The synergistic effect of concatenation in phylogenomics: the case in Pantoea
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...
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PeerJ Inc.
2019-04-01
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| Online Access: | https://peerj.com/articles/6698.pdf |
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| author | Marike Palmer Stephanus N. Venter Alistair R. McTaggart Martin P.A. Coetzee Stephanie Van Wyk Juanita R. Avontuur Chrizelle W. Beukes Gerda Fourie Quentin C. Santana Magriet A. Van Der Nest Jochen Blom Emma T. Steenkamp |
| author_facet | Marike Palmer Stephanus N. Venter Alistair R. McTaggart Martin P.A. Coetzee Stephanie Van Wyk Juanita R. Avontuur Chrizelle W. Beukes Gerda Fourie Quentin C. Santana Magriet A. Van Der Nest Jochen Blom Emma T. Steenkamp |
| author_sort | Marike Palmer |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T07:59:23Z |
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| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:59:23Z |
| publishDate | 2019-04-01 |
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| spelling | doaj.art-2c738682cb524949bca2684dd192a9022023-12-03T00:48:15ZengPeerJ Inc.PeerJ2167-83592019-04-017e669810.7717/peerj.6698The synergistic effect of concatenation in phylogenomics: the case in PantoeaMarike Palmer0Stephanus N. Venter1Alistair R. McTaggart2Martin P.A. Coetzee3Stephanie Van Wyk4Juanita R. Avontuur5Chrizelle W. Beukes6Gerda Fourie7Quentin C. Santana8Magriet A. Van Der Nest9Jochen Blom10Emma T. Steenkamp11Department of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South AfricaDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South AfricaDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South AfricaDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South AfricaDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South AfricaDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South AfricaDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South AfricaDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South AfricaDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South AfricaDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South AfricaBioinformatics and Systems Biology, Justus Liebig Universität Gießen, Giessen, GermanyDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South AfricaWith 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.https://peerj.com/articles/6698.pdfPhylogenomicsConcatenateSuper treesPhylogeneticsPhylogenetic signalPhylogenetic conflict |
| spellingShingle | Marike Palmer Stephanus N. Venter Alistair R. McTaggart Martin P.A. Coetzee Stephanie Van Wyk Juanita R. Avontuur Chrizelle W. Beukes Gerda Fourie Quentin C. Santana Magriet A. Van Der Nest Jochen Blom Emma T. Steenkamp The synergistic effect of concatenation in phylogenomics: the case in Pantoea PeerJ Phylogenomics Concatenate Super trees Phylogenetics Phylogenetic signal Phylogenetic conflict |
| title | The synergistic effect of concatenation in phylogenomics: the case in Pantoea |
| title_full | The synergistic effect of concatenation in phylogenomics: the case in Pantoea |
| title_fullStr | The synergistic effect of concatenation in phylogenomics: the case in Pantoea |
| title_full_unstemmed | The synergistic effect of concatenation in phylogenomics: the case in Pantoea |
| title_short | The synergistic effect of concatenation in phylogenomics: the case in Pantoea |
| title_sort | synergistic effect of concatenation in phylogenomics the case in pantoea |
| topic | Phylogenomics Concatenate Super trees Phylogenetics Phylogenetic signal Phylogenetic conflict |
| url | https://peerj.com/articles/6698.pdf |
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