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Category Archives: Uncategorized
Machine learning for model selection in population genomics
The application of model-based methods in phylogeography helped the field transition from a more qualitative, overlay-a-tree-on-a-map, discipline to one that tests hypotheses in robust statistical frameworks. Many researchers have embraced approximate Bayesian computation (ABC) for model selection since computing the likelihood of … Continue reading
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Measuring dispersal rate in Neotropical fishes in units of 'wallace'
Alfred Russel Wallace often gets second billing compared to Charles Darwin but in a paper recently accepted at Systematic Biology, Tagliacollo et al. define a new term for their analyses (dispersal rate, D) and measure D in units of ‘wallaces‘ (wa) to honor the contributions of Alfred … Continue reading
Posted in methods, phylogenetics, phylogeography, Uncategorized
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Best laid plans are probably not best laid … As I mentioned before, I had every intention of writing up posts on interesting papers as well as highlighting the hosts gracious enough to house/feed/guide us around this summer. Alas, time … Continue reading
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Another uninterpretable epigenetics study
If you looked at your Twitter feed on Sunday you likely saw a lot of buzz about a new study that found that “Holocaust survivors trauma is passed on to children’s genes”. Many people have already taken time to blog … Continue reading
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Survival of the fittest: a marine snail toughs it out through a salty time
For marine organisms, salinity plays an important role in determining how populations and species are distributed across time and space, particularly in the Mediterranean Sea. During the Mesozoic, about 252 to 66 million years ago, the Tethys Ocean, a body … Continue reading
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Inferring kinship from low coverage sequencing data
Knowing the relatedness structure of your population is essential for pretty much any study. Until recently, the only way to determine the kinship structure was to have a detailed pedigree or to estimate relatedness (poorly) using microsatellites. The spurt of … Continue reading
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Should we use Mantel tests in molecular ecology?
No. Stop. At least that is the message from a new publication in Methods in Ecology and Evolution by Pierre Legendre and colleagues (pay-walled, but I found a pdf here). Mantel tests should simply not be used to test hypotheses … Continue reading
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
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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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