For those of you who find yourselves in Kelowna, British Columbia this week, you are hopefully enjoying yourself at the annual Canadian Society for Ecology and Evolution (CSEE) meeting!
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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.
Science Insider reported yesterday that Lamar Smith, a Republican congressman from Texas and the chairman of the U.S. House Committee on Space, Science, and Technology, is planning to introduce legislation to change the way the National Science Foundation decides how to fund proposed projects. The article doesn’t provide access to the full text of the draft bill, but says that it would require NSF director to certify, on the Foundation’s website, that every funded project
1) “… in the interests of the United States to advance the national health, prosperity, or welfare, and to secure the national defense by promoting the progress of science;
2) “… the finest quality, is groundbreaking, and answers questions or solves problems that are of utmost importance to society at large; and
3) “… not duplicative of other research projects being funded by the Foundation or other Federal science agencies.”
This is on the heels of an April 17 hearing in which the committee chairman suggested that “we might be able to improve the process by which NSF makes its funding decisions,” asking acting NSF Director Cora Merrett how the agency could better ensure that it funds projects in “the national interest.”
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As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen-time.
In the journals
Sixty years ago Thursday, Nature published three papers that unravelled (ha!) the molecular structure of DNA. They’re freely available online. But here’s the paper from that archive you mignt not know about already, which was published almost 70 years ago:
Avery, O.T., MacLeod, C.M. & McCarty, M. 1979. Studies on the chemical nature of the substance inducing transformation of pneumococcal types. The Journal of Experimental Medicine 79: 137–159.
Griffith found that mice injected subcutaneously with a small amount of a living R culture derived from Pneumococcus Type II together with a large inoculum of heat-killed Type III (S) cells frequently succumbed to infection … The fact that the R strain was avirulent and incapable by itself of causing fatal bacteremia and the additional fact that the Type III cells contained no viable organisms brought convincing evidence that the R forms growing under these conditions had newly acquired the capsular structure and biological specificity of Type III pneumococci.
Macbeth, G.M., Broderick, D., Buckworth, R.C. & Ovenden, J.R. 2013. Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: A case study on Spanish mackerel (Scomberomorus commerson). G3: Genes|Genomes|Genetics 3: 709–717. doi: 10.1534/g3.112.005124.
A correspondence analysis algorithm was developed to detect and remove outlier genotypes that could possibly be inadvertently sampled from cryptic species or nonbreeding immigrants from genetically separate populations. … When putative immigrants were removed from the empirical data, 95% of the Ne estimates from jacknife resampling were greater than 24,000.
In the news
Grad student stipends aren’t exactly geared towards a life of luxury—at Southern Fried Science, they’re doing a series of posts providing advice for life on the stipend. (Via Scicurious, who adds her own thoughts.)
Trevor Bedford is building a pretty neat online library of his own science visualizations. We especially like the coalescent simulation.
Ken Wissoker, the editorial director of Duke University Press talks about the future of academic publishing, and doesn’t sound too worried.
Update, 20 August 2013: Many readers have requested a copy of the Joshua tree data set used as an example in this post, and I’ve finally secured permission from the coauthors of the original study to post it to Dryad. You can download it right here. Happy coding!
One of our most consistently popular posts of the past few months has been Kim Gilbert’s introduction to using geographic data to make maps in R. But once you’ve made a nice map of your collection sites, you’ve only just started to tap the possibilities of spatial data in R. With a suite of packages anchored by dismo, you can use R and open-sourced climate data to determine the environmental conditions your favorite species requires—by building a species distribution model.
Species distribution models (SDMs) are handy any time you want to extrapolate where a species might be based on where you know it actually is. Maybe you’re trying to figure out where would be fruitful to do more sampling; maybe you want to know where your favorite critters probably lived back during the last ice age; maybe you want to know what regions will be suitable for your favorite critters after another century of global climate change. The basic idea is,
This post provides a little demonstration of what you can do given a reasonably good set of collection sites and a no-longer-cutting-edge laptop. But caveat lector: actually building SDMs for publication-grade analysis requires a lot more work that what I’m presenting here. If you like the possibilities, you should start by reading the “vingnette” documents “Species distribution modeling in R” [pdf] (by dismo developers Roger Hijmans and Jane Elith) and “Boosted regression trees for ecological modeling” [PDF] (by Elith and John Leathwick). Those provide lots of detail and further reading lists, including a relatively recent review by Hijmans and Elith. They’re also the starting point for the demonstrations below.
First, you’ll want some distribution data. For this demonstration, I’ll use coordinates from a 2009 SDM study of Joshua trees by Godsoe et al. (fullest possible disclosure: I’m part of et al.). These are more than 5,000 locations where Joshua trees have been spotted—which is relatively easy, since they’re the tallest things that grow in most of the Mojave Desert—compiled from public databases, then ground-truthed and supplemented by the coauthors. All of those points are plotted in the map up at the beginning of the post; here’s the code that will set that up:
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As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen-time.
In the journals
Amemiya, C.T., Alföldi, J., Lee, A.P., Fan, S., Philippe, H., MacCallum, I., et al. 2013. The African coelacanth genome provides insights into tetrapod evolution. Nature 496: 311–316. doi: 10.1038/nature12027.
Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features.
Parducci, L., Matetovici, I., Fontana, S.L., Bennett, K.D., Suyama, Y., Haile, J., et al. 2013. Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia. Molecular Ecology doi: 10.1111/mec.12298.
Here, we compared pollen-based and metabar- coding approaches to explore the Holocene plant composition around two lakes in cen- tral Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species-specific primers.
In the news
We should all have such a problem: how do you decide what papers to publish first?
Is science’s image problem really a careers problem?
Shameless self-promotion: Jeremy reviews a new book on scientific teaching.
More on E.O. Wilson: maybe the real problem is that he doesn’t understand how collaboration works.
I just finished my registration for Evolution 2013, the joint annual meeting of theAmerican Society of Naturalists, Society of Systematic Biologists, and the Society for the Study of Evolution. This year it’ll run from the 21st to the 26th of June, at the resort town of Snowbird, Utah—which will be a bit trickier as a travel destination, but promises to provide spectacular natural beauty as a backdrop to the biggest conference of evolutionary biologists and ecologists in North America.
Molecular Ecology will be at the meeting as usual, at the Wiley-Blackwell booth, but we haven’t made any formal plans yet for The Molecular Ecologist. Should we make some? Maybe a meet-up for readers and contributors? A hike, or a gathering over some 3.2% beer? Let us know in the comments.
As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen-time.
In the journals
Martins, A.B., De Aguiar, M.A.M. & Bar-Yam, Y. 2013. Evolution and stability of ring species. Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1217034110.
We compare the spatial and genetic properties of a neutral agent-based population model to the greenish warblers’ complex, a well-documented example of an actual ring species in nature. Our results match the distribution of subspecies, the principal components of genetic diversity, and the linear spatial–genetic correlation of the observed data, even though selection is expected to be important for traits of this species.
Schrago, C.G. & Voloch, C.M. 2013. The precision of the hominid timescale estimated by relaxed clock methods. Journal of Evolutionary Biology 26: 746–755. doi: 10.1111/jeb.12076.
By inferring the theoretical limit distribution of posterior densities under a Bayesian frame- work, we show that it is unlikely that lengthier alignments or the availabil- ity of new genomic sequences will provide additional information to reduce the uncertainty associated with the divergence time estimates of the four hominid genera. A reduction of this uncertainty will be achieved only by the inclusion of more informative calibration priors.
In the news
E.O. Wilson says (in an op-ed for the Wall Street Journal) that you don’t need to know much math to be a “great scientist.” Has he gone nuts, or does he have a point? The definitive spot for following the debate is Jeremy Fox’s multiply-updated post at Dynamic Ecology.
“A profession that exploits people’s fear to staff its positions is not one to which you owe loyalty.”
Reed Elsevier bought the popular freemium reference manager/research community Mendeley this week. User responses are mostly not positive. Will this be a good thing for Mendeley? Yes! say the folks at Mendeley. No! says danah boyd. Maybe, says former Mendeley developer Jason Hoyt.
