Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence

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.