedures on twelve nursing mothers has been measured. Some of this information has already been incorporated into the latest guidelines on suspension of feeding after maternal radiopharmaceutical administration. The overall radiation dose that the patients' babies would have sustained had breast feeding not been interrupted has been estimated as an effective dose equivalent. A model has been developed to describe the relationship between clearance of activity from the milk, time between expressions, and the fraction of milk expressed. Some simple guidance is given on calculation of suitable interruption times for any individual mother from counts on her milk samples.

Genetics of aging in Drosophila.

The genetics of aging in Drosophila are reviewed under the separate headings of population genetics, physiological genetics, and molecular genetics. However, connections between these sub-fields are brought forward for discussion.

Evolutionary patterns among measures of aging.

Maximum lifespan has been one of the most common aging measures in comparative studies, while the Gompertz model has recently attracted both proponents and critics of its capacity to adequately describe the acceleration of mortality in the oldest age classes. The Gompertz demographic model describes age-dependent mortality rate acceleration and age-independent mortality using the parameters alpha and A, respectively. Evolutionary biologists have predominantly used average longevity in studies of aging. Little is known about the evolutionary relationships of these measures on the microevolutionary time scale. We have simultaneously compared Gompertz parameters, average longevity, and maximum longevity in 50 related populations of Drosophila melanogaster, many of which have been selected for postponed aging. Overall, these populations have differentiated significantly for the A and alpha parameter of the Gompertz equation, as well as average and maximum longevity. These indices of aging appear to measure the same genetic changes in aging. However, in some specific population comparisons, the relationships among these measures are more complex. In a second experiment, environmental manipulation of longevity had substantially different effects from genetic differentiation, with the A parameter accounting for changes in overall mortality. The adequacy of the maximum lifespan and the Gompertz equation as indices of aging in evolutionary studies is discussed.