In the second interview for the Molecular Ecologist, we feature Dr. Ruth Shaw from the University of Minnesota (full disclosure, Dr. Shaw was my PhD adviser). Dr. Shaw is currently the Editor-in-Chief of the journal Evolution. In her research, she studies the evolutionary consequences of genetic variation using quantitative genetic approaches and has been active in the development of statistical approaches for the analysis of life history data. She has been recognized with the President’s Award from the American Society of Naturalists, the William Skinner Cooper Award from the Ecological Society of America, and the Outstanding Faculty Award from the University of Minnesota Council of Graduate Students. Below, we ask Dr. Shaw about her background, molecular research, and the journal Evolution in this tumultuous age of academic publishing.
1) Can you tell us a bit about how you got started in evolutionary ecology?
I credit my parents with fostering my interest in the natural biota. Both were chemists, but they both knew plants and birds well and routinely consulted the field guides when they took the family on hikes near our home in Pennsylvania and elsewhere. So, though I considered other majors at Oberlin College, I gravitated toward biology, taking all the plant, micro, and math biology courses. In my final year, I took the vertebrate anatomy course, to see what all the pre-meds were complaining about. The professor, Warren Walker, made the subject thoroughly fascinating to me by taking an explicitly evolutionary perspective. That course sparked my interest in studying ongoing evolution of plants, and I was tremendously fortunate to have the opportunity to do my doctoral studies with Janis Antonovics, brilliant scientist, supportive advisor and great friend.
In the journals
E Kazancıoğlu, Arnqvist G. 2013. The maintenance of mitochondrial genetic variation by negative frequency-dependent selection. Ecology Letters. doi: 10.1111/ele.12195.
We assessed the change in mitochondrial haplotype frequencies over 10 generations of experimental evolution in 180 seed beetle populations in the laboratory … We found that haplotypes consistently increased in frequency when they were initially rare and decreased in frequency when initially common.
JE Crawford, Nielsen R. 2013. Detecting adaptive trait loci in non-model systems: divergence or admixture mapping? Molecular Ecology. doi: 10.1111/mec.12562.
Divergence scans of genetic markers for outlier loci, or ‘divergence mapping’, have been used to map locally adapted genes, but this approach is likely to be underpowered when background divergence is elevated. Genotype-phenotype association tests in admixed populations, or ‘admixture mapping’, may provide a useful approach for mapping locally adapted loci when neutral divergence is high.
In the news
Is biology’s future in the computer lab?
The Economist goes off the rails on science’s self-correction.
PubMed is putting a comments section below every article in the archive—and it’s open, to begin, to anyone who’s received funds from NIH or Wellcome Trust.
In the journals
Eckert AJ, JL Wegrzyn, JD Liechty, JM Lee, WP Cumbie, JM Davis, B Goldfarb, CA Loopstra, SR Palle, T Quesada, CH Langley and DB Neale. 2013. The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae). Genetics. doi: 10.1534/genetics.113.157198.
Phenotypes measured at the whole plant level (e.g. disease resistance) exhibit an approximately two-fold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were only apparent when loci were considered at the level of functional sets.
Kajdacsi1 B, F Costa, C Hyseni, F Porter, J Brown, G Rodrigues, H Farias, MG Reis, JE Childs, AI Ko, and A Caccone. 2013. Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil. Molecular Ecology. doi: 10.1111/mec.12455.
Surprisingly, we detected very little relatedness among animals trapped at the same site and found high levels of genetic diversity, as well as structuring across small geographical distances. Most FST comparisons among sites were statistically significant, including sites less than 400 m apart.
In the news
It’s been a really rough week for inclusion in science communication. Here’s hoping we can start to do better.
The U.S. Federal Government is finally open for business again, including the science-related bits.
This week we have a guest post from Markku Karhunen. Markku’s research at the University of Helsinki included the development and implementation of a number of very interesting and useful population genetics methods. In his guest post Markku discusses these novel methods with which researchers can distinguish neutral and non-neutral evolution of quantitative traits.
What does the word ‘random drift’ remind you of? A rowing boat, or a negligent walk through the market street, perhaps. However, there are many instances of this concept also in science. In financial theory, the stock prices are often modeled as randomly drifting, and animal movement could be seen as random drift, too.
In evolutionary theory, people speak of random genetic drift. This means merely the gradual change of allele frequencies from one generation to another. The existence of this phenomenon is trivial; consider for example a lab experiment of 100 generations of fruit flies, with a breeding population of 10 individuals on each generation. Surely you would expect the gene frequencies to change as a result of repeated random sampling.
In the journals
Goodman BA, L Schwarzkopf, & AK Krockenberger. 2013. Phenotypic integration in response to incubation environment adaptively influences habitat choice in a tropical lizard. The American Naturalist, 182(5): 666-73. doi: 10.1086/673299.
Using a split-clutch design, we incubated eggs at thermal regimes that mimicked the thermal environments of nests from two habitat types (forest = warm; rocky = cool). Hatchlings from cool incubation environments had longer limbs and greater running and climbing speeds, which are likely to be beneficial for rocky habitats.
Scheiner SM & LM Bouchie. 2013. The predictive power of NSF reviewers and panels. Frontiers in Ecology and the Environment 11: 406–407. 10.1890/13.WB.017.
Reviewer scores and panel rankings were moderately, but non-significantly, correlated with project outcomes (r = 0.12–0.29), but less so when analyzed by multiple regression. The sole predictive factor was award size for the number of publications (Figure 1; standardized coefficient = 0.64), a relationship consistent with other analyses …
In the news
This week in shutdown science: The CDC sits out an outbreak of drug-resistant salmonella, experiments on hold, lab mice euthanized and an entire season of Antarctic research cancelled.
Science commissioned a sting to test the peer review at open-access journals … but didn’t include a control group.
On the infamous two-body problem.
A big new study finds that papers reporting publicly available data get more citations.
This week I’ve invited a good friend and fellow Homo sapiens, Jacob Tennessen, to contribute a guest post to the Molecular Ecologist. Jacob is a Postdoctoral Scholar at Oregon State University, where he currently works with Mike Blouin and Aaron Liston, but he has also worked at the University of Washington with Josh Akey. It was while he was up in Seattle that Jacob made some profound discoveries that are relevant both to us as a species and as Molecular Ecologists. I’ve invited Jacob to share some of his insights into this fascinating topic…
A non-model organism studies a model organism. Image from Wikipedia.
The term “model species” or “model organism” usually refers to critters like Drosophila that are conducive to basic experimental biology and can yield results relevant to other taxa, including humans. At least, that’s how it gets justified in NIH grant applications: you study non-humans to learn about humans, not the other way around. In molecular ecology, though, the tables have turned. Molecular ecologists study non-humans using methods that were initially tried on humans, and interpret their data in a framework of theoretical population genetics that has been validated with human genetic data. Thus, humans are actually a model species for molecular ecology. Unfortunately, not all molecular ecologists fully appreciate the importance of human genetics to their discipline.
Molecular ecology is essentially population genetics of wild, ecologically interesting species. Because these species are generally difficult to breed or otherwise manipulate in the lab, molecular ecology is often observational rather than experimental. Non-invasive genetics and “natural experiments” are employed to make inferences about evolutionary history, behavior, fitness, and other aspects of natural history. These same restrictions also apply to humans: breeding humans in the lab is as ethically fraught as it is logistically challenging. But, the difference between studying humans and, say, elephant seals is that the established knowledge base for humans is much greater. The combined size of available population genetic datasets in humans is a billion-fold larger than for most species, even some that have already been the target of molecular ecology studies, and these human data are much better annotated and validated. Furthermore, being humans ourselves, we all have an intuitive grasp of the human phenotype, so statements about, say, human genetic diversity are readily placed in the familiar framework of human phenotypic diversity.
In the journals
Petren, K. 2013. The evolution of landscape genetics. Evolution. doi: 10.1111/evo.12278.
Evolutionary landscape genetics is the study of how migration and population structure affects evolutionary processes. As a field it dates back to Sewall Wright and the origin of theoretical population genetics, but empirical tests of adaptive processes of evolution in natural landscapes have been rare
Alberto, F. J., J. Derory, C. Boury, J.-M. Frigerio, N. E. Zimmermann, and A. Kremer. 2013. Imprints of natural selection along environmental gradients in phenology-related genes of Quercus petraea. Genetics 195:495–512. doi: 10.1534/genetics.113.153783.
We investigated whether SNP variation reflected the clinal pattern of bud burst observed in common garden experiments. We used different methods to detect imprints of natural selection (FST outlier, clinal variation at allelic frequencies, association tests) and compared the results obtained for the two gradients.
In the news
Here’s a brief rundown of scientific work and outreach brought to a screeching, experiment-ruining halt by gerrymandering-induced paralysis in Washington this week. And here’s a gallery of screenshots from databases and other online resources hobbled by the shutdown. But the conservative war on the NSF is still underway.
From tweet to review article.
Bard College (where, full disclosure, Jeremy has taught) is initiating a new option for applicants to skip SAT scores and transcripts by writing four 2,500-word research papers. Is that better?
More on the decision by Popular Science to close their website comments system.
A handy guide for male academics who don’t want to be That Dude.
Are you now or have you recently been searching for an academic job? Then you should take this extremely short survey.
Cross posted on ngcrawford.com
From Brant Faircloth
If you attended Evolution 2013, you probably heard quite a lot of chatter about ultra conserved elements. Essentially, ultra conserved elements (UCEs) are parts of the genome that are highly conserved between different species. Although UCEs carry little phylogenetic information, they are surrounded by increasingly variable flanking sequence (see figure). When combined with their flanking sequence these ‘UCE loci’ make ideal markers to study evolutionary relationships across variable time scales. For example, we have used UCEs identified in birds and reptiles to identify homologous UCE loci in amphibians, birds and reptiles. We have also identified these same UCEs in many published mammal genomes.
The first in a series of monthly interviews on the Molecular Ecologist was a logical choice: Dr. Loren Rieseberg, the Chief Editor of our parent journal Molecular Ecology. Dr. Rieseberg is both a Professor in the Department of Botany at the University of British Columbia and a Distinguished Professor at Indiana University. He is best known for his work on the role of hybridization in evolution and speciation, particularly in sunflowers. He has won numerous awards including a MacArthur Fellowship. Below, we ask Dr. Rieseberg about his background, his thoughts on the field of molecular ecology, and how he does everything he does:
1) How did you come to work on sunflowers?
Loren Rieseberg with his favorite plant
When I arrived at Washington State University (WSU) in the fall of 1984 to begin my PhD, my advisor, Doug Soltis, handed me a copy of Verne Grant’s Plant Speciation
and told me to find a problem. I was especially intrigued by Grant’s discussion of the potential role of hybridization in adaptation and speciation. Sunflowers were one of four classic examples of this process discussed by Grant, and were especially attractive to me because the sunflower genus also included two domesticated plants and several weedy species. Thus, it was an easy decision. I wrote and defended my proposal within three months after my arrival at WSU and also worked in a collecting trip to California, where I had the opportunity to take a short excursion with Ledyard Stebbins to observe a sunflower hybrid zone that he had been studying near Davis since the 1940s.
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