Category Archives: bioinformatics

F-statistics Manhattan Plots in R

Characterizing differentiation across individual genomes sampled from different populations can be very informative of the demographic processes that resulted in the differentiation in the first place. Manhattan plots have grown to be very popular representations of genome-wide differentiation statistics in … Continue reading

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Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 2 Comments

To sequence a genome or not to sequence a genome, that is the question

In a paper out last month in the Journal of Phycology, Bhattacharya et al. (2015) provide a perspective on the need for more algal genomes. [A] relevant question on the minds of many phycologists might be: do we really need more algal … Continue reading

Posted in bioinformatics, evolution, genomics, horizontal gene transfer, mutation, next generation sequencing, selection | Tagged , , , , | Leave a comment

sedaDNA sleuths: embracing your inner Sherlock

Awhile back fellow TME contributor Rob Denton posted about a recent review on environmental DNA by Pedersen et al. (2015). Environmental DNA (eDNA) is obtained from samples such as sediments, ice or water and can provide scientific sleuths with tantalizing clues about past … Continue reading

Posted in bioinformatics, domestication, genomics, natural history, next generation sequencing, Paleogenomics | Tagged , , , | Leave a comment

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

Posted in adaptation, bioinformatics, evolution, genomics, phylogenetics, Uncategorized | Leave a comment

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

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

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

Posted in bioinformatics, evolution, genomics, phylogenetics, population genetics | Tagged , , , | 1 Comment

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

Posted in bioinformatics, genomics, howto, R, software | Tagged , | 3 Comments