Dear all,
Excited to open up the second semester Faculty of Biology Seminar Series. The opening seminar will be given by Prof. Sagi Snir from the Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa and President of the Israel Society for Bioinformatics and Computational Biology.
Place and time: Biology auditorium, Monday 27/5 at 13:00.
Title: Harnessing Genome Dynamics for Phylogenetic Reconstruction
Snir lab website: https://sagi-snir.wixsite.com/snir-lab
Looking forward to seeing you all,
Dvir
Harnessing Genome Dynamics for Phylogenetic Reconstruction
The dramatic decrease in time and cost for generating genetic sequence data has opened up vast opportunities in molecular systematics, one of which is the ability to decipher the evolutionary history of strains of a species. Under this fine systematic resolution, the standard markers are often too crude to provide a reliable phylogenetic signal. Nevertheless, among prokaryotes, genome dynamics (GD) in the form of horizontal gene transfer (HGT), the transfer of genetic material between organisms not through lineal descent, seem to provide far richer information by affecting both gene order and gene content.
In modern systematics, a common practice is to assume a stochastic model describing the behavior of the system. Such modelling is valuable, as it allows advanced machine learning approaches to be applied to the data.
Here we provide a first statistical, two-level modeling and analysis, for GD under a very simple operation – the Jump operation. Using this modeling we can infer several essential characteristics for genomes evolving along a tree and analytically infer HGT rate and time.
We applied this model to the new version of the orthology DB EggNOG containing over 4.5K taxa. To the best of our knowledge, this is the largest gene-order-based tree constructed and it overcomes shortcomings found in previous approaches. Constructing a GD-based tree allows to confirm and contrast findings based on other phylogenetic approaches, as we show.
The talk is self-contained and assumes no mathematical background.
Related Papers:
- Katriel, G., Mahanaymi, U., Brezner, S., Kezel, N., Koutschan, C., Zeilberger, D., … & Snir, S. Gene Transfer-based Phylogenetics: Analytical Expressions and Additivity via Birth-Death Theory. Systematic biology, syad060.
- Sevillya, G., D. Doerr, Y. Lerner, J. Stoye, M. Steel, and S. Snir. 2019. Horizontal Gene Transfer Phylogenetics: A Random Walk Approach. Molecular Biology and Evolution (MBE)37:1470–1479.
- Shifman, A., N. Ninyo, U. Gophna, and S. Snir. 2013. Phylo si: a new genome-wide approach for prokaryotic phylogeny. Nucleic acids research (NAR)42:2391–2404.
Short Bio: Sagi Snir graduated in Computer Science from the Technion Israel, focusing on analytical, algebraic, maximum likelihood solutions to phylogenetics. After a postdoc in the Math and the Computer Science depts at UC Berkeley, he returned to the dept of Evolutionary & Environmental biology at the University of Haifa in Israel, where he has established the Bioinformatics program for grad students. He is now a professor of computational evolution at the University of Haifa and the President of the Israeli Society for Bioinformatics and Computational Biology.
His research combines algorithmic approaches to problems from evolution with focus on phylogenetic trees and networks. He has developed the Quartet MaxCut algorithm to combine conflicting signals between evolutionary trees and other fundamental results on maximum likelihood of trees and networks. His papers have been published in both pure theoretical computer science venues and pure evolution venues.
After his army service he traveled for two years on a motorcycle from the tip of South America (Tierra del Fuego) to Alaska.
