The Molecular Ecologist

In the journals
Hughes, K. A., A. E. Houde, A. C. Price, and F. H. Rodd. 2013. Mating advantage for rare males in wild guppy populations. Nature. doi: 10.1038/nature12717.

Hereweuse highly replicatedexperimentalmanipulationsofnatural populations to showthatmales with rare colour patternshave higher reproductive fitness, demonstrating [negative frequency-dependent selection] mediated by sexual selection.

De Mita, S., A. Streng, T. Bisseling, and R. Geurts. 2013. Evolution of a symbiotic receptor through gene duplications in the legume-rhizobium mutualism. New Phytologist. doi: 10.1111/nph.12549.

We show that two rounds of duplication preceded the evolution of the rhizobial symbiosis
in legumes. Molecular evolution patterns indicate that the resulting three paralogous gene copies experienced different selective constraints.

Mendez, M., T. J. Jefferson, S.-O. Kolokotronis, M. Krützen, G. J. Parra, T. Collins, G. Minton, R. Baldwin, P. Berggren, A. Särnblad, O. a. Amir, V. M. Peddemors, L. Karczmarski, A. Guissamulo, B. Smith, D. Sutaria, G. Amato, and H. C. Rosenbaum. 2013. Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters? Molecular Ecology. doi: 10.1111/mec.12535.

The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S. teuszii in the Atlantic off West Africa, S. plumb in the central and western Indian Ocean, S. chinensis in the eastern Indian and West Pacific Oceans, and a new as-yet-unnamed species off northern Australia).

See also coverage by the BBC.
In the news
Why it shouldn’t bother you that no-one reads your blog.
Even as human geneticists are beginning to realize genetics is a lot messier than they thought, and there are good reasons to think that mathematical ability is more in your confidence than your genes, the developer of the Ion Torrent sequencing system is about to drop about a million bucks on a study of mathematicians’ genetics.
Should we send a DNA sequencer to Mars?

In the journals
E Kazancıoğlu, Arnqvist G. 2013. The maintenance of mitochondrial genetic variation by negative frequency-dependent selection. Ecology Letters. doi: 10.1111/ele.12195.

We assessed the change in mitochondrial haplotype frequencies over 10 generations of experimental evolution in 180 seed beetle populations in the laboratory … We found that haplotypes consistently increased in frequency when they were initially rare and decreased in frequency when initially common.

JE Crawford, Nielsen R. 2013. Detecting adaptive trait loci in non-model systems: divergence or admixture mapping? Molecular Ecology. doi: 10.1111/mec.12562.

Divergence scans of genetic markers for outlier loci, or ‘divergence mapping’, have been used to map locally adapted genes, but this approach is likely to be underpowered when background divergence is elevated. Genotype-phenotype association tests in admixed populations, or ‘admixture mapping’, may provide a useful approach for mapping locally adapted loci when neutral divergence is high.

In the news
Is biology’s future in the computer lab?
The Economist goes off the rails on science’s self-correction.
PubMed is putting a comments section below every article in the archive—and it’s open, to begin, to anyone who’s received funds from NIH or Wellcome Trust.

In the journals
Eckert AJ, JL Wegrzyn, JD Liechty, JM Lee, WP Cumbie, JM Davis, B Goldfarb, CA Loopstra, SR Palle, T Quesada, CH Langley and DB Neale. 2013. The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae). Genetics. doi: 10.1534/genetics.113.157198.

Phenotypes measured at the whole plant level (e.g. disease resistance) exhibit an approximately two-fold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were only apparent when loci were considered at the level of functional sets.

Kajdacsi1 B, F Costa, C Hyseni, F Porter, J Brown, G Rodrigues, H Farias, MG Reis, JE Childs, AI Ko, and A Caccone. 2013. Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil. Molecular Ecology. doi: 10.1111/mec.12455.

Surprisingly, we detected very little relatedness among animals trapped at the same site and found high levels of genetic diversity, as well as structuring across small geographical distances. Most F_ST comparisons among sites were statistically significant, including sites less than 400 m apart.

In the news
It’s been a really rough week for inclusion in science communication. Here’s hoping we can start to do better.
The U.S. Federal Government is finally open for business again, including the science–related bits.

In the journals
Goodman BA, L Schwarzkopf, & AK Krockenberger. 2013. Phenotypic integration in response to incubation environment adaptively influences habitat choice in a tropical lizard. The American Naturalist, 182(5): 666-73. doi: 10.1086/673299.

Using a split-clutch design, we incubated eggs at thermal regimes that mimicked the thermal environments of nests from two habitat types (forest = warm; rocky = cool). Hatchlings from cool incubation environments had longer limbs and greater running and climbing speeds, which are likely to be beneficial for rocky habitats.

Scheiner SM & LM Bouchie. 2013. The predictive power of NSF reviewers and panels. Frontiers in Ecology and the Environment 11: 406–407. 10.1890/13.WB.017.

Reviewer scores and panel rankings were moderately, but non-significantly, correlated with project outcomes (r = 0.12–0.29), but less so when analyzed by multiple regression. The sole predictive factor was award size for the number of publications (Figure 1; standardized coefficient = 0.64), a relationship consistent with other analyses …

In the news
This week in shutdown science: The CDC sits out an outbreak of drug-resistant salmonella, experiments on hold, lab mice euthanized and an entire season of Antarctic research cancelled.
Science commissioned a sting to test the peer review at open-access journals … but didn’t include a control group.
On the infamous two-body problem.
A big new study finds that papers reporting publicly available data get more citations.

In the journals
Petren, K. 2013. The evolution of landscape genetics. Evolution. doi: 10.1111/evo.12278.

Evolutionary landscape genetics is the study of how migration and population structure affects evolutionary processes. As a field it dates back to Sewall Wright and the origin of theoretical population genetics, but empirical tests of adaptive processes of evolution in natural landscapes have been rare

Alberto, F. J., J. Derory, C. Boury, J.-M. Frigerio, N. E. Zimmermann, and A. Kremer. 2013. Imprints of natural selection along environmental gradients in phenology-related genes of Quercus petraea. Genetics 195:495–512. doi: 10.1534/genetics.113.153783.

We investigated whether SNP variation reflected the clinal pattern of bud burst observed in common garden experiments. We used different methods to detect imprints of natural selection (FST outlier, clinal variation at allelic frequencies, association tests) and compared the results obtained for the two gradients.

In the news
Here’s a brief rundown of scientific work and outreach brought to a screeching, experiment-ruining halt by gerrymandering-induced paralysis in Washington this week. And here’s a gallery of screenshots from databases and other online resources hobbled by the shutdown. But the conservative war on the NSF is still underway.
From tweet to review article.
Bard College (where, full disclosure, Jeremy has taught) is initiating a new option for applicants to skip SAT scores and transcripts by writing four 2,500-word research papers. Is that better?
More on the decision by Popular Science to close their website comments system.
A handy guide for male academics who don’t want to be That Dude.
Are you now or have you recently been searching for an academic job? Then you should take this extremely short survey.