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Category Archives: bioinformatics
Grasping gorgonians
A recent issue of Heredity focused on the brave new world of environmental genomics. After highlighting the special issue, I started chatting to one of the contributors, Eric Pante and became interested in his work on gorgonians. Eric and his co-authors explored the … Continue reading
Posted in bioinformatics, Coevolution, evolution, genomics, mutation, phylogenetics
Tagged Gorgonians, phylogenetics, pipelines, PyRad, RAD, STACKS
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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 data visualization, genomics, population genetics
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Don't trust your data: reviewing Bioinformatics Data Skills
The Molecular Ecologist receives a small commission for purchases made on Bookshop.org via links from this post. 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 … Continue reading
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 data visualization, genomics, Homo sapiens
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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
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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 Homo sapiens, population genetics
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