Impact of homologous recombination on core genome phylogenies
- PDF / 1,160,872 Bytes
- 10 Pages / 595.276 x 790.866 pts Page_size
- 18 Downloads / 205 Views
RESEARCH ARTICLE
Open Access
Impact of homologous recombination on core genome phylogenies Caroline M. Stott and Louis-Marie Bobay*
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: Phylogeny, Recombination, Prokaryotes, Core genome
Background Phylogenetic approaches have been developed to reconstruct relationships between species and, in sexual organisms, these methods are not applicable to reconstruct relationships between individuals due to the exchange of large chromosomal fragments by crossovers at each generation. In contrast, microbial organisms are technically asexual and the lack of meiosis at each generation opens the possibility to reconstruct the phylogenetic tree of sets of related strains. These approaches have been widely applied to microbial organisms and the entire * Correspondence: [email protected] Department of Biology, University of North Carolina Greensboro, 321 McIver Street, PO Box 26170, Greensboro, NC 27402, USA
core genome (i.e. the set of genes shared by all the strains of the species) is usually used to reconstruct the tree of intraspecies relationships. Multiple artifacts can be encountered when constructing phylogenetic trees as exemplified by the frequent incongruence between gene trees and species trees [1–6], and the source of these incongruencies can be both methodological and biological [7–9]. Several studies have shown that by usin
Data Loading...
