What we’re reading: The phylogenomics of peanut allergens, saving the world with (and from) evolution, and how to make better figures

reading - lectura

In the journals

Ratnaparkhe MB, T-H Lee, X Tan, X Wang, J Li, C Kim, LK Rainville, C Lemke, RO Compton, J Robertson, M Gallo, DJ Bertioli, and AH Paterson. 2014. Comparative and evolutionary analysis of major peanut allergen gene families. Genome Biology and Evolution. doi: 10.1093/gbe/evu189.

The peanut allergen genes are interspersed with low-copy genes and transposable elements. Phylogenetic analyses revealed lineage-specific expansion and loss of low-copy genes between species and homoeologs.

Carroll SP, P Søgaard Jørgensen, MT Kinnison, CT Bergstrom, RF Denison, P Gluckman, TB Smith, SY Strauss, and BE Tabashnik. 2014. Applying evolutionary biology to address global challenges. Science. doi: 10.1126/science.1245993.

Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens and pests that evolve too quickly, and the second from the inability of many valued species to adapt quickly enough.

Rougier NP, M Droettboom, PE Bourne. 2014. Ten simple rules for better figures. PLoS Computational Biology. 10(9): e1003833. doi: 10.1371/journal.pcbi.1003833.

A more accurate definition for scientific visualization would be a graphical interface between people and data. In this short article, we do not pretend to explain everything about this interface … Instead we aim to provide a basic set of rules to improve figure design and to explain some of the common pitfalls.

In the news

“Instead of processing your items in a normal a loop, we’ll show you how to process all your items in parallel, spreading the work across multiple cores.”

“As of last week, I have officially survived my first year as a tenure-track assistant professor!”

“There are no national statistics about how many people are giving up on academic science, but an NPR analysis of NIH data found that 3,400 scientists lost their sustaining grants between 2012 and 2013.”

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What we’re reading: Hyper-mutating symbionts, cichlid genomes, and active learning in biology class

A compulsive reader

In the journals

Remigi P, D Capela, C Clerissi, L Tasse, R Torchet, et al. 2014, Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer. PLoS Biology. 12(9): e1001942. doi: 10.1371/journal.pbio.1001942.

Following introduction of the symbiotic plasmid of Cupriavidus taiwanensis, the Mimosa symbiont, into pathogenic Ralstonia solanacearum we challenged transconjugants to become Mimosa symbionts through serial plant-bacteria co-cultures. We demonstrate that a mutagenesis imuABC cassette encoded on the C. taiwanensis symbiotic plasmid triggered a transient hypermutability stage in R. solanacearum transconjugants that occurred before the cells entered the plant.

Brawand D, CE Wagner, YI Li, M Malinsky, I Keller, et al. 2014. The genomic substrate for adaptive radiation in African cichlid fish. Nature doi: 10.1038/nature13726.

We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms.

In the news

“My big challenge in creating an active-learning lesson is not to decide what to teach but what to not teach.”

“If you have a tendency, like many overwhelmed individuals, to tell yourself that that you’ll get your important work done later — maybe at night or on the weekend — you increase your chance of procrastination during the day.”

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What we’re reading: Genomic selection scans, local adaptation, and the grass is actually pretty green on this side of the publishing fence


In the journals

Cadzow M, J Boocock, HT Nguyen, P Wilcox, TR Merriman and MA Black. 2014. A bioinformatics workflow for detecting signatures of selection in genomic data. Front. Genet. 5:293. doi: 10.3389/fgene.2014.00293.

Here we describe a basic workflow, constructed from open source tools, for detecting and examining evidence of selection in genomic data.

Leamy LJ, C-R Lee, V Cousins, I Mujacic, AJ Manzaneda, K Prasad, T Mitchell-Olds and B-H Song 2014. Large-scale adaptive divergence in Boechera fecunda, an endangered wild relative of Arabidopsis. Ecology and Evolution 2014 4:3175–3186. doi: 10.1002/ece3.1148.

… we assessed the genetic divergence of five quantitative traits in 10 populations of an endangered cruciferous species, Boechera fecunda, found in only several populations in each of two geographic regions (WEST and EAST) in southwestern Montana.

In the news

“More than 50 co-authors from four countries helped collect and analyze the viral sequences. Five of them contracted Ebola virus disease themselves and died.”

“We scientists may whinge about our journals, but they seem to be doing a better job across the board than in other academic fields.”

“The best way to learn how [science communication works] behind the scenes is to get behind the scenes, and to work for funding agencies or for publishers or to try working with the media. But when I do these things, some people make me feel that because I no longer work in a lab, I am now vastly inferior to people who still actively do research.”

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The #IcedBudgetChallenge: Tell Congress to thaw out funding for NSF and NIH!

So a friend nominated me in this viral scheme to raise funds for ALS research, about which you may have heard lately. I’m all in favor of finding a cure for ALS—my grandfather died of it—but I’m also pretty skeptical about raising funds for research one disease-specific social media campaign at a time. So I made my own challenge: I called my Congressional representatives to ask for better funding of NSF and NIH.

The full story is at Nothing in Biology Makes Sense—but I’ll also post the video here:

Really, I don’t care if you douse yourself in ice water or not, but everyone should make the calls. Except for a one-time bump from the 2009 economic stimulus, NSF hasn’t had a significant funding increase in a decade, and NIH hasn’t even kept up with inflation. Block out some time today, look up the numbers at house.gov and senate.gov, and ask for more money for basic science. Then spread the word with my lame pun of a hashtag: #IcedBudgetChallenge.

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What we’re reading: Genetic diversity and life history, evolutionary rescue, and scientists on social media

Sam Reading in Badlands

In the journals

Romiguier, J., P. Gayral, M. Ballenghien, A. Bernard, V. Cahais, A. Chenuil, Y. Chiari, R. Dernat, L. Duret, N. Faivre, E. Loire, J. M. Lourenco, B. Nabholz, C. Roux, G. Tsagkogeorga, A. A.-T. Weber, L. A. Weinert, K. Belkhir, N. Bierne, S. Glémin, and N. Galtier. 2014. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature. doi: 10.1038/nature13685.

The distribution of genetic diversity between species revealed no detectable influence of geographic range or invasive status but was accurately predicted by key species traits related to parental investment: long-lived or low-fecundity species with brooding ability were genetically less diverse than short-lived or highly fecund ones.

Orr, H. A., and R. L. Unckless. 2014. The population genetics of evolutionary rescue. PLoS Genetics. 10:e1004551. doi: 10.1371/journal.pgen.1004551.

Our analysis requires taking into account a subtle population-genetic effect (familiar from the theory of genetic hitchhiking) that involves “oversampling” of those lucky alleles that ultimately sweep to high frequency.

In the news

“If you want to know how often fitness trade-offs evolve under divergent selection (invariably), whether adaptation to a fitness peak typically involves fixation of few or many mutations (few), what the typical rate of substitution is during an adaptive walk, and much more, this book has the numbers.”

“The most-selected activity on both ResearchGate and Academia.edu was simply maintaining a profile in case someone wanted to get in touch … By comparison, Twitter, although used regularly by only 13% of scientists in Nature’s survey, is much more interactive: half of the Twitterati said that they use it to follow discussions on research-related issues, and 40% said that it is a medium for ‘commenting on research that is relevant to my field’ (compared with 15% on ResearchGate).”

“Kim was convinced that she had found the cause of her two diseases, but the only way to know for sure was to get the DNA of her LMNA gene sequenced to see if she had a mutation.”

“The first post doctoral position I was offered was for a fantastic and well-paying position directly related to my Ph.D. work, but I turned it down in no small part because when I did a Google search of the city alongside ‘LGBT’ what came up was a list of murders and shootings.”

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You can evolve there from here. And from here. And here …

Littorina saxatilis

Littorina saxatilis. Photo by Sergey Yeliseev.

If evolutionary history somehow reverted back to the “warm little pond” in which life began, and started over from almost-scratch, would the re-diversification of life end up, four billion years later, pretty much as we see it today? I think most evolutionary biologists would say, after noting that “pretty much as we see it today” is a mighty vague hypothesis statement, that it probably wouldn’t. Especially at the scale of millions of years, world-changing events happen by chance, making the odds pretty slim that a second four-billion year run would go all the way from the origin of life to a planet dominated by ape-descended life-forms who think wireless phones are a pretty neat idea.

On a smaller scale, though, it often does seem that evolutionary history repeats itself. Different populations of the same organism, encountering similar environments or the same natural enemies, adapt similarly—as, for example, in the repeated parallel changes of marine sticklebacks colonizing freshwater, or three different lizard species adapting to the same white sand dune formation. But when the traits that change in the course of adaptation are created by the collective action of many genes, it’s reasonable to think that changes in different subsets of those contributing genes might create similar changes in the visible trait, the phenotype.

As modern sequencing methods let us track genetic changes with greater precision, it’s possible to look for exactly that process—different genetic paths to the same adaptive result. A study just released online ahead of print in Molecular Ecology seems to have found such a case in populations of small snails.

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What we’re reading: Selection for heterozygosity in threatened seals, and testing Fst outlier tests


In the journals

Forcada J and Hoffman JI. 2014. Climate change selects for heterozygosity in a declining fur seal population. Nature. 511:462–465. doi: 10.1038/nature13542.

Variation in SAM [Southern Annular Mode of the Antarctic atmosphere] significantly affects most of the life cycle … During extreme positive SAM anomalies, mean juvenile survival, adult survival and fecundity declined by up to 37.1% (s.e.m. = 7.1%), 41.5% (5.1%) and 32.1% (8.5%) respectively. Survival of pre-breeders was inversely related to HL (Extended Data Fig. 2a), particularly in first-year females.

Lotterhos KE and MC Whitlock. 2014. Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests. Molecular Ecology, 23:2178–2192. doi: 10.1111/mec.12725.

On their best performance, however, the widely used methods had high false-positive rates for IBD and range expansion and were outperformed by methods that accounted for evolutionary nonindependence.

In the news

“It seems quite likely that observed height differences among populations will be partially genetic in nature, and due in part to differential selection, consist with our and Turchin et al’s results. However, to establish this as a scientific finding, rather than a plausible hunch requires much more work.”

“We reject Wade’s implication that our findings substantiate his guesswork. They do not.”

Want to code your own R package? Check out this online book-in-progress.

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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.”

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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.

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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?”

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