What we’re reading: isolation with migration, starch-eating dogs, and politicized science funding

Bookshelf

As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen time.

In the journals

Mailund, T., Halager, A.E., Westergaard, M., Dutheil, J.Y., Munch, K., Andersen, L.N., et al. 2012. A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS genetics 8: e1003125. doi: 10.1371/journal.pgen.1003125.

We provide a test for whether divergence is gradual or instantaneous, and we apply the model to three key divergence processes in great apes: (a) the bonobo and common chimpanzee, (b) the eastern and western gorilla, and (c) the Sumatran and Bornean orang-utan. We find that the bonobo and chimpanzee appear to have undergone a clear split, whereas the divergence processes of the gorilla and orang-utan species occurred over several hundred thousands years with gene flow stopping quite recently. We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation.

Axelsson, E., Ratnakumar, A., Arendt, M.-L., Maqbool, K., Webster, M.T., Perloski, M., et al. 2013. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature, doi: 10.1038/nature11837.

The results presented here demonstrate a striking case of parallel evolution whereby the benefits of coping with an increasingly starch- rich diet during the agricultural revolution caused similar adaptive responses in dog and human.

Cromie, G.A., Hyma, K.E., Ludlow, C.L., Garmendia-torres, C., Teresa, L., May, P., et al. n.d. Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq. arXiv: 1303.4835.

Here, we apply a multiplexed, reduced genome sequencing strategy (known as RAD- seq) to genotype a large collection of S. cerevisiae strains, isolated from a wide range of geographical locations and environmental niches. The method permits the sequencing of the same 1% of all genomes, producing a multiple sequence alignment of 116,880 bases across 262 strains.

In the news

The U.S. Senate voted this week to forbid the National Science Foundation from funding political science.

Nature has a cool article about long-term scientific experiments.

Concerning the decision to send a paper to PLoS ONE.

A new, more complete version of the Neanderthal genome has just been released.

The SMBE satellite meeting on “Eukaryotic-omics” at UC Davis, which Holly Bik is organizing, is coming up soon—the extended deadline for abstracts is today!

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About Jeremy Yoder

Jeremy Yoder is an Assistant Professor of Biology at California State University, Northridge. He also blogs at Denim and Tweed, and tweets under the handle @jbyoder.
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