Impact of homologous recombination on core genome phylogenies

Abstract

Background: Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate.

Results: In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts.

Conclusions: Overall, these results have important implications for the application of core genome phylogenies in prokaryotes.

Keywords: Core genome; Phylogeny; Prokaryotes; Recombination.

Fig. 1

Robustness of tree topology to recombination. a Phylogenetic tree built on the clonal simulation of the core genome of A. pittii. The tree was evolved in silico without recombination. b Phylogenetic tree obtained from the simulated core genome of A. pittii recombined in silico. Each site of the clonal core genome with phylogenetic signal was exposed to exactly one recombination event. As a result, nearly all informative sites (96.4%) are incongruent with the true topology of the tree

Fig. 2

Impact of recombination rate (r/m) on tree inference. We evolved the core genome of 100 species with various levels of recombination rates. The tree topology score (TTS) represents the % of identical nodes between the simulated trees and the real trees. Reported TTS and r/m values on the graph represent the average values computed across the set of 100 species. Grey areas represent the standard deviation across the 100 species. Horizontal green lines represent the average (plain line) percent and standard deviation (dashed lines) of nodes expected to be identical if the trees were random

Fig. 3

Impact of recombination rate on bootstrap supports. a Average bootstrap supports of the trees inferred with the core genomes of A. pittii simulated with different recombination rates (r/m). The trees and their bootstrap supports were inferred with RAxML. The blue dashed line represents the average bootstrap supports estimated across all the simulated trees of A. pittii. The blue solid line represents the average bootstrap support of the real tree of A. pittii. b Relationship between the average bootstrap supports of the trees of A. pittii simulated with various recombination rates and their tree topology score relative to the real tree of A. pittii

Fig. 4

Impact of phylogenetic method on tree topology inference from core genome simulated with different levels of recombination. a Tree topology scores relative to recombination rates from trees inferred with RAxML. b Tree topology scores relative to recombination rates from trees inferred with BIONJ. c Relative performance of both phylogenetic approaches. Green line represents identical tree topology scores

Fig. 5

Correlation between average bootstrap values of the real tree and the average tree topology score. Bootstrap supports were inferred for the real tree of each species. The y-axis represents the average percent of nodes identical between the real tree and the simulated trees evolved with different recombination rates (i.e. each dot represents the average % of topology scores across the trees simulated with the different recombination rates for each species)

Fig. 6

Impact of average branch length and selective pressures on tree robustness to recombination. a Correlation between average branch lengths of the tree and tree topology scores. b Correlation between average genomic dN/dS and tree topology scores