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Sampling strategy optimization to increase statistical power in landscape genomics: A simulation-based approach.

ABSTRACT: An increasing number of studies are using landscape genomics to investigate local adaptation in wild and domestic populations. Implementation of this approach requires the sampling phase to consider the complexity of environmental settings and the burden of logistical constraints. These important aspects are often underestimated in the literature dedicated to sampling strategies. In this study, we computed simulated genomic data sets to run against actual environmental data in order to trial landscape genomics experiments under distinct sampling strategies. These strategies differed by design approach (to enhance environmental and/or geographical representativeness at study sites), number of sampling locations and sample sizes. We then evaluated how these elements affected statistical performances (power and false discoveries) under two antithetical demographic scenarios. Our results highlight the importance of selecting an appropriate sample size, which should be modified based on the demographic characteristics of the studied population. For species with limited dispersal, sample sizes above 200 units are generally sufficient to detect most adaptive signals, while in random mating populations this threshold should be increased to 400 units. Furthermore, we describe a design approach that maximizes both environmental and geographical representativeness of sampling sites and show how it systematically outperforms random or regular sampling schemes. Finally, we show that although having more sampling locations (between 40 and 50 sites) increase statistical power and reduce false discovery rate, similar results can be achieved with a moderate number of sites (20 sites). Overall, this study provides valuable guidelines for optimizing sampling strategies for landscape genomics experiments.

SUBMITTER: Selmoni O

PROVIDER: S-EPMC6972490 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Sampling strategy optimization to increase statistical power in landscape genomics: A simulation-based approach.

Selmoni Oliver O Vajana Elia E Guillaume Annie A Rochat Estelle E Joost Stéphane S

Molecular ecology resources 20191021 1

An increasing number of studies are using landscape genomics to investigate local adaptation in wild and domestic populations. Implementation of this approach requires the sampling phase to consider the complexity of environmental settings and the burden of logistical constraints. These important aspects are often underestimated in the literature dedicated to sampling strategies. In this study, we computed simulated genomic data sets to run against actual environmental data in order to trial lan ...[more]

PMID: 31550072

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Project description:ObjectivesObservational work sampling is often used in occupational studies to assess categorical biomechanical exposures and occurrence of specific work tasks. The statistical performance of data obtained by work sampling is, however, not well understood, impeding informed measurement strategy design. The purpose of this study was to develop a procedure for assessing the statistical properties of work sampling strategies evaluating categorical exposure variables and to illustrate the usefulness of this procedure to examine bias and precision of exposure estimates from samples of different sizes.MethodsFrom a parent data set of observations on 10 construction workers performing a single operation, the probabilities were determined for each worker of performing four component tasks and working in four mutually exclusive trunk posture categories (neutral, mild flexion, severe flexion, twisted). Using these probabilities, 5000 simulated data sets were created via probability-based resampling for each of six sampling strategies, ranging from 300 to 4500 observations. For each strategy, mean exposure and exposure variability metrics were calculated at both the operation level and task level and for each metric, bias and precision were assessed across the 5000 simulations.ResultsEstimates of exposure variability were substantially more uncertain at all sample sizes than estimates of mean exposures and task proportions. Estimates at small sample sizes were also biased. With only 600 samples, proportions of the different tasks and of working with a neutral trunk posture (the most common) were within 10% of the true target value in at least 80% of all the simulated data sets; rarer exposures required at least 1500 samples. For most task-level mean exposure variables and for all operation-level and task-level estimates of exposure variability, performance was low, even with 4500 samples. In general, the precision of mean exposure estimates did not depend on the exposure variability between workers.ConclusionsThe suggested probability-based simulation approach proved to be versatile and generally suitable for assessing bias and precision of data collection strategies using work sampling to estimate categorical data. The approach can be used in both real and hypothetical scenarios, in ergonomics, as well as in other areas of occupational epidemiology and intervention research. The reported statistical properties associated with sample size are likely widely relevant to studies using work sampling to assess categorical variables.

Project description:BackgroundSchistosoma mansoni is a parasite of major public health importance in developing countries, where it causes a neglected tropical disease known as intestinal schistosomiasis. However, the distribution of the parasite within many endemic regions is currently unknown, which hinders effective control. The purpose of this study was to characterize the prevalence and intensity of infection of S. mansoni in a remote area of western Tanzania.Methodology/principal findingsStool samples were collected from 192 children and 147 adults residing in Gombe National Park and four nearby villages. Children were actively sampled in local schools, and adults were sampled passively by voluntary presentation at the local health clinics. The two datasets were therefore analysed separately. Faecal worm egg count (FWEC) data were analysed using negative binomial and zero-inflated negative binomial (ZINB) models with explanatory variables of site, sex, and age. The ZINB models indicated that a substantial proportion of the observed zero FWEC reflected a failure to detect eggs in truly infected individuals, meaning that the estimated true prevalence was much higher than the apparent prevalence as calculated based on the simple proportion of non-zero FWEC. For the passively sampled data from adults, the data were consistent with close to 100% true prevalence of infection. Both the prevalence and intensity of infection differed significantly between sites, but there were no significant associations with sex or age.Conclusions/significanceOverall, our data suggest a more widespread distribution of S. mansoni in this part of Tanzania than was previously thought. The apparent prevalence estimates substantially under-estimated the true prevalence as determined by the ZINB models, and the two types of sampling strategies also resulted in differing conclusions regarding prevalence of infection. We therefore recommend that future surveillance programmes designed to assess risk factors should use active sampling whenever possible, in order to avoid the self-selection bias associated with passive sampling.

Dataset Information

Sampling strategy optimization to increase statistical power in landscape genomics: A simulation-based approach.

Publications

Sampling strategy optimization to increase statistical power in landscape genomics: A simulation-based approach.

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