The synergistic effect of concatenation in phylogenomics : the case in Pantoea

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dc.contributor.author Palmer, Marike
dc.contributor.author Venter, S.N. (Stephanus Nicolaas)
dc.contributor.author McTaggart, Alistair R.
dc.contributor.author Coetzee, Martin Petrus Albertus
dc.contributor.author Van Wyk, Stephanie
dc.contributor.author Avontuur, Juanita R.
dc.contributor.author Beukes, Chrizelle Winsie
dc.contributor.author Fourie, Gerda
dc.contributor.author Santana, Quentin C.
dc.contributor.author Van der Nest, Magrieta Aletta
dc.contributor.author Blom, Jochen
dc.contributor.author Steenkamp, Emma Theodora
dc.date.accessioned 2020-08-24T09:49:54Z
dc.date.available 2020-08-24T09:49:54Z
dc.date.issued 2019-04
dc.description Supplementary Information 1: Multi-species coalescent model phylogeny DOI: 10.7717/peerj.6698/supp-1 en_ZA
dc.description Supplementary Information 2: Consensus network of 1,357 gene trees DOI: 10.7717/peerj.6698/supp-2 en_ZA
dc.description Supplementary Information 3: Neighbour-Joining phylogeny from ANI-based distances DOI: 10.7717/peerj.6698/supp-3 en_ZA
dc.description Supplementary Information 4: AML concatenated phylogenies constructed after the exclusion of backbone supporting genes and genes with no signal DOI: 10.7717/peerj.6698/supp-4 en_ZA
dc.description Supplementary Information 5: AML concatenated phylogenies of backbone supporting genes and genes with no signal DOI: 10.7717/peerj.6698/supp-5 en_ZA
dc.description Supplementary Information 6: Strict consensus trees of subset datasets DOI: 10.7717/peerj.6698/supp-6 en_ZA
dc.description Supplementary Information 7: Python script Raw Data: FastTree python script for the construction of individual gene trees DOI: 10.7717/peerj.6698/supp-7 en_ZA
dc.description Supplementary 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-8 en_ZA
dc.description Supplementary 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-9 en_ZA
dc.description Supplementary 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-10 en_ZA
dc.description Supplementary Information 11: Nucleotides with conflicting signal Nucleotide positions with conflicting signal as determined from the NeighborNet. DOI: 10.7717/peerj.6698/supp-11 en_ZA
dc.description Supplementary Information 12: Recombination detection data Results obtained from the recombination detection program regarding potential recombination breakpoints. DOI: 10.7717/peerj.6698/supp-12 en_ZA
dc.description Supplementary 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-13 en_ZA
dc.description.abstract With 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_ZA
dc.description.department Biochemistry en_ZA
dc.description.librarian pm2020 en_ZA
dc.description.uri https://peerj.com en_ZA
dc.identifier.citation Palmer 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. en_ZA
dc.identifier.issn 2167-8359 (online)
dc.identifier.other 10.7717/peerj.6698
dc.identifier.uri http://hdl.handle.net/2263/75868
dc.language.iso en en_ZA
dc.publisher PeerJ en_ZA
dc.rights © 2019 Palmer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. en_ZA
dc.subject Phylogenetic conflict en_ZA
dc.subject Phylogenetic signal en_ZA
dc.subject Phylogenetics en_ZA
dc.subject Super trees en_ZA
dc.subject Concatenate en_ZA
dc.subject Phylogenomics en_ZA
dc.title The synergistic effect of concatenation in phylogenomics : the case in Pantoea en_ZA
dc.type Article en_ZA


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