Oct 2012 Moving to Stanford
For the last year of my HFSP fellowship, I will move to Stanford and join Dmitri Petrov's lab. My new website will be here.
Oct 2012 Short movie on milk now available in French and German
Thanks to my collaborator in France (Yannick Mahé), our short movie on the evolution of milk drinking with professors Sarah Tishkoff and Joachim Burger is now also available in German and in French. If you visit our Evolution of Life youtube channel, you will find our other movies in English, German and French. Some of them even have Spanish and Romanian subtitles. Enjoy!
Aug 2012 R code to calculate Jost D for mtDNA sequences
In my paper in JEB from 2011, I calculated Jost D for microsatellites and for mtDNA. We deposited the data and the code on Dryad, but for some reason I forgot to include the code to calculate Jost D for mtDNA. Because several people have asked for the code, I decided to publish it after all. I hope it can still be added to the Dryad package (Dryad will certainly live longer than this website), but for now it can be downloaded here:
rget_d_mtdna_penningsjeb2011.r July 2012 New paper - new movie
In 2009 and 2010 I spent some time in the field in New York and West Virginia with Susanne Foitzik (evolutionary biology professor in Mainz), Tobias Pamminger (PhD student), Andreas Modlmeier (PhD student) and Stefan Suette (Diplom student). In 2010 we did a field experiment that gave us very surprising results. In short: it allowed us to see the benefit of aggression for ants (Temnothorax longispinosus) when dealing with a slavemaker ant.
The paper is behind a paywall. You can see the abstract on the Biology Letters website. Here is a preprint (with almost the same text as the published paper):
All five authors during our 2009 fieldwork trip. From left to right: Stefan Suette, me, Susanne Foitzik, Tobias Pamminger and Andreas Modlmeier.
June 2012 The Scientist has a story about my PLoS Comp Bio paper
You can read the story on The Scientist's website. The story explains what I have done and then asks what others from the field think of it, which shows that some people agree with me and some don't. Here are some quotes from the piece by Sabrina Richards:
“The paper is interesting, and may be important for getting scientists to think about evolution of drug resistance,” said Andrew Read [...].
Not everyone agrees that one mutation can establish drug resistance. “I feel it is too simplistic and not entirely plausible” that one mutation would be enough for multi-drug therapy to fail, said Roger Kouyos.
[...] But this simplicity may be good, argued Sergei Kosakovsky Pond [...]. If models get too complicated, he explained, “you can make them do almost anything” by plugging in the right numbers.
Andrew Read is at Penn State, Roger Kouyos is at the ETH in Zurich and Sergei Kosakovsky Pond is at UC San Diego.
Paper on HIV drug resistance in PLoS Comp Bio
Today (June 7th 2012), my paper will come out in PLoS Comp Bio. The paper should become available on the PLoS website at 5PM Boston time. Have a look here for the paper. And have a look here for my video abstract on Vimeo. For some more background information about the paper, click on "HIV project" in the main menu of this site.
May 2012 Manuscript on slavemaking ants accepted for publication
Tobias Pamminger is the first author on this paper, the other authors are Susanne Foitzik, Annette Leingärtner and myself. We looked at the survival of pupae of slavemaking ants, in nests where slave ants are "supposed" to take care of the slavemaker pupae. We find that slavemaker pupae have a hard time surviving to adulthood, worst off are the queens in West Virginia. The paper will be published in Evolutionary Ecology. If you read dutch, please look at a description of a related study on the sciencepalooza blog.
May 2012 Manuscript on dense Lasius colonies accepted for publication
Corinna Steinmeyer, Susanne Foitzik and I coauthored a paper on extremely dense colonies of the ant species Lasius flavus. It will be published later this year in "Insectes Sociaux".
April 2012 Manuscripts accepted for publication
My manuscript on the role of standing genetic variation for the evolution of drug resistance in HIV is accepted for publication in PLoS Computional Biology. A recent version can be downloaded from here: arXiv.
I also recently collaborated with Vera Domingues, Hopi Hoekstra and others on a population genetic study of adaptation in beach mice. The manuscript is accepted for publication in Evolution.
April 2012 Milk Movie published
We have just published the last short movie of the Evolution-of-Life project. The movie shows what Joachim Burger (University of Mainz) and Sarah Tishkoff (University of Pennsylvania) have discovered about milk and why some people can digest milk whereas others can't. The movie is available in English, with German or French subtitles.
Jan 2012 Microbial evolution seminar series starts again
We have finalized the schedule for the microbial evolution seminars for the spring semester. We have found 10 speakers, who agreed to tell us about their exciting work on evolution in microbes. Most of the speakers are from Harvard (though from many different departments), but we also have a speaker from Tufts and one from MIT. The series starts on Jan 26th with a talk by co-organizer Sergey Kryazhimskyi.
Nov 2011 Paper on the arXiv
My manuscript on standing genetic variation and the evolution of drug resistance in HIV is now available for download from the arXiv. For this manuscript, I used lots of previously published data to estimate this probability and find that for patients who are treated with ART with an NNRTI or an unboosted PI, the probability is approximately 6%. When treatment is interrupted for a while and then started again, there is again a 6% probability that drug resistance evolves due to mutations that occurred during the interruption.
Look at the HIV project tab of this website for some more information on the manuscript.
Oct 2011 Video about movie-project
Last year, Yannick Mahé and I won an award for our project Evolution of Life for the best European educational multimedia collaboration. Now, the organization that gave us the award (Medea) made a short documentary about our project, based on an interview with Yannick. It can be seen on YouTube.
Oct 2011 Book chapter published
Together with Rebecca Meredith and Meike Wittmann, I wrote a book chapter about the evolution of drug resistance in bacteria, malaria, HIV and cancer. The chapter is published in a book on modern evolutionary biology for German biology teachers. See here.
July 2010 Welcome to my homepage
The picture of me on this site was made by Martijn van Egmond of Tot en met ontwerpen in Amsterdam.
My e-mail address is pennings at fas dot harvard dot edu. I love to discuss new ideas and to drink a coffee, so if you would like to meet for either or both, drop me a line!