Dataset Information

When do we have the power to detect biological interactions in spatial point patterns?

ABSTRACT: Uncovering the roles of biotic interactions in assembling and maintaining species-rich communities remains a major challenge in ecology. In plant communities, interactions between individuals of different species are expected to generate positive or negative spatial interspecific associations over short distances. Recent studies using individual-based point pattern datasets have concluded that (a) detectable interspecific interactions are generally rare, but (b) are most common in communities with fewer species; and (c) the most abundant species tend to have the highest frequency of interactions. However, it is unclear how the detection of spatial interactions may change with the abundances of each species, or the scale and intensity of interactions. We ask if statistical power is sufficient to explain all three key results.We use a simple two-species model, assuming no habitat associations, and where the abundances, scale and intensity of interactions are controlled to simulate point pattern data. In combination with an approximation to the variance of the spatial summary statistics that we sample, we investigate the power of current spatial point pattern methods to correctly reject the null model of pairwise species independence.We show the power to detect interactions is positively related to both the abundances of the species tested, and the intensity and scale of interactions, but negatively related to imbalance in abundances. Differences in detection power in combination with the abundance distributions found in natural communities are sufficient to explain all the three key empirical results, even if all pairwise interactions are identical. Critically, many hundreds of individuals of both species may be required to detect even intense interactions, implying current abundance thresholds for including species in the analyses are too low. Sy n thesis. The widespread failure to reject the null model of spatial interspecific independence could be due to low power of the tests rather than any key biological process. Since we do not model habitat associations, our results represent a first step in quantifying sample sizes required to make strong statements about the role of biotic interactions in diverse plant communities. However, power should be factored into analyses and considered when designing empirical studies.

SUBMITTER: Rajala T

PROVIDER: S-EPMC6472561 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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When do we have the power to detect biological interactions in spatial point patterns?

Rajala Tuomas T Olhede Sofia Charlotta SC Murrell David John DJ

The Journal of ecology 20181023 2

Uncovering the roles of biotic interactions in assembling and maintaining species-rich communities remains a major challenge in ecology. In plant communities, interactions between individuals of different species are expected to generate positive or negative spatial interspecific associations over short distances. Recent studies using individual-based point pattern datasets have concluded that (a) detectable interspecific interactions are generally rare, but (b) are most common in communities wi ...[more]

PMID: 31007275

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Project description:BackgroundIdentifying interaction effects between genes is one of the main tasks of genome-wide association studies aiming to shed light on the biological mechanisms underlying complex diseases. Multifactor dimensionality reduction (MDR) is a popular approach for detecting gene-gene interactions that has been extended in various forms to handle binary and continuous phenotypes. However, only few multivariate MDR methods are available for multiple related phenotypes. Current approaches use Hotelling's T2 statistic to evaluate interaction models, but it is well known that Hotelling's T2 statistic is highly sensitive to heavily skewed distributions and outliers.ResultsWe propose a robust approach based on nonparametric statistics such as spatial signs and ranks. The new multivariate rank-based MDR (MR-MDR) is mainly suitable for analyzing multiple continuous phenotypes and is less sensitive to skewed distributions and outliers. MR-MDR utilizes fuzzy k-means clustering and classifies multi-locus genotypes into two groups. Then, MR-MDR calculates a spatial rank-sum statistic as an evaluation measure and selects the best interaction model with the largest statistic. Our novel idea lies in adopting nonparametric statistics as an evaluation measure for robust inference. We adopt tenfold cross-validation to avoid overfitting. Intensive simulation studies were conducted to compare the performance of MR-MDR with current methods. Application of MR-MDR to a real dataset from a Korean genome-wide association study demonstrated that it successfully identified genetic interactions associated with four phenotypes related to kidney function. The R code for conducting MR-MDR is available at https://github.com/statpark/MR-MDR .ConclusionsIntensive simulation studies comparing MR-MDR with several current methods showed that the performance of MR-MDR was outstanding for skewed distributions. Additionally, for symmetric distributions, MR-MDR showed comparable power. Therefore, we conclude that MR-MDR is a useful multivariate non-parametric approach that can be used regardless of the phenotype distribution, the correlations between phenotypes, and sample size.

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When do we have the power to detect biological interactions in spatial point patterns?

Publications

When do we have the power to detect biological interactions in spatial point patterns?

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