The Molecular Ecologist

In the journals
Carlson, C. S., Matise, T. C., North, K. E., Haiman, C. a., Fesinmeyer, M. D., Buyske, S., … Kooperberg, C. L. (2013). Generalization and dilution of association results from European GWAS in populations of non-European ancestry: The PAGE study. PLoS Biology, 11(9):e1001661. doi: 10.1371/journal.pbio.1001661.

… 25% of tagSNPs identified in EA [European ancestry] GWAS have significantly different effect sizes in at least one non-EA population, and these differential effects were most frequent in African Americans where all differential effects were diluted toward the null.

Peischl, S., Dupanloup, I., Kirkpatrick, M., & Excoffier, L. (2013). On the accumulation of deleterious mutations during range expansions. Molecular Ecology. doi: 10.1111/mec.12524.

We find that deleterious mutations accumulate steadily on the wave front during range expansions, thus creating an expansion load. Reduced fitness due to the expansion load is not restricted to the wave front but occurs over a large proportion of newly colonized habitats.

In the news
Popular Science closes its comments section, citing evidence that they’re bad for science communication.
More advice during academic job-hunting season: the one way to guarantee you don’t get a position is, don’t apply to it.
A new “task view” for R focuses on packages necessary to interact with online resources and websites.

In the journals
Cho YS et al. 2013. The tiger genome and comparative analysis with lion and snow leopard genomes. Nature Communications 4:2433. doi: 10.1038/ncomms3433.

Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats’ hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met394Lys39), which is likely to be associated with adaptation to high altitude.

Ferretti L, SE Ramos-Onsins, and M Pérez-Enciso. Population genomics from pool sequencing. Molecular Ecology doi: 10.1111/mec.12522.

Next generation sequencing of pooled samples is an effective approach for studies of variability and differentiation in populations. In this paper we provide a comprehensive set of estimators of the most common statistics in population genetics based on the frequency spectrum, namely the Watterson estimator θW , nucleotide pairwise diversity Π, Tajima’s D, Fu and Li’s D and F , Fay and Wu’s H, McDonald-Kreitman and HKA tests and Fst, corrected for sequencing errors and ascertainment bias.

In the news
Identifying functional variation across the genome using transcriptome sequencing.
Concerning the infamous two-body problem.
An insider account of how faculty hiring committees work.
No, PhDs finding non-academic careers is not a sign that we should make more PhDs.
“She was a professor?” Yeah, but she was an adjunct.

In the journals
Skotte L, TS Korneliussen, and A Albrechtsen. 2013. Estimating individual admixture proportions from next generation sequencing data. Genetics doi: 10.1534/genetics.113.154138.

This paper presents a new method for inferring individ- ual’s ancestry that takes the uncertainty introduced in next generation sequencing data into account. This is achieved by working directly with genotype likelihoods which contains all relevant information of the unobserved genotypes.

Scholle SO, RJF Ypma, AL Lloyd, and K Koelle. 2013. Viral substitution rate variation can arise from the interplay between within-host and epidemiological dynamics. The American Naturalist 182(4):494-513. doi: 10.1086/672000.

This work shows that even in neutrally evolving viral populations, epidemiological dynamics can alter substitution rates via the interplay between within-host replication dynamics and population-level disease dynamics.

In the news
Charles Goodnight on quantitative genetics in metapopulations.
A list of (rather more than) ten things to keep in mind when you sit down to work with that nice new dataset.
And some personal logrolling
Tim presented some worrying results from a study of the accessibility of old (and not-even-that-old) datasets at the International Congress on Peer Review and Biomedical Publication last week.
Jeremy posted the first preliminary analysis from a project on LGBTQ experiences in scientific careers.

In the journals
Deorowicz, S., A. Danek, and S. Grabowski. 2013. Genome compression: A novel approach for large collections. Bioinformatics 1–7. doi: 10.1093/bioinformatics/btt460.

More precisely, our novel Ziv-Lempel-style compression algorithm squeezes a single
human genome to ~400KB. The key to high compression is to look for similarities across the whole collection, not just against one refer- ence sequence, what is typical for existing solutions.

Kosheleva, K. a, and M. M. Desai. 2013. The dynamics of genetic draft in rapidly adapting populations. Genetics 1–46. doi: 10.1534/genetics.113.156430.

In both asexually reproducing organisms and in regions of low recombination in sexual organisms, the chance congregation of beneficial mutations on competing genetic backgrounds skews evolutionary dynamics. Because of this “clonal interference” effect, the success of a mutation depends not only on its fitness effect, but also on the quality of the genetic background in which it occurs and the fortune of the mutant’s progeny in amassing more beneficial mutations …

In the news
At what point have we shared enough data?
A top-notch long-form piece on the vital importance of gene expression.
How post-publication peer review fails.
An exceptionally detailed guide to the R base graphics package.