In every eukaryotic genome there are DNA sequences that have recently lost their function. These could be inactive genes (pseudogenes) or mobile retroelements. We study the patterns of mutation that accumulate in these types of element to describe baseline patterns of mutation in different species. Comparison with these baselines can reveal the signatures of selection elsewhere in the genome. We are also interested in studying new insertions, deletions and duplications in natural populations, and this has recently become possible because of advances in long-read genome sequencing.
Carr, M, Bensasson, D, Bergman C.M. 2012 “Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.” PLoS ONE. 7 (11) e50978.
Liti, G., Carter D.M., Moses A.M., Warringer J., Parts L, James S.A., Davey R.P., Roberts I.N., Burt A., Koufopanou V., Tsai I.J., Bergman C.M., Bensasson D. et al. 2009 “Population genomics of domestic and wild yeasts”. Nature. 458 337-341.
Bergman C.M. and Bensasson, D. 2007 “Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in D. melanogaster”. Proc. Nat. Acad. Sci. USA. 104(27) 11340- 11345.
Keller, I., Bensasson, D., Nichols, R.A. 2007 “Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes”. PLoS Genetics. 3(2) e22.
Bensasson, D., Feldman, M.W., & Petrov, D.A. 2003 “Rates of DNA duplication and mtDNA insertion in the human genome” J. Mol. Evol. 57(3) 343-354
Bensasson, D., Petrov, D.A., Zhang, D-X., Hartl, D.L., Hewitt, G.M. 2001 “Genomic gigantism: DNA loss is slow in mountain grasshoppers.” Mol. Biol. Evol. 18(2) 246-253.
Related code on github