The Molecular Ecologist

In the journals
Nishino J. 2013. Detecting selection using time-series data of allele frequencies with multiple independent reference loci. G3. 3:2151-2161. doi: 10.1534/g3.113.008276.

Recently, in 2013 Feder et al. proposed the frequency increment test (FIT), which evaluates natural selection at a single diallelic locus by the use of time-series data of allele frequencies. … Here, we expand upon the FIT by introducing a test that explicitly allows for changes in population size by using information from independent reference loci.

Aagaard JE, George RD, Fishman L, MacCoss MJ, Swanson WJ. 2013. Selection on plant male function genes identifies candidates for reproductive isolation of yellow monkeyflowers. PLoS Genetics 9(12): e1003965. doi:10.1371/journal.pgen.1003965.

We use isotopic labeling in combination with shotgun proteomics to identify more than 2,000 male function (pollen tube) proteins within maternal reproductive structures (styles) of M. guttatus flowers where pollen competition occurs. We then sequence array-captured pollen tube exomes from a large outcrossing population of M. guttatus, and identify those genes with evidence of selective sweeps or balancing selection consistent with their role in pollen competition.

In the news
Nature takes a look at its own representation of women in science.
What do you do when your standards, as a peer reviewer, are higher than the standards of the journal you’re reviewing for?
How wet lab scientists have made the transition from lab work to programming.
Is the missing heritability for human psychological traits … just not actually there?

In the journals
Petren, K. 2013. The evolution of landscape genetics. Evolution 67:3383–5 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. Now, with recent developments in technology, methodology, and modeling tools, we are poised to trace adaptive genetic variation across space and through time.

And see the entire Special Section.
Caballero A, A García-Dorado. Allelic diversity and its implications for the rate of adaptation. Genetics 195: 1373-84. doi: 10.1534/genetics.113.158410.

… allelic-diversity variables are better predictors of long-term adaptation than gene-frequency variables. This observation is also extended to unlinked neutral markers as a result of the information they convey on the demographic population history.

In the news
David Dobbs goes looking for new metaphors in a world of non-Mendelian genetics. But see also; and also.
Want to buy an authorship? Apparently doing that is shockingly direct.
Bad news gets worse: On funding rates for the NIH.

In the journals
Caulfield T, Evans J, McGuire A, McCabe C, Bubela T, et al. (2013) Reflections on the Cost of “Low-Cost” Whole Genome Sequencing: Framing the Health Policy Debate. PLoS Biol 11(11): e1001699. doi:10.1371/journal.pbio.1001699

Given the interest and significant investment in genomics, this seems an ideal time to consider what the evidence tells us about potential benefits and harms, particularly in the context of health care policy.

In the news
The personal genotyping service by 23andMe got smacked down by the U.S. FDA; but it probably won’t slow down the rush to consumer genomics.

In the journals
Guillot, G., L. Schilling, E. Porcu, and M. Bevilacqua. n.d. Validity of covariance models for the analysis of geographical variation. ArXiv: 1311.4136v1. See also Haldane’s Sieve.

We also outline how to construct alternative covariance models for the analysis of geographical variation that are both mathematically well behaved and easily implementable.

Keller, I., J. M. Alexander, R. Holderegger, and P. J. Edwards. 2013. Widespread phenotypic and genetic divergence along altitudinal gradients in animals. J. Evol. Biol. 26:2527–2543. doi: 10.1111/jeb.12255.

Several lines of evidence suggest that some of the observed differences are adaptively relevant, but rigorous tests of local adaptation or the link between specific phenotypes and fitness are sorely lacking. Evidence for a role of altitudinal adaptation also exists for a number of candidate genes, most prominently haemoglobin, and for anonymous molecular markers.

In the news
Requiescat, Frederick Sanger.
An in-depth look at the death of a Duquesne University adjunct professor suggests that the University (and its associated community) did more to try and help her than has been credited—but it also reemphasizes what a lousy deal adjunct positions can be.
Charles Goodnight explains the statistics of selection on correlated quantitative traits.
Are academic disciplines like frats?
How much should we care about replicating specific results?
Now that PLOS is reporting a profit, it’s looking for the next big change in peer-reviewed publishing.

In the journals
Sánchez-Guillén RA, A Córdoba-Aguilar, A Cordero-Rivera, M Wellenreuther. 2013. Genetic divergence predicts reproductive isolation in damselflies. Journal of Evolutionary Biology. doi: 10.1111/jeb.12274.

Our results indicate a positive and strong correlation between reproductive isolation and genetic distance using both mitochondrial and nuclear genes cytochrome oxidase II … Hybridization thresholds range from −0.43 to 1.78% for COII and −0.052–0.71% for 18S–28S, and both F1-hybrids and backcrosses were detected in wild populations of two pairs of Ischnura species with overlapping thresholds. Our study suggests that threshold values are suitable to identify species prone to hybridization and that positive isolation–divergence relationships are taxonomically widespread.

Fischer MC, C Rellstab, A Tedder, S Zoller, F Gugerli, KK Shimizu, R Holderegger, A Widmer. 2013. Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps. Molecular Ecology. 22:5594-5607. doi: 10.1111/mec.12521.

Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using F_ST-based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection.

In the news
SWIRL—statistics with interactive R learning—promises to teach statistics, and R coding, from within the R terminal.
There’s now an ArXive for biology—bioRXiv.
Phylogenetic methods find the grandmother of “Little Red Riding Hood”—the story, not the character.

In the journals
Brandvain, Y., T. Slotte, K. M. Hazzouri, S. I. Wright, and G. Coop. 2013. Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella. PLoS Genet. 9:e1003754. doi: 10.1371/journal.pgen.1003754.

Due to the recency of [their] split, much of the variation within C. rubella is also found within C. grandiflora. We can therefore identify genomic regions where two C. rubella individuals have inherited the same or different segments of ancestral diversity (i.e. founding haplotypes) present in C. rubella’s founder(s). Based on this analysis, we show that C. rubella was founded by multiple individuals drawn from a diverse ancestral population closely related to extant C. grandiflora, that drift and selection have rapidly homogenized most of this ancestral variation since C. rubella’s founding, and that little novel variation has accumulated within this time.

Han, F., J. Faraco, X. S. Dong, H. M. Ollila, L. Lin, J. Li, P. An, S. Wang, K. W. Jiang, Z. C. Gao, L. Zhao, H. Yan, Y. N. Liu, Q. H. Li, X. Z. Zhang, Y. Hu, J. Y. Wang, Y. H. Lu, C. J. Lu, W. Zhou, J. Hallmayer, Y. S. Huang, K. P. Strohl, T. Pollmächer, and E. Mignot. 2013. Genome wide analysis of narcolepsy in China implicates novel immune loci and reveals changes in association prior to versus after the 2009 H1N1 influenza pandemic. PLoS Genet. 9:e1003880. doi: 10.1371/journal.pgen.1003880.

Our results illustrate how genetic association can change in the presence of new environmental challenges and suggest that the monitoring of genetic architecture over time may help reveal the appearance of novel triggers for autoimmune diseases.

In the news
Authors who retract their own papers are less likely to see a decline in citations of their other work than those who have papers retracted for them.
Is there life after graduate school? It looks like there is if your dissertation advisor was David Hillis.
How Nazi-era scientific work haunts us to this day, including in U.S. abortion politics.
DNA barcoding discovers herbal supplements containing fillers, the wrong thing, toxic alternatives, and no detectable trace of herbs.