The Molecular Ecologist

In the journals
Arnegard M.E., M.D. McGee, B. Matthews, K.B. Marchinko, G.L. Conte, S. Kabir, N. Bedford, S. Bergek, Y.F. Chan, F.C. Jones, D.M. Kingsley, C.L. Peichel, D. Schluter. 2014. Genetics of ecological divergence during speciation. Nature doi: 10.1038/nature13301.

Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions.

Ronald P.C. 2014. Lab to farm: Applying research on plant genetics and genomics to crop improvement. PLoS Biology 12(6): e1001878. doi: 10.1371/journal.pbio.1001878.

In this Essay, I describe how basic research advances have been translated into crop improvement, explore some lessons learned, and discuss the potential for current and future contribution of plant genetic improvement technologies to continue to enhance food security and agricultural sustainability.

In the news
“Everyone is, to some degree, winging it. Your career decisions may be as much serendipity as serious long term planning.”
“In our study, a low-frequency variant in HNF1A — present in 2 percent of type 2 diabetes cases and 0.4 percent of healthy controls — quintupled risk of type 2 diabetes, the largest effect ever observed for a type 2 diabetes variant found in more than 0.1 percent of the population.”

In the journals
Campitelli, B. E., and J. R. Stinchcombe. 2014. Population dynamics and evolutionary history of the weedy vine Ipomoea hederacea in North America. G3: Genes, Genomes, Genetics, doi: 10.1534/g3.114.011700.

We further found significant genetic differentiation at sequenced loci, but nearly 4-fold stronger differentiation at the leaf shape locus, strengthening evidence that the leaf shape locus is under divergent selection.

Lohmueller, K. E. 2014. The impact of population demography and selection on the genetic architecture of complex traits. PLOS Genetics. 10:e1004379. doi: 10.1371/journal.pgen.1004379.

Under a model where a mutation’s effect on a trait is correlated with its effect on fitness, rare variants explain a greater portion of the additive genetic variance of the trait in a population that has recently expanded than in a population that did not recently expand.

In the news
“I would argue then that the need to strive for top-tier non-OA journals is greatest for research-active faculty at institutions that are actually most harmed by predatory scientific publishing structures (see the list above).”
How to write the introduction to an ecology (or any scientific) paper: a flowchart.
“Two months after the implementation of the PLOS journals’ data policy, what have we learned from our authors, reviewers, editors, correspondents, and commenters in the blogosphere?”
Stop wasting your time writing faculty job application packages and just plug your publication stats into this regression-based widget to calculate the odds you’ll become a PI. (But see also.)

In the journals
Bozek K, Wei Y, Yan Z, Liu X, Xiong J, et al. 2014. Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PLoS Biology 12(5): e1001871. doi: 10.1371/journal.pbio.1001871.

We found that the evolution of the metabolome largely reflects genetic divergence between species and is not greatly affected by environmental factors. In the human lineage, however, we observed an exceptional acceleration of metabolome evolution in the prefrontal cortical region of the brain and in skeletal muscle.

Alcaide M, Scordato ESC, Price TD, Irwin DE. 2014. Genomic divergence in a ring species complex. Nature 10.1038/nature13285.

These results cast doubt on the hypothesis that the greenish warbler should be viewed as a rare example of speciation by distance, but demonstrate that the greenish warbler displays a continuum from slightly divergent neighbouring populations to almost fully reproductively isolated species.

In the news
“For a career in science you need to combine curiosity and creativity with hard work and stamina, as well salesmanship and confidence …”
“Being quite selective has worked out very well for me so far. I’ve been fortunate enough to attract several really great graduate students. But lately I’m wondering if I need to be less selective.”
“Now, even when I have other newish finds that I’ve yet to present, I submit [conference] abstracts for projects that still lack a rudimentary answer.”

In the journals
Coon, K. L., K. J. Vogel, M. R. Brown, and M. R. Strand. 2014. Mosquitoes rely on their gut microbiota for development. Molecular Ecology. 2727–2739. doi: 10.1111/mec.12771.

Functional assays showed that axenic larvae of each species failed to develop beyond the first instar. Experiments with Ae. aegypti indi- cated several members of the microbial community and Escherichia coli successfully colonized axenic larvae and rescued development.

Myers, R. B., B. Millman, and M. A. F. Noor. 2014. Genetics and evolution: An iOS application to supplement introductory courses in transmission and evolutionary genetics. G3: Genes, Genomes, Genetics. 4:779–781. doi: 10.1534/g3.114.010215.

The app provides demonstrations of Mendelian inheritance and population genetics, it assists with calculations common in genetics classes associated with these principles (e.g., recombination fraction), and it generates unique practice problems with which students can practice or professors can design assessments.

In the news
“It seems that negative events are necessary and we use them to avoid making the same mistakes again. It doesn’t need to be dramatic, it can be something as apparently positive as constructively worded critical feedback.”
“Wade wants us to cut up human diversity into five races not because that’s what the statistical analyses show, but because thinking about it as a gradient is hard.”
“Our key point here is that it is possible to have multiple potential comparisons, in the sense of a data analysis whose details are highly contingent on data, without the researcher performing any conscious procedure of fishing or examining multiple p-values.”

In the journals
Ferretti, L., E. Raineri, and S. Ramos-Onsins. 2012. Neutrality tests for sequences with missing data. Genetics 191:1397–401. doi: 10.1534/genetics.112.139949.

At present, most packages for population genetics analyses like DNAsp (Librado and Rozas 2009) deal with missing data simply by removing individuals and/or positions affected with incomplete data. This is a good strategy as long as missing data represent a very minor fraction of the alleles, since in this case they do not affect the power of the analysis. However, there could be situations in which a large amount of missing data are unavoidable.

Szkiba, D., M. Kapun, A. von Haeseler, and M. Gallach. 2014. SNP2GO: Functional analysis of genome-wide association studies. Genetics 197:285–289. doi: 10.1534/genetics.113.160341.

If candidate genes are significantly overrepresented, then one typically concludes that the GO term also contains an overrepresentation of candidate SNPs. While this may be true in many instances, it is certainly not always the case.

In the news
“Git can be an invaluable tool for researchers. It does, however, have a bit of a high activation energy.”
“What’s more important, you might ask, a nice doctor or a good one? A nice professor, or one who knows what she’s talking about? Well of course the answer is, why can’t she be both?”
“… the presence of male experimenters caused mice to display 35 percent less pain than when filmed remotely or in the presence of a female experimenter.”
“The level of criticism it would take to prove a wrong study wrong is higher than that almost any existing study can withstand. That is not encouraging for existing studies.”