This project will develop statistical theory and methodology to characterize adaptive evolution in DNA sequences using whole genome polymorphism data. These approaches will significantly improve the identification and localization of recent selective events, and provide long sought information regarding the genomic distributions of the strengths and rates of beneficial fixations. This work is especially timely given the rapid increase in the availability of genomic data. Understanding of the products and processes of adaptation is of fundamental importance to linking genetic and phenotypic information. This project will enhance the infrastructure for research by continuing to foster partnerships between computational and empirical groups, as well as functional and evolutionary labs.

Project Report

This research starter grant was used to purchase a computer cluster for my Lab. As my group is computational and theoretical - this cluster is our primary tool. As such, this award has directly contributed to eleven publications in 2010-11 (see below), and has supported all additional research by myself, my postdoctoral fellow, my four PhD students, and six rotation students. Projects range from theory to analysis to method development - on topics spanning Neandertal genomics to yeast experimental evolution to Drosophila population genetics. Crisci, J., A. Wong, J. Good, and J.D. Jensen, On characterizing adaptive events unique to modern humans. In press, Genome Biology & Evolution. Albert, F.W., E. Hodges, J.D. Jensen, F. Besnier, Z. Xuan, M. Rooks, A. Bhattacharjee, L. Brizuela, J.M. Good, R. E. Green, H. Burbano, I.Z. Plyusnina, L. Trut, L. Andersson, T. Schoneberg, O. Carlborg, G.J. Hannon, and S. Paabo, 2011. Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. In press, Heredity. Jensen, J.D. and D. Bachtrog, 2011. Characterizing the influence of effective population size on the rate of adaptation: Gillespie’s Darwin Domain. In press, Genome Biology & Evolution. Renzette, N., B. Bhattarcharjee, J.D. Jensen, L. Gibson, and T.F. Kowalik, 2011. The existence of the human cytomegalovirus quasispecies as revealed by high throughput sequencing. PLoS Pathogens 7(5): e1001344. Hietpas, R.T., J.D. Jensen, and D.N.A. Bolon, 2011. Experimental dissection of a fitness landscape. Proc Natl Acad Sci USA 108: 7896-901. Cutler, D.J. and J.D. Jensen. 2010. To pool, or not to pool. Genetics 186: 41-3. Pavlidis, P., J.D. Jensen, and W. Stephan. 2010. Searching for footprints of positive selection in whole-genome SNP data from non-equilibrium populations. Genetics 185: 907-22. Jensen, J.D., and O.J. Rando. 2010. Recent evidence for pervasive adaptation targeting gene expression attributable to population size change. Proc Natl Acad Sci USA 107: E109-110. Jensen, J.D. and D. Bachtrog. 2010. Characterizing recurrent positive selection at fast evolving genes in Drosophila miranda. Genome Biology & Evolution 2: 371-8. Green, R.E., J. Krause, A.W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, M. H-Y. Fritz, N. Hansen, E.Y. Durand, A.-S. Malaspinas, J.D. Jensen, T. Marques-Bonet, C. Alkan, M. Meyer, K. Prufer, H.A. Burbano, J.M. Good, R. Schultz, A. Aximu-Petri, A. Butthof, B. Hober, B. Hoffner, M. Siegemund, A. Weihmann, C. Nusbaum, E.S. Lander, C. Russ, N. Novod, J. Affourtit, M. Egholm, P. Rudan, D. Brajkovic, Z. Kucan, I. Gusic, V.B. Doronichev, L.V. Golovanova, C. Lalueza-Fox, M. de la Rasilla, J. Fortea, A. Rosas, R. Schmitz, P. Johnson, E.E. Eichler, D. Flash, E. Birney, J.C. Mullikin, M. Slatkin, R. Nielsen, J. Kelso, M. Lachmann, D. Reich, and S. Paabo. 2010. A draft sequence of the Neandertal genome. Science 328: 710-722. *Awarded the AAAS Newcomb-Cleveland Prize Pool, J. E., I. Hellmann, J.D. Jensen, and R. Nielsen. 2010. Population genomics and next-generation sequencing technology. Genome Research 20: 291-300.

National Science Foundation (NSF)
Division of Environmental Biology (DEB)
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Samuel M. Scheiner
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University of Massachusetts Medical School
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