Monthly Archives: May 2015

Differential gene expression turns on salamander attack mode

Posted on 13 May, 2015 by Rob Denton

The transcriptomics field is boomin’. Approaches like RNA-seq have opened the flood gates to hundreds and hundreds of investigations that compare gene expression between biologically-interesting phenotypes, variants, species, etc. Plastic phenotypes have been a fascinating area of study for decades … Continue reading →

Posted in Molecular Ecology, the journal, transcriptomics | Tagged , | 2 Comments

Another lesson in genomics experimental design and avoiding batch effects

Posted on 12 May, 2015 by Noah Snyder-Mackler

Twitter has been abuzz with Orna Man and Yoav Gilad’s (re)analysis of the data from a recent PNAS paper: “Comparison of the transcriptional landscapes between human and mouse tissues”. The PNAS paper concluded that the gene expression profiles of different … Continue reading →

Posted in bioinformatics, genomics, next generation sequencing, RNAseq | Tagged , , | 3 Comments

Next generation sequencing: more replicates or more sequence?

Posted on 11 May, 2015 by Melissa DeBiasse

The field of evolutionary biology changed drastically with the advent of next generation sequencing technologies. One thing that has stayed the same, however, is the importance of a well-planned experimental design, which ensures the data we collect have the power … Continue reading →

Posted in Uncategorized | Leave a comment

When genomes duplicate

Posted on 8 May, 2015 by Stacy Krueger-Hadfield

Whole genome duplication events have played an important role in the evolutionary history of plants. Vallejo-Marín et al. (2015) describe origins of a new polyploid species, Mimulus peregrines, found on the Scottish mainland as well as the Orkney Islands. It was formed within … Continue reading →

Posted in bioinformatics, evolution, genomics, natural history, plants | Tagged , , | 1 Comment

Gene flow and Population Fitness

Posted on 7 May, 2015 by Arun Sethuraman

Fitness effects of gene flow (both advantageous and deleterious) have garnered plenty of recent press and scientific exploration. At the population level, the concepts and consequences are notoriously familiar. In the context of immigration, they reduce to existing genetic variation, … Continue reading →

Posted in adaptation, evolution, genomics, natural history, population genetics, selection, speciation, theory | Tagged , , , , , | 1 Comment

To review or not to review, that is the question

Posted on 6 May, 2015 by Mark Christie

Imagine this scenario. You are industriously working away on your most recent paper (ignoring other pressing data analyses, administrative duties, and grant proposals). You have just begun to get into the zone of intense focus, writing nirvana, when DING!!! a … Continue reading →

Posted in career, peer review, science publishing | 3 Comments

Polyploidy can melt the frozen niche

Posted on 6 May, 2015 by Rob Denton

The rabbit hole of asexual reproduction literature is full of weird detours in the evolution of life. There are asexual lineages that facultatively have sex, asexuals that still need sperm from other species,  and asexuals that steal sperm from other species, … Continue reading →

Posted in DNA barcoding, natural history, plants | Tagged , , | Leave a comment

The death of the p-value? Probably not.

Posted on 5 May, 2015 by Noah Snyder-Mackler

In February, a social psychology journal, Basic and Applied Social Psychology , made the bold (and extreme) move to ban the use of p-values, F-statistics, T-values, and any other form of Null Hypothesis Testing (NHT) method. This major move generated … Continue reading →

Posted in methods, politics, science publishing | Tagged , , | 3 Comments

Sous les mers: cradles or museums of biodiversity?

Posted on 2 May, 2015 by Stacy Krueger-Hadfield

While thinking about environmental genomics and writing this post on a recent article in Heredity, I interviewed Eric Pante.

Posted in adaptation, bioinformatics, Coevolution, evolution, genomics, interview | Tagged , , , , | Leave a comment

Grasping gorgonians

Posted on 1 May, 2015 by Stacy Krueger-Hadfield

A recent issue of Heredity focused on the brave new world of environmental genomics. After highlighting the special issue, I started chatting to one of the contributors, Eric Pante and became interested in his work on gorgonians. Eric and his co-authors explored the … Continue reading →

Posted in bioinformatics, Coevolution, evolution, genomics, mutation, phylogenetics | Tagged , , , , , | 1 Comment