Category Archives: bioinformatics

Interspecific gene flow enhances vectorial capacity

There are charismatic cases of gene flow between species, such as Neanderthals (see also Arun’s posts here and here), but the role of introgression in evolution remains poorly documented. Recently diverged species have incomplete reproductive isolation and can hybridize. Rapid … Continue reading

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Twice Mixed? Testing hypotheses of Neanderthal Introgression

Human migration in, and out of Africa was wrought with complex patterns of admixture (see my previous post summarizing the story so far). Of note were some recent findings on the disparity in amounts of Neanderthal introgression/ancestry between East Asians … Continue reading

Posted in adaptation, bioinformatics, evolution, genomics, mutation, Paleogenomics, population genetics | Tagged , | 1 Comment

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

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Phonemes and Genomes

Human phonemes and genomes are thought to have evolved hand-in-glove out of Africa. Several recent studies have attempted to capture a picture of this global variation in languages and peoples, often supporting (and rejecting) a serial founder model (eg. see … Continue reading

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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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Totally RAD

Puritz et al. (2014) weigh the pros and cons of, the aptly titled, “RAD fad” in a comment recently published online in Molecular Ecology. They challenge: (1) the assertion that the original RAD protocol minimizes the impact of PCR artifacts … Continue reading

Posted in bioinformatics, genomics, methods, next generation sequencing, Uncategorized | 3 Comments

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

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Using GitHub with R and RStudio

A few weeks back, the Molecular Ecologist released an article about GitHub and also created an organization where you can fork or simply download code shared by the Molecular Ecology community. A few of you out there may still be … Continue reading

Posted in bioinformatics, howto, R, software | 18 Comments

Sequencer to the stars

No single person is responsible for the revolution in genetic data collection that has reshaped biology over just a handful of decades, but if you had to make a list of people deserving credit, Craig Venter’s name would be among … Continue reading

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Want to share your code?

In this line of work, we have all encountered tasks that are tedious, time consuming, and repetitive.  (Or if not, maybe give it a bit more time.) When confronted with these situations, people tend to fall into one of two … Continue reading

Posted in bioinformatics, community, genomics, howto, methods, next generation sequencing, phylogenetics, population genetics, quantitative genetics, R, software, theory | 14 Comments