Category Archives: bioinformatics

The brave new world of environmental genomics

A new special issue of Heredity reflects on the recent advances in environmental genomics (see other posts about eDNA here and here) and highlights the ways NGS can aid in characterizing complex biological systems. The cryptic, as well as the rare but active … Continue reading

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Posted in bioinformatics, Coevolution, DNA barcoding, evolution, genomics | Tagged , , , | Leave a comment

Gorillas (genomes) in the mist

Mountain gorillas are an endangered great ape subspecies that number around 800 individuals, inhabiting mountain ranges in central Africa. They have been the subject of numerous field studies, but few genetic analyses have been carried out. Xue et al. (2015) sequenced … Continue reading

Posted in bioinformatics, conservation, evolution, genomics, natural history, next generation sequencing, primates | Tagged , , , | Leave a comment

Visualizing Linkage Disequilibrium in R

Patterns of Linkage Disequilibrium (LD) across a genome has multiple implications for a population’s ancestral demography. For instance, population bottlenecks predictably result in increased LD, LD between SNP’s in loci under natural selection affect each others rates of adaptive evolution, selfing/inbreeding populations … Continue reading

Posted in bioinformatics, howto, population genetics, R | Tagged , , | 1 Comment

Don’t trust your data: reviewing Bioinformatics Data Skills

There is little debate on the importance of bioinformatics for the present and future of science. As molecular ecologists, we are likely more aware of this than most disciplines due to the data explosion that has accompanied the wide application of … Continue reading

Posted in bioinformatics, book review, genomics, software | Tagged | 1 Comment

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

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 , , , | 1 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

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