The Molecular Ecologist

In the journals
Carstens, B. C., T. a Pelletier, N. M. Reid, and J. D. Satler. 2013. How to fail at species delimitation. Molecular Ecology 22:4369–4383. doi: 10.1111/mec.12413.

… in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.

Etienne, L., and M. Emerman. 2013. The mongoose, the pheasant, the pox, and the retrovirus. PLoS Biology 11:e1001641. doi: 10.1371/journal.pbio.1001641.

The genomes of two species of mongooses and an egg-laying mammal called an echidna show that a virus currently present in poultry, the reticuloendotheliosis virus (REV), is actually of ancient exotic mammalian origin.

In the news
The latest word on “sequestration” budget cuts in the U.S. is that they’ll cut the purchasing power of the National Institutes of Health by 25 percent, relative to ten years ago.
A plant geneticist working on breeding a better mass-market tomato uses modern genetics to guide old-fashioned controlled crosses.

In the journals
Johnston SE, J Gratten, C Berenos, JG Pilkington, TH Clutton-Brock, JM Pemberton, and J Slate. 2013. Life history trade-offs at a single locus maintain sexually selected genetic variation. Nature doi: 10.1038/nature12489.

We found that an allele conferring larger horns, Ho⁺, is associated with higher reproductive success, whereas a smaller horn allele, Ho^P, confers increased survival, resulting in a net effect of overdominance (that is, heterozygote advantage) for fitness at RXFP2.

Almbro M and LW Simmons. 2013. Sexual selection can remove an experimentally induced mutation load. Evolution doi: 10.1111/evo.12238.

Here we induced mutations in the dung beetle Onthophagus taurus using ionizing radiation, and tested the efficacy of sexual selection in their removal. … Two generations of sexual selection were sufficient to remove mutations that affected male strength, but not testes mass.

In the news
Rosie Redfield’s continued digging into the fine print of Creative Commons licensing finds that CC-BY is not a blank check.
Memo to grad students and other early-career researchers: it’s not going to get easier.
Here’s a list of more than 60 resources for learning how to do stuff in R—and many of them are free.
The Onion reports that scientists are finally pronouncing the human genome.

In the journals
Hedrick, PW. 2013. Adaptive introgression in animals: examples and
comparison to new mutation and standing variation as sources of adaptive variation. Molecular Ecology doi: 10.1111/mec.12415.

… potential examples of adaptive introgression in animals, including balancing selection for multiple alleles for major histocompatibility complex (MHC), S and csd genes, pesticide resistance in mice, black colour in wolves and white colour in coyotes, Neanderthal or Denisovan ancestry in humans, mimicry genes in Heliconius butterflies, beak traits in Darwin’s finches, yellow skin in chickens and non-native ancestry in an endangered native salamander, are examined.

(Hat-tip to Graham Coop for this one.)
Goudie F, MH Allsopp, and BP Oldroyd. 2013. Selection on overdominant genes maintains heterozygosity along multiple chromosomes in a clonal lineage of honey bee. Evolution doi: 10.1111/evo.12231.

Correlations between fitness and genome-wide heterozygosity … have been reported across a wide range of taxa. The genetic basis of these correlations is controversial: do they arise from genome-wide inbreeding (‘general effects’) or the ‘local effects’ of overdominant loci acting in linkage disequilibrium with neutral loci?

In the news
Apple Academic Publishing, an outfit not (apparently) affiliated with the gadget manufacturer, is selling $100 books consisting entirely of papers previously published under CC-BY licenses, the kind used by most open-access journals. And they’re not asking authors’ permission first. How do you feel about that? Rosie Redfield wants to know.
Remembering the lives of pioneering field biologists Ted Parker and Al Gentry, 20 years after their deaths in a plane crash.
A non-inclusive, non-normative list of upsides to being a woman in science.

In the journals
Staats, M., R. H. J. Erkens, B. van de Vossenberg, J. J. Wieringa, K. Kraaijeveld, B. Stielow, J. Geml, J. E. Richardson, and F. T. Bakker. 2013. Genomic treasure troves: Complete genome sequencing of herbarium and insect museum specimens. PLoS ONE 8:e69189. doi: 10.1371/journal.pone.0069189.

Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling.

Chao, D.-Y., B. Dilkes, H. Luo, A. Douglas, E. Yakubova, B. Lahner, and D. E. Salt. 2013. Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. Science 658:10–12. doi: 10.1126/science.1240561.

We found that the cytotype of the root, and not the genotype, determined the majority of heritable natural variation in leaf potassium (K) concentration in Arabidopsis thaliana. Autopolyploidy also provided resistance to salinity and may represent an adaptive outcome of the enhanced K accumulation of plants with higher ploidy.

In the news
The Ecological Society of America met in Minneapolis this week. And there was coverage at Dynamic Ecology and the EEB & Flow, and of course all over Twitter
How pipes turn Unix into a chainsaw.
“Zen” and the art of responding to reviewer comments.
Want to contribute information about your menstrual cycle, sexual practices, and success at conception to an effort in fertility-related data-mining? There’s an app for that.

In the journals
Berg, J. J., and G. Coop. 2013. The population genetic signature of polygenic local adaptation. arXiv: 1307.7759v1. See also Haldane’s Sieve.

We exploit the fact that GWAS provide an estimate of the additive effect size of many loci, to estimate the mean additive genetic value for a give phenotype across many populations as simple weighted sums of allele frequencies. While these genetic values may be poor predictors of true phenotypes, they contain a great deal of information about the genetic variation underlying the phenotype of interest, and they lend themselves to a reasonably complete description under a simple null model of genetic drift.

ffrench-Constant, R. H. 2013. The molecular genetics of insecticide resistance. Genetics 194:807–815. doi: 10.1534/genetics.112.141895.

Key questions addressed are therefore: How many mutations per gene cause resistance? How many mechanisms are there per species (genome)? How many independent genetic origins (mutations) give rise to each mechanism? What new mechanisms are still undiscovered and how might they arise?

Charlesworth, B. 2013. Stabilizing selection, purifying selection and mutational bias in finite populations. Genetics 194:955–971. doi: 10.1534/genetics.113.151555.
In the news
What kind of license should you use for your open-access article?
Is the tenure track worth it even if you never get tenure?
Finally, are biologists starting too many sentences with adverbs? (via Dynamic Ecology)