The Molecular Ecologist

As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen time.
In the journals
Tsai, I.J., Zarowiecki, M., Holroyd, N., Garciarrubio, A., Sanchez-Flores, A., Brooks, K.L., et al. 2013. The genomes of four tapeworm species reveal adaptations to parasitism. Nature doi: 10.1038/nature12031.

Tapeworms have specialized detoxification pathways, metabolism that is finely tuned to rely on nutrients scavenged from their hosts, and species-specific expansions of non-canonical heat shock proteins and families of known antigens. We identify new potential drug targets, including some on which existing pharmaceuticals may act.

Gaspar, J.M. & Thomas, W.K. 2013. Assessing the consequences of denoising marker-based metagenomic data. PLoS ONE 8: e60458. doi: 10.1371/journal.pone.0060458.

… we processed a real 16S rRNA metagenomic dataset through five denoising pipelines. By reconstituting the sequence reads at each stage of the pipelines, we determined how the reads were being altered.

Fourcade, Y., Chaput-Bardy, A., Secondi, J., Fleurant, C. & Lemaire, C. 2013. Is local selection so widespread in river organisms? Fractal geometry of river networks leads to high bias in outlier detection. Molecular Ecology 2065–2073. doi: 10.1111/mec.12158.

… using simulations we showed that F_ST outlier tests pro- vided a high rate of false-positives (up to 60%) in fractal environments such as river net- works. Surprisingly, the number of sampled demes was correlated with parameters of population genetic structure, such as the variance of F_STs, and hence strongly influenced the rate of outliers.

In the news
The trouble with Big Data is that big != useful.
Round and wrinkly peas got your genetics students snoozing? Try teaching Mendelian inheritance with ball pythons.

As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen-time.
In the journals
McTavish, E.J., Decker, J.E., Schnabel, R.D., Taylor, J.F. & Hillis, D.M. 2013. New World cattle show ancestry from multiple independent domestication events. Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1303367110.

In this study, we show that, although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants.

Van Wijk, S.J., Taylor, M.I., Creer, S., Dreyer, C., Rodrigues, F.M., Ramnarine, I.W., et al. 2013. Experimental harvesting of fish populations drives genetically based shifts in body size and maturation. Frontiers in Ecology and the Environment, doi: 10.1890/120229.

Here, we quantify genetic versus environmental change in response to size-selective harvesting for small and large body size in guppies (Poecilia reticulata) across three generations of selection. We document for the first time significant changes at individual genetic loci, some of which have previously been associated with body size.

Zhan, X., Pan, S., Wang, Junyi, Dixon, A., He, J., Muller, M.G., et al. 2013. Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nature Genetics, doi: 10.1038/ng.2588.

Analysis of 8,424 orthologs in both  falcons, chicken, zebra finch and turkey identified consistent  evidence for genome-wide rapid evolution in these raptors.

In the news
A new startup proposes to target advertising using genetic information. (What could possibly be wrong with that?)
Our co-blogger Tim Vines takes the “post-publication review” at F1000 Research to the metaphorical woodshed.
In a sort of followup to our most recent Molecular ecology view, here’s a video about surveying salmon spawning with a “hexacopter” drone.

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!