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| Main Authors: | , , , , , , , , , , , |
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| Format: | Artículo científico |
| Language: | en |
| Published: |
Plant diversity
2026
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| Online Access: | https://pubmed.ncbi.nlm.nih.gov/41726818/ |
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| _version_ | 1868266082215657473 |
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| author | Nie, Liyun Wang, Jie Huang, Lei Kong, Jiali Nie, Bao Tembrock, Luke R Dong, Shanshan Tiwari, Ravi Wang, Hui Kan, Shenglong Zou, Xinhui Wu, Zhiqiang |
| author_facet | Nie, Liyun Wang, Jie Huang, Lei Kong, Jiali Nie, Bao Tembrock, Luke R Dong, Shanshan Tiwari, Ravi Wang, Hui Kan, Shenglong Zou, Xinhui Wu, Zhiqiang Nie, Liyun Wang, Jie Huang, Lei Kong, Jiali Nie, Bao Tembrock, Luke R Dong, Shanshan Tiwari, Ravi Wang, Hui Kan, Shenglong Zou, Xinhui Wu, Zhiqiang |
| collection | PubMed - marine biology |
| contents | Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence. Nie, Liyun Wang, Jie Huang, Lei Kong, Jiali Nie, Bao Tembrock, Luke R Dong, Shanshan Tiwari, Ravi Wang, Hui Kan, Shenglong Zou, Xinhui Wu, Zhiqiang Deep relationships in the angiosperm tree of life remain highly controversial. To address this, we first assembled the complete mitochondrial genomes for and , confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data. To dissect this classic cyto-nuclear conflict, we developed the 'PhyloForensics' framework, a novel diagnostic approach to systematically identify sources of phylogenetic instability. This framework revealed that signal heterogeneity (topological entropy variance) and information content (the proportion of informative sites) are the primary drivers of gene-tree conflict. Empirically validating this, we show that removing a small subset of "loudly conflicted" genes resolves deep-level incongruence, yielding a single, highly-supported topology previously obscured by noise. Finally, complementing this sequence-based resolution, we demonstrate that mitogenome architecture provides powerful phylogenetic signals, revealing predictable, mitogenome-wide evolutionary patterns, such as a significant negative correlation between branch length and both GC content and RNA editing sites. By integrating a validated conflict-resolution framework with architectural genomics, our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories. |
| format | Artículo científico |
| id | pubmed_41726818 |
| institution | PubMed |
| language | en |
| publishDate | 2026 |
| publisher | Plant diversity |
| record_format | pubmed |
| spellingShingle | Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence. Nie, Liyun Wang, Jie Huang, Lei Kong, Jiali Nie, Bao Tembrock, Luke R Dong, Shanshan Tiwari, Ravi Wang, Hui Kan, Shenglong Zou, Xinhui Wu, Zhiqiang Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence. Nie, Liyun Wang, Jie Huang, Lei Kong, Jiali Nie, Bao Tembrock, Luke R Dong, Shanshan Tiwari, Ravi Wang, Hui Kan, Shenglong Zou, Xinhui Wu, Zhiqiang Deep relationships in the angiosperm tree of life remain highly controversial. To address this, we first assembled the complete mitochondrial genomes for and , confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data. To dissect this classic cyto-nuclear conflict, we developed the 'PhyloForensics' framework, a novel diagnostic approach to systematically identify sources of phylogenetic instability. This framework revealed that signal heterogeneity (topological entropy variance) and information content (the proportion of informative sites) are the primary drivers of gene-tree conflict. Empirically validating this, we show that removing a small subset of "loudly conflicted" genes resolves deep-level incongruence, yielding a single, highly-supported topology previously obscured by noise. Finally, complementing this sequence-based resolution, we demonstrate that mitogenome architecture provides powerful phylogenetic signals, revealing predictable, mitogenome-wide evolutionary patterns, such as a significant negative correlation between branch length and both GC content and RNA editing sites. By integrating a validated conflict-resolution framework with architectural genomics, our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories. |
| title | Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence. |
| url | https://pubmed.ncbi.nlm.nih.gov/41726818/ |