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...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.展开更多
Chronological data underpin paleoclimate studies.Age constraints provided by magnetostratigraphic methods can be supplemented by orbital tuning to establish higher-resolution age controls on sediments.Orbital tuning p...Chronological data underpin paleoclimate studies.Age constraints provided by magnetostratigraphic methods can be supplemented by orbital tuning to establish higher-resolution age controls on sediments.Orbital tuning primarily involves statistical and classical tuning.This paper reviews the principles and applications of these two methods.We applied the evolutionary correlation coefficient(eCOCO/COCO)obtained from statistical tuning,and visual tuning from classical tuning to the redness(a*)value record of the Pliocene Dongwan section(10–30 m)on the Chinese Loess Plateau.We then compared the age models constructed from these two approaches.The results demonstrate that,due to local factors(e.g.,micro-topography,vegetation change,and minor erosion),sedimentation rates in terrestrial sequences,such as eolian deposits,exhibit significant variability.Sedimentation rates from statistical tuning can deviate considerably from those obtained by magnetostratigraphic studies.These discrepancies become particularly pronounced when the precession signal in the strata is weak or absent.Given that eolian deposits are often able to be dated with high-precision magnetostratigraphic methods,visual tuning can more effectively reduce the age uncertainties caused by variations in the sedimentation rate,which yields a more accurate astronomical timescale.Nevertheless,statistical tuning is a viable alternative for sequences with limited age-control points and is better suited for marine and lacustrine deposits with relatively stable sedimentation rates.展开更多
基金funded by the Shenzhen Science and Technology Program(Grant No.JCYJ20241202130723030)the National Natural Science Foundation of China(Grant No.32170238)+2 种基金the Guangdong Pearl River Talent Program(Grant No.2021QN02N792)the Shenzhen Fundamental Research Program(Grant No.JCYJ20220818103212025)the Chinese Academy of Agricultural Sciences Elite Youth Program(110243160001007)to Z.W.
文摘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.
基金supported by the National Natural Science Foundation of China(Grant No.42488201)the Second Tibetan Plateau Scientific Expedition and Research Program(Grant No.2024QZKK0301)。
文摘Chronological data underpin paleoclimate studies.Age constraints provided by magnetostratigraphic methods can be supplemented by orbital tuning to establish higher-resolution age controls on sediments.Orbital tuning primarily involves statistical and classical tuning.This paper reviews the principles and applications of these two methods.We applied the evolutionary correlation coefficient(eCOCO/COCO)obtained from statistical tuning,and visual tuning from classical tuning to the redness(a*)value record of the Pliocene Dongwan section(10–30 m)on the Chinese Loess Plateau.We then compared the age models constructed from these two approaches.The results demonstrate that,due to local factors(e.g.,micro-topography,vegetation change,and minor erosion),sedimentation rates in terrestrial sequences,such as eolian deposits,exhibit significant variability.Sedimentation rates from statistical tuning can deviate considerably from those obtained by magnetostratigraphic studies.These discrepancies become particularly pronounced when the precession signal in the strata is weak or absent.Given that eolian deposits are often able to be dated with high-precision magnetostratigraphic methods,visual tuning can more effectively reduce the age uncertainties caused by variations in the sedimentation rate,which yields a more accurate astronomical timescale.Nevertheless,statistical tuning is a viable alternative for sequences with limited age-control points and is better suited for marine and lacustrine deposits with relatively stable sedimentation rates.
