March 13, 2019 –
Title: An Integrated Framework for Domain, Gene and Species Reconciliation
Ph.D. Candidate: Lei Li
Major Advisor: Dr. Mukul Bansal
Associate Advisors: Dr. Ion Mandoiu, Dr. Yufeng Wu
Day/Time: Wednesday, March 13th, 2019 9:00 AM
Location: HBL Class of 1947 Conference Room
In this thesis I demonstrate an integrated framework for domain, gene and species reconciliations, combined with the computational analysis and algorithms.
Genes, as functional fragments of DNA sequences, evolve inside genomes through complex mechanisms, and are often treated as the minimal evolutionary unit. However, biological studies in the recent decades showed that majority of genes in eukaryotes consist of multiple protein domains that can be independently lost or gained during evolution. Despite the fact that a large amount of research have been conducted on protein domains, these works usually focus on domain architectures or use domain content information as an auxiliary to analyzing gene evolutionary history. Thus, the study of domain evolution itself is still in its infancy. And the relationship of domain level and gene level evolution has never been explored.
Reconciliation is a technique for inferring the evolutionary history, traditionally for genes evolving inside species. In this thesis I present an integrated reconciliation model of domain evolution that explicitly captures the interdependence of domain-, gene-, and species-level evolution. The computational problem of finding the optimal DGS scenario is proved to be NP-hard, therefore, I propose two algorithms: An effective heuristic algorithm and an exact algorithm on a slightly restricted version of the problem. Both algorithms are tested on a genome-wide data set contains thousands of domain families and gene families. I also present an extended version of DGS model which reconciles multiple domain trees, multiple gene trees and a species tree simultaneously.