The Molecular Ecologist

(Flickr: vamapaull)

… 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.”

(Flickr: amanda tipton)

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.”

(Flickr: Éole Wind)

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.”

(Flickr: Jens Schott Knudsen)

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.”

(Flickr: Chris Wieland)

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.”

(Flickr: Chris Blakeley)

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.”