Monthly Archives: August 2013

What we’re reading: Species delimitation failure, the twisty history of a retrovirus, and breeding a better tomato

In the journals Carstens, B. C., T. a Pelletier, N. M. Reid, and J. D. Satler. 2013. How to fail at species delimitation. Molecular Ecology 22:4369–4383. doi: 10.1111/mec.12413. … in most contexts it is better to fail to delimit species … Continue reading

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Want to share your code?

In this line of work, we have all encountered tasks that are tedious, time consuming, and repetitive.  (Or if not, maybe give it a bit more time.) When confronted with these situations, people tend to fall into one of two … Continue reading

Posted in bioinformatics, community, genomics, howto, methods, next generation sequencing, phylogenetics, population genetics, quantitative genetics, R, software, theory | 14 Comments

What we’re reading: Rams’ horns, beetles’ testes, the rules of CC-BY reuse, and “Gatcaatgaggtgga …”

In the journals Johnston SE, J Gratten, C Berenos, JG Pilkington, TH Clutton-Brock, JM Pemberton, and J Slate. 2013. Life history trade-offs at a single locus maintain sexually selected genetic variation. Nature doi: 10.1038/nature12489. We found that an allele conferring … Continue reading

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By popular request …

The original data set of Joshua tree presence locations, which I used as an example in my post about estimating species distribution models in R, is now available for download from Dryad. Thanks to my coauthors for agreeing to share … Continue reading

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Making heatmaps with R for microbiome analysis

Arianne Albert is the Biostatistician for the Women’s Health Research Institute at the British Columbia Women’s Hospital and Health Centre. She earned a PhD from the University of British Columbia under the tutelage of Dolph Schluter before branching off into … Continue reading

Posted in howto, microbiology, R, software | Tagged , , | 71 Comments

What we’re reading: Adaptive introgression reviewed, overdominance and heterozygosity, and predatory re-publication of CC-BY articles

In the journals Hedrick, PW. 2013. Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation. Molecular Ecology doi: 10.1111/mec.12415. … potential examples of adaptive introgression in animals, including balancing selection for … Continue reading

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Domesticated genes gone wild

Artificial selection of domesticated plants and animals has been cited as a test case for natural selection since Charles Darwin first conceived the latter concept. But we generally consider that these two forms of selection operate to very different ends—that … Continue reading

Posted in adaptation, domestication, population genetics | 4 Comments