The Molecular Ecologist

In the journals
Cortez, D., R. Marin, D. Toledo-Flores, L. Froidevaux, A. Liechti, P. D. Waters, F. Grützner, and H. Kaessmann. 2014. Origins and functional evolution of Y chromosomes across mammals. Nature 508:488–93. doi: 10.1038/nature13151.

Despite expression decreases in therians, Y/W genes show notable conservation of proto-sex chromosome expression patterns, although various Y genes evolved testis-specificities through differential regulatory decay. Thus, although some genes evolved novel functions through spatial/temporal expression shifts, most Y genes probably endured, at least initially, because of dosage constraints.

Schueler, S., W. Falk, J. Koskela, F. Lefèvre, M. Bozzano, J. Hubert, H. Kraigher, R. Longauer, and D. C. Olrik. 2014. Vulnerability of dynamic genetic conservation units of forest trees in Europe to climate change. Global Change Biology 20:1498–511. doi: 10.1111/gcb.12476.

Compared to the overall climate niche of the analysed target species populations at the warm and dry end of the species niche are underrepresented in the network. However, by 2100, target species in 33–65 %of conservation units, mostly located in southern Europe, will be at the limit or outside the species’ current climatic niche as demonstrated by favourabilities below required model sensitivities of 95%.

In the news
“… the take home message is that there is currently no definitive evidence one way or another about whether most results are false.”
“So in summary, my recommendations are: learn to turn your research outputs into papers, and learn how to produce research outputs in a short space of time; learn skills that are rare and in high demand; and learn how to take projects to completion.”
“As scientists, we like to think that we are measuring things accurately, and tend to be disturbed at the idea that we might be systematically biased in our measurements. So, the idea that we might systematically be underestimating the abilities of a large portion of our students is something most of us would find disturbing.”

In the journals
Williams PD, AP Dobson, KV Dhondt, DM Hawley, and AA Dhondt. 2014. Evidence of trade-offs shaping virulence evolution in an emerging wildlife pathogen. Journal of Evolutionary Biology. doi: 10.1111/jeb.12379.

Relationships between pathogen traits are also investigated, with transmission and recovery rates being significantly negatively correlated, whereas transmission and virulence, measured as average eye lesion score over the course of infection, are positively correlated.

Tellier A, and C Lemaire. 2014. Coalescence 2.0: a multiple branching of recent theoretical developments and their applications. Molecular Ecology. doi: 10.1111/mec.12755.

We explain how these new models take into account various pervasive ecological and biological characteristics, life history traits or life cycles which were not accounted in previous theories such as 1) the skew in offspring production typical of marine species, 2) fast adapting microparasites (virus, bacteria and fungi) exhibiting large variation in population sizes during epidemics, 3) the peculiar life cycles of fungi and bacteria alternating sexual and asexual cycles, and 4) the high rates of extinction-recolonization in spatially structured populations.

In the news
“Institutions that successfully reduce false positives in their research output could then sell off their surplus permits to other institutions that have exceeded their allocation. This flexibility would create incentives for researchers to find innovative ways to reduce false positives.”
“I feel that as long as I am productive, as long as my peeps are doing well and they are productive, as long as the distress and discomfort to the animals is as low as I can get it, and they are not wasted, its OK not to use Every Bit Of Data.”
“Scientific collecting is important in many ways, and not just in describing and defining biodiversity.”
Because of course you want to start a script with this: require("wesanderson")
“Professors, then, worked 51 hours during the official workweek and then, in addition, put in ten hours over the weekend.”

In the journals
Comeault, A. a., V. Soria-Carrasco, Z. Gompert, T. E. Farkas, C. A. Buerkle, T. L. Parchman, and P. Nosil. 2014. Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae. The American Naturalist. 183:711–727. doi: 10.1086/675497.

Here we quantitatively describe the genetic architecture of traits that are subject to known intensities of differential selection between host plant species in Timema cristinae stick insects.

Anderson, J. D., W. J. Karel, C. E. Mace, B. L. Bartram, and M. P. Hare. 2014. Spatial genetic features of eastern oysters (Crassostrea virginica Gmelin) in the Gulf of Mexico: northward movement of a secondary contact zone. Ecology and Evolution. doi: 10.1002/ece3.1064.

Recent hydrological changes in the area of secondary contact may be promoting migration in areas that were previously inhospitable to eastern oysters, and observed differences in the timing of spawning may limit hybridization between populations. Comparison of these findings with the results of an earlier study of oysters in Texas suggests that the secondary contact zone has shifted approximately 27 km north, in as little as a 23-year span.

In the news
“Dear Academia, I loved you, but I’m leaving you. This relationship is hurting me.”
“If you do have a paper that is going to get a lot attention I think it’s also fair to say that you now should be highly confident in your result prior to publication.”
“I cannot find any serious fault with this joke. Leeson is fully qualified to make it, and has done so carefully and thoroughly. The joke is funny and of comparable quality to jokes found in peer journals. I score it 3/10 and recommend rejection.”
“In short, no, good science does not REQUIRE replication.”
“Tired of generic mass produced palettes for your plots? Short of adding an owl and dressing up your plot in a bowler hat, here’s the most indie thing you can do to one. First round of palettes derived from the amazing Tumblr blog Wes Anderson Palettes.”

In the journals
de Vladar HP, N Barton. 2014. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. doi: 10.1534/genetics.113.159111.

The interplay between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of 2√μ/S remain polymorphic, whereas those with larger effects are fixed.

Gray MM, D Wegmann, RJ Haasl, MA White, SI Gabriel, JB Searle, RJ Cuthbert, PG Ryan, and BA Payseur. 2014. Demographic history of a recent invasion of house mice on the isolated Island of Gough. Molecular Ecology. 23:1923–1939. doi: 10.1111/mec.12715.

Gough Island mice showed substantial reductions in mitochondrial and nuclear sequence variation and weak reductions in microsatellite diversity compared with Western European populations, consistent with a population bottleneck. Approximate Bayesian computation (ABC) estimated that mice recently colonized Gough Island (~100 years ago) and experienced a 98% reduction in population size followed by a rapid expansion.

In the news
“While trying to bluff your way through a qualifying exam isn’t a good strategy, it’s also not going to harm anyone else. In other situations, though, failing to recognize and/or acknowledge what you do and do not know is really important, with the potential to cause harm.”
“In the fight for attention from researchers, there are winners and there are civets.”
“More than 60 percent of Americans in every state favor government-imposed limits on greenhouse gas emissions from businesses and power plants.”

In the journals
Boots M., A. White, A. Best, and R. Bowers. 2014. How specificity and epidemiology drive the coevolution of static trait diversity in hosts and parasites. Evolution. doi: 10.1111/evo.12393

We examine theoretically how epidemiological feedbacks and the characteristics of the interaction between host types and parasites strains determine the coevolution of host–parasite diversity.

Manichanh C., A. Eck, E. Varela, J. Roca, J.C. Clemente, A. González, et al. 2014. Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet. Gut. 63(3):401-8. doi: 10.1136/gutjnl-2012-303013.

When challenged with flatulogenic diet, patients’ microbiota developed instability in composition, exhibiting variations in the main phyla and reduction of microbial diversity, whereas healthy subjects’ microbiota were stable. Taxa from Bacteroides fragilis or Bilophila wadsworthia correlated with number of gas evacuations or volume of gas evacuated, respectively.

In the news
“I’ve developed a data scraper that gathers information on student dissertations, such as page length, year and month of graduation, major, and primary advisor.”
“I hate the phrase next-generation sequencing (NGS) with a passion. Here’s why …” [Plus addendum.]