The Molecular Ecologist

In the journals
Harrisson K.A., A. Pavlova, M. Telonis-Scott and P. Sunnucks. 2014. Using genomics to characterize evolutionary potential for conservation of wild populations. Evolutionary Applications. doi: 10.1111/eva.12149.

… screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s).

Lozier J.D. 2014. Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing. Molecular Ecology. 23:788–801. doi: 10.1111/mec.12636.

Previous microsatellite-based analyses have shown that gene diversity is lower in the declining [Bombus] pensylvanicus than in B. impatiens. RADseq nucleotide diversities appear much more similar in the two species.

Petchey O.L., J.W. Fox, L. Haddon. 2014. Imbalance in individual researcher’s peer review activities quantified for four British Ecological Society journals, 2003-2010. PLoS ONE 9: e92896. doi: 10.1371/journal.pone.0092896. (See also discussion by author Jeremy Fox at Dynamic Ecology)

The majority of researchers (64%) did not have balanced contributions and withdrawals. Depending on assumptions, 12% to 44% contributed more than twice as much as required; 20% to 52% contributed less than half as much as required.

In the news
“In the face of climate change, scientists like [Ruth] Shaw have begun to measure how effective evolution might be as a survival strategy.”
“Observers lauded [David] Wright’s appointment in December 2011 … But on 25 February, he fired off a fiery resignation letter to his boss (see below), HHS Assistant Secretary for Health (ASH) Howard Koh.”
“But after a few years … you are given the chance to reflect and summarize, even rewrite your own narrative. You’ve identified collaborators and programs that make your collective program greater than the sum of its parts.”
“But just as the spherical cow is logically rigorous but of limited empirical insight, so the relentless tautologies of adaptationism leave us in the dark as to how human cultural and social diversity came about.”
“The problem is that most people don’t know what ‘the flu’ is, and relying on Google searches by people who may be utterly ignorant about the flu does not produce useful information.”
“So upon their predictable failure (in the free national labor market!) to turn up a qualified candidate, they wound up with a man whose views on issues relevant to the course are not only outside the scientific mainstream, but are demonstrably, factually incorrect and who likely has in the past abused such a position to advance his agenda.”

In the journals
Falk, K. L., J. Kästner, N. Bodenhausen, K. Schramm, C. Paetz, D. G. Vassão, M. Reichelt, D. von Knorre, J. Bergelson, M. Erb, J. Gershenzon, and S. Meldau. 2013. The role of glucosinolates and the jasmonic acid pathway in resistance of Arabidopsis thaliana against molluscan herbivores. Molecular Ecology. 1188–1203.

Our data highlight the function of well-known antiherbivore defence pathways in resistance against slugs and snails and suggest an important role for the diurnal regulation of defence metabolites against nocturnal molluscan herbivores.

Smemo, S., J. J. Tena, K.-H. Kim, E. R. Gamazon, N. J. Sakabe, C. Gómez-Marín, I. Aneas, F. L. Credidio, D. R. Sobreira, N. F. Wasserman, J. H. Lee, V. Puviindran, D. Tam, M. Shen, J. E. Son, N. A. Vakili, H.-K. Sung, S. Naranjo, R. D. Acemel, M. Mazanares, A. Nagy, N. J. Cox, C.-C. Hui, J. L. Gomez-Skarmeta, and M. A. Nóbrega. 2014. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature. doi: 10.1038/nature13138.

Genome-wide association studies (GWAS) have reproducibly assoc- iated variants within introns of FTO with increased risk for obesity and type 2 diabetes (T2D). Although the molecular mechanisms linking these noncoding variants with obesity are not immediately obvious, subsequent studies in mice demonstrated that FTO expression levels influence body mass and composition phenotypes. However, no direct connection between the obesity-associated variants and FTO expression or function has been made. Here we show that the obesity-associated noncoding sequences within FTO are functionally connected, at megabase distances, with the homeobox gene IRX3.

In the news
“In a new policy, PLoS requires PIs to cut and deposit one of their fingers every time they submit a paper, or at least that is the sense you get after reading the reactions about ‘new policy’ online.”
“… consider that one could easily have applied nearly all of the arguments people having been making in the blogosphere these past two weeks to that dastardly scientific timesink that is the common Methods sections.”
“The papers’ comment threads on PubPeer have attracted some 40000 viewers. It’s hardly surprising they caught issues that three overworked referees and a couple of editors did not.”

In the journals
Kunte K., W. Zhang, A. Tenger-Trolander, D. H. Palmer, A. Martin, R. D. Reed, S. P. Mullen, and M. R. Kronforst. 2014. doublesex is a mimicry supergene. Nature. doi: 10.1038/nature13112.

Using an integrative approach combining genetic and association mapping, transcriptome and genome sequencing, and gene expression analyses, we show that a single gene, doublesex, controls supergene mimicry in Papilio polytes.

(See also commentary by David Loehlin and Sean Carroll.)
Fraïsse C., J. A. D. Elderfield, and J. J. Welch. 2014. The genetics of speciation: are complex incompatibilities easier to evolve? J. Evolutionary Biology. doi: 10.1111/jeb.12339.

Experimental crosses show that such Dobzhansky–Muller incompatibilities (DMIs) are often complex (involving alleles at three or more loci) and asymmetrical (such that reciprocal introgressions have very different effects on fitness). One possible explanation is that asymmetrical and complex DMIs are ‘easier to evolve’, because they block fewer of the possible evolutionary paths between the parental genotypes.

In the news
“I’d like to think that people want to work with me because of what I can bring to the table other than my data, but I’m not keen on testing that working hypothesis.”
“So I say suck it up, share the data behind the paper, manage your data well, and let’s all get on with our lives.”
“Ask anyone in academics whether you’d rather have 6 citations from awesome papers or 6 awesome papers and 100% of them will take the papers.”
“This is an R wrapper to the NOAA climate data API.”
“I would like to place a vertical bar next to all the tips descended for a node that I specify [on my phylogeny]. How do I do this?”