Graduate Fellow
Comparative sequence analyses are rudimentary for understanding genome evolution and gene function. Such analyses are often focused on a certain species or lineage in order to infer their unique genomic traits. The commonly used approaches for such analyses focus on a single gene and try to determine whether it has undergone adaptive evolutionary changes characterized by excess of nonsynonymous over synonymous substitutions. These approaches however, are not designed to detect other scenarios of radical changes in the selection regime operating on a gene such as changes in the intensity of purifying selection. In addition, a single gene analysis may miss valuable information present in multigene data. I propose to develop an approach that alleviates these limitations. This method will be designed to analyze multigene data and detect genes and specific clades in which radical changes in the selection regime have occurred. Specifically, this method will search for genes in which the phylogenetic signal is incongruent with that obtained from compared genes, pointing to accelerations or decelerations in the evolutionary rate in a certain clade of the phylogeny. This methodology can be used to test whether certain functionally related genes underwent concerted radical evolutionary changes in a certain clade, e.g., brain related genes in the primate clade and specifically in the human lineage. In addition, the proposed method will impact other aspects related to evolutionary methodology such as model selection criteria.
Detection of clade-specific accelerations and decelerations in gene evolutionary rates
| PI(s): | Nimrod D Rubinstein (Tel-Aviv University) |
| Start Date: | 20-Sep-2010 |
| End Date: | 10-Dec-2010 |
| Keywords: | maximum likelihood, phylogenetics, mathematical modeling |
Comparative sequence analyses are rudimentary for understanding genome evolution and gene function. Such analyses are often focused on a certain species or lineage in order to infer their unique genomic traits. The commonly used approaches for such analyses focus on a single gene and try to determine whether it has undergone adaptive evolutionary changes characterized by excess of nonsynonymous over synonymous substitutions. These approaches however, are not designed to detect other scenarios of radical changes in the selection regime operating on a gene such as changes in the intensity of purifying selection. In addition, a single gene analysis may miss valuable information present in multigene data. I propose to develop an approach that alleviates these limitations. This method will be designed to analyze multigene data and detect genes and specific clades in which radical changes in the selection regime have occurred. Specifically, this method will search for genes in which the phylogenetic signal is incongruent with that obtained from compared genes, pointing to accelerations or decelerations in the evolutionary rate in a certain clade of the phylogeny. This methodology can be used to test whether certain functionally related genes underwent concerted radical evolutionary changes in a certain clade, e.g., brain related genes in the primate clade and specifically in the human lineage. In addition, the proposed method will impact other aspects related to evolutionary methodology such as model selection criteria.Related products
Publications- Evolutionary models accounting for layers of selection in protein coding genes and their impact on the inference of positive selection Nimrod D. Rubinstein, Adi Doron-Faigenboim, Itay Mayrose, and Tal Pupko 2011 Evolutionary models accounting for layers of selection in protein coding genes and their impact on the inference of positive selection Mol Biol Evol doi:10.1093/molbev/msr162
- The Operonic Location of Auto-Transcriptional Repressors is Highly Conserved in Bacteria Nimrod D. Rubinstein, David Zeevi, Yaara Oren, Gil Segal, and Tal Pupko 2011 The Operonic Location of Auto-Transcriptional Repressors is Highly Conserved in Bacteria Mol Biol Evol doi:10.1093/molbev/msr163
