The Molecular Ecologist

In the journals
Orona-Tamayo D., Wielsch N., Blanco-Labra A., Svatos A., Farías-Rodríguez R., Heil M., 2013 Exclusive rewards in mutualisms: ant proteases and plant protease inhibitors create a lock-key system to protect Acacia food bodies from exploitation. Molecular Ecology 22: 4087–4100. doi: 10.1111/mec.12320.

[Protease inhibitors] extracted from Acacia [food bodies] were biologically active, as they effectively reduced the trypsin-like and elastase-like proteolytic activity in the guts of seed-feeding beetles (Prostephanus truncatus and Zabrotes subfasciatus), which were used as non-adapted herbivores representing potential exploiters. By contrast, the legitimate mutu- alistic consumers maintained high proteolytic activity dominated by chymotrypsin 1, which was insensitive to the FB PIs.

Wray N. R., Yang J., Hayes B. J., Price A. L., Goddard M. E., Visscher P. M., 2013 Pitfalls of predicting complex traits from SNPs. Nature Reviews Genetics 14: 507–515. doi: 10.1038/nrg3457.

We have highlighted what we believe are limitations to genetic risk prediction as well as the most important pitfalls to befall researchers, and we have discussed how these can be avoided. Most problems occur in the validation stage, when data are not fully independent from those in the dis- covery phase, but care is also needed to ensure that the discovery and validation samples are representative of the popula- tion in which the predictor will be applied.

In the news
Want to make maps of changing climate? There’s a library for that in R.
On the importance of doubt in science, and science careers.
Advice for keeping up with the scientific literature: just give up already. (Except don’t!)

In the journals
Assis J., Castilho Coelho N., Alberto F., Valero M., Raimondi P., Reed D., Alvares Serrão E., 2013 High and distinct range-edge genetic diversity despite local bottlenecks (SJ Goldstien, Ed.). PLoS ONE 8: e68646. doi: 10.1371/journal.pone.0068646.

As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.

Brown A. M. V., Huynh L. Y., Bolender C. M., Nelson K. G., McCutcheon J. P., 2013 Population genomics of a symbiont in the early stages of a pest invasion. Molecular Ecology. doi: 10.1111/mec.12366.

We were primarily interested in determining the role of the symbiont in causing the emergence of the pest phenotype in the US. We found strong evidence that the genotype of US Ishikawaella in M. cribraria functionally resembles the Ishikawaella strain that confers the pest status in Japan, in M. punctatissima. Thus, we suggest the initial population of invading insects was probably able to infest soybeans, a surprising result given the resemblance of the host insect to nonpests in Asia.

In the news
What’s it feel like to watch the popular science media rehash a controversy that your field resolved years ago? “… like I am trapped under that fridge.”
A method to suppress expression from a whole chromosome could treat Down’s Syndrome.
How to identify functional transcription factors: come up with a null hypothesis and a standard for comparison.
Will increased data sharing lead to more false positives?

Peter, B.M., and M. Slatkin. 2013. Detecting range expansions from genetic data. Evolution online early. doi: 10.1111/evo.12202.

We introduce a statistic ψ (the directionality index) that detects asymmetries in the two-dimensional allele frequency spectrum of pairs of population. These asymmetries are caused by the series of founder events that happen during an expansion and they arise because low frequency alleles tend to be lost during founder events, thus creating clines in the frequencies of surviving low-frequency alleles.

Bolfíková B., Konečný A., Pfäffle M., Skuballa J., Hulva P., 2013 Population biology of establishment in New Zealand hedgehogs inferred from genetic and historical data: conflict or compromise? Molecular Ecology 22: 3709–3720. doi: 10.1111/mec.12331.

One of the most problematic NZ invasions is that of the West European hedgehog (Erinaceus europaeus). A series of introductions from the United Kingdom last- ing until early in the 20th century has been dated to 1869 (Brockie 1990). Recently, this species has reached considerable population densities, even higher than in the native range in the case of the North Island (Brockie 1990).

In the journals
Leviyang S., 2013  Computational inference methods for selective sweeps arising in acute HIV infection. Genetics 194: 737–752. doi: 10.1534/genetics.113.150862.

HIV escape from CTL [cytotoxic T-lymphocyte] response forms a complex, selective sweep that is difficult to analyze. In this work, we develop a model of initial infection, based on the well-known standard model, that allows for a description of multi-epitope response and the complex mutation pathways of HIV escape.

Lanfear R., Ho S. Y. W., Jonathan Davies T., Moles A. T., Aarssen L., Swenson N. G., Warman L., Zanne A. E., Allen A. P., 2013  Taller plants have lower rates of molecular evolution. Nature Communications 4: 1879. doi: 10.1038/ncomms2836.

Crucially, the long-term rate of mitosis in the apical meristem is likely to be lower in taller plants, because growth slows as plants increase in size and because there are physical limits to the delivery of water and nutrients to apical meristems as they increase in distance from the root system.

In the blogosphere
The story of this retracted Nature paper involves a break-in, tampering with experimental materials, and a hidden camera. Forget the lost publication—who’s got the movie rights?