The Molecular Ecologist

In the journals
Jalasvuori M & J Lehtonen. 2014. Virus epidemics can lead to a population-wide spread of intragenomic parasites in a previously parasite-free asexual population. Molecular Ecology. 23(5):987–991. doi: 10.1111/mec.12662.

Endogenous retroviruses are retroviruses that have integrated to the germ line cells and are inherited thereafter vertically. They can also replicate within the genome similarly to retrotransposons as well as form virus particles and infect previously uninfected cells. This highlights the possibility that endogenous retroviruses could play a role in the evolution of sexual reproduction.

Kleindorfer S, JA O’Connor, RY Dudaniec, SA Myers, J Robertson, & FJ Sulloway. 2014. Species collapse via hybridization in Darwin’s tree finches. The American Naturalist. 183(3):325-341. doi: 10.1086/674899.

The results presented here go to the heart of evolutionary biology: by what criteria do we denote species, and by what criteria do new species form or collapse? Here we present evidence that three sympatric species of Darwin’s tree finches in the 1900s have collapsed, under conditions of hybridization, into two species by the 2000s.

In the news
“Data should be in the form in which it was originally collected, before summarizing, analyzing or reporting.” —The PLOS journals are instituting a sweeping new data-sharing policy that appears to require sharing “raw” data. This has made some people very angry, while others are all in favor. But regardless, that data archiving mandate won’t be a panacea.
“Why filter and not just let anybody publish whatever they want?” —A nice multi-part discussion of the how’s and why’s of peer review.
“… you should contact several POs from different programs to put your name on their radar.” —Why you should probably be angling to sit on an NSF review panel, and applying for a CAREER grant.
“I can, at least in principle, imagine a creationist professor who taught the contents of a microbiology curriculum, complete with the common descent of life on Earth, and never breathed a word of his personal beliefs in the classroom.” —Can a young-Earth creationist be trusted to teach an introductory biology course at Jeremy’s alma mater?

In the journals
Wang J. 2014. Marker-based estimates of relatedness and inbreeding coefficients: an assessment of current methods. J. Evol. Biol. 27:518–530. doi: 10.1111/jeb.12315.

… F and r estimates can be misleading and become biased and marker dependent when a sample containing a high proportion of highly inbred and/or closely related individuals is used as reference.

Worobey M, G-Z Han, A Rambaut. 2014. A synchronized global sweep of the internal genes of modern avian influenza virus. Nature. doi: 10.1038/nature13016.

Here we show that explicitly allowing [influenza A virus] host lineages to have independent rates of molecular evolution is necessary for reliable phylogenetic inference of IAV and that methods that do not do so, including ‘relaxed’ molecular clock models9, can be positively misleading.

In the news
“The irony is that when UK statistician Ronald Fisher introduced the P value in the 1920s, he did not mean it to be a definitive test.” —So how then should we judge statistical significance?
“I make the drawings on a small whiteboard and record it with my iPhone.” —You, too, can make a whiteboard movie.

In the journals
Morlon, H. 2014. Phylogenetic approaches for studying diversification. Ecology Letters. doi: 10.1111/ele.12251.

A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment.

Da Silva, J., and S. K. Wyatt. 2014. Fitness valleys constrain HIV-1’s adaptation to its secondary chemokine coreceptor. J. Evol. Biol. doi: 10.1111/jeb.12329.

We have identified four fitness valleys from a previous study of fitness epistasis in adaptation to CXCR4 and use estimates of the within-patient variance Ne for different patient treatment statuses and infection stages (conditions) to estimate times to cross the valleys.

In the news
“Cortex in Metallic Pastels represents a stylized section of the cerebral cortex, in which axons, dendrites, and other features create a scene reminiscent of a copse of silver birch at twilight. ” —Have you seen the winners of the AAAS/NSF 2013 International Science and Engineering Visualization Challenge yet?
“Analyses like this are bound to come up with results that look like a caricature, since they are obtained in much the same way that a caricature is drawn, by finding and highlighting the most extreme and distinctive aspects.” —A cautionary note about clustering algorithms.
“When it comes to science, online news outlets are more important than ever, but newspapers are still key. … But what struck me was the importance of television.” —Breaking down a new NSF report on public understanding of and support for scientific research.
“If the ultimate goal is to evaluate a person’s true overall role as a scientist, I think we should be considering how they communicate with all people not just other scientists.” —A proposed “influence metric” would combine your h-index, social media followers, and press mentions.
“It is not hard to peddle incoherent math to biologists, many of whom are literally math phobic. … Similarly, it isn’t hard to fool mathematicians into believing biological fables.” —What can happen when you mix math and biologists.

In the journals
Li Y, R Cheng, KA Spokas, AA Palmer, and JO Borevitz. 2014. Genetic Variation for Life History Sensitivity to Seasonal Warming in Arabidopsis thaliana. Genetics 196:569-77. doi: 10.1534/genetics.113.157628.

The identified genetic architecture allowed accurate prediction of flowering phenotypes (R² > 0.95) that has application for genomic selection of adaptive genotypes for future environments

Harris RB, MD Carling, IJ Lovette. 2014. The influence of sampling design on species tree inference: A new relationship for the New World chickadees (Aves: Poecile). Evolution. 68:501-13. doi: 10.1111/evo.12280.

Collectively, our analyses contrast with previous studies and support a sister relationship between the Black-capped and Carolina Chickadee, two superficially similar species that hybridize along a long zone of contact. … Our results suggest that relatively few loci with high information content may be sufficient for estimating an accurate species tree, but that substantially more loci are necessary for accurate parameter estimation.

In the news
“I can’t believe I sat through 2 hours and 45 minutes of that.” —P.Z. Meyers watched Bill Nye the Science Guy debate a creationist so you don’t have to. But did it do any good?
“It is the first time since the reading-habit questionnaire began in 1977 that manuscript consumption has not increased.” —In 2012, scientists reported reading about as many papers as they did in 2005, but more in electronic formats.
“For every PeerJ or Figshare (and these are ultimately just as dependent on continued public financing of research as any grant-driven project), we also need more innovative organizations like the Internet Archive, wholly dedicated to the public good and not the relentless pressure to commoditize everything (especially their patrons’ privacy).” —Is Open Science too focused on turning a profit?

In the journals
Hong J, Gresham D. 2014. Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments. PLoS Genetics 10(1):e1004041. doi:10.1371/journal.pgen.1004041.

The identification of repeatedly selected variation at functionally related loci that interact epistatically suggests that gene network polymorphisms (GNPs) may be a frequent outcome of adaptive evolution.

Rodriguez D, CG Becker, NC Pupin, CFB Haddad, KR Zamudio. 2014. Long-term endemism of two highly divergent lineages of the amphibian-killing fungus in the Atlantic Forest of Brazil. Molecular Ecology 23:774-787. doi:10.1111/mec.12615.

Focusing on the Atlantic Forest (AF) of Brazil, we used qPCR assays to determine the presence or absence of [Batrachochytrium dendrobatidis] on 2799 preserved postmetamorphic anurans collected between 1894 and 2010 and used semi-nested PCRs to determine the frequency of rRNA ITS1 haplotypes from 52 samples. Our earliest date of detection was 1894.

In the news
“One of the great things about academic freedom is that we have broad latitude over what happens in our classrooms.” —Does it make sense to assign novels in a biology class?
“It does make me wonder what someone would do if they weren’t happy with their gender gap.” —What should we do about the gender ratio in our collaborations?
“They didn’t understand, no matter how many times I told them, that I didn’t have summers off.” —What it’s like being the only academic in the village family.
Farmer, Miner, Cowboy, Jailer … —What kind of genomics researcher are you?