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Monthly Archives: May 2015
Differential gene expression turns on salamander attack mode
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
Next generation sequencing: more replicates or more sequence?
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
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When genomes duplicate
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 genomics, invasion, polyploids
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Gene flow and Population Fitness
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
To review or not to review, that is the question
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
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The death of the p-value? Probably not.
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 null hypothesis testing, p-value, statistics
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Sous les mers: cradles or museums of biodiversity?
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 Evolution, genomics, Gorgonians, interview, seamounts
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Grasping gorgonians
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 Gorgonians, phylogenetics, pipelines, PyRad, RAD, STACKS
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