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

RedditDiggMendeleyPocketShare and Enjoy
Posted in linkfest | Leave a comment

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

Posted in linkfest | Leave a comment

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

Posted in data archiving, howto, methods | Leave a comment

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 , , | 45 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

Posted in linkfest | Leave a comment

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

What we’re reading: Genomes from museum specimens, adaptive polyploidy, and “crowdsourced” fertility planning

In the journals Staats, M., R. H. J. Erkens, B. van de Vossenberg, J. J. Wieringa, K. Kraaijeveld, B. Stielow, J. Geml, J. E. Richardson, and F. T. Bakker. 2013. Genomic treasure troves: Complete genome sequencing of herbarium and insect … Continue reading

Posted in linkfest | Leave a comment

How to Backup and Store your Next-Generation Sequencing (NGS) data

Congratulations!  You have recently received a file path to retrieve your hard-earned next-generation sequencing data.  You quickly transfer the files to the computing cluster you work on or perhaps, if you only have a few lanes of data, to your … Continue reading

Posted in bioinformatics, data archiving, genomics, howto | 1 Comment

What we’re reading: mutational bias, local adaptation, insecticide resistance, and CC-BY licensing

In the journals Berg, J. J., and G. Coop. 2013. The population genetic signature of polygenic local adaptation. arXiv: 1307.7759v1. See also Haldane’s Sieve. We exploit the fact that GWAS provide an estimate of the additive effect size of many … Continue reading

Posted in linkfest | 2 Comments