A haplotype method detects diverse scenarios of local adaptation from genomic sequence variation

Identifying genomic targets of population‐specific positive selection is a major goal in several areas of basic and applied biology. However, it is unclear how often such selection should act on new mutations versus standing genetic variation or recurrent mutation, and furthermore, favoured alleles may either become fixed or remain variable in the population. Very few population genetic statistics are sensitive to all of these modes of selection. Here, we introduce and evaluate the Comparative Haplotype Identity statistic (χ_MD), which assesses whether pairwise haplotype sharing at a locus in one population is unusually large compared with another population, relative to genomewide trends. Using simulations that emulate human and Drosophila genetic variation, we find that χ_MD is sensitive to a wide range of selection scenarios, and for some very challenging cases (e.g. partial soft sweeps), it outperforms other two‐population statistics. We also find that, as with F_ST, our haplotype approach has the ability to detect surprisingly ancient selective sweeps. Particularly for the scenarios resembling human variation, we find that χ_MD outperforms other frequency‐ and haplotype‐based statistics for soft and/or partial selective sweeps. Applying χ_MD and other between‐population statistics to published population genomic data from D. melanogaster, we find both shared and unique genes and functional categories identified by each statistic. The broad utility and computational simplicity of χ_MD will make it an especially valuable tool in the search for genes targeted by local adaptation.     

Extended Rank Analysis of Covariance as a More Efficient Matched Analysis Considering Trend Information

Classical matched analysis, regarded as analysis of covariance (ANOCOVA) in a broad sense, makes no attempt in modeling and may therefore be inefficient. In this paper, we discuss the relative efficiencies of the ERMP (extended rank and matched‐pair) test (Chen and Quade , 2000) to standard matched methods, and extend it to the case of multivariate covariables X . Taking advantage of trend information between the response Y and the covariables X by ranking after matching, ERMP test achieves better efficiency than a proposed class of weighted matched statistics. When Y is dichotomous, the optimal weighted matched statistic is equivalent to the Mantel‐Haenszel statistic. Example and simulation results also suggest the conclusion.     

Effects of folic acid fortification on spina bifida prevalence in Brazil

BACKGROUND: To assess spina bifida birth prevalence changes after folic acid fortification of wheat and maize flours began in Brazil in June 2004. METHODS: Cross‐sectional study of Brazilian live births in 2004 and 2006. Spina bifida birth prevalence from the Live Births Information System (SINASC: Sistema de Informações sobre Nascidos Vivos) in a prefortified period was compared to a period fortified with folic acid in each state. Observed prevalence rates in 2004 were used to calculate the expected prevalence rates in 2006 under the null hypothesis that both were similar. The observed/expected (O/E) ratios were tested by two‐tailed Z‐test. To minimize ascertainment differences among states, the O/E ratio of each one of the 27 Brazilian states was adjusted for the number of births with the Mantel‐Haenszel statistic. RESULTS The reduction in spina bifida birth prevalence in 2006 was 39% (O/E = 0.61; 95% confidence interval [CI], 0.55‐0.67), and 40% (O/E = 0.60; 95% CI, 0.53–0.68), after adjusting for state birth number. This reduction was significant (p < 0.0001), and heterogeneous among states (χ² = 72.96; p < 0.0001). CONCLUSIONS: Using SINASC data, there was a significant reduction in spina bifida birth prevalence in Brazil, probably related to the folic acid food fortification program. Birth Defects Research (Part A) 2011. © 2011 Wiley‐Liss, Inc.     

Small Sample Comparison of Modified Chi‐Square Test Statistics for Survey Data

The problem of categorial data analysis in survey sampling arises because of non‐independence of sample elements of the sample obtained through imposed sampling design. In this article the performance of modified χ² statistic for testing independence of attributes have been evaluated for small sample sizes with the help of log‐linear models with respect to its achieved level of significance for fixed nominal level at 5%, through simulation technique. It hase been observed that the perfiormance of these test statistics depends on average and coefficient of variation of eigen values of design effect matrix. The first order corrected statistic is able to capture the effect of sampling design to a great extent but the performance of second order corrected statistic is much better. Further, these modified χ² test statistics were applied to a real survey data and their performance were evaluated with respect to their achievied level of significance.     

Comparing Power Behaviours for Some Goodness-of-Fit Test Statistics in Sparse Multinomials

This paper is concerned with the power behaviour of four goodness-of-fit test statistics in sparse multinomials with k cells. Most previous work has been concerned only with both Pearson's X² and the likelihood ratio test statistics. We consider in this study, two additional test statistics, namely, the Cressie-Read test statistic – I(2/3) and the modified Freeman-Tukey test (FT) statistic. Because k ≥ 10 in this study, a Monte Carlo procedure based on 1000 simulated samples is used to estimate the powers for the four test statistics. Alternatives on various line segments are employed. Results suggest that none of the test statistics completely dominate the other and that the choice of which test to use depends on the nature of the alternative hypothesis. These results are consistent with those obtained by West and Kempthorne (1972), although, the Pearson's χ² test statistic may be preferred because of its closer approximation to the χ² distribution in terms of the attained α levels.     

Comparing Species Assemblages Via Species Accumulation Curves

Summary Comparing species assemblages given incidence‐based data is of importance in ecological studies, often done by a visual inspection of estimated species accumulation curves or by an ad hoc use of 95% pointwise confidence bands of these curves. It is shown that comparing species assemblages is a challenging problem. A χ² test is proposed. An adjustment using an eigenvalue decomposition is proposed to overcome computational difficulties. The bootstrap method is also suggested to approximate the distribution of the proposed test statistic. The eigenvalue adjusted (Eva) χ² test and the Eva‐bootstrap test are assessed by a simulation study. Both the Eva‐χ² and the Eva‐bootstrap tests are applied to a study that involves two woody seedling species assemblages.     

An Improved Goodness of Fit Statistic for Probability Prediction Models

We consider the general case of probability prediction models having two or more outcomes and propose an adjusted χ² statistic which can be used to assess the goodness of fit of these models. We present a simulation study to show that our proposed statistic has an approximate χ² distribution under the null hypothesis. Two applications are provided to illustrate the use of the new statistic. The first application examines the fit of a logistic regression model using both the proposed statistic and the popular Hosmer-Lemeshow statistic and we compare and contrast these two methods. The second application evaluates the goodness of fit of a polychotomous regression model.     

A Truncated Proportional Hazards Test

We present two truncated proportional hazards tests. The first, which is applicable to those cases in which the time of action of an agent or treatment is known, was studied in two forms: One uses expected Fisher information and the other observed Fisher information. In this case the expected information statistic, C₁(a₀), had properties superior to the observed information statistic and is recommended. The use of the X² distribution with one degree of freedom for percentiles appears to be satisfactory. When the time of action is unknown, a statistic based on the maximum of the C₁(a) statistics is used. A simulation study gives empirical percentiles for the Max C₁(a) statistic which agree with those given in a study by Muenz, Green and Byar (1977).     

Exact Power of Conditional Tests for Several Binomial Populations

An efficient recursive polynomial multiplication method is proposed for exact unconditional power calculation for unordered 2 × K contingency table with up to moderate sample size. Our method can be applied to the family of cell-additive statistics which includes the Freeman-Halton statistic, the Pearson χ² statistic and the likelihood ratio statistic. We illustrate our proposed method by several numerical examples.     

Racemization of the aqua-{N-salicylidene-(S)-alaninato}copper(II) by reaction with potassium cyanate

Copper(II) N-salicylidene-(S)-alaninate trihydrate reacting as the S-enantiomeric parent compound with KOCN in hot diluted methanol yielded by slow crystallisation from the cooled reaction mixture (in the course of 1 day) the racemic product K[Cu{sal-(RS)-ala}(NCO)]. The parameters of the axial type EPR spectrum in X-band region and the LF band position in the electronic spectrum are typical of an axially distorted square pyramidal coordination of the Cu(II) atom in this complex. The spectral properties of the complex cuprate prepared and its basal crystallographic data are consistent with those of the earlier studied¹⁵ K₂[Cu₂{sal-(RS)-ala}₂(μ-NCO)₂] synthetized by using [Cu{sal-(RS)-ala}(H₂O)].H₂O as the racemic parent complex in the reaction mixture with KOCN.     

Quantifying the lag time to detect barriers in landscape genetics

Understanding how spatial genetic patterns respond to landscape change is crucial for advancing the emerging field of landscape genetics. We quantified the number of generations for new landscape barrier signatures to become detectable and for old signatures to disappear after barrier removal. We used spatially explicit, individual‐based simulations to examine the ability of an individual‐based statistic [Mantel’s r using the proportion of shared alleles’ statistic (Dps)] and population‐based statistic (F_ST) to detect barriers. We simulated a range of movement strategies including nearest neighbour dispersal, long‐distance dispersal and panmixia. The lag time for the signal of a new barrier to become established is short using Mantel’s r (1–15 generations). F_ST required approximately 200 generations to reach 50% of its equilibrium maximum, although G’_ST performed much like Mantel’s r. In strong contrast, F_ST and Mantel’s r perform similarly following the removal of a barrier formerly dividing a population. Also, given neighbour mating and very short‐distance dispersal strategies, historical discontinuities from more than 100 generations ago might still be detectable with either method. This suggests that historical events and landscapes could have long‐term effects that confound inferences about the impacts of current landscape features on gene flow for species with very little long‐distance dispersal. Nonetheless, populations of organisms with relatively large dispersal distances will lose the signal of a former barrier within less than 15 generations, suggesting that individual‐based landscape genetic approaches can improve our ability to measure effects of existing landscape features on genetic structure and connectivity.     

Group characteristics,site fidelity,and photo‐identification of harbor porpoises,Phocoena phocoena,in Burrows Pass,Fidalgo Island,Washington

Little is known about harbor porpoises at the individual level or local group structure. Group characteristics, site fidelity, and photo‐identification of harbor porpoises were investigated off Fidalgo Island, Washington State. Harbor porpoise presence was affected by season and rip tide strength (Wald χ² P < 0.04); calf presence was influenced by season and tide (Wald χ² P < 0.0075). Average group size (2.32 ± 1.38, n = 266) was influenced by season, behavior, and calf presence (F₇ = 9.71, P < 0.0001, R² = 0.294). Fifty‐three individuals were identified using a matrix of primary, secondary, and confirmation markings that were stable over months/years. Over 35% were resighted in more than 1 mo (range 1–7, = 1.83); 15.1% were seen in more than 1 yr, suggesting some level of residency. Despite having higher effort, presence and group size were significantly lower in Summer. Variations in the significance of rip tide strength and tides relate to calf presence and support other findings that harbor porpoise population structure is complex and varies at small spatiotemporal scales and may also vary between populations and habitats. This study identifies variables affecting group characteristics and emphasizes the importance of research on local populations of harbor porpoises.     

Morningness: Protective Factor for Sleep-Related and Emotional Problems in Childhood and Adolescence?

The relationship between morningness/eveningness, sleep, and psychological problems is well documented in adults as well as in adolescents. However, research on the circadian orientation and its concomitants in younger children is scarce. The authors investigated the distribution of morningness/eveningness and its connection to sleeping and psychological problems in 91 children and 151 adolescents in Austria. The authors found that morning (M) types had less sleep-related and psychological problems than intermediate (I) and evening (E) types, respectively. Among children, M-types suffered less from daytime sleepiness (females: χ²₍₂₎?=?8.1, p?=?.017; males: χ²₍₂₎?=?14.8, p?=?.001). Among adolescents, M-types showed fewer sleep-wake problems (females: χ²₍₂₎?=?17.5, p?<?.001; males: χ²₍₂₎?=?19.8, p?<?.001), and female M-types showed less externalizing (χ²₍₂₎?=?8.7, p?=?.013) as well as internalizing problem behavior (χ²₍₂₎?=?9.0, p?=?.011). In conclusion, these findings indicate that morningness may act as a protective factor against the development of sleep-related problems in childhood and sleep-related and psychological problems in adolescence, especially in females. (Author correspondence: gloriagelbmann@gmx.at)     

The boundary layer and the apparent responses of stomatal conductance to wind speed and to the mole fractions of CO2 and water vapour in the air

The experiments and simulations reported in this paper show that, for stomata sensitive to both CO₂ and water vapour concentrations, responses of stomatal conductance (g^w_s) to boundary layer thickness have two components, one resulting from changes in intercellular CO₂ concentration (χ^c_i) and another from changes in leaf surface water vapour saturation deficit (D^w_s). The experiments and simulations also show that the boundary layer conductance (g^w_b) can significantly alter the apparent response of g^w_s to ambient air CO₂ mole fraction (χ^c_a) and water vapour mole fraction (χ^w_a). Because of the feedback loop involved the responses of g^w_s for χ^c_a and χ^w_a each include responses to both χ^c_i and D^w_s. The boundary layer alters the state of the variables sensed by the guard cells—i.e. χ^c_i and D^w_s—and so it is a source of feedback. Thus, when scaling up from responses of stomata to the response of g^w_s for a whole leaf, the effect of the boundary layer must be considered. The results indicate that, for given responses of g^w_s to χ^c_i and D^w_s, the apparent responses of g^w_s to D^w_a and χ^c_a depend on the size of the leaf and wind speed, showing that this effect of the boundary layer should be considered when comparing data measured under different conditions, or with different methods.     

Relative contributions of adiposity and muscularity to physical function in community-dwelling older adults

Objective: To determine the relative contributions of adiposity and muscularity to multi‐dimensional performance‐based and perceived physical function in older adults living independently. Methods and Procedures: Data from 109 women and men, aged 60 or older, with low serum dehydroepiandrosterone (DHEA) sulfate levels were included in this cross‐sectional analysis of baseline measures from a single‐site, randomized, controlled trial of DHEA replacement therapy. Physical function was determined by means of performance on the 100‐point Continuous Scale‐Physical Functional Performance (CS‐PFP) test and by self‐reporting using the physical function subscale of the Medical Outcomes Short Form‐36 (SF36_PF). Body composition was measured by dual‐energy X‐ray absorptiometry (DXA). Linear regression analyses were used to determine the contributions of body mass index (BMI; kg body mass/m²), fat index (FI; kg fat/m²), and appendicular skeletal muscle index (ASMI; kg muscle/m²) to the CS‐PFP and SF36_PF scores, adjusted for age and sex. Results: Age‐adjusted regression analyses indicated that FI, but not ASMI, was a significant (P < 0.001) determinant of CS‐PFP (R ² = 0.54) and SF36_PF (R ² = 0.37). When adjusted for age and sex, BMI was nearly as good a predictor of CS‐PFP (R ² = 0.50) and SF36_PF (R ² = 0.34) as FI. Discussion: Adiposity was a stronger predictor of measured and self‐reported physical function than was muscularity in older adults living independently. BMI, adjusted for sex, is a reasonable substitute for adiposity in the prediction of physical function.     

Association between nutrition and the prosthetic condition in edentulous elderly

Objectives: The aim of this study was to assess the possible risk of malnutrition among the elderly population. Subjects: twenty‐three pairs of complete dentures were made for a group of patients and 17 upper complete dentures with implant‐supported lower dentures were made for a different group. Methods: The study was performed at the University of São Paulo – Dental Branch, Brazil. The patients were submitted to a nutritional test, as well as to a clinical examination and interview. Chewing ability and patient's satisfaction with their prostheses were evaluated. The nonparametric statistics proof of chi‐squared, level 0.05 was performed and because of the low frequencies. The Fischer test was also used. Results: Patients wearing mandibular implant‐supported dentures were considered well nourished (76.47%) when compared with complete dentures users (43.48%). There was a significant difference between the two groups, concerning to chewing ability (χ² = 5.79) and nutritional status (χ² = 4.35). Conclusion: The risk of malnutrition was higher for elderly wearing complete dentures. The psychological state influences the interest in diet and choice of food.     

Comparison of techniques for sex determination of American martens

Accurate determination of sex in harvested species is critical for understanding demography and developing population models for management. We used genetic-based sex identification to assess accuracy of external carcass and pelt examination at registration and maximum canine root area (MRA) to determine sex of American martens (Martes americana) trapped in the Upper Peninsula of Michigan, 2000–2004. Overall percent similarity between MRA and genetic-based sex determination was 98.4% (n = 188). In contrast, only 84.6% (n = 421) of martens were similarly classified using external examination. For external examination, percent similarity to genetic-based sex determination for juveniles (<1-yr old) and adults (≥1-yr old; Wald χ²₁ = 2.168, P = 0.141), as well as for males and females (Wald χ²₁ = 0.005, P = 0.946), was similar. We recommend MRA as a suitable technique for sex determination of martens; thus, marten sex and age (using cementum annuli counts) can be obtained from one lower canine tooth. We do not recommend use of external examination at registration to identify sex of martens without implementing additional quality assurance measures. © 2010 The Wildlife Society.     

Effect of Intracluster Correlation on the R-Square Statistic

R²-statistic is a popular and very widely used statistic in regression analysis to estimate the square multiple correlation (SMC), ρ², between a response variable Y and p predictor variables, _X1, …, _Xp. Numerous articles are available in the statistical literature on the properties of R² as an estimator of ρ² when the observations are uncorrelated. However, relatively little is known about the behavior of R² when the available observations are correlated such as the data that result from complex sampling schemes. In this paper, we study the behavior R² in the presence of two-stage sampling data. An approximate expressions for the variance and the bias of R² in the presence of two-stage cluster sampling data with positive intracluster correlation (ρ*) are obtained. It is evident from these formulas and from a simulation study that R² is a poor estimator of ρ² except when ρ* is small. As such, we consider several alternative estimators of ρ² and evaluate their theoretical properties and finite sample performance using a simulation study.