What we’re reading: A meta-analysis of meta-analyses, plants’ cytoplasmic genomes, and science under political attack

In the journals

Koricheva, J. and J. Gurevitch. 2014. Uses and misuses of meta-analysis in plant ecology. Journal of Ecology, 102: 828–844. doi: 10.1111/1365-2745.12224.

We found many cases of imprecise and inaccurate usage of the term ‘meta-analysis’ in plant ecology, particularly confusion between meta-analysis and vote counting and incorrect application of statistical techniques designed for primary studies to meta-analytical data, without recognition of the violation of statistical assumptions of the analyses.

Bock, D.G., R.L. Andrew, and L.H. Rieseberg. 2014. On the adaptive value of cytoplasmic genomes in plants. Molecular Ecology, 23: 4899–4911. doi: 10.1111/mec.12920.

Is DNA variation maintained in organelle genomes selectively neutral? The answer to this question has important implications for many aspects of ecology and evolution. While traditionally the answer has been ‘yes’, recent studies in animals have shown that, on the contrary, mitochondrial DNA polymorphism is frequently adaptive. In plants, however, the neutrality assumption has not been strongly challenged.

In the news

“The blackboard-centered classroom offers more than pedagogical efficiency; it also offers an effective set of teaching possibilities. … The teacher is not the focus of the class but rather a lens through which the lesson is created and clarified.”

“… although humanity as a whole may manage in an evolving world, failure to moderate our use of chemical agents will mean a future of real, individual people sickened by un-killable bacteria and left hungry by impervious agricultural pests.”

“My options seemed obvious: don’t respond to an obviously ill-intentioned inquiry and risk looking guilty, or respond and hopefully discourage Hunter from writing the article in the first place (after all, why bother writing it without the concluding ‘gotcha’?). So I wrote Hunter back. I don’t have to summarize what I wrote here, because a week later she essentially reprinted my email in its entirety.”

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What we’re reading: QTLs of pine growth, climate-niche evolution, and the shape of Twitter conversations

In the journals

Li Z., H.R. Hällingback, S. Abrahamsson, A Fries, B.A. Gull, M.J. Sillanpää and M.R. García-Gil. 2014. Functional multi-locus QTL mapping of temporal trends in Scots pine wood traits. G3: Genes | Genomes | Genetics. doi: 10.1534/g3.114.014068.

Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 – 9 timepoints, 91 – 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP) and single nucleotide polymorphism (SNP) markers.

Lawson A.M. and J.T. Weir. 2014. Latitudinal gradients in climatic-niche evolution accelerate trait evolution at high latitudes. Ecology Letters. 17: 1427–1436. doi: 10.1111/ele.12346.

We then tested whether divergence of the climatic-niche was associated with evolution in traits important in ecological differentiation (body mass) and reproductive isolation (song), and found that climatic divergence is associated with faster rates in both measures.

In the news

“If a topic is political, it is common to see two separate, polarized crowds [of Twitter users] take shape. They form two distinct discussion groups that mostly do not interact with each other. … The participants within each separate group commonly mention very different collections of website URLs and use distinct hashtags and words.”

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How many markers does it take to make a dataset “genomic”?

One size fits all. Welcome to the 80's

Actually, no. (Flickr: Stephan van Es)

A new paper in Ecology Letters by Matthew Fitzpatrick and Stephen Keller proposes to use some a class of statistical methods developed for understanding the distribution of species in different environments to understand the distribution of genetic variants in different environments. It’s an interesting idea, and a cool possible point of cross-pollination between the emerging field of landscape genomics and the more established field of community ecology. But there was one sentence that got my dander up:

In analyses, we have run on a computer with a 2.95 GHz quad-core processor, [this analysis method] took 0.5 h to analyse 2314 SNP loci, which is not unreasonable compared to other genetic analysis methods for detecting local adaptation.

Half an hour to analyze more than 2,000 genetic markers might sound “not unreasonable” to the authors, but if the computation time necessary for their analysis scales linearly with the number of markers, that implies a run time of 500 hours—almost 21 days—for a 2 million SNP dataset such as the one I’ve been lucky to play with in my postdoctoral research. (And, depending on how exactly the method incorporates data from multiple loci, computation time might increase quite a bit faster than linearly with additional markers.) Yes, we’d hope to have more powerful computing resources for a larger dataset, and maybe the analysis can be parallelized to spread the work across many linked computer processors—but that is still not what I’d call an efficient analysis. For comparison, a much simpler genotype-environment association scan I did with 2 million SNPs in 200 lines of Medicago truncatula took about 8 hours, if I recall correctly.

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Posted in association genetics, genomics, next generation sequencing, population genetics, software | 5 Comments

House science committee is digging for dirt in NSF’s confidential records of peer review

ScienceInsider reports that aides for the U.S. House Committee on Science, Space, and Technology have been spending the summer digging through records of grant the grant review process that the National Science Foundation usually keeps confidential:

The Republican aides were looking for anything that Representative Lamar Smith (R–TX), their boss as chair of the House Committee on Science, Space, and Technology, could use to support his ongoing campaign to demonstrate how the $7 billion research agency is “wasting” taxpayer dollars on frivolous or low-priority projects, particularly in the social sciences. The Democratic staffers wanted to make sure that their boss, Representative Eddie Bernice Johnson (D–TX), the panel’s senior Democrat, knew enough about each grant to rebut any criticism that Smith might levy against the research.

The article describes an “escalating” “feud” between NSF’s allies on the committee (all Democrats) and the Republican chair. But, as I noted when the first rumblings of this “feud” started, it’s not nearly so two-sided as that language implies.

It looks like Republicans are bent on making NSF into the next National Endowment for the Arts. After years of ginned-up controversy about specific, often deliberately mis-read, works of art, NEA’s funding in 2012 was less than it was in 1979—and that’s without adjusting for inflation.

Smith doesn’t care a whit for scientific integrity or the quality of the grant review process—he’s looking for any excuse to reduce and eliminate the already stingy Federal support of basic science.

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What we’re reading: Sorting out whole-genome duplication, adaptation without tradeoffs, and is science leaving its logistic growth phase?

In the journals

McGrath CL, J-F Gout, P Johri, TG Doak, and M Lynch. Differential retention and divergent resolution of duplicate genes following whole-genome duplication. 2014. Genome Res. 24: 1665-1675. doi: 10.1101/gr.173740.114.

Finally, multiple sources of evidence indicate that [Paramecium] sexaurelia diverged from the two other lineages immediately following, or perhaps concurrent with, the recent WGD, with approximately half of gene losses between P. tetraurelia and P. sexaurelia representing divergent gene resolutions (i.e., silencing of alternative paralogs), as expected for random duplicate loss between these species.

McGee LW, EW Aitchison, SB Caudle, AJ Morrison, L Zheng, et al. 2014. Payoffs, not tradeoffs, in the adaptation of a virus to ostensibly conflicting selective pressures. PLoS Genetics 10(10): e1004611. doi: 10.1371/journal.pgen.1004611.

We selected for individual mutations under fluctuating selective pressures for a ssDNA microvirid bacteriophage by alternating selection for increased growth rate with selection on biophysical properties of the phage capsid in high-temperature or low-pH conditions. Surprisingly, none of the seven unique mutations identified showed a pleiotropic cost; they all improved both growth rate and pH or temperature stability, suggesting that single mutations even in a simple genetic system can simultaneously improve two distinct traits.

In the news

“So, this is an attempt to compile a list of videos that people have found helpful for teaching about concepts typically covered in ecology courses (or the ecology section of courses like Intro Bio).”

“… many people around the world carry potentially harmful parasites, from tapeworms to treponema. Shooting these up your anus is a bad idea.”

“Thus, the proportion of scientists relative to the total human population has been increasing for decades, if not centuries. Price makes the startling but obvious outcomes of this observation very clear: either everyone on earth will be a scientist one day, or the growth rate of science must decrease from its previous long-term trends.”

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We’re looking for a few good Molecular Ecologists (UPDATED)

Update, 6 October: Thanks to everyone who has written in to apply for a position! I’ll try to respond to your inquiries in the next day or so; we’ll continue to accept applications until next Monday, 13 October before making any final decisions. —Jeremy

The Molecular Ecologist is seeking new regular contributors to join our community of commenters discussing population genetics in ecology and evolutionary biology.

We are interested in contributors with expertise and experience in our core topic, the applications of genetic data in understanding the past and future of living populations. Preference is given for senior graduate students, postdoctoral researchers, and other working scientists who can discuss basic science on a level that engages our core community of research biologists. Ideal candidates will also be interested in explaining fundamental molecular ecology concepts to the general public.

Successful candidates will recieve a small stipend in exchange for meeting posting goals over a 6-month term, with the option to renew pending availability and satisfactory performance.

To apply, please e-mail a brief cover letter explaining why you want to write for The Molecular Ecologist, with a writing sample, to Jeremy Yoder at jbyoder@gmail.com.

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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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Posted in adaptation, association genetics, genomics | Tagged | 1 Comment

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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