Category Archives: genomics

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

Migration Circos plots in R

Posted on 11 Dec, 2014 by Arun Sethuraman

We’ve all seen them – colorful, and I daresay, pretty darn informative. Circos plots are fun visualizations of large data-sets. I’ve seen them used in two contexts in comparative genomics – to represent structural variants in homologous chromosome segments in … Continue reading →

Posted in bioinformatics, genomics, howto, R, software | Tagged , | 11 Comments

Et tu, Brute? Black-legged ticks use genes co-opted from bacteria to fight bacterial infection

Posted on 8 Dec, 2014 by Melissa DeBiasse

Horizontal gene transfer occurs when genes are passed between individuals by mechanisms other than reproduction. It is common in bacteria and occasionally happens between highly divergent groups (for example, monocot genes transferred to eudicots, fungal genes transferred to aphids, bacterial genes transferred … Continue reading →

Posted in adaptation, genomics, horizontal gene transfer, microbiology | Leave a comment

The Evolution of Recombination

Posted on 4 Dec, 2014 by Arun Sethuraman

In a recent publication, Lesecque et al (2014). provide key evidence that fills in some of the blanks to an age old question – how do recombination hotspots evolve? Their analyses of major PRDM9 (a polymorphic zinc finger protein with … Continue reading →

Posted in adaptation, genomics, mutation, population genetics, theory | Tagged , | 2 Comments

Compensatory evolution: a possible mechanism of population divergence

Posted on 1 Dec, 2014 by Melissa DeBiasse

After spending my graduate career using genetic data to reconstruct historical demographic events, one of the things that excite me the most about my postdoc work is the opportunity to use experimental methods to make evolution happen (insert mad scientist laugh … Continue reading →

Posted in adaptation, genomics, mutation, yeast | 3 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

Consuming raw or undercooked frogs may increase your risk of getting a rare tapeworm in your brain

Posted on 25 Nov, 2014 by Noah Snyder-Mackler

A 50-year-old UK resident had been living with an unwelcome visitor for the past 4 years and it was such a headache. Surgeons from Addenbrooke’s Hospital in Cambridge removed the tapeworm during a biopsy after noticing a small circular lesion … Continue reading →

Posted in genomics, medicine, phylogenetics | Tagged , , | 2 Comments

The latest gadget for the molecular ecologist’s toolkit

Posted on 21 Nov, 2014 by Stacy Krueger-Hadfield

Designing a sampling scheme to collect an organism of interest for a population genetic/genomic study can be fraught with difficulty. How best to sample? Randomly? Or, along a grid? How many individuals to sample? Thirty? Or, perhaps, the sample size … Continue reading →

Posted in genomics, methods, Molecular Ecology, the journal, natural history, pedigree, population genetics, software | 2 Comments