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The phylum Nematoda remains very poorly sampled for mtDNA, with a strong bias toward parasitic, economically important or model species of the Chromadoria lineage. Most chromadorian mitogenomes share a specific order of genes encoded on one mtDNA strand. However, the few sequenced representatives of the Dorylaimia lineage exhibit a variable order of mtDNA genes encoded on both strands. While the ancestral arrangement of nematode mitogenome remains undefined, no evidence has been reported for Enoplia, the phylum's third early divergent major lineage. We describe the first mitogenome of an enoplian nematode, Campydora demonstrans, and contend that the complete 37-gene repertoire and both-strand gene encoding are ancestral states preserved in Enoplia and Dorylaimia versus the derived mitogenome arrangement in some Chromadoria. The C. demonstrans mitogenome is 17,018 bp in size and contains a noncoding perfect inverted repeat with 2013 bp-long arms, subdividing the mitogenome into two coding regions. This mtDNA arrangement is very rare among animals and instead resembles that of chloroplast genomes in land plants. Our report broadens mtDNA taxonomic sampling of the phylum Nematoda and adds support to the applicability of cox1 gene as a phylogenetic marker for establishing nematode relationships within higher taxa., (© 2024 Wiley Periodicals LLC.)

Multiple primary lung cancer (MPLC) is an increasingly prevalent subtype of lung cancer. According to recent genomic studies, the different lesions of a single MPLC patient exhibit functional similarities that may reflect evolutionary convergence. We perform whole-exome sequencing for a unique cohort of MPLC patients with multiple samples from each lesion found. Using our own and other relevant public data, evolutionary tree reconstruction reveals that cancer driver gene mutations occurred at the early trunk, indicating evolutionary contingency rather than adaptive convergence. Additionally, tumors from the same MPLC patient are as genetically diverse as those from different patients, while within-tumor genetic heterogeneity is significantly lower. Furthermore, the aberrant molecular functions enriched in mutated genes for a sample show a strong overlap with other samples from the same tumor, but not with samples from other tumors or other patients. Overall, there is no evidence of adaptive convergence during the evolution of MPLC. Most importantly, the similar between-tumor diversity and between-patient diversity suggest that personalized therapies may not adequately account for the genetic diversity among different tumors in an MPLC patient. To fully exploit the strategic value of precision medicine, targeted therapies should be designed and delivered on a per-lesion basis., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest to disclose., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The concept of homology lies in the heart of comparative biological science. The distinction between homology as structure and analogy as function has shaped the evolutionary paradigm for a century and formed the axis of comparative anatomy and embryology, which accept the identity of structure as a ground measure of relatedness. The advent of single-cell genomics overturned the classical view of cell homology by establishing a backbone regulatory identity of cell types, the basic biological units bridging the molecular and phenotypic dimensions, to reveal that the cell is the most flexible unit of living matter and that many approaches of classical biology need to be revised to understand evolution and diversity at the cellular level. The emerging theory of cell types explicitly decouples cell identity from phenotype, essentially allowing for the divergence of evolutionarily related morphotypes beyond recognition, as well as it decouples ontogenetic cell lineage from cell-type phylogeny, whereby explicating that cell types can share common descent regardless of their structure, function or developmental origin. The article succinctly summarizes current progress and opinion in this field and formulates a more generalistic view of biological cell types as avatars, transient or terminal cell states deployed in a continuum of states by the developmental programme of one and the same omnipotent cell, capable of changing or combining identities with distinct evolutionary histories or inventing ad hoc identities that never existed in evolution or development. It highlights how the new logic grounded in the regulatory nature of cell identity transforms the concepts of cell homology and phenotypic stability, suggesting that cellular evolution is inherently and massively network-like, with one-to-one homologies being rather uncommon and restricted to shallower levels of the animal tree of life., (© 2023 Wiley Periodicals LLC.)

We consider the main aspects of detailed dynamics of the reactions of direct three-body ion-ion recombination Cs + + X - + R → CsX + R (X - = F - , I - and R = Ar, Xe) for non-central encounters of the ions. The reactions are simulated by the quasiclassical trajectory method using diabatic semiempirical potential energy surfaces proposed previously. The recombination mechanisms are studied via visualization of randomly selected trajectories for each of the four systems. Comparison of trajectories for different systems with identical sets of initial conditions is carried out. For most of the presented trajectories, the ion encounter energy and the third body energy are equal to 1 eV. The characteristic function of recombination is defined, this function depends on 13 arguments including eight kinematic parameters. It is shown that the transfer of excess energy from the ion pair to the neutral atom can occur, in particular, via an encounter of the R atom with the Cs + ion, via an encounter of the R atom with the X - ion, or via successive encounters of the R atom with both the ions, as well as via an "insertion" of the R atom between the ions.

The direct three-body recombination reactions Cs + + X - + R → CsX + R (X = F, I and R = Ar, Xe) are studied within the quasiclassical trajectory method using diabatic semiempirical potential energy surfaces, the encounters of the ions being non-central. The collision energies range between 1 and 10 eV (values typical for low temperature plasma), while the so-called delay parameter, which characterizes the delay in the arrival of the neutral atom R in relation to the time instant when the distance between the ions attains its minimum, is equal to 0 or 20%. The calculation results include the recombination excitation functions, the opacity functions, and the vibrational and rotational energy distributions of the recombination products. All the four reactions considered exhibit similar overall statistical dynamics, but each process has its own features. On the whole, for both the recombining pairs Cs + + F - and Cs + + I - , xenon is more effective than argon as an acceptor of excess energy from the ion pair. The rotational energy distributions of the salt molecules CsF and CsI are almost equilibrium, whereas the vibrational energy distributions are strongly non-equilibrium.

Two enigmatic groups of morphologically simple parasites of invertebrates, the Dicyemida (syn. Rhombozoa) and the Orthonectida, since the 19th century have been usually considered as two classes of the phylum Mesozoa. Early molecular evidence suggested their relationship within the Spiralia (=Lophotrochozoa), however, high rates of dicyemid and orthonectid sequence evolution led to contradicting phylogeny reconstructions. Genomic data for orthonectids revealed that they are highly simplified spiralians and possess a reduced set of genes involved in metazoan development and body patterning. Acquiring genomic data for dicyemids, however, remains a challenge due to complex genome rearrangements including chromatin diminution and generation of extrachromosomal circular DNAs, which are reported to occur during the development of somatic cells. We performed genomic sequencing of one species of Dicyema , and obtained transcriptomic data for two Dicyema spp. Homeodomain (homeobox) transcription factors, G-protein-coupled receptors, and many other protein families have undergone a massive reduction in dicyemids compared to other animals. There is also apparent reduction of the bilaterian gene complements encoding components of the neuromuscular systems. We constructed and analyzed a large dataset of predicted orthologous proteins from three species of Dicyema and a set of spiralian animals including the newly sequenced genome of the orthonectid Intoshia linei . Bayesian analyses recovered the orthonectid lineage within the Annelida. In contrast, dicyemids form a separate clade with weak affinity to the Rouphozoa (Platyhelminthes plus Gastrotricha) or (Entoprocta plus Cycliophora) suggesting that the historically proposed Mesozoa is a polyphyletic taxon. Thus, dramatic simplification of body plans in dicyemids and orthonectids, as well as their intricate life cycles that combine metagenesis and heterogony, evolved independently in these two lineages.

Biodiversity of sphagnum bogs is one of the richest and less studied, while these ecosystems are among the top ones in ecological, conservation, and economic value. Recent studies focused on the prokaryotic consortia associated with sphagnum mosses, and revealed the factors that maintain sustainability and productivity of bog ecosystems. High-throughput sequencing technologies provided insight into functional diversity of moss microbial communities (microbiomes), and helped to identify the biochemical pathways and gene families that facilitate the spectrum of adaptive strategies and largely foster the very successful colonization of the Northern hemisphere by sphagnum mosses. Rich and valuable information obtained on microbiomes of peat bogs sets off the paucity of evidence on their eukaryotic diversity. Prospects and expectations of reliable assessment of taxonomic profiles, relative abundance of taxa, and hidden biodiversity of microscopic eukaryotes in sphagnum bog ecosystems are briefly outlined in the context of today's metagenomics.

The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.

Background: A long recognized problem is the inference of the supertree S that amalgamates a given set {G(j)} of trees G(j), with leaves in each G(j) being assigned homologous elements. We ground on an approach to find the tree S by minimizing the total cost of mappings α(j) of individual gene trees G(j) into S. Traditionally, this cost is defined basically as a sum of duplications and gaps in each α(j). The classical problem is to minimize the total cost, where S runs over the set of all trees that contain an exhaustive non-redundant set of species from all input G(j)., Results: We suggest a reformulation of the classical NP-hard problem of building a supertree in terms of the global minimization of the same cost functional but only over species trees S that consist of clades belonging to a fixed set P (e.g., an exhaustive set of clades in all G(j)). We developed a deterministic solving algorithm with a low degree polynomial (typically cubic) time complexity with respect to the size of input data. We define an extensive set of elementary evolutionary events and suggest an original definition of mapping β of tree G into tree S. We introduce the cost functional c(G, S, f) and define the mapping β as the global minimum of this functional with respect to the variable f, in which sense it is a generalization of classical mapping α. We suggest a reformulation of the classical NP-hard mapping (reconciliation) problem by introducing time slices into the species tree S and present a cubic time solving algorithm to compute the mapping β. We introduce two novel definitions of the evolutionary scenario based on mapping β or a random process of gene evolution along a species tree., Conclusions: Developed algorithms are mathematically proved, which justifies the following statements. The supertree building algorithm finds exactly the global minimum of the total cost if only gene duplications and losses are allowed and the given sets of gene trees satisfies a certain condition. The mapping algorithm finds exactly the minimal mapping β, the minimal total cost and the evolutionary scenario as a minimum over all possible distributions of elementary evolutionary events along the edges of tree S. The algorithms and their effective software implementations provide useful tools in many biological studies. They facilitate processing of voluminous tree data in acceptable time still largely avoiding heuristics. Performance of the tools is tested with artificial and prokaryotic tree data., Reviewers: This article was reviewed by Prof. Anthony Almudevar, Prof. Alexander Bolshoy (nominated by Prof. Peter Olofsson), and Prof. Marek Kimmel.

Despite the ubiquity of recombination processes in nature and various technologies, presently little is known about the dynamics of these processes. This article reports on a quasi-classical trajectory study of the dynamics of the direct three-body recombination of Cs(+) and Br(-) ions in the presence of a Xe atom at energies of the ion encounter and that of the third body ranging from 0.2 to 10 eV. Several dynamical mechanisms of stabilization of the recombining ion pair have been found. Head-on ion encounters are characterized by two mechanisms of removing the energy from the recombining pair. In the case of nonzero impact parameters of ion encounters, the dynamics leading to the stabilization of the nascent CsBr molecule becomes much more complicated and three new mechanisms appear. They depend mainly on the energy of the ion encounter, on the energy of the collision of the ion pair with the third body, and on the impact parameter of the ion encounter and the impact parameter of the third body. The common feature of all the three mechanisms is the transfer of a fraction of the rotational energy of the recombining pair to the third body. This transfer plays a key role in the stabilization of the molecule. The dynamical peculiarities observed are expected to be common for the recombination of the charged and neutral particles.

For over a century, Haeckel's Gastraea theory remained a dominant theory to explain the origin of multicellular animals. According to this theory, the animal ancestor was a blastula-like colony of uniform cells that gradually evolved cell differentiation. Today, however, genes that typically control metazoan development, cell differentiation, cell-to-cell adhesion, and cell-to-matrix adhesion are found in various unicellular relatives of the Metazoa, which suggests the origin of the genetic programs of cell differentiation and adhesion in the root of the Opisthokonta. Multicellular stages occurring in the complex life cycles of opisthokont protists (mesomycetozoeans and choanoflagellates) never resemble a blastula. Here, we discuss a more realistic scenario of transition to multicellularity through integration of pre-existing transient cell types into the body of an early metazoon, which possessed a complex life cycle with a differentiated sedentary filter-feeding trophic stage and a non-feeding blastula-like larva, the synzoospore. Choanoflagellates are considered as forms with secondarily simplified life cycles.

We present a laser driven soft x-ray source based on a novel solid argon filament. The continuously flowing micron-sized filament (diameter approximately 56 microm, flow speed approximately 5 mms) was used as a laser target in order to generate a plasma source of high brightness in the "water window" (2.2-4.4 nm) spectral range. The emission properties of the source were characterized in detail with respect to crucial parameters such as positional and energy stability using an extreme ultraviolet (XUV) sensitive pinhole camera and an XUV spectrometer. The results are compared with an argon plasma based on a gas puff target operated under the same experimental conditions showing an increase of the brilliance by a factor of 84. By changing the capillary geometry from a constant diameter to a convergent shape the flow speed of the filament was significantly increased up to 250 mms, facilitating the operation at higher repetition rates.

High resolution HF product time-of-flight spectra measured for the reactive scattering of F atoms from n-H2(p-H2) molecules at collision energies between 69 and 81 meV are compared with exact coupled-channel quantum mechanical calculations based on the Stark-Werner ab initio ground state potential energy surface. Excellent agreement between the experimental and computed rotational distributions is found for the HF product vibrational states v'=1 and v'=2. For the v'=3 vibrational state the agreement, however, is less satisfactory, especially for the reaction with p-H2. The results for v'=1 and v'=2 confirm that the reaction dynamics for these product states is accurately described by the ground electronic state 1 (2)A' potential energy surface. The deviations for HF(v'=3, j' > or =2) are attributed to an enhancement of the reaction resulting from the 25% fraction of excited ((2)P(12)) fluorine atoms in the reactant beam.

It is shown that in hard sphere (impulsive) collisions of atoms with diatomic molecules, complete conversion of the collision energy into the internal energy of the diatomic partner is possible for any number of impacts between the elastic balls representing the particles. The corresponding collision geometries and relations between the masses of the particles are described in detail.

The HeH2 van der Waals complex has been identified in a molecular beam produced by a cryogenic (T0=24.7 K) free jet expansion of a 1% H2 mixture in 99% 4He gas. The weakly bound HeH2 complexes in the beam are identified via their first order diffraction angles after passing through a 100 nm period transmission grating. An electron impact mass spectrometer analysis of the diffraction patterns is used to discriminate against ion fragments of the constituent gas clusters.

The connection between the salient features of the potential energy surface (PES) and the dynamical characteristics of the elementary collision process is studied using a correlation approach based on quasiclassical trajectory simulations. The method is demonstrated for the reaction F + D2 --> D + DF for which the scattering characteristics were calculated on a model family of PES's based on a London-Eyring-Polanyi-Sato-type five-parameter equation. The correlations between the reactive cross section and the vibrational and rotational quantum numbers and the scattering angle of the DF product, and the various parameters of the collinear and noncollinear PES's, such as the location and height of the minimal barrier and the Sato coefficients, are reported. Although usually correlations between two variables suffice, in some cases coefficients of correlation among three variables are required. The role of nonlinear parameter dependencies in computing the correlation coefficients is also considered. The correlation approach makes it possible to examine a large set of potential surfaces without intermediate human control and obtain quantitative information., ((c) 2004 American Institute of Physics)