Population Genomics of Transposable Elements in Drosophila

Transposable elements (TEs) are the primary contributors to the genome bulk in many organisms and are major players in genome evolution. TEs in Drosophila melanogaster come in a large diversity of families with individual familes varying in size from a few to over a hundred copies per genome. In a paper that was just published in Molecular Biology and Evolution, we carried out the first global population genomic analysis of ~800 TEs from all of the major families (55 in total) in 75 D. melanogaster strains. We found strong evidence that TEs in Drosophila are deleterious because ectopic recombination among dispersed TE copies generates inviable gametes. We showed that strength of this selection varies predictably with recombination rate, length of individual TEs, and copy number and length of other TEs in the same family. These rules do not appear to vary across orders, suggesting that selection based on ectopic recombination is a universal force preventing the uncontrolled spread of TEs in the Drosophila genome. Consistently with this notion we were able to build a statistical model that considered only individual TE-level (such as the TE length) and family-level properties (such as the copy number) and explained more than 40% of the variation in TE frequencies.

Ruth Hershberg accepts a tenure track faculty position offer from Technion

We are very happy to announce that Ruth Hershberg has just accepted a tenure track position at the Ruth & Bruce Rappaport Faculty of Medicine at the Technion (Israel Institute of Technology). Ruth will establish an interdisciplinary lab, combining evolutionary theory, bioinformatics, computational and experimental genomics, and microbiology. She will continue studying the most fundamental driving forces in evolution: mutation and natural selection, and elucidating how each of these process shapes microbial genomic variation. More specifically Ruth will pursue the following topics: (i) Elucidating variation in the efficacy with which natural selection acts on different bacteria, and understanding the consequences of such variation on the evolution of bacterial genomes, (ii) Studying variation in mutational patterns across bacteria, (iii) Quantifying changes in mutational rates and patterns in response to stress, (iv) Understanding the evolutionary processes that drive codon usage bias, (v) The bacterial species concept.
The Technion is one of Israel’s top Universities, and provides some of the best research resources available in Israel. Ruth has been a star in the lab, publishing several beautiful papers, showing: (i) how the identity of optimal codons is chosen in evolution, (ii) that mutation is universally biased towards AT in bacteria and that variable genomic GC content is likely driven by natural selection, (iii) that the reduced selection on M. tuberculosis leads to high functional diversity, and (iv) that the reduced selection on Shigella led to a loss of many genes. We will miss her very much and hope to collaborate with her in the future. Anyone interested in joining Ruth’s lab, as either a postdoc, graduate or undergraduate student, or in collaborating with Ruth in any other way should contact her at rutihersh@gmail.com.