Tag Archives: methods

On false positives in Isolation with Migration analyses

The IM suite of tools (IM, IMa, IMa2, IMa2p, etc.) are used widely by molecular ecologists at large for the analyses and estimation of ancestral demography under an Isolation with Migration (IM) model. However, these tools come with fundamental assumptions … Continue reading

Posted in evolution, genomics, howto, IMa2, methods, Molecular Ecology views, natural history, population genetics, software, theory | Tagged , , , , , , , | 1 Comment

Sweptaway – Part 2

Numerous methods have been developed over the last few years for the detection of selective sweeps (hard and soft – see my previous post). This week, we look at three new studies that (a) compare existing methods to detect sweeps … Continue reading

Posted in adaptation, bioinformatics, evolution, genomics, methods, population genetics, selection, software, theory | Tagged , , , | Leave a comment

Sweptaway – Part 1

Brace yourselves for a series of new posts on selection, especially with articles from the special Molecular Ecology issue on “Detecting selection in natural populations: making sense of genome scans and towards alternative solutions” starting to roll out! Selective sweeps … Continue reading

Posted in adaptation, evolution, genomics, mutation, population genetics, selection, speciation, theory | Tagged , , , , , | Leave a comment

Should we use Mantel tests in molecular ecology?

No. Stop. At least that is the message from a new publication in Methods in Ecology and Evolution by Pierre Legendre and colleagues (pay-walled, but I found a pdf here). Mantel tests should simply not be used to test hypotheses … Continue reading

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IBE/IBD Contour plots in R

Rob’s post from yesterday motivated me to find an alternate way of visualizing correlations between matrices of geographical or ecological data, and genetic data. I have seen plenty of Mantel, or partial Mantel tests of correlation, as well as plots … Continue reading

Posted in bioinformatics, howto, population genetics, R, software | Tagged , , , | 5 Comments

Exploring color palettes in R

How often have you had to squint at figures with unpleasant color palettes in a manuscript online or in print, and ultimately given up on distinguishing between fifty (or maybe just around 30) shades of gray? I found the RColorBrewer … Continue reading

Posted in howto, population genetics, R, software, STRUCTURE | Tagged , , | 8 Comments

SpaceMix, and a brief history of Spatial Genetics

Incorporating spatial data to inform studies of the population demography of a species has a long history of interest. From inferring geographical clines in Principal Components Analyses (Menozzi et al. 1978), using location data as “informative priors” during model-based estimation … Continue reading

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Migration Circos plots in R

We’ve all seen them – colorful, and I daresay, pretty darn informative. Circos plots are fun visualizations of large data-sets. I’ve seen them used in two contexts in comparative genomics – to represent structural variants in homologous chromosome segments in … Continue reading

Posted in bioinformatics, genomics, howto, R, software | Tagged , | 11 Comments

The big chief at Molecular Ecology Resources: Interviewing Shawn Narum

What are the most exciting parts of doing science? The first look at results? The sheen of your publication finally in print? That initial foray out into the field? What about the moment you figure out a way to make a … Continue reading

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Dramatically reducing sequencing error via Duplex Tag sequencing

An exciting new study was published in PNAS last month, an open access paper entitled “Detection of ultra-rare mutations by next-generation sequencing”. This new method has the potential to open up a new frontier in Next-gen sequencing bioinformatics, since it allows … Continue reading

Posted in methods, next generation sequencing | Tagged , , , , | 5 Comments