QLS Talk: Pangenome evolution on human time scales
Channel: Ludmer Centre
Date: 2020-10-20

McGill’s Quantitative Life Sciences and Medicine lecture series

Title: Pangenome evolution on human time scales

Guest: Jesse Shapiro, McGill University

Date: Oct. 6, 2020

Abstract: A pangenome is the total set of genes encoded by all members of a species or population. In bacteria, pangenomes can be orders of magnitude larger than an individual genome size, due to extensive gene mobility by horizontal gene transfer (HGT). It is actively debated to what extent mobile gene evolution (and resulting pangenome structure) is shaped by selection (niche adaptation) or drift (neutral evolution). I have recently suggested that this controversy can be resolved by explicitly considering natural selection at the level of the gene versus at the level of the genome. Crucially, whether mobile genes are considered ‘adaptive’ or not depends on the time scale considered. For example, we have identified very recent horizontal gene transfer (HGT) events into Vibrio cholerae from other species in the human gut microbiome. Most of these events are likely only a few days old, since cholera infections are very short. Some of these HGT events may be adaptive within an infection (e.g. modulating biofilm formation) but are likely maladaptive over long time scales – since they are never observed in other patients. Building upon these results, I will describe an analysis of mobile genes in the healthy human gut to test whether global patterns of mobile gene evolution (i.e. over millions of years of evolution, and without ecological context) also hold over short evolutionary time scales, among genes and genomes that are ecologically connected in the same environment. To do so, we used public microbiome data estimate to ask how mobile gene evolution (i.e. census and effective population size) is driven by the human host, the mobile gene family, or the bacterial host genome, and discuss the implications for our models of the population genetics of pangenomes.

About the lecture series:
McGill’s Quantitative Life Sciences (QLS) PHD program, the Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM), the McGill initiative in Computational Medicine (MiCM), and the Ludmer Center for Neuroinformatics & Mental Health have join forces to offer this weekly interdisciplinary seminars. To see the program and abstracts, as well as information on the PhD program, visit: https://www.mcgill.ca/qls/seminars .