The Molecular Ecologist

In the journals

Pemberton, T.J., Degiorgio, M. & Rosenberg, N. a. 2013. Population structure in a comprehensive genomic data set on human microsatellite variation. G3: Genes, Genomes, Genetics 3: 891–907. doi: 10.1534/g3.113.005728.

Here, we combine eight human population-genetic data sets at the 645 microsatellite loci they share in common, accounting for procedural differences in the production of the different data sets, to assemble a single data set containing 5,795 individuals from 267 worldwide populations.

(Hat tip to Razib Khan, who calls this “the mother of all microsatellite papers.”)

Henss, J.M., Moeller, J.R., Theim, T.J. & Givnish, T.J. 2013. Spatial scales of genetic structure and gene flow in Calochortus albus (Liliaceae). Ecology and Evolution 3: 1461–1470. doi: 10.1002/ece3.566.

Our data on SGS imply that the root-mean-square distance of gene dispersal σ is between 5 and 43 m, and that neighborhood size is between 52 and 194 individuals. Limited gene flow provides a potential explanation for local differentiation seen within species of Calochortus (e.g., in C. albus from the northern Sierras vs. south Coast Ranges [Ownbey 1940]), the high level of local endemism seen across species, the geographic coherence of individual clades of Calochortus, and the parallel adaptive radiations the genus has undergone for several traits in different areas.

Stachowicz, J.J., Kamel, S.J., Hughes, a R. & Grosberg, R.K. 2013. Genetic relatedness influences plant biomass accumulation in eelgrass (Zostera marina). The American Naturalist 181: 715–24. doi: 10.1086/669969.

… contrary to the pattern observed in multispecies assemblages, maximum biomass occurred in assemblages of more closely related individuals.

In the news

The U.S. Supreme Court rules (as most folks seem to be interpreting it) that naturally occurring DNA sequences may not be patented. But the text of the decision [PDF] is drawing complaints from people who know actual biology, and one justice admitted in his concurrence that he doesn’t understand the science.

On the danger of false positives in high-throughput sequencing results.

Thinking about tenure as a safety net.

A good idea for a new blog: Nice R Code. (Get it?)

In the journals

Moreno-Estrada, A., Gravel, S., Zakharia, F., Mccauley, J.L., Jake, K., Gignoux, C.R., et al. n.d. Reconstructing the population genetic history of the Caribbean. arXive: 1306.0558.

Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade.

Bastide, H., Betancourt, A., Nolte, V., Tobler, R., Stöbe, P., Futschik, A., et al. 2013. A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster. PLoS Genetics 9: e1003534. doi: 10.1371/journal.pgen.1003534.

We conducted the first genome-wide scan for polymorphism associated with pigmentation variation in a large natural sample of D. melanogaster, and found SNPs near two genes, tan and bric-a`-brac 1, affecting the trait. The SNPs associated with pigmentation variation in these genes appear to act by affecting the regulation of the pigmenta- tion genes, rather than their protein coding sequence.

In the journals

Arnqvist, G. 2013. Editorial rejects? Novelty, schnovelty! Trends in Ecology & Evolution 5: 2012–2013. doi: 10.1016/j.tree.2013.05.007.

Firstly, because an assessment of novelty critically depends upon a reader’s knowledge and perspective, the degree of novelty is arguably more demanding than many other criteria that can be used in editorial assessments. Because single associate editors cannot be experts in every subdomain, which is required for an informed and fair assessment of novelty, this increases the rate of poorly informed and mistaken editorial decisions.

Nystedt, B., Street, N.R., Wetterbom, A., Zuccolo, A., Lin, Y.-C., Scofield, D.G., et al. 2013. The Norway spruce genome sequence and conifer genome evolution. Nature, doi: 10.1038/nature12211.

Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the .100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism.

In the journals

Almany, G.R., Hamilton, R.J., Bode, M., Matawai, M., Potuku, T., Saenz-Agudelo, P., et al. 2013. Dispersal of grouper larvae drives local resource sharing in a coral reef fishery. Current Biology 23: 626–630. doi: 10.1016/j.cub.2013.03.006.

Using genetic parentage analysis, we measured larval dispersal from a single, managed spawning aggregation of squaretail coral grouper (Plectropomus areolatus) and determined its contribution to fisheries replenishment within five community tenure areas up to 33 km from the aggregation at Manus Island, Papua New Guinea.

Moe, A.M. & Weiblen, G.D. 2012. Pollinator-mediated reproductive isolation among dioecious fig species (Ficus, Moraceae). Evolution 66: 3710–21. doi: 10.1111/j.1558-5646.2012.01727.x.

Selection on pollinators maintaining host specificity appears to be an important mechanism of contemporary reproductive isolation among these taxa that could potentially influence their diversification.

In the news

On the mounting costs of the U.S. “sequester” for science funding.

NSF pushes back on Congressional prying into peer review.

“I’m very glad that I went to graduate school—my life would be different, and definitely worse, without it. But when I’m asked to give students advice about what they should do, I’m stumped.”

In the journals

Dudley, J.T., Chen, R., Sanderford, M., Butte, A.J. & Kumar, S. 2012. Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery. Molecular Biology and Evolution 29: 2087–94. doi: 10.1093/molbev/mss079.

We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position.

Ralph, P. & Coop, G. 2013. The geography of recent genetic ancestry across Europe. PLoS Biology 11: e1001555. doi: 10.1371/journal.pbio.1001555.

 We find that a pair of modern Europeans living in neighboring populations share around 2–12 genetic common ancestors from the last 1,500 years, and upwards of 100 genetic ancestors from the previous 1,000 years.

See also: the authors’ FAQ on the article and very nice discussion by Carl Zimmer.

In the news

More (not particularly optimistic) thoughts on political interference with peer review.

What do you do to help make your lab a nice place to work?

Jeremy’s launching a new side project: surveying LGBTQ folks working in science. If that describes you or any of your friends or colleagues, take the survey and pass along the link!

As we head into the weekend, here’s a few things we’ve noticed that are worth your screen-time.

In the journals

Navon, O., Sul, J.H., Han, B., Conde, L., Bracci, P., Riby, J., et al. 2013. Rare variant association testing under low-coverage sequencing. Genetics, doi: 10.1534/genetics.113.150169.

In this paper, we propose two novel methods for detecting association of rare SNPs with disease risk, using low coverage, error-prone sequencing. We show by simulation that our methods outperform previous methods under both low and high coverage sequencing, and under different disease architectures.

Petschenka, G., Fandrich, S., Sander, N., Wagschal, V., Boppré, M. & Dobler, S. n.d. Stepwise evolution of resistance to toxic cardenolides via genetic substitutions in the Na+/K+-ATPase of milkweed butterflies (Lepidoptera: Danaini). Evolution, doi: 10.1111/evo.12152.

Despite the monarch butterfly (Danaus plexippus) being famous for its adaptations to the defensive traits of its milkweed host plants, little is known about the macroevolution of these traits.

In the news

Infuriating: Sixteen-year-old conducts a DIY chemistry experiment that probably all of us have seen done, ends up charged with a felony.

Still more on the increasingly worrying politics around U.S. government funding for science by Phil Plait.