The Molecular Ecologist

In the journals
Moreira B., MC Castellanos, and JG Pausas. 2014. Genetic component of flammability variation in a Mediterranean shrub Molecular Ecology. doi: 10.1111/mec.12665.

Our general hypothesis is that flammability-enhancing traits are adaptive; here we test whether they have a genetic component. … We found that at least 42% of the phenotypic variation in flammability was explained by the genetic divergence in a subset of AFLP loci.

Yoder JB, J Stanton-Geddes, P Zhou, R Briskine, ND Young, and P Tiffin. 2014. Genomic signature of local adaptation to climate in Medicago truncatula. Genetics. doi: 10.1534/genetics.113.159319.

Genotypes at [climate-associated] candidate loci also predicted the performance of an independent sample of plant accessions grown in climate-controlled conditions. … candidates for two climate gradients, AMT and PWM, were significantly enriched for genic regions; and genome segments flanking genic AMT and PWM candidates harbored less nucleotide diversity, elevated differentiation between haplotypes carrying alternate alleles, and an overrepresentation of the most common haplotypes.

In the news
“… the biggest consumers of peer review seem to contribute the least to the process.” — Should journals refuse to take submissions from authors who don’t review for them?
“The mistake made by all bibliometricians is that they fail to consider the content of papers, because they have no desire to understand research.” — Why “altmetrics,” and other numeric proxies of a paper’s impact, are bunk.
“The FDA approved a machine called the MiSeqDx, ‘the first FDA-regulated test system that allows laboratories to develop and validate sequencing of any part of a patient’s genome.’ ” — Why the 23andMe decision doesn’t mean the FDA is opposed to genetic testing.
“We are a culture where boasting contests about who’s busier and who’s getting less sleep are not uncommon.” — Are you too busy thinking about tomorrow’s experiment to celebrate today’s results?

In the journals
Gazave E, L Ma, D Chang, A Coventry, F Gao, D Muzny, E Boerwinkle, RA Gibbs, CF Sing, AG Clark, and A Keinan. 2013. Neutral genomic regions refine models of recent rapid human population growth
PNAS doi: 10.1073/pnas.1310398110.

Here, to study recent human history with minimal confounding by selection, we sequenced and examined genetic variants far from genes. These data point to the human population size growing by about 3.4% per generation over the last 3,000–4,000 y, resulting in a greater than 100-fold increase in population size over that epoch.

Freedman AH, I Gronau, RM Schweize, D Ortega-Del Vecchyo, E Han, et al. 2014. Genome Sequencing Highlights the Dynamic Early History of Dogs. PLoS Genetics 10(1): e1004016. doi: 10.1371/journal.pgen.1004016.

Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary.

In the news
On being poor in graduate school.
What does it take to get Hope Jahren to take a principled stand? Misogynistic nonsense in the pages of Nature, apparently.
On what counts in doing science: experience, rather than genius.

Why are academics so vulnerable to online outrage?

In the journals
Castillo JA, CW Epps, AR Davis, SA Cushman. 2014. Landscape effects on gene flow for a climate-sensitive montane species, the American pika. Molecular Ecology doi: 10.1111/mec.12650.

Pikas are heat intolerant and restricted to cool microclimates, thus range contractions have been predicted as climate changes. We evaluated the correlation between landscape variables and genetic distance using partial Mantel tests in a causal modeling framework, and used spatially-explicit simulations to evaluate methods of model optimization including a novel approach based on relative support and reciprocal causal modeling.

Edelsparre AH, A Vesterberg, JH Lim, M Anwari, MJ Fitzpatrick. 2014. Alleles underlying larval foraging behaviour influence adult dispersal in nature. Ecology Letters doi:10.1111/ele.12234.

Using laboratory and field experiments, we demonstrate that natural allelic variation in a gene underlying a foraging polymorphism in larval fruit flies (for), also influences their dispersal tendencies as adults.

In the news
Nature covers Jeremy’s project on LGBTQ scientists.
The cellular basis of blue petunias.
The surprisingly simple genetics of an experimental evolutionary change in E. coli.
What happened when a Hawaiian city councilman decided to learn the facts on genetically modified crops.
Yet another roundup of the many capabilities of R.

In the journals
Niskanen AK, LJ Kennedy, M Ruokonen, I Kojola, H Lohi, M Isomursu, E Jansson, T Pyhäjärvi, J Aspi, J. 2014. Balancing selection and heterozygote advantage in MHC loci of the bottlenecked Finnish wolf population. Molecular Ecology doi: 10.1111/mec.12647.

MHC allele frequency distributions in the Finnish population were more even than expected under neutrality, implying balancing selection. In addition an excess of nonsynonymous compared to synonymous polymorphisms indicated historical balancing selection. … MHC-heterozygous wolves were less often infected by Trichinella spp. and carriers of specific MHC alleles, SNP haplotypes and SNP alleles had less helminth infections.

Sexton JP, SB Hangartner, AA Hoffmann. 2014. Genetic isolation by environment or distance: Which pattern of gene flow is most common? Evolution. 68:1558-646. doi: 10.1111/evo.12258.

Of 70 studies, we found evidence of IBD in 20.0%, IBE in 37.1%, and both patterns in 37.1%. In addition, 10.0% of studies exhibited counter-gradient gene flow. In total, 74.3% showed significant IBE patterns.

In the news
About 7% funded, with the median P.I. about 10 years post-Ph.D.: The depressing, depressing summary statistics from NSF grant funding in 2013.
Liam Revell continues to wrap new PHYLIP sub-programs into his RPhylip package.
Can American universities ever quit football?

In the journals
Zanne AE, DC Tank, WK Cornwell, et al. 2013. Three keys to the radiation of angiosperms into freezing environments. Nature doi: 10.1038/nature12872.

Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits5 and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. … By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait).

Hübner S, E Rashkovetsky, YB Kim, JH Oh, K Michalak, D Weiner, AB Korol, E Nevo, P Michalak. 2013.Genome differentiation of Drosophila melanogaster from a microclimate contrast in Evolution Canyon, Israel. PNAS 110:21059-21064. doi: 10.1073/pnas.1321533111.

Long-term studies of Drosophila melanogaster populations inhabiting the canyon have exhibited significant interslope divergence in thermal and drought stress resistance, candidate genes, mobile elements, habitat choice, mating discrimination, and wing-shape variation, all despite close physical proximity of the contrasting habitats, as well as substantial interslope migration. To examine patterns of genetic differentiation at the genome-wide level, we used high coverage sequencing of the flies’ genomes.

In the news
Will new moves to control university employees’ use of online media force online academics to go pseudonymous?
Richard Lenski’s Ten Commandments of statistical inference, and one very important Golden Rule.

In the journals
Althoff DM, KA Segraves, MTJ Johnson. 2013. Testing for coevolutionary diversification: linking pattern with process. Trends in Ecology & Evolution. doi: 10.1016/j.tree.2013.11.003.

In this review, we highlight potential mechanisms of coevolutionary diversification, outline approaches to examine this process across temporal scales, and propose a set of minimal requirements for demonstrating coevolutionary diversification.

Vines TH, AYK Albert, RL Andrew, F Débarre, DG Bock, MT Franklin, KJ Gilbert, J-S Moore, S Renaut, DJ Rennison 2013. The availability of research data declines rapidly with article age. Current Biology. doi: 10.1016/j.cub.2013.11.014.

For papers where the authors gave the status of their data, the odds of a data set being extant fell by 17% per year. In addition, the odds that we could find a working e-mail address for the first, last, or corresponding author fell by 7% per year.

See also coverage by The American Scientist, Science Insider, and Nature News.
In the news
“The deal represents a step in the right direction, but a small one.” — How the new U.S. budget deal will affect research funding.
“… if it really takes a year for a study to be reproduced, if your finding is that fragile, this is something that researchers should know about right away from reading the article.” — Formal replication is hard, but it’s still important.
“… a mandatory data archiving policy was much more effective than either recommending archiving or having no policy at all.” — The American Scientist covers Tim’s research on data archiving.
“The secret for sane use is to use Excel only for data entry; any data manipulation … or analysis is done in statistical software.” — When it actually makes sense to use Microsoft Excel.
“Goofus says, ‘George Price published a paper in Nature. He must be really smart. And I am smart because I have smartly recognized his smartness.'” — Jon F. Wilkins on the recent dustup about “luxury” journals.