Category Archives: methods

Mixed modeling of methylation measures (increase your power by 60%)

Do you want to increase your power to detect differentially methylated CpG sites by 60%*? Yes?! Then do I have the pre-print for you.

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Posted in bioinformatics, genomics, methods, next generation sequencing, software | Tagged , , | Leave a comment

Conversation starter: common mistakes in population genetics

When interpreting the results, it is important to focus more on biological relevance than on statistical significance. That does not mean that significance is unimportant; results that have a straightforward interpretation but are not significant should not be considered. On the … Continue reading

Posted in community, methods, Molecular Ecology, the journal | Tagged , , | Leave a comment

Easy as ABC

Determining the whens and hows of biological invasions using genetic data is a major goal of molecular ecology. One such tool is approximate Bayesian computation (ABC) which is being used for inferring invasion histories. In a new paper in Heredity, Benazzo et … Continue reading

Posted in evolution, methods, population genetics | Tagged , , | Leave a comment

The death of the p-value? Probably not.

In February, a social psychology journal, Basic and Applied Social Psychology , made the bold (and extreme) move to ban the use of p-values, F-statistics, T-values, and any other form of Null Hypothesis Testing (NHT) method. This major move generated … Continue reading

Posted in methods, politics, science publishing | Tagged , , | 2 Comments

A transcriptomic approach for reduced representation in population genomics

                    Many population genomics studies use methods that provide a reduced representation of the genome, for example RADseq or UCEs. Targeting a subset of the genome reduces the cost of sequencing … Continue reading

Posted in genomics, howto, methods, Molecular Ecology, the journal, next generation sequencing, RNAseq | Leave a comment

Coral conservation through assisted evolution

Coral reefs occupy a tiny portion of the world’s oceans (see map below) but their biodiversity is hugely disproportionate to their size. More than 450 million people from 109 countries live in close proximity to coral reefs and depend upon the … Continue reading

Posted in adaptation, conservation, evolution, methods | Leave a comment

Show me the power

Describing the patterns of genetic structure and mating system variation in presents challenges from the outset of sample collection to data analysis (see this post and this post). At the beginning of February, I had the pleasure to collaborate with Sean … Continue reading

Posted in conservation, evolution, genomics, interview, methods, population genetics, software, Uncategorized | 1 Comment

The results are in for the journal selection survey

Two weeks ago I wrote a post about a recent paper by Salinas and Munch that presented a model-based method for determining to which journal an author should submit a manuscript for publication. I was curious to know how the readers … Continue reading

Posted in career, Impact Factors, methods, peer review, science publishing | 2 Comments

Genome-wide effects of artificial selection

Humans have been artificially selecting for favorable traits in crops, pets, and livestock over millennia. Years of theoretical predictions and experimental evolution studies have shown the detrimental effects of increased homozygosity, and the population-wide advantages of artificially maintaining heterozygosity. Two … Continue reading

Posted in bioinformatics, evolution, genomics, methods, mutation, population genetics, theory | Leave a comment

Breaking free of the guide tree: two new species delimitation methods

A couple of weeks ago I wrote about a new method to incorporate morphology and DNA sequences into species delimitation. Including both data types improved the results but a couple of tricky spots remained: 1) correctly assigning individuals to putative species and 2) estimating … Continue reading

Posted in methods, species delimitation | Leave a comment