What we're reading, and zooming


As we head into the weekend, here’s a few things we found this week that might be worth your screen time:
In the journals:
Minoche, A. E., J. C. Dohm and H. Himmelbauer. 2011. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome biology 12:R112. BioMed Central Ltd. DOI: 10.1186/gb-2011-12-11-r112

We provide quantifications and evidence for GC bias, error rates, error sequence context, effects of quality filtering, and the reliability of quality values. By combining different filtering criteria we reduced error rates 7-fold at the expense of discarding 12.5% of alignable bases. While overall error rates are low in HiSeq data we observed regions of accumulated wrong base calls.

Malek, T. B., J. W. Boughman, I. Dworkin and C. L. Peichel. 2012. Admixture mapping of male nuptial colour and body shape in a recently formed hybrid population of threespine stickleback. Molecular Ecology 5265–5279. DOI: 10.1111/j.1365-294X.2012.05660.x

Here, we demonstrate the utility of admixture mapping in a naturally occurring hybrid population of threespine sticklebacks (Gasterosteus aculeatus) from Enos Lake, British Columbia. … By genotyping males with nuptial colour at the two extremes of the phenotypic distribution, we identified seven genomic regions on three chromosomes associated with divergence in male nuptial colour. These genomic regions are also associated with variation in body shape, suggesting that tight linkage and/or pleiotropy facilitated adaptation to divergent environments in benthic–limnetic species pairs.

Mayer, K. F. X., R. Waugh, P. Langridge, T. J. Close, R. P. Wise, et al. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature DOI: 10.1038/nature11543

We implemented a hierarchical approach to further anchor the physical and genetic maps (Methods, Supplementary Note 4). A total of 3,241 genetically mapped gene-based single-nucleotide variants (SNV) and 498,165 sequence-tag genetic markers14 allowed us to use sequence homology to assign 4,556 sequence-enriched physical map contigs spanning 3.9 Gb to genetic positions along each barley chromosome.

Rosindell, J. and L. J. Harmon. 2012. OneZoom: A Fractal Explorer for the Tree of Life. PLoS Biology 10:e1001406. DOI: 10.1371/journal.pbio.1001406
Rather than an abstract, here’s the introductory video from the OneZoom site, which presents big phylogenetic trees in a zoomable “fractal” format:

In the blogosphere:
Holly’s at a QIIME-VAMPS meeting in Boulder (sponsored by the Sloan program for Microbiology of the Built Environment), and notes that everyone from the meeting is tweeting about data analysis under the hashtag #microbenet — she’ll make a Storify out of it later.
Over on Slate: photos of birds, taken using techniques usually used for portraits of humans.

About Jeremy Yoder

Jeremy B. Yoder is an Associate Professor of Biology at California State University Northridge, studying the evolution and coevolution of interacting species, especially mutualists. He is a collaborator with the Joshua Tree Genome Project and the Queer in STEM study of LGBTQ experiences in scientific careers. He has written for the website of Scientific American, the LA Review of Books, the Chronicle of Higher Education, The Awl, and Slate.
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