Category Archives: next generation sequencing

sedaDNA sleuths: embracing your inner Sherlock

Posted on 6 Mar, 2015 by Stacy Krueger-Hadfield

Awhile back fellow TME contributor Rob Denton posted about a recent review on environmental DNA by Pedersen et al. (2015). Environmental DNA (eDNA) is obtained from samples such as sediments, ice or water and can provide scientific sleuths with tantalizing clues about past … Continue reading →

Posted in bioinformatics, domestication, genomics, natural history, next generation sequencing, Paleogenomics | Tagged , , , | 1 Comment

Rescue me

Posted on 6 Feb, 2015 by Stacy Krueger-Hadfield

Whiteley et al. (2015) review genetic rescue (GR), or the increase in population fitness (growth) owing to immigration of new alleles, in a new paper in TREE. Genetic rescue is a controversial and hasn’t been applied to any great extent … Continue reading →

Posted in adaptation, evolution, genomics, next generation sequencing | Tagged , , | Leave a comment

Night at the museum

Posted on 5 Feb, 2015 by Stacy Krueger-Hadfield

Many population genetic and genomic studies document snapshots of a given population’s genetic diversity. Yet, there are many reasons to document changes over time in population parameters in response to perturbations, such as biological invasions (both in terms of the invader … Continue reading →

Posted in DNA barcoding, evolution, genomics, natural history, next generation sequencing, phylogenetics, population genetics, speciation, Uncategorized | Tagged , , , | Leave a comment

Mike Sovic on what comes AftrRAD

Posted on 4 Feb, 2015 by Rob Denton

We’ve recently been highlighting some discussions comparing different protocols for restriction site-associated DNA sequencing (RADseq). We’ve seen the pros and cons of multiple techniques, but what happens when you finally have thousands of shiny SNPs sitting on your hard drive? Multiple … Continue reading →

Posted in interview, Molecular Ecology views, next generation sequencing | Tagged , | Leave a comment

New to the genome sequencing $8 menu: Nextera library preps!

Posted on 20 Jan, 2015 by Noah Snyder-Mackler

Researchers are thrifty. We’re always looking for ways to make our expensive supplies and reagents go the extra mile. This shit has been going on for decades – hell, probably even centuries: I remember when I was a kid and … Continue reading →

Posted in genomics, methods, next generation sequencing | Tagged , , , , | 7 Comments

Species and sensibility

Posted on 9 Jan, 2015 by Stacy Krueger-Hadfield

Pante et al. (2014) performed a literature review of marine population connectivity in order to illustrate the biased estimates of connectivity which can result from the failure to recognize an evolutionary-relevant unit, such as a species. When exploring the connectivity … Continue reading →

Posted in adaptation, community ecology, conservation, DNA barcoding, natural history, next generation sequencing, phylogenetics, population genetics, speciation, theory | 6 Comments

Totally RAD, Part 2

Posted on 7 Jan, 2015 by Rob Denton

Edit (8/20/15): I used the wrong web address for Kimberly Andrews! Go check out her work here. Sorry Kim! Restriction site-associated DNA sequencing (RADseq) is quickly becoming the go-to methodology for collecting population genetic data, and the methodological difficulties of … Continue reading →

Posted in genomics, Molecular Ecology views, next generation sequencing, population genetics | Tagged , , | 1 Comment

Transcriptomics in the wild (populations)

Posted on 6 Jan, 2015 by Noah Snyder-Mackler

The genomics revolution is coming has already come. The past decade has seen countless advances in genomic techniques – many of which are now commonly found in any molecular ecologist’s toolbox. For example, instead of measuring gene expression in one … Continue reading →

Posted in genomics, next generation sequencing | Tagged , , | 1 Comment

Totally RAD

Posted on 12 Dec, 2014 by Stacy Krueger-Hadfield

Puritz et al. (2014) weigh the pros and cons of, the aptly titled, “RAD fad” in a comment recently published online in Molecular Ecology. They challenge: (1) the assertion that the original RAD protocol minimizes the impact of PCR artifacts … Continue reading →

Posted in bioinformatics, genomics, methods, next generation sequencing, Uncategorized | 4 Comments

Caught sweeping 'cross the sea

Posted on 28 Nov, 2014 by Stacy Krueger-Hadfield

  The salmon louse Lepeophtheirus salmonis is an ectoparasite linked to declines in wild salmonid populations as well as causing huge economic losses in salmon farms. Previous studies, using a variety of molecular markers, yielded conflicting results ranging from strong … Continue reading →

Posted in adaptation, genomics, mutation, next generation sequencing | Leave a comment