What we’re reading: Estimating linkage in resequencing data, genomics of host-parasite coevolution, and scientific work-life balance

Hammock Lounging

In the journals

Maruki, T., and M. Lynch. 2014. Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data. Genetics 197:1303–1313. doi: 10.1534/genetics.114.165514.

… we developed a maximum-likelihood estimator of linkage disequilibrium for use with error-prone sampling data. Computer simulations indicate that the estimator is nearly unbiased with a sampling variance at high coverage asymptotically approaching the value expected when all relevant information is accurately estimated.

Tellier, A., S. Moreno-Gámez, and W. Stephan. 2014. Speed of adaptation and genomic footprints of host-parasite coevolution under arms race and trench warfare dynamics. Evolution 68:2211–24. doi: 10.1111/evo.12427.

Our results suggest that deterministic models of coevolution with infinite population sizes do not predict reliably the observed genomic signatures, and it may be best to study parasite rather than host populations to find genomic signatures of coevolution, such as selective sweeps or balancing selection.

In the news

“I’m saying ‘no’ to ‘Would you like to chair this blah blah blah…’ and ‘yes’ to ‘Would you like to sit in this chair and drink a cocktail?’ And I’m enjoying my family and my life in a way that I haven’t been able to since…well, since I started graduate school back in 1999.”

“Normal working hours and time off aren’t just okay – they are important for productivity.”

“The idea is that when you do require(nothing) you express that you don’t need anything, and therefore nothing assumes you are fine just using the base package, so it detaches all other packages.”

“My advice to junior people is to get more than one idea in the system. Yes, you’ll have you favorite proposal, but you need to be floating more than that at all times. Two is better. Three is even better.”

RedditDiggMendeleyPocketShare and Enjoy
Posted in linkfest | Leave a comment

How many genes does it take to make a new species?

Gasterosteus aculeatus 1879.jpg


Gasterosteus aculeatus 1879” by Alexander Francis Lydon (1836-1917) – British fresh water fishes. Image via Wikimedia Commons.

Three-spined sticklebacks are speciation machines. When retreating glaciers exposed lakes and rivers around the coasts of northern North America and Eurasia, these armor-plated little fish colonized the new freshwater habitats from the ocean, and adapted to the threats and resources they found there. But colonists kept coming from the ocean, and sometimes they found not an empty lake or a population of sticklebacks like themselves, but unfamiliar fishes that ate some of the same things they did.

Competition between the new arrivals and their evolutionary cousins gave an advantage to fish that relied less on the resources they both used. And, eventually, in many of those freshwater lakes, there were two types of stickleback: one that made a living in the shallow limnetic zone of ponds, eating free-swimming plankton; and one in the deeper benthic zone, snapping up prey from the bottom sediment or off of rocks and vegetation. Across many different bodies of water where they’ve been found, benthic and limnetic sticklebacks mate mostly within their types, meeting the classical definition of separate species.

The specific genetic differences between freshwater sticklebacks and their oceanic ancestors have been dissected in detail—they mostly boil down to change at a single gene that reduced the bony armor plating in freshwater populations. Now, a study published recently in Nature has dissected the genetic differences between the benthic and limnetic forms, and it shows that the genetic basis of sticklebacks’ repeated ecological speciation has been quite a bit more complicated than their move from the ocean.

Continue reading

Posted in genomics, population genetics, quantitative genetics, speciation | Tagged , | 5 Comments

What we’re reading: resurrected rodent teeth, the genetic origin of sex, and what’s in your ANOVA?

Life Without Principle

In the journals

Harjunmaa E, K Seidel, T Häkkinen, E Renvoisé, IJ Corfe, A Kallonen, Z-Q Zhang, Alistair R. Evans, ML Mikkola, I Salazar-Ciudad, OD Klein, and & J Jernvall. 2014. Replaying evolutionary transitions from the dental fossil record. Nature. doi: 10.1038/nature13613.

By identifying development-based character inter-dependencies, we show how to predict morphological patterns of teeth among mammalian species. Finally, in vivo inhibition of sonic hedgehog signalling in Eda null teeth enabled us to reproduce characters deep in the rodent ancestry.

Geng S, P De Hoff, and JG Umen. 2014. Evolution of Sexes from an Ancestral Mating-Type Specification Pathway. PLoS Biology 12(7): e1001904. doi: 10.1371/journal.pbio.1001904.

Here we show that, contrary to predictions, a single conserved mating locus (MT) gene in volvocine algae—MID, which encodes a RWP-RK domain transcription factor—evolved from its ancestral role in C. reinhardtii as a mating-type specifier, to become a determinant of sperm and egg development in [Volvox] carteri.

In the news

“There is no dark corner of academic metrics to expose when the people you’re mocking are the ones least well positioned to respond.”

“It is everything a big idea paper should be – confident, persuasive, suggesting that simple tradeoffs may allow us to predict broad ecological patterns. And while with time I feel that some of the logic in the paper is flawed or at least unsupported, it definitely is a reminder of how exciting thinking big can be (and 1870 citations suggests others agree).”

“So really, what I’m asking is, exactly what hypotheses do you prefer to test when doing ANOVA with >1 factor?”

Posted in linkfest | Leave a comment

What we’re reading: The creosote-eating gut microbes of wood rats, the molecular taxonomy of bats’ diets, and drift in experimental evolution

Hammock Lounging

In the journals

Kohl, K. D., Weiss, R. B., Cox, J., Dale, C., Denise Dearing, M. (2014), Gut microbes of mammalian herbivores facilitate intake of plant toxins. Ecology Letters. doi: 10.1111/ele.12329.

Creosote toxins altered the population structure of the gut microbiome to facilitate an increase in abundance of genes that metabolise toxic compounds. In addition, woodrats were unable to consume creosote toxins after the microbiota was disrupted with antibiotics.

Burgar, J. M., Murray, D. C., Craig, M. D., Haile, J., Houston, J., Stokes, V. and Bunce, M. (2014), Who’s for dinner? High-throughput sequencing reveals bat dietary differentiation in a biodiversity hotspot where prey taxonomy is largely undescribed. Molecular Ecology. 23: 3605–3617. doi: 10.1111/mec.12531.

We used high-throughput sequencing (HTS) and bioinformatic analyses to phylogenetically group DNA sequences into molecular operational taxonomic units (MOTUs) to examine predator–prey dynamics of three sympatric insectivorous bat species in the biodiversity hotspot of south-western Australia. We could only assign between 4% and 20% of MOTUs to known genera or species, depending on the method used, underscoring the importance of examining dietary diversity irrespective of taxonomic knowledge in areas lacking a comprehensive genetic reference database.

In the news

“Harpak and Sella start from a premise that has been less widely-appreciated in the serial-transfer context: namely, that the other forces of evolution, including drift and demography, are also active in serial-transfer contexts.”

I love Science because it lets me be a child, to play in the dirt and laugh. I love Science because it lets me be a teenager, to rebel and defy the university and demand to borrow its car keys on the same day. I love Science because it lets me be an adult, responsible for machines that cost more than my house.”

Posted in linkfest | Leave a comment

What we’re reading: Experimental evolution of beetles’ immunity, adaptive introgression in mussels, and sexual harassment in the field

Summer afternoon

In the journals

Joop G., O. Roth, P. Schmid-Hempel, and J. Kurtz. 2014. Experimental evolution of external immune defences in the red flour beetle. Journal of Evolutionary Biology, 27: 1562–1571. doi: 10.1111/jeb.12406.

Intriguingly, we found indication for an interme- diate quinone secretion, as in unselected wild-type bee- tles, being closest to optimal and by such providing one of the rare examples for potential optimal immune defence.

Fraïsse, C., C. Roux, J. J. Welch, and N. Bierne. 2014. Gene flow in a mosaic hybrid zone: Is local introgression adaptive? Genetics 197:939–951. doi: 10.1534/genetics.114.161380.

Here we conduct a scan for unusual patterns of differentiation in a mosaic hybrid zone between two mussel species, Mytilus edulis and M. galloprovincialis. One outlying locus, mac-1, showed a characteristic footprint of local introgression, with abnormally high frequency of edulis-derived alleles in a patch of M. galloprovincialis enclosed within the mosaic zone, but low frequencies outside of the zone.

Clancy K.B.H., R.G. Nelson, J.N. Rutherford, K. Hinde. 2014. Survey of Academic Field Experiences (SAFE): Trainees Report Harassment and Assault. PLoS ONE 9(7): e102172. doi: 10.1371/journal.pone.0102172.

Women trainees were the primary targets; their perpetrators were predominantly senior to them professionally within the research team. Male trainees were more often targeted by their peers at the research site.

In the news

“I only started this blog in 2009, and what I didn’t realize until 2010 was that a whole bunch of super useful TT search advice-related posts were written in 2007 and 2008 by some of your favorite faculty bloggers.”—And The Spandrel Shop has launched a corresponding pre-tenure blog carnival.

“A trial of double-blind peer reviewing is going on at Nature Publishing Group (NPG), which owns Nature. Since June 2013, Nature Geoscience and Nature Climate Change have offered double-blind peer review as an option for those submitting manuscripts.”

“He suspected that only a few scientists are able to publish papers year in, year out. But the finding that less than 1% do so surprised him, he says.”

Posted in linkfest | Leave a comment

Peer review, reviewed

Partners in crime

Revise and resubmit.

Rebecca Schuman, who has almost single-handedly turned Slate into one of best big websites for coverage of the many trials and tribulations of academia, turns to peer review for scholarly journals, in which an author’s academic peers volunteer to weigh in on whether a manuscript is worthy of publication. Schuman discusses the problems of of both how long the process takes—routinely more than a year, especially with the back-and-forth of revisions—and tone:

Think of your meanest high school mean girl at her most gleefully, underminingly vicious. Now give her a doctorate in your discipline, and a modicum of power over your future. That’s peer review.

And she suggests something that might sound familiar to those of us who hang out in the evolutionary ecology blog-o-verse: enforced reviewing reciprocity.

… what if in order to be eligible to submit an academic article to a journal, a scholar had first to volunteer to review someone else’s article for that same journal? … You want to publish and not perish? First you have to earn that right by making a punctual, non-petty investment into the publishing enterprise.

Continue reading

Posted in peer review, science publishing | 6 Comments

What we’re reading: Sexual selection and fish placentas, SNPs versus observational pedigrees, and the stupidest statement ever on replication

Reading

In the journals

Pollux BJA, RW Meredith, MS Springer, DN Reznick. 2014. The evolution of the placenta drives a shift in sexual selection in livebearing fish. Nature. doi: 10.1038/nature13451.

We show that post-zygotic maternal provisioning by means of a placenta is associated with the absence of bright coloration, courtship behaviour and exaggerated ornamental display traits in males. Furthermore, we found that males of placental species have smaller bodies and longer genitalia, which facilitate sneak or coercive mating and, hence, circumvents female choice.

Bérénos C, PA Ellis, JG Pilkington, and JM Pemberton. 2014. Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches. Molecular Ecology, 23: 3434–3451. doi: 10.1111/mec.12827.

We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics studies in natural populations.

In the news

“Whether they mean to or not, authors and editors of failed replications are publicly impugning the scientific integrity of their colleagues.”

“Trying to prevent anyone from replicating your work, however, IS a knock on integrity. On the scientific integrity of that person who does not wish anyone to try to replicate his or her work, that is.”

“We are pleased to report that Molecular Ecology is now the first journal to surpass 1000 data packages in Dryad!”

“It’s okay to be competitive. It’s okay to strive to be the leader. But don’t define your success that way or you will undoubtedly spend more time chasing windmills than developing your career.”

Posted in linkfest | Leave a comment

What we’re reading: Fish gut microbes, Denisovan origins of Tibetan altitude adaptation, and the curious costs of journal subscriptions

Konzentration auf Strand

In the journals

Bolnick, D. I., L. K. Snowberg, P. E. Hirsch, C. L. Lauber, R. Knight, J. G. Caporaso, and R. Svanbäck. 2014. Individuals’ diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch). Ecology Letters. 17:979–987. doi: 10.1111/ele.12301.

Unexpectedly, in most cases individuals with more generalised diets had less diverse microbiota than dietary specialists, in both natural and laboratory populations. This negative association between diet diversity and microbial diversity was small but significant, and most apparent after accounting for complex interactions between sex, size and diet.

Huerta-Sánchez, E., X. Jin, Z. Bianba, B. M. Peter, N. Vinckenbosch, Y. Liang, X. Yi, M. He, M. Somel, P. Ni, B. Wang, X. Ou, J. Luosang, Z. X. P. Cuo, K. Li, G. Gao, Y. Yin, W. Wang, X. Zhang, X. Xu, H. Yang, Y. Li, J. Wang, J. Wang, and R. Nielsen. 2014. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature, doi: 10.1038/nature13408.

… the length of the haplotype, and the fact that it is not found in any other populations, makes it unlikely that the haplotype sharing between Tibetans and Denisovans was caused by incomplete ancestral lineage sorting rather thanintrogression.

In the news

“Typically ‘gene’ is misused most when followed by ‘for.'”

“Some universities are paying nearly twice what universities of seemingly similar size and research output pay for access to the very same journals.”

“[Wright] basically thought that a medium size population would have a balance of drift and selection that it would allow the population to drift away from an adaptive peak and randomly explore the adaptive landscape.”

Posted in linkfest | Leave a comment

Bayesian Markov-chain Monte Carlo in population genetics

IMGP3678

Bayes’s Theorem in neon. Photo by Matt Buck.

This is a guest post by Arun Sethuraman, a postdoctoral associate with Jody Hey, studying statistical models for divergence population genetics in the Department of Biology at Temple University. You can also find him on Twitter, and on his short story blog.

Prompted by the great response to my talk at Evolution 2014 on “Parallel MCMC and inference of ancient demography under the IM model”, I wanted to throw together a quick and dirty review of Bayesian MCMC, and why and how it works for the uninitiated, as well as highlight some of the important problems surrounding the method and its implementation.

Continue reading

Posted in methods, population genetics, software | Tagged , | 1 Comment

#Evol2014 in tweets

I think it’s fair to say that I was a pioneer of Twitter at the Evolution meetings—back when I set up the website for Evolution 2009, I created an account for the conference, and signed up for one myself. I think maybe six unique people ever tweeted the #Evol2009 hashtag, and they mostly used it to exchange notes about where to find better coffee than what the University of Idaho catering service provided.

Five years later, at this year’s iteration of the meeting in Raleigh, North Carolina, Evolution was all over Twitter. Far from being worried about over-publicizing preliminary work, attendees broadcast everything from their talk slides to mockery of the tiny, absurd protest outside the convention center.

When I ran a search for the meeting hashtag, #Evol2014, on ScraperWiki, I ended up with a file containing almost 9,000 tweets (including retweets) from 20 to 24 June. Here’s what they looked like on an hourly basis:

Evol2014_twitter_infographic

I may play around with some additional analysis of this dataset, but I’m not sure when I’ll have time—so I thought I’d use it as an excuse to (finally) try out Figshare. If your interest is piqued, you can download the original data here, and see what you can do with it.

Yoder, JB. 2014. #Evol2014 in tweets. figshare. doi: 10.6084/m9.figshare.1083874

Posted in blogging, community, conferences | Tagged , | 3 Comments