What we're reading

2007.06.23 - am I in there?

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
Maughan, H., P. W. Wang, J. Diaz Caballero, P. Fung, Y. Gong, S. L. Donaldson, L. Yuan, S. Keshavjee, Y. Zhang, Y. C. W. Yau, V. J. Waters, D. E. Tullis, D. M. Hwang and D. S. Guttman. 2012. Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions. PLoS ONE 7:e45791. DOI: 10.1371/journal.pone.0045791

The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways in which microbial communities affect ecosystem functioning and human health. Here we describe Serial Illumina Sequencing (SI-Seq): a method for deep sequencing of the bacterial 16S rRNA gene using next- generation sequencing technology.

Huang, X., N. Kurata, X. Wei, Z.-X. Wang, A. Wang, Q. Zhao, Y. Zhao, K. Liu, H. Lu, W. Li, Y. Guo, Y. Lu, C. Zhou, D. Fan, Q. Weng, C. Zhu, T. Huang, L. Zhang, Y. Wang, L. Feng, H. Furuumi, T. Kubo, T. Miyabayashi, X. Yuan, Q. Xu, G. Dong, Q. Zhan, C. Li, A. Fujiyama, A. Toyoda, T. Lu, Q. Feng, Q. Qian, J. Li and B. Han. 2012. A map of rice genome variation reveals the origin of cultivated rice. Nature, online ahead of publication. DOI: 10.1038/nature11532

Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication.

Domingues, V. S., Y.-P. Poh, B. K. Peterson, P. S. Pennings, J. D. Jensen and H. E. Hoekstra. 2012. Evidence of adaptation from ancestral variation in young populations of beach mice. Evolution; international journal of organic evolution 66:3209–3223. DOI: 10.1111/j.1558-5646.2012.01669.x

There are still few cases in which the precise mutations (and hence, defined alleles) that contribute to adaptive change have been identified in nature; one exception is the genetic basis of camouflaging pigmentation of oldfield mice (Peromyscus polionotus) that have colonized the sandy dunes of Florida’s Gulf Coast. To quantify the genomic impact of colonization as well as the signature of selection, we resequenced 5000 1.5-kb noncoding loci as well as a 160-kb genomic region surrounding the melanocortin-1 receptor (Mc1r), a gene that contributes to pigmentation differences, in beach and mainland populations. … we show that all beach subspecies share a single derived light Mc1r allele, which was likely selected from standing genetic variation that originated in the mainland.

In the blogosphere
Biologists at the Argonne National Lab turn microbial diversity datasets into music.
A study by Dunkin’ Donuts concludes that scientists drink more coffee than members of any other profession.

About Jeremy Yoder

Jeremy B. Yoder is an Assistant 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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