Identifying Signatures of Selection in Genetic Time Series

Both genetic drift and natural selection cause the frequencies of alleles in a population to vary over time. Discriminating between these two evolutionary forces, based on a time series of samples from a population, remains an outstanding problem with increasing relevance to modern data sets. Even in the idealized situation when the sampled locus is independent of all other loci this problem is difficult to solve, especially when the size of the population from which the samples are drawn is unknown. A standard $\chi^2$-based likelihood ratio test was previously proposed to address this problem. Here we show that the $\chi^2$ test of selection substantially underestimates the probability of Type I error, leading to more false positives than indicated by its $P$-value, especially at stringent $P$-values. We introduce two methods to correct this bias. The empirical likelihood ratio test (ELRT) rejects neutrality when the likelihood ratio statistic falls in the tail of the empirical distribution obtained under the most likely neutral population size. The frequency increment test (FIT) rejects neutrality if the distribution of normalized allele frequency increments exhibits a mean that deviates significantly from zero. We characterize the statistical power of these two tests for selection, and we apply them to three experimental data sets. We demonstrate that both ELRT and FIT have power to detect selection in practical parameter regimes, such as those encountered in microbial evolution experiments. Our analysis applies to a single diallelic locus, assumed independent of all other loci, which is most relevant to full-genome selection scans in sexual organisms, and also to evolution experiments in asexual organisms as long as clonal interference is weak. Different techniques will be required to detect selection in time series of co-segregating linked loci.Comment: 24 pages, 6 figures, 4 tables, 7 supplementary figures and table

Tax Policy and Returns to Education

This paper considers how asymmetric tax treatment, where labour market earnings are taxed but household production is untaxed, aspects educational choice and labour supply. We show that taxes on labour market earnings can generate a large (non-marginal) switch to home production and the ensuing deadweight losses are large. Using a cross-country panel, we find that gender differences in labour supply responses to tax policy can explain differences in aggregate labour supply and years of education across countries.Increasing returns; tax policy; gender; labour supply; education

Electron microscopic measurement of the size of the optical focus in laser scanning microscopy

We describe a method for measuring the lateral focal spot size of a multiphoton laser scanning microscope (LSM) with unprecedented accuracy. A specimen consisting of an aluminum film deposited on a glass coverslip was brought into focus in a LSM and the laser intensity was then increased enough to perform nanoablation of the metal film. This process leaves a permanent trace of the raster path usually taken by the beam during the acquisition of an optical image. A scanning electron microscope (SEM) was then used to determine the nanoablated line width to high accuracy, from which the lateral spot size and hence resolution of the LSM can be determined. To demonstrate our method, we performed analysis of a multiphoton LSM at various infrared wavelengths, and we report measurements of optical lateral spot size with an accuracy of 20 nm, limited only by the resolution of the SEM

Applying the Biopsychosocial Model: Factors Associated with Depression in Mexican-American Adults

Although professionals in psychiatry, psychology and medicine claim to endorse the biopsychosocial model as proposed by George L. Engel (1977), clinicians in all three fields still tend to underutilize it. Some academics have also criticized the model for its inadequate emphasis on cultural contextualization. To improve upon the model, I sought to empirically establish the relationship between culturally-specific social factors and psychological disorder, in this case depressive symptoms in Mexican-American adults. Eighty-six Mexican-American participants living on the US-Mexico border completed scales measuring depressive symptoms, bidirectional acculturation, living situation, diabetes, and health beliefs regarding the origins of diabetes. The results revealed that diabetes, acculturation, and gender were not associated with depressive symptoms in this population, even when controlling for mental health biases. This finding is in contrast to findings from other literature that associated diabetes, low acculturation and gender with depression in Hispanic adults. Extended family cohabitation was also not associated with lower numbers of depressive symptoms, despite the importance of familism and the extended family unit in Mexican-American culture. Unemployment was significantly related to number of depressive symptoms in both genders. There was no significant relationship between acculturation and health beliefs. These results indicate the importance of studying psychological disorders within the context of specific population groups that transcend vague censual terms. The discussion addresses methodological concerns and further directions for research concerning gender roles, chronic illness, depression and out-of-home employment in Mexican-American adults

A Randomized Controlled Trial of Device Guided, Slow-Paced Respiration in Women with Overactive Bladder Syndrome.

PurposeWe evaluated the effects of device guided, slow-paced respiration on urgency associated urinary symptoms, perceived stress and anxiety, and autonomic function in women with overactive bladder syndrome.Materials and methodsWe performed a randomized, parallel group trial of slow-paced respiration to improve perceived stress and autonomic dysfunction as potential contributors to overactive bladder. Ambulatory women who reported at least 3 voiding or incontinence episodes per day associated with moderate to severe urgency were randomized to use a portable biofeedback device to practice daily, slow, guided breathing exercises or a control device which appeared identical and was reprogrammed to play music without guiding breathing. During 12 weeks we evaluated changes in urinary symptoms by voiding diaries, perceived stress and anxiety by validated questionnaires, and autonomic function by heart rate variability and impedance cardiography.ResultsIn the 161 randomized participants, including 79 randomized to paced respiration and 82 randomized to the control group, the average ± SD baseline frequency of voiding or incontinence associated with moderate to severe urgency was 6.9 ± 3.4 episodes per day. Compared to controls the participants randomized to paced respiration demonstrated greater improvement in perceived stress (average Perceived Stress Scale score decrease 2.8 vs 1.1, p=0.03) but not in autonomic function markers. During 12 weeks the average frequency of voiding or incontinence associated with moderate to severe urgency, which was the study primary outcome, decreased by a mean of 0.9 ± 3.2 episodes per day but no significant between group difference was detected.ConclusionsAmong women with overactive bladder slow-paced respiration was associated with a modest improvement in perceived stress during 12 weeks. However, it was not superior to a music listening control for reducing urinary symptoms or changing autonomic function

Effects of virus infection on release of volatile organic compounds from insect-damaged bean, Phaseolus vulgaris

Insects can serve as important vectors of plant pathogens, especially viruses. Insect feeding on plants causes the systemic release of a wide range of plant volatile compounds that can serve as an indirect plant defense by attracting natural enemies of the herbivorous insect. Previous work suggests that the Mexican bean beetle (Epilachna varivestis) prefers to feed on plants infected by either of two viruses that it is known to transmit: Southern bean mosaic virus (SBMV) or Bean pod mottle virus (BPMV). A possible explanation for the preferred feeding on virus-infected tissues is that the beetles are attracted by volatile signals released from leaves. The purpose of this work was to determine whether volatile compounds from virus-infected plants are released differentially from those emitted by uninfected plants. To test the hypothesis, common bean plants (Phaseolus vulgaris cv. Black Valentine) were inoculated with either BPMV, SBMV, or a mixture of both viruses, and infected plants were compared to uninfected plants. An Ouchterlony assay was used with SBMVand BPMV-specific antisera to confirm the presence of virus in inoculated plants. RNA blot analysis was performed on tissue from each plant and indicated that a well-characterized defense gene, encoding phenylalanine ammonia-lyase (PAL), was not induced in systemic tissue following virus infection. Plant volatiles were collected—and analyzed via gas chromatography (GC)—from plants that were either undamaged or beetle-damaged. In undamaged plants, there were no measurable differences in profiles or quantities of compounds released by uninfected and virus-infected plants. After Mexican bean beetles were allowed to feed on plants for 48 h, injured plants released several compounds that were not released from undamaged plants. Lower quantities of volatile compounds were released from virus-infected plants suggesting that enhanced release of plant-derived volatile organic compounds is not the cause for attraction of Mexican bean beetles to virus-infected plants