Palmer, MarikeVenter, S.N. (Stephanus Nicolaas)McTaggart, Alistair R.Coetzee, Martin Petrus AlbertusVan Wyk, StephanieAvontuur, Juanita RayleenBeukes, Chrizelle WinsieFourie, GerdaSantana, Quentin C.Van der Nest, Magrieta AlettaBlom, JochenSteenkamp, Emma Theodora2020-08-242020-08-242019-04Palmer M, Venter SN, McTaggart AR, Coetzee MPA, Van Wyk S, Avontuur JR, Beukes CW, Fourie G, Santana QC, Van Der Nest MA, Blom J, Steenkamp ET. 2019. The synergistic effect of concatenation in phylogenomics: the case in Pantoea. PeerJ 7:e6698 http://doi.org/10.7717/peerj.6698.2167-8359 (online)10.7717/peerj.6698http://hdl.handle.net/2263/75868Supplementary Information 1: Multi-species coalescent model phylogeny DOI: 10.7717/peerj.6698/supp-1Supplementary Information 2: Consensus network of 1,357 gene trees DOI: 10.7717/peerj.6698/supp-2Supplementary Information 3: Neighbour-Joining phylogeny from ANI-based distances DOI: 10.7717/peerj.6698/supp-3Supplementary Information 4: AML concatenated phylogenies constructed after the exclusion of backbone supporting genes and genes with no signal DOI: 10.7717/peerj.6698/supp-4Supplementary Information 5: AML concatenated phylogenies of backbone supporting genes and genes with no signal DOI: 10.7717/peerj.6698/supp-5Supplementary Information 6: Strict consensus trees of subset datasets DOI: 10.7717/peerj.6698/supp-6Supplementary Information 7: Python script Raw Data: FastTree python script for the construction of individual gene trees DOI: 10.7717/peerj.6698/supp-7Supplementary Information 8: NeighborNet Network Raw Data: A nexus file for the NeighborNet Network constructed from the concatenated nucleotide data matrix (Fig. 2). DOI: 10.7717/peerj.6698/supp-8Supplementary Information 9: Consensus Network Raw data: A nexus file for the consensus network constructed from the individual gene trees (Fig. S2). DOI: 10.7717/peerj.6698/supp-9Supplementary Information 10: Backbone supporting and no signal gene trees Datasets and trees for the individual gene trees marked as supporting the backbone and those with no signal. DOI: 10.7717/peerj.6698/supp-10Supplementary Information 11: Nucleotides with conflicting signal Nucleotide positions with conflicting signal as determined from the NeighborNet. DOI: 10.7717/peerj.6698/supp-11Supplementary Information 12: Recombination detection data Results obtained from the recombination detection program regarding potential recombination breakpoints. DOI: 10.7717/peerj.6698/supp-12Supplementary Information 13: Randomised subset datasets Data pertaining to the randomised subset datasets constructed from 20, 50, 60, 70, 80, 90, 100, 110 and 120 randomly selected genes. DOI: 10.7717/peerj.6698/supp-13With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of single gene trees, concatenated analyses of genes that were identified as having no signal resulted in a phylogeny that resembled the species phylogeny of Pantoea. This distribution of signal and noise across the genome presents the ideal situation for phylogenetic inference, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and our data suggests that this finding may also hold true for smaller datasets. We thus argue that, by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes.en© 2019 Palmer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License.Phylogenetic conflictPhylogenetic signalPhylogeneticsSuper treesConcatenatePhylogenomicsArticle