Tag Archives: genomics

The Truth

Spoiler Alert: I’ve taken plenty of care to try and not spill the beans on any plotlines, but you have been forewarned that there may be some aspects of the science that’s discussed on the show that I attempt to … Continue reading

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The 2016 Workshop on Genomics summary

I recently had the pleasure to spend two and a half weeks in the beautiful medieval town of Český Krumlov, Czech Republic. The reason was the popular Workshop on Genomics that was running and I was one of the TAs … Continue reading

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The Neanderthal admixture plot thickens…

Previous studies of archaic admixture from Altai Neanderthals and Denisovans into modern humans outside of Africa have put forth several lines of evidence for gene flow from Neanderthals into common ancestors of Eurasian populations, from Denisovans into ancestors of modern … Continue reading

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Posted in bioinformatics, evolution, genomics, mutation, natural history, next generation sequencing, Paleogenomics, population genetics, speciation | Tagged , , , | 2 Comments

Clinal genomic variation in Drosophila species

Two recent manuscripts describe adaptive evolutions to clinal/latitudinal variations in Drosophila species to supplement a growing wealth of recent studies on geographic variation and adaptive evolution in natural populations of fruitflies (eg. see Kao et al. 2015, Zhao et al. … Continue reading

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2D Posterior Density Plots in R

I have been grappling with visualizing two dimensional histograms of posterior density distributions of parameters, as estimated by one of your favorite programs – IMa2, MIGRATE-n, MSVAR, etc. All these programs print out distributions of estimated parameters, and here’s a … Continue reading

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

A Nice opinion on confronting uncertainty and modeling it for GBS data

Just over a week ago, I had the opportunity to work in Chris Nice‘s lab at Texas State University. I was accompanied by one of our MS students, Ben, and my colleague, Erik Sotka, to prep libraries for a genomic … Continue reading

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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

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

Introgression history in sticklebacks and oaks

Speciation theory has many monikers for differential gene flow – migration, introgression, admixture, hybridization, secondary contact. As a homogenizing process, gene flow at large acts to reduce differentiation between populations post-divergence. However, selection and demography affect the rates of gene … Continue reading

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Posted in adaptation, evolution, genomics, natural history, phylogenetics, population genetics, selection, speciation, species delimitation | Tagged , , , , , | 1 Comment

Sweptaway – Part 3 – Adaptation genomics of White Sands Lizards

Recent colonization events offer juicy insights into the adaptive evolution of species in response to natural selection of novel habitats – however, they are confounded by demographic changes (eg. bottlenecks, differential migration). In a recent study, Laurent et al. (2015) … Continue reading

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Posted in adaptation, Coevolution, evolution, genomics, natural history, population genetics, selection | 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

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