Author Archives: Reid Brennan

About Reid Brennan

I am an evolutionary ecologist and a PhD candidate at UC Davis. I am generally interested in mechanisms allowing populations to evolve and respond to environmental stressors. Specifically, I combine physiological and genomic approaches to understand how fish have evolved to inhabit divergent abiotic environments.

Conifer convergence

Convergent local adaptation is typically studied within a species or between closely related species. In these cases, it is perhaps not unexpected to observe parallel evolution due to common genetic variation, constraints, etc. Convergence between species is somewhat less studied, … Continue reading

Posted in adaptation, association genetics, genomics, plants, selection, Uncategorized | Tagged , , | 1 Comment

The trouble with PCR duplicates

The sequencing center just sent your lane of Illumina data. You’re excited. Life is great. You begin to process the data. You align the data. You check for PCR duplicates. 50 percent. Half of your data is garbage. Everything is … Continue reading

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

New insight into the genetic basis of industrial melanism

The evolution of coloration in peppered moths during the industrial revolution is one of the most well known examples of natural selection in action. Part of the appeal of the system is the apparent simplicity. The once-abundant light colored morph … Continue reading

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Steelhead in a random forest: identifying the genetic basis of migration

Genome-wide association studies (GWAS) have been quite successful in identifying variants associated with various phenotypes (I suppose there is some debate surrounding this statement. For an interesting, if dated, discussion look here). While most of this work was originally conducted … Continue reading

Posted in association genetics, bioinformatics, conservation, genomics, next generation sequencing | Leave a comment

The simpler cichlid: a recent adaptive radiation

If I was asked to name a few of the most compelling systems in evolutionary biology, I’d certainly start with Darwin’s Finches. Next might come peppered moths, African cichlids, stickleback, Caribbean Anolis lizards, or Lenski’s E. coli. What’s interesting about … Continue reading

Posted in adaptation, evolution, selection, speciation | Leave a comment

Genomic Islands of Speciation… are real?

I really want genomic islands of speciation to be real. Those great studies that seemed so convincing over the last ~10 years have been squashed due to, among other things, the trickiness of low genetic diversity (stay with me, I’ll … Continue reading

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A different perspective on genetic architecture

As an ecological geneticist, I’m constantly reminded how much we don’t understand about the genetic nature of adaptive variation. Sure, we have lots of examples of genes/pathways/regions that seem to be responsible for adaptation, but we don’t really know if … Continue reading

Posted in association genetics, evolution, genomics, mutation, quantitative genetics, theory | Leave a comment