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Category Archives: population genetics
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
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
Posted in bioinformatics, howto, population genetics, R, software
Tagged data visualization, genomics, population genetics, R
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On getting empirical with the obvious
I’ve been thinking lately about the value in doing “simple” things. As a PhD student, my time is constantly incentivised by productivity (what am I doing right now that is working towards a publication?). But that doesn’t jive well with … Continue reading
Posted in population genetics, theory, Uncategorized
Tagged Daphnia, drift, population size
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Genomics of domestication in chicken and cattle
Two recent studies attempt to understand the process of adaptive evolution in domestication and artificial selection by characterizing (a) sweeps, and their association with phenotypes in extant hybrid lines (Sheng et al. 2015), and (b) phylogenomic position of an extinct … Continue reading
Posted in adaptation, bioinformatics, domestication, evolution, genomics, natural history, Paleogenomics, phylogeography, population genetics, selection, speciation, STRUCTURE
Tagged domestication, ecological speciation, Evolution, hybridization, natural selection, population genetics, population structure
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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
Posted in evolution, genomics, howto, IMa2, methods, Molecular Ecology views, natural history, population genetics, software, theory
Tagged Evolution, gene flow, genomics, IM, isolation with migration, methods, migration, population genetics
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Along the Mackerel Road
We left Hokkaido and flew to Osaka where we collected our next rental car (our first teeny tiny one!) As our flight was delayed due to weather in Hokkaido, we decided to break the journey between Osaka and Obama (it … Continue reading
Posted in adaptation, blogging, community, haploid-diploid, natural history, population genetics, speciation
Tagged Gracilaria, Japan, Kamiya, sampling, seaweed, tourist sites, Ulva
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Genetic distance predicts the spread of deadly fungal infections in bats
You’ve probably heard about White-Nose Syndrome (WNS), the particularly nasty fungal pathogen that has decimated North American bat populations over the last decade. Not only has WNS been extremely deadly, but the speed at which it’s spread has been alarming. Really alarming: Understanding … Continue reading
Posted in Molecular Ecology, the journal, phylogeography, population genetics
Tagged pathogens, RADseq
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On background selection in Ficedula flycatchers
Several recent studies (including those I wrote about last week) use genome-wide scans of differentiation to understand evolutionary mechanisms behind high or low divergence. However, there has been contentious support for and against these differentiation islands being due to differential … Continue reading
An unspoiled frontier
“An unspoiled frontier, an escape from industrialized Japan and a chance to connect with nature …” or so says the Rough Guide to Japan (6th edition, September 2014). We had experienced a bit of the city-scene in Hakodate, but the rest … Continue reading
Posted in blogging, conservation, evolution, natural history, population genetics
Tagged Field work, Gracilaria, Hokkaido, Japan
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