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Monthly Archives: July 2015
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
When and how to "go for the genes"
A new special issue of Molecular Ecology, entitled “Detecting selection in natural populations: making sense of genome scans and towards alternative solutions”, is coming down the line, and a few articles from that issue are starting to appear as newly-accepted. Seeing those … Continue reading
Posted in adaptation, association genetics, Molecular Ecology, the journal
Tagged opinion, phenotype, QTL
1 Comment
The Tao of open science for ecology
I think we can all agree that science needs to be transparent, shared, and reproducible. Recently, however, the discussion about “open science” has been conducted mostly in online forums and less so in publications (hopefully Open Access ones!). This is … Continue reading
Current archival practices limit our ability to reuse genetic data
Archiving genetic data is important for a lot of reasons, like ensuring reproducibility and transparency of results. Being able to access previously published data is also important given that the same set of data can often help answer a diversity of … Continue reading
Posted in Uncategorized
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Dozens of talks from the Evolution 2015 meetings are on YouTube
If, like me, you didn’t make it to the 2015 Evolution meetings — maybe the logistics of a trip to Brazil were beyond your financial and/or temporal means — you can make up for it with the big cache of … Continue reading
Posted in community, conferences, phylogeography, population genetics
Tagged Evolution 2015
3 Comments
Dispersal and the rainbow trout takeover
I’m going to keep rolling on the dispersal theme from last week and share a new paper by Ryan Kovach and colleagues that demonstrates the balance between dispersal and selection. Specifically, the authors show that this balance dictates the hybridization … Continue reading
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
1 Comment
Dispersal by land or by sea
Here, we compare and contrast the traits and selective forces influencing the evolution of dispersal in marine and terrestrial systems. From this comparison, a unifying question emerges: when is dispersal for dispersal and when is dispersal a by-product of selection … Continue reading