Category Archives: Uncategorized

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

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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

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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

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Genomics: the “four-headed beast” of Big Data

When I bought my first laptop in 2005, it came with a free 64MB flash drive*, which I thought was pretty awesome. Given the rate at which genomic data generation has increased in the past decade, the storage capacity of … Continue reading

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Gene expression analysis- are we doing it wrong?

In the last few weeks, three new preprints have come out suggesting that like Jack Butler dropping his kids off at school in the movie Mr. Mom, when it comes to differential gene expression analyses, we’re doing it wrong.

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The evolution of phylogeography in the next gen era: 20 years in review

Phylogeographers have long known about the limitations of single locus studies (ie, the effects of selective sweeps, stochasticity in lineage sorting among loci) and that adding loci improves the accuracy of demographic parameter estimates. As we continue to shift towards collecting multi-locus datasets thanks to high throughput … Continue reading

Posted in evolution, genomics, Molecular Ecology, the journal, next generation sequencing, phylogeography, Uncategorized | 2 Comments