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Species retaining ancestral features, such as species called living fossils, are often regarded as less derived than their sister groups, but such discussions are usually based on qualitative enumeration of conserved traits. This approach creates a major barrier, especially when quantifying the degree of phenotypic evolution or degree of derivedness, since it focuses only on commonly shared traits, and newly acquired or lost traits are often overlooked. To provide a potential solution to this problem, especially for inter-species comparison of gene expression profiles, we propose a new method named “derivedness index” to quantify the degree of derivedness. In contrast to the conservation-based approach, which deals with expressions of commonly shared genes among species being compared, the derivedness index also considers those that were potentially lost or duplicated during evolution. By applying our method, we found that the gene expression profiles of penta-radial phases in echinoderm tended to be more highly derived than those of the bilateral phase. However, our results suggest that echinoderms may not have experienced much larger modifications to their developmental systems than chordates, at least at the transcriptomic level. In vertebrates, we found that the mid-embryonic and organogenesis stages were generally less derived than the earlier or later stages, indicating that the conserved phylotypic period is also less derived. We also found genes that potentially explain less derivedness, such as Hox genes. Finally, we highlight technical concerns that may influence the measured transcriptomic derivedness, such as read depth and library preparation protocols, for further improvement of our method through future studies. We anticipate that this index will serve as a quantitative guide in the search for constrained developmental phases or processes. 

The electronic character of photoexcited molecules can abruptly change at avoided crossings and conical intersections. Here, we report direct mapping of the coupled interplay between electrons and nuclei in a prototype molecule, iodine monobromide (IBr), by using attosecond transient absorption spectroscopy. A few-femtosecond visible pulse resonantly excites the B ( Π 3 0 + ) , Y(0 + ), and Z(0 + ) states of IBr, and the photodissociation dynamics are tracked with an attosecond extreme-ultraviolet pulse that simultaneously probes the I-4 d and Br-3 d core-level absorption edges. Direct comparison with quantum mechanical simulations unambiguously identifies the absorption features associated with adiabatic and diabatic channels at the B/Y avoided crossing and concurrent two-photon dissociation processes that involve the Y/Z avoided crossing. The results show clear evidence for rapid switching of valence-electronic character at the avoided crossing. 

Ultrafast X-ray/XUV transient absorption spectroscopy is a powerful tool for real-time probing of chemical dynamics. Interpretation of the transient absorption spectra requires knowledge of core-excited potentials, which necessitates assistance from high-level electronic-structure computations. In this study, we investigate Br-3d core-excited electronic structures of hydrogen bromide (HBr) using spin-orbit general multiconfigurational quasidegenerate perturbation theory (SO-GMC-QDPT). Potential energy curves and transition dipole moments are calculated from the Franck-Condon region to the asymptotic limit and used to construct core-to-valence absorption strengths for five electronic states of HBr (Σ10+, 3Π1, 1Π1, 3Π0+, 3Σ1) and two electronic states of HBr+ (2Π3∕2, 2Σ1∕2). The results illustrate the capabilities of Br-3d edge probing to capture transitions of the electronic-state symmetry as well as nonadiabatic dissociation processes that evolve across avoided crossings. Furthermore, core-to-valence absorption spectra are simulated from the neutral Σ10+ state and the ionic Π21/2,3/2 states by numerically solving the time-dependent Schrödinger equation and exhibit excellent agreement with the experimental spectrum. The comprehensive and quantitative picture of the core-excited states obtained in this work allows for transparent analysis of the core-to-valence absorption signals, filling gaps in the theoretical understanding of the Br-3d transient absorption spectra.