Haldane’s Sieve

Haldane_Sieve_betterThis week we have a guest post by Graham Coop and Joe Pickrell. Here, Graham [GC] and Joe [JKP] answer a few questions we had about the development and future of their blog, Haldane’s Sieve. If you’re interested in population genetics it’s definitely worth your time to take a look at and follow the blog. We would also like to hear what the readers of the The Molecular Ecologist think of Haldane’s Sieve and its place in the research community, so feel free to post in the comments section below.

1. Can you explain what Haldane’s Sieve is, and what service it provides to the science community?

Haldane’s Sieve is a site designed for the promotion and discussion of preprints in evolutionary genetics and genomics. Each day we post abstracts and links to the preprints that have appeared on the arXiv & bioRxiv and fall broadly in evolutionary genomics. We also invite authors to write posts giving informal summaries of their work,  e.g. explaining the story behind the paper or highlighting some part of the work that they find particularly exciting. All papers also have comment threads where readers can give feedback, and we also have the occasional post with a detailed review of a paper.

[GC] It’s been really great to see so many people in the community embracing preprints over the past few years, and evolutionary genetics and genomics being central to the move towards preprints in biology. It’s great that Haldane’s sieve has played some role in that, especially as it started from a idle chat on a saturday afternoon that hit on a great name for a preprint website. It’s also been wonderful to see a number of biology journals change towards preprint friendly policies in response to authors really wanting to engage with preprints.

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Genetics reveal the diversity of pollinators’ other cargo: fungi

Rufous-tailed Hummingbird (Amazilia tzacatl jucunda)

What else is this pollinator carrying? (Flickr: Lip Kee Yap)

The following is a cross-posting from the Stanford CEHG Blog by Jeremy Hsu, a graduate student in Elizabeth Hadley’s lab at Stanford University.

Many animals that visit flowers are known to carry microfungal communities; these fungi are important ecologically because they have the potential to alter the attractiveness of nectar to these pollinators, thus influencing plant-animal interactions. The pollinators also act as vectors for the microfungi, helping distribute communities throughout the local ecosystem. In a recent paper in Fungal Ecology, Melinda Belisle, a then-graduate student in the Department of Biology in CEHG faculty member Tad Fukami’s lab, led a team of researchers at Stanford and in Costa Rica to investigate these relationships further and examine how the distribution of microfungi varies in space and time in a local ecosystem.

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What we’re reading: The color of cichlids, projected genomes, and simplifying NSF proposals

In the journals

Albertson RC, KE Powder, Y Hu, KP Coyle, RB Roberts, and KJ Parsons. 2014. Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichlid fishes. Molecular Ecology, 23: 5135–5150. doi: 10.1111/mec.12900.

… we crossed two divergent cichlid species to generate an F2 mapping population that exhibited extensive variation in pigmentation levels and patterns. Our experimental design is robust in that it combines traditional quantitative trait locus (QTL) analysis with population genomics, which has allowed us to move efficiently from QTL interval to candidate gene. In total, we detected 41 QTL and 13 epistatic interactions that underlie melanocyte- and xanthophore-based coloration across the fins and flanks of these fishes.

Yang MA, K Harris and M Slatkin. 2014. The projection of a test genome onto a reference population and applications to humans and archaic hominins. Genetics, doi: 10.1534/genetics.112.145359.

We introduce a method for comparing a test genome with numerous genomes from a reference population. … Using analytic theory, numerical analysis, and simulations, we show how the projection depends on the time of population splitting, the history of admixture and changes in past population size.

In the news

“So here’s an idea: what if NSF preproposals were the proposals? After all, one way to encourage reviewers to focus on the big ideas rather than picky methodological details is to not provide them with any methodological details in the first place.”

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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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