Contributor Kim Gilbert’s photos of molecular ecology in action.
The “PCR gods” keep the old thermal cyclers going. Photo courtesy Kim Gilbert.
Our first response to the call for photos of molecular ecology in action.
Anne Dalziel places a minnow trap for stickleback collection. Photo courtesy Simone Des Roches.
As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen-time.
In the journals
Smith, S.A., Beaulieu, J.M., Stamatakis, A. & Donoghue, M.J. 2011. Understanding angiosperm diversification using small and large phylogenetic trees. American Journal of Botany 98: 404–14. doi: 10.3732/ajb.1000481.
… we found that diversification rate shifts are not directly associated with the major named clades examined here, with the sole exception of Fabaceae in the GenBank mega-phylogeny. These agreements are encouraging and may support a generality about angiosperm evolution: major shifts in diversification may not be directly associated with major named clades, but rather with clades that are nested not far within these groups.
Makowsky, R., Pajewski, N.M., Klimentidis, Y.C., Vazquez, A.I., Duarte, C.W., Allison, D.B., et al. 2011. Beyond missing heritability: prediction of complex traits. PLoS Genetics 7: e1002051. doi: 10.1371/journal.pgen.1002051.
Using data from the Framingham Heart Study, we explore the genomic prediction of human height in training and validation samples while varying the statistical approach used, the number of SNPs included in the model, the validation scheme, and the number of subjects used to train the model. In our training datasets, we are able to explain a large proportion of the variation in height (h2 up to 0.83, R2 up to 0.96). However, the proportion of variance accounted for in validation samples is much smaller (ranging from 0.15 to 0.36 depending on the degree of familial information used in the training dataset)
In the blogosphere
Requiescat: Godfrey Hewitt.
PLOS Genetics cuts some ethical corners to publish a paper using crowdsourced human genome data.
Where should you submit your next paper?
Molecular Ecology Notes published its first issue back in March 2001 – an issue containing a brief editorial, four technical notes, and 35 primer notes. The latter, brief papers describing new primer pairs useful for studying natural populations, have been the main output for the journal for the last twelve years: we have published almost 2,500 of them, and archived 35,000 primer pairs on the MER primer database.
A few things have happened in the last five years that have undermined the importance of primer notes (aka Permanent Genetic Resources Notes). First, in silico techniques and the wide availability of EST or Next Generation Sequence data mean that optimising 10-20 microsatellites is much easier than it used to be, and this was the primary reason behind our switch to the summary article format for primer notes at the start of 2009. Our ability to generate large volumes of sequence data has progressed very quickly, to the extent that microsats will soon be replaced by SNP and sequence data in many projects, with analyses based on individual assignment (e.g. paternity analysis) being the likely exception.
Given the declining importance of primer notes, and the existence of other good outlets (e.g. Cons. Gen. Resources and APPS), we will stop considering them for publication at the end of March 2013. This is the end of an era for ME Resources, but we feel it’s important to keep moving things forward.
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Fire ants, Solenopsis invicta. Photo by Flickr user HankPlank.
As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen-time.
In the journals
Epps, C.W., Wasser, S.K., Keim, J.L., Mutayoba, B.M. & Brashares, J.S. 2013. Quantifying past and present connectivity illuminates a rapidly changing landscape for the African elephant. Molecular Ecology. doi: 10.1111/mec.12198
The connectivity of elephant populations in Tanza- nian protected areas reflects a landscape in transition: elephants are still moving surprising distances outside protected areas (Fig. 2), even over steep terrain and near human settlements, but areas of dense human set- tlement and poaching threats have likely greatly reduced or eliminated many such movements (Figs 3 and 4).
Sunday, J.M. & Hart, M.W. 2013. Sea star populations diverge by positive selection at a sperm-egg compatibility locus. Ecology and Evolution. doi: 10.1002/ece3.487
We find a different pattern of selection in the bindin locus in two geographically separated populations of a single species. Our results specifically indicate that there are sites under positive selection (dN > dS) in one population that are under purifying or neutral selection in the other population (dN ≤ dS), and the sites found to be under positive selection differed between the two populations.
In the blogosphere
A non-exhaustive list of hurdles for crowdfunding science.
The U.S. National Science Foundation Division of Environmental Biology (NSF-DEB) has launched a blog.
This week I’ve invited a friend and colleague, Hayley Lanier, to contribute a guest post to the Molecular Ecologist. Hayley is a Postdoctoral Fellow at the University of Michigan, where she works with Lacey Knowles. She has contributed an excellent post on getting the most out of the mentor/mentee relationship….
My research is focused on species tree estimation, phylogeography, and population structure, but I’ve opted not to talk about any of that today. Instead, I’d like to focus on mentorship, and how having a good support system can make the uncertain waters of academia easier to navigate.
Noted science blogger and marine scientist Kevin Zelnio hung up his quill this week and moved on to greener pastures (a microbrewery and hostel in Sweden). He chronicles his journey from enthusiastic graduate student to discouraged PhD seeker and how his scientific blogging and freelance writing have developed through the years over at Deep Sea News. His enthusiastic writings and witty posts at DSN and The Other 95% will be missed. Although we have never personally met, Kevin strikes me as a clearly intelligent individual with an amazing capacity for communicating science, and yet his journey through graduate school left him feeling embittered and discouraged. While Kevin identifies many factors that contributed to his disillusionment with academia, one of the things that really stuck out to me was the role that his mentors have played in his frustration (and successes) in science.
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Anyone who’s hung around the blogosphere long enough is familiar with the “View From Your Window” feature at Andrew Sullivan’s blog, in which readers send in photos of, well, exactly what it says on the tin. The result is a stream of posts showcasing the worldwide community gathered around Sullivan’s site, and it’s really quite lovely.
Well, you know what other blog has a worldwide audience that must surely include many a talented amateur photographer? The Molecular Ecologist! Okay, yes, we’re not exactly on the same level as the Daily Dish, but we’d love to see the diversity of molecular ecology through the eyes of the working scientists who read this blog.
So here’s the proposition: We’d like you, our readers, to send in your photos and images of molecular ecology in action—from the lab, from the field, and from the greenhouse. Photos of scientists at work or their favorite study organisms are what we’re mostly interested in, but we’d also love to see your very best data visualizations—the more colorful, creative, and informative, the better. We’ll post submissions to the blog and in a gallery on our Facebook page—and we’ll incorporate the very best ones into our rotating list of header images.
To submit, post a Creative Commons-licensed copy of the photo to Flickr with the tag MolecularEcologistView; or e-mail a high-resolution image to Jeremy. (This may seem obvious, but: By submitting a photo or image, you’re understood to be giving The Molecular Ecologist permission to post it to the blog and use it as a header image, and to make any modifications necessary to do so.)
We can’t wait to see what you’ll send in!
As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen-time.
In the journals
Rodelo-Urrego, M., Pagán, I., González-Jara, P., Betancourt, M., Moreno-Letelier, a, Ayllón, M. a, et al. 2013. Landscape heterogeneity shapes host-parasite interactions and results in apparent plant-virus codivergence. Molecular Ecology, doi: 10.1111/mec.12232.
Also, environ- mental heterogeneity similarly shaped the spatial genetic structures of host and viruses. This resulted in the congruence between host and virus phylogenies, which does not seem to be due to host-virus co-evolution.
Dart, S. & Eckert, C.G. 2013. Experimental and genetic analyses reveal that inbreeding depression declines with increased self-fertilization among populations of a coastal dune plant. Journal of Evolutionary Biology, doi: 10.1111/jeb.12075.
Based on lifetime measures of dry mass and flower production, ID [inbreeding depression] was stronger in nine [outcrossing] populations [mean ∂ = 1-(fitness of selfed seed/fitness of outcrossed seed) = 0.39] than 16 [selfing] populations (mean ∂ = 0.03). However, predispersal ID during seed maturation was not stronger for LF populations, and ID was not more pronounced under simulated drought, a pervasive stress in sand dune habitat.
In the blogosphere
Our own Tim Vines discusses how to decide what to put in a public archive on the Dryad blog.
An adjunct lecturer explains why her course syllabus instructs her students not to call her “professor.”
A new study concludes that there’s no racial bias in NIH funding, but the sample size is, um, kind of underwhelming.
Where’s the heritability?
