A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes

Eliran Avni,Sagi Snir

doi:10.1038/s41598-020-62446-5

Abstract

It is well established nowadays that among prokaryotes, various families of orthologous genes exhibit conflicting evolutionary history. A prime factor for this conflict is horizontal gene transfer (HGT) - the transfer of genetic material not via vertical descent. Thus, the prevalence of HGT is challenging the meaningfulness of the classical Tree of Life concept. Here we present a comprehensive study of HGT representing the entire prokaryotic world. We mainly rely on a novel analytic approach for analyzing an aggregate of gene histories, by means of the quartet plurality distribution (QPD) that we develop. Through the analysis of real and simulated data, QPD is used to reveal evidence of a barrier against HGT, separating the archaea from the bacteria and making HGT between the two domains, in general, quite rare. In contrast, bacteria’s confined HGT is substantially more frequent than archaea’s. Our approach also reveals that despite intensive HGT, a strong tree-like signal can be extracted, corroborating several previous works. Thus, QPD, which enables one to analytically combine information from an aggregate of gene trees, can be used for understanding patterns and rates of HGT in prokaryotes, as well as for validating or refuting models of horizontal genetic transfers and evolution in general.

Highlights

Deciphering the history of life on Earth is among the most fundamental and ancient task in biology
This part of the work focuses on analyzing the plurality quartets derived from a collection of 6901 prokaryotic genes based on 41 archaea and 59 bacteria Quartet Plurality Distribution. (QPD), a concept that was introduced in[32] and is further developed here we introduce and develop, is used to show that in the collection of genes that we analyze, horizontal gene transfer (HGT) events are divided into three major categories: (1) Bacteria’s confined HGTs, that are most common; (2) Archaea’s confined HGTs, that are moderately common; and (3) HGTs between archaea and bacteria (Inter-domain), that are least common
Through the development of the concept of quartet plurality distribution (QPD32), which enables one to combine information about quartet topologies from an aggregate of gene trees, we reveal evidence for an average low propensity for inter-domain HGTs, which implies the existence of an archaea-bacteria HGT barrier

Summary

Introduction

Deciphering the history of life on Earth is among the most fundamental and ancient task in biology. A basic and ubiquitous step in phylogenomic studies is the inference of an ancestor-descendant relationship in the form a tree, dubbed as a gene tree, for every family of genes in a dataset These studies have found widespread disagreements between these gene trees[3], leading some to doubt the relevance of the Tree of Life concept[4,5,6,7,8,9]. There is ample evidence that a strong tree-like signal can be extracted, even in the presence of extensive HGT These results often rely on a blend of phylogenetic signals, including pairwise gene distances, a comparison to a reference species tree, theoretical studies, and the analysis of simulative and empirical data[3,18,19,20,21,22,23]. Statistical computations show that these differences in HGT frequency are highly significant

Methods

Results

Discussion

Conclusion