What we’re reading: A guide to Bioconductor, Latin American admixture, and the sordid truth about academic job hunting

In the journals

Lawrence M., M. Morgan. 2014. Scalable genomics with R and Bioconductor. arXiv:1409.2864.

This paper reviews strategies for solving problems encountered when analyzing large genomic data sets and describes the implementation of those strategies in R by packages from the Bioconductor project.

Ruiz-Linares A., K. Adhikari, V. Acuña-Alonzo, M. Quinto-Sanchez, C. Jaramillo, et al. 2014. Admixture in Latin America: Geographic structure, phenotypic diversity and self-perception of ancestry based on 7,342 individuals. PLoS Genetics. 10(9): e1004572. doi: 10.1371/journal.pgen.1004572.

Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry.

In the news

“If you say it works, then show us data. Anecdotes are subject to suspicion.”

“Academics lucky enough to be on the tenure track rarely—let’s just round down to never—have a choice about where they live. Their home for the rest of their lives is dependent entirely on which departments can hire in which specialties in a given year.”

“Ever since joining social media I’ve been bemusedly struck by those people who choose to put “Doctor” or “PhD” or even “Professor” in their handles and blog titles- whether they go by a pseudonym or not. Now, of course, I am thinking about whether they were in a boundary condition when they came up with those identifiers.”

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What we’re reading: Bayesian phylogenetics for whole genomes and coevolutionary interactions in epidemiology

In the journals

Aberer A.J., K. Kobert, and A. Stamatakis. 2014. ExaBayes: Massively parallel Bayesian tree inference for the whole-genome era. Mol. Biol. Evol. 31(10): 2553-2556. doi: 10.1093/molbev/msu236.

Modern sequencing technology now allows biologists to collect the entirety of molecular evidence for reconstructing evolutionary trees. We introduce a novel, user-friendly software package engineered for conducting state-of-the-art Bayesian tree inferences on data sets of arbitrary size.

Kodaman N., R.S. Sobota, R Mera, B.G. Schneider, and S.M. Williams. 2014. Disrupted human–pathogen co-evolution: a model for disease. Frontiers in Genetics. 5:290. doi: 10.3389/fgene.2014.00290.

We suggest that disrupted co-evolution between a pathogen and its human host can explain variation in disease outcomes, and that genome-by-genome interactions should therefore be incorporated into genetic models of disease caused by infectious agents

In the news

“There is a fundamental and culturally learned power imbalance between men and women, and it follows us into the workplace. The violence born of this imbalance follows us also. We would like to believe that it stops short of following us into the laboratory and into the field — but it does not.”

“Our students are counting on us to create an environment that enables their success. Safety always comes first. Safety requires an aware environment and respectful attitude in the workplace. The workplace includes the field.”

“Amid a wave of recent journal article retractions, researchers are taking to social media to discuss a perennial favourite: a three-year-old paper looking at the relationship between a journal’s impact factor and its retraction frequency.”

“I recommend that we drop the preproposals, go to a single full proposal a year, and as a community commit to careful review of the adhoc proposals we receive.”

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Fishing for genetic signals of adaptation

One of the biggest promises of modern DNA sequencing methods is the ability to track the adaptation of living populations at a fine genetic scale, in essentially real time. It’s already been done in a number of experimental evolution systems: collect lots of DNA sequence data from a population, subject that population to selection, then sequence its selected descendants and compare them to the pre-selection sequences to identify genetic variants that became more common over the course of adaptation. More and more, it’s getting to be possible to do that in the—I would say—more interesting case of natural populations responding to selection by conditions we may not even know with any specificity. A paper in the latest issue of Molecular Ecology is a nice example of the possibilities from an in nature “evolve and re-sequence” study—but it also shows how much work will be necessary to truly realize the promise of the approach.

The paper, by Vincent Bourret, Mélanie Dionne, and Louis Bernatchez at the Université Laval and the Ministère des Forêts, de la Faune, et de Parcs in Québec, Canada, tests for adaptive genetic change over the course of a single generation in Atlantic salmon. Salmon are interesting as an economically important species, but their lifestyle also makes them particularly suitable for fine-scaled studies of adaptation.

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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

Book

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

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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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