A tale of two Dryad submissions

Posted on 20 Mar, 2013 by Jeremy Yoder


As it happens, the last two scientific papers I’ve had accepted for publication are also the first two papers for which my first-authorial duties included some substantial journal-mandated archiving of supporting data (beyond uploading a handful of DNA sequences to GenBank). The respective journals that are publishing the two papers each require authors to upload data supporting published papers to some public repository, and both strongly suggested that the repository be Dryad.
And that’s about where the similarities end. The differences, I think, suggest that there’s still some work to be done before journals, authors, and public data archives settle on a set of standard procedures that will make the data collected in publicly funded scientific research easily available with a minumum of fuss.
The first paper went to Systematic Biology. It’s a phylogenetic analysis using data collected by the Medicago HapMap Project. (I described the results briefly over at Nothing in Biology Makes Sense! last week.) Like most genome projects, the MHP has its own infrastructure for making its data available, and I’d cited that website in the MS and figured we’d done our duty. But the afternoon after I submitted the manuscript, I recieved an e-mail from the editorial office reminding me that (1) Systematic Biology expects authors to upload supplementary figures (the MS had a couple) to Dryad and (2) we were also expected to make supporting data available to reviewers at the time of submission … so why not put the data in the same Dryad package?
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Discussion, now with Disqus

Posted on 15 Mar, 2013 by Jeremy Yoder

Screen Shot 2013-03-15 at 9.18.36 AM

A screenshot of the new comments form.


Readers may have noticed that our comments forms have changed—because we’ve installed the Disqus commenting platform for this site. (Old comments are currently being imported into the new system, which should be done within 24 hours.)
Disqus offers some nice features above and beyond the old native WordPress system: it lets you comment using a login identity from Facebook, Twitter, or Google+ (though you can still just type in any old name to comment); allows more flexibility for formatting and embedding media (images or video, say); and lets the commenter community help moderate the discussion by flagging inappropriate posts for moderators’ attention. Also, because Disqus is a widely used commenting platform, it effectively connects this blog to commenting communities with overlapping interests all across the Web, including at NPR, The Atlantic, BoingBoing, and many smaller sites.
In the end, we’re mainly hopeful that Disqus will make it easier to participate in and follow discussion right here at the Molecular Ecologist. Dare we ask that you let us know what you think in the comments?

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What we're reading

Posted on 15 Mar, 2013 by Jeremy Yoder

Reading

As we head into the weekend, here are a few things we’ve noticed that might be worth your screen-time.
In the journals
Bell, G. 2013. The phylogenetic interpretation of biological surveys. Oikos. doi: 10.1111/j.1600-0706.2013.00405.x.

I describe a method of nested sister-group analysis for estimating ecological similarity based on landscape features or on co-distribution. The phylogeny is dissected into triplets, each comprising two sister taxa and their outgroup. For a triplet at any phylogenetic level, the similarity of sister groups with respect to some given character can be compared with their joint similarity to the outgroup to give a single test of similarity by descent.

Poisot, T., Péquin, B. & Gravel, D. 2013. High-throughput sequencing: A roadmap toward community ecology. Ecology and Evolution. doi: 10.1002/ece3.508.

Here, we showcase how HTS can be put in practice by revisiting classical questions pertaining to the distribution and dynamics of ecological diversity. In particular, we start from characterization of α-diversity, and scale up to the integration of species interactions in species distribution. Doing so, we highlight how these techniques can rapidly transform modern ecology by bringing new answers general ecologists are concerned about.

Linnen, C.R., Poh, Y.-P., Peterson, B.K., Barrett, R.D.H., Larson, J.G., Jensen, J.D., et al. 2013. Adaptive evolution of multiple traits through multiple mutations at a single gene. Science 339: 1312–1316. doi: 10.1126/science.1233213.

We identified distinct regions within the Agouti locus associated with each color trait and found that only haplotypes associated with light trait values have evidence of selection. Thus, local adaptation is the result of independent selection on many mutations within a single locus, each with a specific effect on an adaptive phenotype, thereby minimizing pleiotropic consequences.

In the blogosphere
If you celebrated “pi day” yesterday, you might want to consider celebrating “tau day” instead, next year.
How to get a faculty job in 20 not-so-easy steps.
A view from the front lines of the fight against antibiotic resistant bacteria. It ain’t pretty.

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Syndication, really simple (and, how will you subscribe?)

Posted on 14 Mar, 2013 by Jeremy Yoder

the postman always rings thrice

With the recent announcement that Google Reader’s days are numbered, it’s occurred to me to clean up the options for RSS (really simple syndication) subscriptions here at The Molecular Ecologist. To that end, I’ve installed a shiny new Feedburner RSS feed, which should give us more control over what readers get in their RSS reader, as well as more information about how many people use the service. As a bonus, Feedburner offers subscriptions via e-mail. [Edit: the service is activated, but it doesn’t seem to be working just yet. Will upate when it’s online! … Okay, now it’s working—subscribe to your heart’s content.] Both options are now prominently placed in our sidebar, for your convenience.
(The original site feed, http://www.molecularecologist.com/feed remains up and running, so you shouldn’t have any issues if you’re subscribed to that; but please consider switching to the new system!)
And, while we’re on the subject, am I the only one in the Molecular Ecologist community who’s mourning the passing of Google Reader? What alternatives are you folks out there using, or considering? In my initial panicked casting around last night, I tried out feedly, then paid a few bucks for Reeder. Both of these are essentially clients for Google Reader, but the developers of each are promising work-arounds before the GR goes down on 1 July. I’ll probably swap between them for a little while until I decide which fits my needs best.

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Hitchhiking microbes

Posted on 12 Mar, 2013 by kimgilbert

108-365 Fresh Bread

Saccharomyces cerevisae is effectively a domesticated species. Photo by Flickr user bcymet.


It is quite clear that humans play a major role in altering ecosystems today. Historic migration of human populations has been shown to have many interesting associated evolutionary consequences1,2. Worldwide travel makes it difficult to stop anything from going anywhere, and there is now even discussion about the impact of microbes catching a ride to Mars on space shuttles!
The interesting associated migration I’d like to discuss here is that of our good friend, the budding yeast Saccharomyces cerevisiae. My previous interests in this delightful organism were limited to its use in fermenting some of my favorite beverages. However, there is so much more to this microscopic morphon than meets the eye. Not until yeast geneticist Duncan Greig came to UBC did it become clear to me how little we know of this species in nature. But the idealistic thoughts of having field sites at vineyards in French wine country were quickly washed away by his description of how difficult it can be to find the right yeast, which is not easy to identify to the species level3.
Yet the point about vineyards is intriguing. It might be argued that S. cerevisiae is now a domesticated species. These microbes are not motile on their own, and human use has been shown to impact the evolution of different strains since the origin of alcohol production in pre-historic human populations4. Populations of yeast exhibit genetic differentiation associated with different alcohol breweries or distilleries and different geographic regions across the globe.
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What we're reading

Posted on 8 Mar, 2013 by Jeremy Yoder

Bookshelf
As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen-time.
In the journals
Garud, N.R., Messer, P.W., Buzbas, E.O. & Petrov, D.A. Soft selective sweeps are the primary mode of recent adaptation in. arXiv: 1303.0906.

Here, we developed a statistical test based on a haplotype statistic, H12, capable of detecting both hard and soft sweeps with similar power. We used H12 to identify multiple genomic regions that have undergone recent and strong adaptation using a population sample of fully sequenced Drosophila melanogaster strains (DGRP). We then developed a second statistical test based on a statistic H2/H1 | H12, to test whether a given selective sweep detected by H12 is hard or soft. Surprisingly, when applying the test based on H2/H1 | H12 to the top 50 most extreme H12 candidates in the DGRP data, we reject the hard sweep hypothesis in every case.

Lee, M.-C. & Marx, C.J. 2013. Synchronous waves of failed soft sweeps in the laboratory: Remarkably rampant clonal interference of alleles at a single locus. Genetics 193: 943–952. doi: 10.1534/genetics.112.148502.

Here we uncovered a dramatic example of clonal interference between multiple similar mutations occurring at the same locus within replicate populations of Methylobacterium extorquens AM1. … Despite conferring a large selective benefit, the majority of these alleles rose and then fell in frequency due to other lineages emerging that were more fit.

In the blogosphere
How reliable (or, well, consistent) are the species descriptions in field guides?
New to Tim: Stephen Jay Gould may have fudged the numbers on his exposé of number-fudging in The Mismeasure of Man.
There is a Tumblr of beautiful scientific illustrations, because of course there is.

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Molecular ecology views: Shenandoah butternuts

Posted on 7 Mar, 2013 by Jeremy Yoder

Sean Hoban, a postdoc at the Università di Ferrara, Italy, sends along these photos from his Ph.D. fieldwork on endangered butternut trees in beautiful Shenandoah National Park, USA. Many more pictures of Sean’s field work in forests across the eastern US and Canada, and some botanic gardens, can be found here.
If you have photos of your own molecular ecology in action that you’d like to share, send them our way!
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Speciation with gene flow and the virtual beanbag: Genome-level effects increase divergence during ecological speciation, but linkage is not required

Posted on 6 Mar, 2013 by Jeremy Yoder

This post is a guest contribution by Dylan Goldade, Kathryn Theiss, and Chris Smith, from the Biology Department at Willamette University. See below for the coauthors’ afflilations and research interests.

In a famous address given on the hundredth anniversary of the publication of The Origin of Species, Ernst Mayr (Figure 1) critiqued the work of early 20th-Century population geneticists, including Fisher and Haldane, as ‘beanbag genetics’ (Provine 2004). Mathematical models of natural selection that consider only a single locus in isolation, Mayr argued, overlook the importance of epistatic interactions between loci. Very strong interactions between loci in the form of ‘coadapted gene complexes’, Mayr later argued, might play a major role in peripatric speciation; ‘genetic revolutions’ following population bottlenecks might allow small populations to move between two genetic equilibria.

Figure 1: Ernst Mayr in 1994

Ernst Mayr in 1994, after receiving an honorary degree at the University of Konstanz. Image from Meyer A. (2005).


Mayr foresaw that genome-level effects could be important in understanding the formation of new species. Although Mayr was almost monomaniacally focused on allopatric speciation, new simulation results produced by Sam Flaxman, Jeff Feder, and Patrik Nosil (Flaxman et al. 2013) suggest that ecological speciation is also more likely to occur in models that incorporate genome-level effects. However, contrary to the predictions made by a number of authors, linkage seems to play little role in facilitating speciation with gene flow.
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What we're reading

Posted on 1 Mar, 2013 by Jeremy Yoder

reading

As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen-time.
In the journals
Lindsey, H.A., Gallie, J., Taylor, S. & Kerr, B. 2013. Evolutionary rescue from extinction is contingent on a lower rate of environmental change. Nature 494: 463–467. doi: 10.1038/nature11879.

We allowed hundreds of populations of Escherichia coli to evolve under variable rates of increase in concentration of the antibiotic rifampicin. We then genetically engineered all com- binations of mutations from isolates evolved under lower rates of environmental change. By assessing fitness of these engineered strains across a range of drug concentrations, we show that certain genotypes are evolutionarily inaccessible under rapid environ- mental change.

Wright, K.M., Lloyd, D., Lowry, D.B., Macnair, M.R. & Willis, J.H. 2013. Indirect evolution of hybrid lethality due to linkage with selected locus in Mimulus guttatus. PLoS Biology 11: e1001497. doi: 10.1371/journal.pbio.1001497.

Here we show, using high-resolution genome mapping, that copper tolerance and hybrid lethality are not caused by the same gene but are in fact separately controlled by two tightly linked loci. We further show that selection on the copper tolerance locus indirectly caused the hybrid incompatibility allele to go to high frequency in the copper mine population because of hitchhiking.

Graur, D., Zheng, Y., Price, N., Azevedo, R.B.R., Zufall, R. a & Elhaik, E. 2013. On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution 1–43. doi: 10.1093/gbe/evt028.

The ENCODE Consortium aims to convince its readers that almost every nucleotide in the human genome has a function and that these functions can be maintained indefinitely without selection. ENCODE accomplishes these aims mainly by playing fast and loose with the term “function,” by divorcing genomic analysis from its evolutionary context and ignoring a century of population genetics theory, and by employing methods that consistently overestimate functionality, while at the same time being very careful that these estimates do not reach 100%.

In the blogosphere
Was J.P. Morgan’s “rogue trader” undone because he made a copy-paste error in Microsoft Excel?
Do nice folks finish last in academia?
Carl Zimmer describes how biologists tracked down a multidrug resistant bacterial strain in a National Institutes of Health hospital.

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Molecular Ecology views: This [spruce] bud's for you

Posted on 28 Feb, 2013 by Jeremy Yoder

Processing spruce buds for DNA collection, on the banks of the Skeena River, northern British Columbia. Photo courtesy Jill Hamilton.

Processing spruce buds for DNA collection by the banks of the Skeena River, northern British Columbia. Photo courtesy Jill Hamilton.


Jill Hamilton sends in her view of molecular ecology in action:

After a long day of clipping spruce buds from trees for DNA extraction there was a need to process the samples a bit further as we reached our sample sites way before bud flush (see additional photo of bud size). But pulling the little bits of green tissue from the protection of their bud scales night after night was never too onerous with a cold drink, an amazing landscape and a great field assistant/friend.

Continue reading →

Posted in Molecular Ecology views | 1 Comment