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Category Archives: howto
Best practices in sample naming
Wherein I try to save me from myself Let’s imagine a young scientist, bursting to the seems with enthusiasm and schemes to uncover the secrets of the biological world. Everything is new and she learns as she goes! Let’s call … Continue reading
Molecular ecology, the flowchart
Towards the end of last semester my department’s evolutionary genetics journal club read Rasmus Nielsen’s terrific 2005 review of tests for recent natural selection in genetic data. Nielsen provides figures illustrating the effects of a recent selective sweep and the … Continue reading
Phylogenetic trees in R using ggtree
Recently, one R package which I like to use for visualizing phylogenetic trees got published. It’s called ggtree, and as you might guess from the name it is based on the popular ggplot2 package. With ggtree, plotting trees in R has … Continue reading
Posted in bioinformatics, howto, phylogenetics, R
Tagged ggtree, phylogenetics, phylogenomics, R
2 Comments
Handling microbial contamination in NGS data
Until recently, I had given little thought to the potential for unwanted microbial contamination in high throughput sequence data. I suspect that if you’re a molecular ecologist who doesn’t primarily study microbes or work with ancient DNA, you’re in a … Continue reading
Unbalanced population sampling and STRUCTURE
The utility and intuition offered by the program STRUCTURE, and more generally, the ‘admixture’ model of Pritchard et al. (2000) are unquestioned – with tens of thousands of citations, it retains its lead among the most popular population genetics software. … Continue reading
Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE
Tagged gene flow, methods, population structure
1 Comment
Video Tutorial: editing R plots in Adobe Illustrator
Adobe Illustrator is a powerful tool for creating and editing figures; unfortunately, it’s also really intimidating. So today at The Molecular Ecologist we’re trying something a little different: a screen-capture video tutorial about using Adobe Illustrator to enhance and edit plots … Continue reading
Posted in howto, R
Tagged Adobe, Figures, how to, Illustrator, Plots, R, Screen Capture, Tutorial, Video
3 Comments
On (mis)interpreting STRUCTURE/ADMIXTURE results
STRUCTURE, ADMIXTURE and other similar software are among the most cited programs in modern population genomics. They are algorithms that estimate allele frequencies and admixture proportions under the premise that sampled genotypes are derived from one of “K” ancestral populations, … Continue reading
Making Maps in R, volume 2: ggplots
The open-source statisical programming environment R is truly a Swiss Army knife for molecular ecology. With the right code, R can processes genetic data and trait measurements, analyze how genetic variants relate to traits, reconstruct phylogenetic trees, and illustrate the … Continue reading
10 simple rules for designing a scientific poster
Conference season is upon us! Around the world, thousands of scientists face a daunting task: designing a scientific poster. It should be sleek, yet informative; eye-catching, yet professional; and most of all it should attract the attention of your future … Continue reading
How to make the most out of your phylogenetic study
Phylogenetic studies are crucial for ecology and evolution. However, their usefulness for comparative biology or meta-analyses can vary considerably. Especially the inclusion of unidentified species (“Balanus sp.”) obstructs their use in comparative studies. How can I attach life history or morphological data … Continue reading
Posted in data archiving, evolution, howto, phylogenetics, Uncategorized
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