2005. Implementing false discovery rate control: increasing your power. Á/ Oikos 108: 643 Á/647. Popular procedures to control the chance of making type I errors when multiple statistical tests are performed come at a high cost: a reduction in power. As the number of tests increases, power for an individual test may become unacceptably low. This is a consequence of minimizing the chance of making even a single type I error, which is the aim of, for instance, the Bonferroni and sequential Bonferroni procedures. An alternative approach, control of the false discovery rate (FDR), has recently been advocated for ecological studies. This approach aims at controlling the proportion of significant results that are in fact type I errors. Keeping the proportion of type I errors low among all significant results is a sensible, powerful, and easy-to-interpret way of addressing the multiple testing issue. To encourage practical use of the approach, in this note we illustrate how the proposed procedure works, we compare it to more traditional methods that control the familywise error rate, and we discuss some recent useful developments in FDR control.The appropriate threshold to declare a test statistic's p value significant becomes complex when more than one test is performed. In the absence of a true effect each test has a chance of a to yield a significant result, and the chance of drawing at least one false conclusion increases rapidly with the number of tests performed. Protection against false rejections of the null hypothesis, or type I errors, is usually achieved via a Bonferroni-type correction procedure (Holm 1979). By performing individual tests at error rates that are a fraction of the overall nominal a, the chance of making even a single type I error can be maintained at the desired a level (usually 5%). This is called control of the familywise error rate (FWER). With an increasing number of tests, maintaining a low chance of making even one type I error comes at the direct cost of making more type II errors, i.e. not recognizing a true effect as significant. The classical Bonferroni procedure, which performs each of m tests at a type I error rate of a/m, is undesirable because of this trade-off: only a very strong effect is likely to be recognized as significant when many tests are performed. Several improvements to the classical Bonferroni have been proposed in order to reduce the problem of low power (reviewed by García 2004). For instance, the well known Holm's step-down or sequential Bonferroni procedure (Holm 1979, popularized among evolutionary biologists and ecologists by Rice 1989) performs tests in order of increasing p values, and conditional on having rejected tests with smaller p values an increasingly permissive threshold can be used while maintaining the FWER at the desired level (5%). Further power gains are possible with the sequential approach by using a step-up instead of a step-down procedure (that is, testing in order of decreasing p values, Hochberg 1988), by estimating the number of true nu...

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Growing evidence makes a strong case that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology from dissecting developmental processes to understanding aspects of human health and disease. In ecology, recent studies have merged ecological experimental design with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress response, adaptation to habitat, or species range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, many studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which allow for a more mechanistic understanding but have limited ecological realism. To understand the true significance of epigenetics for plant ecology and evolution, we must combine both approaches transferring knowledge and methods from model-species research to genomes of evolutionarily divergent species, and examining responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration between molecular epigeneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Absolute abundances (concentrations) of dinoflagellate cysts are often determined through the addition of Lycopodium clavatum marker-grains as a spike to a sample before palynological processing. An interlaboratory calibration exercise was set up in order to test the comparability of results obtained in different laboratories, each using its own preparation method. Each of the 23 laboratories received the same amount of homogenized splits of four Quaternary sediment samples. The samples originate from different localities and consisted of a variety of lithologies. Dinoflagellate cysts were extracted and counted, and relative and absolute abundances were calculated. The relative abundances proved to be fairly reproducible, notwithstanding a need for taxonomic calibration. By contrast, excessive loss of Lycopodium spores during sample preparation resulted in non-reproducibility of absolute abundances. Use of oxidation, KOH, warm acids, acetolysis, mesh sizes larger than 15 µm and long ultrasonication (N 1 min) must be avoided to determine reproducible absolute abundances. The results of this work therefore indicate that the dinoflagellate cyst worker should make a choice between using the proposed standard method which circumvents critical steps, adding Lycopodium tablets at the end of the preparation and using an alternative method.

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