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Journal article
Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence
Plant diversity, In Press
2025
Abstract
Deep relationships in the angiosperm tree of life remain highly controversial. To address this, we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius, 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.
Details
- Title
- Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence
- Authors/Creators
- Liyun Nie - Agricultural Genomics Institute at ShenzhenJie Wang - Agricultural Genomics Institute at ShenzhenLei Huang - Shaanxi Normal UniversityJiali Kong - Agricultural Genomics Institute at ShenzhenBao Nie - Agricultural Genomics Institute at ShenzhenLuke R. Tembrock - Colorado State UniversityShanshan Dong - Fairy Lake Botanical GardenRavi Tiwari - Murdoch UniversityHui Wang - Fairy Lake Botanical GardenShenglong Kan - Agricultural Genomics Institute at ShenzhenXinhui Zou - State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaZhiqiang Wu - Agricultural Genomics Institute at Shenzhen
- Publication Details
- Plant diversity, In Press
- Publisher
- Elsevier B.V
- Identifiers
- 991005828144407891
- Copyright
- © 2025 Kunming Institute of Botany, Chinese Academy of Sciences.
- Murdoch Affiliation
- School of Medical, Molecular and Forensic Sciences
- Language
- English
- Resource Type
- Journal article
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