Want to see us in your Facebook News Feed? You should probably do this one weird thing.

Click this, please.

Click this, please.

A whole lot of folks—875!—have “liked” the Molecular Ecologist page on Facebook, which ought to mean that all those people see new posts from the site right in their Facebook News Feed. But we’ve found that our Facebook posts are typically seen by a lot fewer than 875 folks—and the number seems to be declining. This may be a symptom of something happening with Facebook pages in general—fewer posts are reaching the people who’ve “liked” pages, possibly because there are just more pages to “like.” The solution offered by FB is to pay for placement in people’s news feeds, but this “promotion” can reach a lot of people who really aren’t interested, and that’s not why we have a Facebook page in the first place.

If you want to ensure that posts from The Molecular Ecologist make it into your News Feed, there is one thing you can do: Turn on the “get notifications” option on our page. This is illustrated above—it’s in a drop-down menu attached to the “Like” button itself. Selecting “get notifications” tells Facebook’s News Feed algorithm to give our posts priority in your feed.

And, if you want a less convoluted option, you can also receive Molecular Ecologist posts on Twitter, via RSS subscription, and even by e-mail, using the tools in our sidebar.

(Hat tip to the Facebook page for Small Pond Science for pointing me toward that recent article about the declining audience for FB pages. Ironic sourcing? Yes, maybe.)

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Crowd-sourcing natural history

Lygopodium palmatum

What I think of as my first “real” science job was a year I spent in Pittsburgh, interning for the Western Pennsylvania Conservancy. One of my most enjoyable duties was assisting a WPC ecologist on systematic surveys of plant diversity at a series of study plots out in the mountains. If I recall correctly, the point of the project was actually to assess collateral damage done to spring ephemerals and other understory plants by various herbicides that timber companies wanted to use to prevent striped maple from taking over recently clear-cut tracts of forest.

But before I could be much use out in the woods, I needed to learn to identify the plant species we’d be tracking. So my boss took me down to the Carnegie Museum of Natural History, where I spent a few afternoons leafing through specimen sheets at the herbarium. It wasn’t the same thing as seeing actual, live plants in the field, but it gave me a head start on learning the distinguishing characteristics of the species we were most likely to find.

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Posted in citizen science, community, methods | 7 Comments

What we’re reading: Arabidopsis vs slugs, the long reach of a GWAS hit, and post-pub peer review comes into its own?


In the journals

Falk, K. L., J. Kästner, N. Bodenhausen, K. Schramm, C. Paetz, D. G. Vassão, M. Reichelt, D. von Knorre, J. Bergelson, M. Erb, J. Gershenzon, and S. Meldau. 2013. The role of glucosinolates and the jasmonic acid pathway in resistance of Arabidopsis thaliana against molluscan herbivores. Molecular Ecology. 1188–1203.

Our data highlight the function of well-known antiherbivore defence pathways in resistance against slugs and snails and suggest an important role for the diurnal regulation of defence metabolites against nocturnal molluscan herbivores.

Smemo, S., J. J. Tena, K.-H. Kim, E. R. Gamazon, N. J. Sakabe, C. Gómez-Marín, I. Aneas, F. L. Credidio, D. R. Sobreira, N. F. Wasserman, J. H. Lee, V. Puviindran, D. Tam, M. Shen, J. E. Son, N. A. Vakili, H.-K. Sung, S. Naranjo, R. D. Acemel, M. Mazanares, A. Nagy, N. J. Cox, C.-C. Hui, J. L. Gomez-Skarmeta, and M. A. Nóbrega. 2014. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature. doi: 10.1038/nature13138.

Genome-wide association studies (GWAS) have reproducibly assoc- iated variants within introns of FTO with increased risk for obesity and type 2 diabetes (T2D). Although the molecular mechanisms linking these noncoding variants with obesity are not immediately obvious, subsequent studies in mice demonstrated that FTO expression levels influence body mass and composition phenotypes. However, no direct connection between the obesity-associated variants and FTO expression or function has been made. Here we show that the obesity-associated noncoding sequences within FTO are functionally connected, at megabase distances, with the homeobox gene IRX3.

In the news

“In a new policy, PLoS requires PIs to cut and deposit one of their fingers every time they submit a paper, or at least that is the sense you get after reading the reactions about ‘new policy’ online.”

“… consider that one could easily have applied nearly all of the arguments people having been making in the blogosphere these past two weeks to that dastardly scientific timesink that is the common Methods sections.”

“The papers’ comment threads on PubPeer have attracted some 40000 viewers. It’s hardly surprising they caught issues that three overworked referees and a couple of editors did not.”

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The broom of the system: Tracking soft selective sweeps in bacteria colonizing the gut

ποντίκι / μυς, mouse (Mus musculus) by George Shuklin

Evolution inside this mouse’s gut (and yours) is more complex than you might think.

A growing body of population genetic evidence suggests that adaptive evolutionary change often proceeds via soft selective sweeps, in which beneficial mutations on multiple genetic backgrounds—and potentially at multiple loci—all increase in frequency, but none achieve fixation. This process has been directly tracked in populations of HIV within patients receiving antiretroviral drugs; and now a recent paper in PLOS Genetics finds that soft sweeps are integral in the adaptation of bacteria to the mammalian gut.

João Barroso-Batista and colleagues at the Instituto Gulbenkian de Ciência and Instituto de Tecnologia Química e Biológica in Portugal first treated mice with streptomycin to clear their guts of bacteria, then fed them cultures of Escherichia coli that were genetically uniform—except that half the E. coli cells in the culture had been engineered to produce a blue fluorescent protein, and half had been engineered to produce a yellow fluorescent protein. Any adaptation to the mouse guts would have to occur via new mutation, which might pop up in either a blue or a yellow cell. If a single mutation made that one cell so successful that its descendants entirely dominated the gut, the authors would be able to tell—by checking the color of the host mouse’s poop.

Yes, you read that correctly.

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What we’re reading: A single gene for Batesian mimicry, the genetics of interspecies incompatibility, and further debate over data sharing

book reading

In the journals

Kunte K., W. Zhang, A. Tenger-Trolander, D. H. Palmer, A. Martin, R. D. Reed, S. P. Mullen, and M. R. Kronforst. 2014. doublesex is a mimicry supergene. Nature. doi: 10.1038/nature13112.

Using an integrative approach combining genetic and association mapping, transcriptome and genome sequencing, and gene expression analyses, we show that a single gene, doublesex, controls supergene mimicry in Papilio polytes.

(See also commentary by David Loehlin and Sean Carroll.)

Fraïsse C., J. A. D. Elderfield, and J. J. Welch. 2014. The genetics of speciation: are complex incompatibilities easier to evolve? J. Evolutionary Biology. doi: 10.1111/jeb.12339.

Experimental crosses show that such Dobzhansky–Muller incompatibilities (DMIs) are often complex (involving alleles at three or more loci) and asymmetrical (such that reciprocal introgressions have very different effects on fitness). One possible explanation is that asymmetrical and complex DMIs are ‘easier to evolve’, because they block fewer of the possible evolutionary paths between the parental genotypes.

In the news

“I’d like to think that people want to work with me because of what I can bring to the table other than my data, but I’m not keen on testing that working hypothesis.”

“So I say suck it up, share the data behind the paper, manage your data well, and let’s all get on with our lives.”

“Ask anyone in academics whether you’d rather have 6 citations from awesome papers or 6 awesome papers and 100% of them will take the papers.”

“This is an R wrapper to the NOAA climate data API.”

“I would like to place a vertical bar next to all the tips descended for a node that I specify [on my phylogeny]. How do I do this?”

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2014 NGS Field Guide: Resistance is Futile (mostly, at least for a while)

Alineando secuencias (1)

Photo by Shary.

This year, to introduce the 2014 update to his Next Generation Sequencing Field Guide—perennially our most-accessed community resource—Travis Glenn has a bit more to say than just what goes in the tables. So here it is as a guest post!

Welcome to the 2014 update of the NGS Field Guide. Previously, I have presented the data & left the interpretation of those data to the readers, other than my “grades” about the utility of specific platforms for specific applications (i.e., Tables 1a, 1b, and 1c). However, many of the people that I have corresponded with have asked me to cut to the chase and just make a recommendation. So, by popular demand, in this year’s edition I am being much more direct about my recommendations.

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Posted in howto, methods, next generation sequencing | Leave a comment

What we’re reading: Sex and the single endogenous retrovirus, extinction by hybridization, and the PLOS data-sharing policy

Read a book

In the journals

Jalasvuori M & J Lehtonen. 2014. Virus epidemics can lead to a population-wide spread of intragenomic parasites in a previously parasite-free asexual population. Molecular Ecology. 23(5):987–991. doi: 10.1111/mec.12662.

Endogenous retroviruses are retroviruses that have integrated to the germ line cells and are inherited thereafter vertically. They can also replicate within the genome similarly to retrotransposons as well as form virus particles and infect previously uninfected cells. This highlights the possibility that endogenous retroviruses could play a role in the evolution of sexual reproduction.

Kleindorfer S, JA O’Connor, RY Dudaniec, SA Myers, J Robertson, & FJ Sulloway. 2014. Species collapse via hybridization in Darwin’s tree finches. The American Naturalist. 183(3):325-341. doi: 10.1086/674899.

The results presented here go to the heart of evolutionary biology: by what criteria do we denote species, and by what criteria do new species form or collapse? Here we present evidence that three sympatric species of Darwin’s tree finches in the 1900s have collapsed, under conditions of hybridization, into two species by the 2000s.

In the news

“Data should be in the form in which it was originally collected, before summarizing, analyzing or reporting.” —The PLOS journals are instituting a sweeping new data-sharing policy that appears to require sharing “raw” data. This has made some people very angry, while others are all in favor. But regardless, that data archiving mandate won’t be a panacea.

“Why filter and not just let anybody publish whatever they want?” —A nice multi-part discussion of the how’s and why’s of peer review.

“… you should contact several POs from different programs to put your name on their radar.” —Why you should probably be angling to sit on an NSF review panel, and applying for a CAREER grant.

“I can, at least in principle, imagine a creationist professor who taught the contents of a microbiology curriculum, complete with the common descent of life on Earth, and never breathed a word of his personal beliefs in the classroom.” —Can a young-Earth creationist be trusted to teach an introductory biology course at Jeremy’s alma mater?

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What’s more isolating—environmental distance or … plain old distance?


We molecular ecologists spend a lot of time thinking about how we can differentiate the effects of natural selection acting on populations in different environments—local adaptation—from the simple isolating effects of, well, being in different places—isolation-by-distance. There’s a considerable literature of studies using genetic data to try and make that differentiation, and the very first paper of 2014 in the journal Evolution was a review that tries to extract some broad trends from that literature.

Jason Sexton, Sandra Hangartner, and Ary Hoffman searched Google Scholar and the Web of Science for papers estimating gene flow rates with respect to geography and environmental variation. They filtered the results list to include only field studies on natural populations outside hybrid zones, using neutral genetic markers to estimate gene flow—which left 110 papers that were relevant for the question of how locally variable selection interacts with gene flow.

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What we’re reading: estimating relatedness and inbreeding, the evolution of influenza, and a new spin on p-values

Dr. Scot Brown's Book Reading

In the journals

Wang J. 2014. Marker-based estimates of relatedness and inbreeding coefficients: an assessment of current methods. J. Evol. Biol. 27:518–530. doi: 10.1111/jeb.12315.

… F and r estimates can be misleading and become biased and marker dependent when a sample containing a high proportion of highly inbred and/or closely related individuals is used as reference.

Worobey M, G-Z Han, A Rambaut. 2014. A synchronized global sweep of the internal genes of modern avian influenza virus. Nature. doi: 10.1038/nature13016.

Here we show that explicitly allowing [influenza A virus] host lineages to have independent rates of molecular evolution is necessary for reliable phylogenetic inference of IAV and that methods that do not do so, including ‘relaxed’ molecular clock models9, can be positively misleading.

In the news

“The irony is that when UK statistician Ronald Fisher introduced the P value in the 1920s, he did not mean it to be a definitive test.” —So how then should we judge statistical significance?

“I make the drawings on a small whiteboard and record it with my iPhone.” —You, too, can make a whiteboard movie.

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What we’re reading: Phylogenetic analyses of diversification, how HIV crosses fitness valleys, and gorgeous science visualizations

Love For Books

In the journals

Morlon, H. 2014. Phylogenetic approaches for studying diversification. Ecology Letters. doi: 10.1111/ele.12251.

A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment.

Da Silva, J., and S. K. Wyatt. 2014. Fitness valleys constrain HIV-1’s adaptation to its secondary chemokine coreceptor. J. Evol. Biol. doi: 10.1111/jeb.12329.

We have identified four fitness valleys from a previous study of fitness epistasis in adaptation to CXCR4 and use estimates of the within-patient variance Ne for different patient treatment statuses and infection stages (conditions) to estimate times to cross the valleys.

In the news

Cortex in Metallic Pastels represents a stylized section of the cerebral cortex, in which axons, dendrites, and other features create a scene reminiscent of a copse of silver birch at twilight. ” —Have you seen the winners of the AAAS/NSF 2013 International Science and Engineering Visualization Challenge yet?

“Analyses like this are bound to come up with results that look like a caricature, since they are obtained in much the same way that a caricature is drawn, by finding and highlighting the most extreme and distinctive aspects.” —A cautionary note about clustering algorithms.

“When it comes to science, online news outlets are more important than ever, but newspapers are still key. … But what struck me was the importance of television.” —Breaking down a new NSF report on public understanding of and support for scientific research.

“If the ultimate goal is to evaluate a person’s true overall role as a scientist, I think we should be considering how they communicate with all people not just other scientists.” —A proposed “influence metric” would combine your h-index, social media followers, and press mentions.

“It is not hard to peddle incoherent math to biologists, many of whom are literally math phobic. … Similarly, it isn’t hard to fool mathematicians into believing biological fables.” —What can happen when you mix math and biologists.

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