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 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. Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Marike Palmer [verfasserIn] Stephanus N. Venter [verfasserIn] Alistair R. McTaggart [verfasserIn] Martin P.A. Coetzee [verfasserIn] Stephanie Van Wyk [verfasserIn] Juanita R. Avontuur [verfasserIn] Chrizelle W. Beukes [verfasserIn] Gerda Fourie [verfasserIn] Quentin C. Santana [verfasserIn] Magriet A. Van Der Nest [verfasserIn] Jochen Blom [verfasserIn] Emma T. Steenkamp [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	Phylogenomics Concatenate Super trees Phylogenetics Phylogenetic signal Phylogenetic conflict

Übergeordnetes Werk:	In: PeerJ - PeerJ Inc., 2013, 7, p e6698(2019)
Übergeordnetes Werk:	volume:7, p e6698 ; year:2019

Links:	Link aufrufen Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.7717/peerj.6698

Katalog-ID:	DOAJ024027960

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allfields	10.7717/peerj.6698 doi (DE-627)DOAJ024027960 (DE-599)DOAJ2c738682cb524949bca2684dd192a902 DE-627 ger DE-627 rakwb eng QH301-705.5 Marike Palmer verfasserin aut The synergistic effect of concatenation in phylogenomics: the case in Pantoea 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Phylogenomics Concatenate Super trees Phylogenetics Phylogenetic signal Phylogenetic conflict Medicine R Biology (General) Stephanus N. Venter verfasserin aut Alistair R. McTaggart verfasserin aut Martin P.A. Coetzee verfasserin aut Stephanie Van Wyk verfasserin aut Juanita R. Avontuur verfasserin aut Chrizelle W. Beukes verfasserin aut Gerda Fourie verfasserin aut Quentin C. Santana verfasserin aut Magriet A. Van Der Nest verfasserin aut Jochen Blom verfasserin aut Emma T. Steenkamp verfasserin aut In PeerJ PeerJ Inc., 2013 7, p e6698(2019) (DE-627)736558624 (DE-600)2703241-3 21678359 nnns volume:7, p e6698 year:2019 https://doi.org/10.7717/peerj.6698 kostenfrei https://doaj.org/article/2c738682cb524949bca2684dd192a902 kostenfrei https://peerj.com/articles/6698.pdf kostenfrei https://peerj.com/articles/6698/ kostenfrei https://doaj.org/toc/2167-8359 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7, p e6698 2019
spelling	10.7717/peerj.6698 doi (DE-627)DOAJ024027960 (DE-599)DOAJ2c738682cb524949bca2684dd192a902 DE-627 ger DE-627 rakwb eng QH301-705.5 Marike Palmer verfasserin aut The synergistic effect of concatenation in phylogenomics: the case in Pantoea 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Phylogenomics Concatenate Super trees Phylogenetics Phylogenetic signal Phylogenetic conflict Medicine R Biology (General) Stephanus N. Venter verfasserin aut Alistair R. McTaggart verfasserin aut Martin P.A. Coetzee verfasserin aut Stephanie Van Wyk verfasserin aut Juanita R. Avontuur verfasserin aut Chrizelle W. Beukes verfasserin aut Gerda Fourie verfasserin aut Quentin C. Santana verfasserin aut Magriet A. Van Der Nest verfasserin aut Jochen Blom verfasserin aut Emma T. Steenkamp verfasserin aut In PeerJ PeerJ Inc., 2013 7, p e6698(2019) (DE-627)736558624 (DE-600)2703241-3 21678359 nnns volume:7, p e6698 year:2019 https://doi.org/10.7717/peerj.6698 kostenfrei https://doaj.org/article/2c738682cb524949bca2684dd192a902 kostenfrei https://peerj.com/articles/6698.pdf kostenfrei https://peerj.com/articles/6698/ kostenfrei https://doaj.org/toc/2167-8359 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7, p e6698 2019
allfields_unstemmed	10.7717/peerj.6698 doi (DE-627)DOAJ024027960 (DE-599)DOAJ2c738682cb524949bca2684dd192a902 DE-627 ger DE-627 rakwb eng QH301-705.5 Marike Palmer verfasserin aut The synergistic effect of concatenation in phylogenomics: the case in Pantoea 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Phylogenomics Concatenate Super trees Phylogenetics Phylogenetic signal Phylogenetic conflict Medicine R Biology (General) Stephanus N. Venter verfasserin aut Alistair R. McTaggart verfasserin aut Martin P.A. Coetzee verfasserin aut Stephanie Van Wyk verfasserin aut Juanita R. Avontuur verfasserin aut Chrizelle W. Beukes verfasserin aut Gerda Fourie verfasserin aut Quentin C. Santana verfasserin aut Magriet A. Van Der Nest verfasserin aut Jochen Blom verfasserin aut Emma T. Steenkamp verfasserin aut In PeerJ PeerJ Inc., 2013 7, p e6698(2019) (DE-627)736558624 (DE-600)2703241-3 21678359 nnns volume:7, p e6698 year:2019 https://doi.org/10.7717/peerj.6698 kostenfrei https://doaj.org/article/2c738682cb524949bca2684dd192a902 kostenfrei https://peerj.com/articles/6698.pdf kostenfrei https://peerj.com/articles/6698/ kostenfrei https://doaj.org/toc/2167-8359 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7, p e6698 2019
allfieldsGer	10.7717/peerj.6698 doi (DE-627)DOAJ024027960 (DE-599)DOAJ2c738682cb524949bca2684dd192a902 DE-627 ger DE-627 rakwb eng QH301-705.5 Marike Palmer verfasserin aut The synergistic effect of concatenation in phylogenomics: the case in Pantoea 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Phylogenomics Concatenate Super trees Phylogenetics Phylogenetic signal Phylogenetic conflict Medicine R Biology (General) Stephanus N. Venter verfasserin aut Alistair R. McTaggart verfasserin aut Martin P.A. Coetzee verfasserin aut Stephanie Van Wyk verfasserin aut Juanita R. Avontuur verfasserin aut Chrizelle W. Beukes verfasserin aut Gerda Fourie verfasserin aut Quentin C. Santana verfasserin aut Magriet A. Van Der Nest verfasserin aut Jochen Blom verfasserin aut Emma T. Steenkamp verfasserin aut In PeerJ PeerJ Inc., 2013 7, p e6698(2019) (DE-627)736558624 (DE-600)2703241-3 21678359 nnns volume:7, p e6698 year:2019 https://doi.org/10.7717/peerj.6698 kostenfrei https://doaj.org/article/2c738682cb524949bca2684dd192a902 kostenfrei https://peerj.com/articles/6698.pdf kostenfrei https://peerj.com/articles/6698/ kostenfrei https://doaj.org/toc/2167-8359 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7, p e6698 2019
allfieldsSound	10.7717/peerj.6698 doi (DE-627)DOAJ024027960 (DE-599)DOAJ2c738682cb524949bca2684dd192a902 DE-627 ger DE-627 rakwb eng QH301-705.5 Marike Palmer verfasserin aut The synergistic effect of concatenation in phylogenomics: the case in Pantoea 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Phylogenomics Concatenate Super trees Phylogenetics Phylogenetic signal Phylogenetic conflict Medicine R Biology (General) Stephanus N. Venter verfasserin aut Alistair R. McTaggart verfasserin aut Martin P.A. Coetzee verfasserin aut Stephanie Van Wyk verfasserin aut Juanita R. Avontuur verfasserin aut Chrizelle W. Beukes verfasserin aut Gerda Fourie verfasserin aut Quentin C. Santana verfasserin aut Magriet A. Van Der Nest verfasserin aut Jochen Blom verfasserin aut Emma T. Steenkamp verfasserin aut In PeerJ PeerJ Inc., 2013 7, p e6698(2019) (DE-627)736558624 (DE-600)2703241-3 21678359 nnns volume:7, p e6698 year:2019 https://doi.org/10.7717/peerj.6698 kostenfrei https://doaj.org/article/2c738682cb524949bca2684dd192a902 kostenfrei https://peerj.com/articles/6698.pdf kostenfrei https://peerj.com/articles/6698/ kostenfrei https://doaj.org/toc/2167-8359 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7, p e6698 2019
language	English
source	In PeerJ 7, p e6698(2019) volume:7, p e6698 year:2019
sourceStr	In PeerJ 7, p e6698(2019) volume:7, p e6698 year:2019
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Phylogenomics Concatenate Super trees Phylogenetics Phylogenetic signal Phylogenetic conflict Medicine R Biology (General)
isfreeaccess_bool	true
container_title	PeerJ
authorswithroles_txt_mv	Marike Palmer @@aut@@ Stephanus N. Venter @@aut@@ Alistair R. McTaggart @@aut@@ Martin P.A. Coetzee @@aut@@ Stephanie Van Wyk @@aut@@ Juanita R. Avontuur @@aut@@ Chrizelle W. Beukes @@aut@@ Gerda Fourie @@aut@@ Quentin C. Santana @@aut@@ Magriet A. Van Der Nest @@aut@@ Jochen Blom @@aut@@ Emma T. Steenkamp @@aut@@
publishDateDaySort_date	2019-01-01T00:00:00Z
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callnumber-first	Q - Science
author	Marike Palmer
spellingShingle	Marike Palmer misc QH301-705.5 misc Phylogenomics misc Concatenate misc Super trees misc Phylogenetics misc Phylogenetic signal misc Phylogenetic conflict misc Medicine misc R misc Biology (General) The synergistic effect of concatenation in phylogenomics: the case in Pantoea
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topic_title	QH301-705.5 The synergistic effect of concatenation in phylogenomics: the case in Pantoea Phylogenomics Concatenate Super trees Phylogenetics Phylogenetic signal Phylogenetic conflict
topic	misc QH301-705.5 misc Phylogenomics misc Concatenate misc Super trees misc Phylogenetics misc Phylogenetic signal misc Phylogenetic conflict misc Medicine misc R misc Biology (General)
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title	The synergistic effect of concatenation in phylogenomics: the case in Pantoea
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title_full	The synergistic effect of concatenation in phylogenomics: the case in Pantoea
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author_browse	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
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title_sort	synergistic effect of concatenation in phylogenomics: the case in pantoea
callnumber	QH301-705.5
title_auth	The synergistic effect of concatenation in phylogenomics: the case in Pantoea
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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	The synergistic effect of concatenation in phylogenomics: the case in Pantoea
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The synergistic effect of concatenation in phylogenomics: the case in Pantoea

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