The infinitely many genes model with horizontal gene transfer

TL;DR

This paper extends the infinitely many genes model to include horizontal gene transfer in bacteria, providing a genealogical framework and calculating key genetic statistics for bacterial pangenomes.

Contribution

It introduces the Ancestral Gene Transfer Graph to model bacterial gene evolution with horizontal transfer, advancing understanding of pangenome dynamics.

Findings

Derived moments of gene difference statistics

Computed gene frequency spectrum under the model

Provided a genealogical construction for bacterial pangenomes

Abstract

The genome of bacterial species is much more flexible than that of eukaryotes. Moreover, the distributed genome hypothesis for bacteria states that the total number of genes present in a bacterial population is greater than the genome of every single individual. The pangenome, i.e. the set of all genes of a bacterial species (or a sample), comprises the core genes which are present in all living individuals, and accessory genes, which are carried only by some individuals. In order to use accessory genes for adaptation to environmental forces, genes can be transferred horizontally between individuals. Here, we extend the infinitely many genes model from Baumdicker, Hess and Pfaffelhuber (2010) for horizontal gene transfer. We take a genealogical view and give a construction -- called the Ancestral Gene Transfer Graph -- of the joint genealogy of all genes in the pangenome. As application, we compute moments of several statistics (e.g. the number of differences between two individuals and the gene frequency spectrum) under the infinitely many genes model with horizontal gene transfer.