Category Archives: genomics

Genomes are coming: Sequence libraries from the honey bee reflect associated microbial diversity

Posted on 20 Jul, 2017 by Kelle Freel

One of the coolest of reasons that cheap sequencing is nifty, in my opinion, is that it has allowed researchers to study individual eukaryotic organisms, and their associated microbes (their microbiome). Let’s be real, we are in the midst of … Continue reading →

Posted in Coevolution, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing | Tagged , , | Leave a comment

This new review explains why soft sweeps are the bane — and the baseline — of ecological genetics

Posted on 18 Jul, 2017 by Jeremy Yoder

If you’ve done ecological genetics research in the last decade, you’ve almost certainly cited a series of papers by Pleuni Pennings and Joachim Hermisson, which broke down the problem of soft selective sweeps. Pennings and Hermisson have revisited soft sweeps … Continue reading →

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When less might be more: The evolution of reduced genomes

Posted on 23 Jun, 2017 by Kelle Freel

The advent of affordable genome sequencing has provided us with a wealth of data. Researchers have sequenced everything from Escherichia coli (4.6 Mbp genome size), to sea urchins (810 Mbp), chimpanzees (3.3 Gbp), and humans (3.2 Gbp). Then there are the … Continue reading →

Posted in adaptation, Coevolution, evolution, genomics, microbiology, population genetics, selection | Tagged , , , | Leave a comment

On hyRAD-X, another option for museum genomics

Posted on 9 Jun, 2017 by Ethan Linck

Last year, I profiled Suchan et al.’s “hyRAD” method for reduced-representation genome sequencing of degraded sources of DNA using RAD probes. While it’s too early to say whether hyRAD will be widely used by molecular ecologists looking to integrate historic … Continue reading →

Posted in genomics, methods, natural history, next generation sequencing, phylogenetics, phylogeography, population genetics, RNAseq, selection, transcriptomics | Tagged , , , | Leave a comment

Shared patterns of genomic diversity across populations of distantly related taxa

Posted on 5 Jun, 2017 by Arun Sethuraman

Genomic diversity is shaped by the complex interplay between the effects of genetic drift and natural selection among populations. Several of these effects, especially those of linked selection at neutral sites, adaptive introgression, and barriers to migration (often called “genomic … Continue reading →

Posted in adaptation, bioinformatics, birds, evolution, genomics, population genetics, selection | Tagged , , , , , | Leave a comment

Molecular adaptation in a deep-sea alien…*ahem* amphipod

Posted on 24 May, 2017 by Kelle Freel

Space: the final frontier…or is it? I was inspired Jeremy’s post yesterday to talk about that deep dark abyss that takes up the vast majority of our mostly blue planet. For the record, I’m in agreement with the assessments for the … Continue reading →

Posted in adaptation, evolution, genomics, Molecular Ecology, the journal, next generation sequencing | Tagged , , | Leave a comment

Relatively rare tropical trees all agree: avoiding the 'rain of death' seems like a good call

Posted on 5 May, 2017 by Kelle Freel

When you think of a tropical jungle, what’s the first thing that comes to mind? Probably a lush green landscape with trees, vines, flowers, and let’s be real, at least one toucan. Tropical forests are made up of diverse groups … Continue reading →

Posted in genomics, Molecular Ecology, the journal, next generation sequencing, plants, transcriptomics | Tagged , | Leave a comment

N50 for transcriptome assemblies

Posted on 3 May, 2017 by Elin Videvall

This is the sixth in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transcriptome assemblies. Transcriptome assemblies are inherently different … Continue reading →

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(Un)usual sources of ancient DNA

Posted on 27 Apr, 2017 by Patrícia Chrzanová Pečnerová

Working with ancient DNA can be quite painful at times, but hard work pays off (or so they say) and scientists are starting to reap great benefits from their effort by exploring more and more things to extract DNA from.

Posted in evolution, genomics, methods, Paleogenomics | Tagged , , , | 2 Comments

A solution to the N50 misassembly problem

Posted on 26 Apr, 2017 by Elin Videvall

This is the fifth in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transcriptome assemblies. The misassembly problem of N50 that … Continue reading →

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