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


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!


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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