The Molecular Ecologist

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.”

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.”

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.”

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.”

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.

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.”