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Category Archives: bioinformatics
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
Posted in adaptation, bioinformatics, evolution, genomics, methods, population genetics, selection, software, theory
Tagged genomics, methods, natural selection, population structure
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Notes from Edmonton and #Botany2015
As noted previously, I broke with my usual habit and skipped the Evolution meetings this year. Instead, I attended Botany 2015, a joint meeting of multiple U.S. and Canadian plant-focused scholarly societies held in Edmonton, Alberta — I’d never been … Continue reading
Posted in bioinformatics, conferences, genomics, natural history, phylogenetics, plants, population genetics
Tagged Botany 2015
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PCA of multilocus genotypes in R
An earlier post from Mark Christie showed up on my feed on calculating allele frequencies from genotypic data in R, and I wanted to put together a quick tutorial on making PCA (Principal Components Analysis) plots using genotypes. I used … Continue reading
Posted in bioinformatics, genomics, howto, population genetics, R, software
Tagged data visualization, Homo sapiens, R
6 Comments
What do with all those pesky mtDNA reads in your NGS experiment
Have you ever noticed how many reads from your high throughput sequencing project map to the tiny fraction of your genome that is the mitochondrial genome (mtDNA)? Pretty much any NGS experiment (e.g., RNA-seq, DNA-seq, capture-based sequencing) leave you with … Continue reading
Posted in bioinformatics, genomics, howto, mutation, software, Uncategorized
Tagged mitochondria, mtDNA
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IMa2p – Parallel Isolation with Migration Analyses
I figured that it was time to write an update on my post from a year ago on Bayesian MCMC in inferring ancestral demography. Recently, my postdoctoral advisor, Jody Hey and I released a version of the popular IMa2 program, … Continue reading
Posted in bioinformatics, genomics, howto, software, theory
Tagged Evolution, genomics, isolation, isolation with migration, migration, population genetics
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IBE/IBD Contour plots in R
Rob’s post from yesterday motivated me to find an alternate way of visualizing correlations between matrices of geographical or ecological data, and genetic data. I have seen plenty of Mantel, or partial Mantel tests of correlation, as well as plots … Continue reading
Posted in bioinformatics, howto, population genetics, R, software
Tagged data visualization, landscape genetics, methods, population genetics
5 Comments
When genomes duplicate
Whole genome duplication events have played an important role in the evolutionary history of plants. Vallejo-Marín et al. (2015) describe origins of a new polyploid species, Mimulus peregrines, found on the Scottish mainland as well as the Orkney Islands. It was formed within … Continue reading
Posted in bioinformatics, evolution, genomics, natural history, plants
Tagged genomics, invasion, polyploids
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Sous les mers: cradles or museums of biodiversity?
While thinking about environmental genomics and writing this post on a recent article in Heredity, I interviewed Eric Pante.
Posted in adaptation, bioinformatics, Coevolution, evolution, genomics, interview
Tagged Evolution, genomics, Gorgonians, interview, seamounts
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