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Abstract Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages. The redundancy created by WGDs typically results in a phase of massive gene loss. However, some WGD–derived paralogs are maintained over long evolutionary periods, and the relative contributions of different selective pressures to their maintenance are still debated. Previous studies have revealed a history of three successive WGDs in the lineage of the ciliate Paramecium tetraurelia and two of its sister species from the Paramecium aurelia complex. Here, we report the genome sequence and analysis of 10 additional P. aurelia species and 1 additional out group, revealing aspects of post-WGD evolution in 13 species sharing a common ancestral WGD. Contrary to the morphological radiation of vertebrates that putatively followed two WGD events, members of the cryptic P. aurelia complex have remained morphologically indistinguishable after hundreds of millions of years. Biases in gene retention compatible with dosage constraints appear to play a major role opposing post-WGD gene loss across all 13 species. In addition, post-WGD gene loss has been slower in Paramecium than in other species having experienced genome duplication, suggesting that the selective pressures against post-WGD gene loss are especially strong in Paramecium. A near complete lack of recent single-gene duplications in Paramecium provides additional evidence for strong selective pressures against gene dosage changes. This exceptional data set of 13 species sharing an ancestral WGD and 2 closely related out group species will be a useful resource for future studies on Paramecium as a major model organism in the evolutionary cell biology. 

Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant Tree of Life continues to improve. The intersection of these two research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a “model clade”. These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis thaliana and the family Brassicaceae. We promote the utility of such a “model clade” and make suggestions for building global networks to support future studies in the model order Brassicales.

 

Abstract By modeling the homoeologous gene losses that occurred in 50 genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes, or yeasts. We show that many of the events show a relative rate of duplicate gene loss before the first postpolyploidy speciation that is significantly higher than in later phases of their evolution. The relatively weak selective constraint experienced by the single-copy genes these losses produced leads us to suggest that most of the purely selectively neutral duplicate gene losses occur in the immediate postpolyploid period. Nearly all of the events show strong evidence of biases in the duplicate losses, consistent with them being allopolyploidies, with 2 distinct progenitors contributing to the modern species. We also find ongoing and extensive reciprocal gene losses (alternative losses of duplicated ancestral genes) between these genomes. With the exception of a handful of closely related taxa, all of these polyploid organisms are separated from each other by tens to thousands of reciprocal gene losses. As a result, it is very unlikely that viable diploid hybrid species could form between these taxa, since matings between such hybrids would tend to produce offspring lacking essential genes. It is, therefore, possible that the relatively high frequency of recurrent polyploidies in some lineages may be due to the ability of new polyploidies to bypass reciprocal gene loss barriers. 

Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Extensive heteroplasmy is observed in D. obtusa, where the high level of intraclonal divergence must have resulted from a biparental-inheritance event, and recombination in the mitochondrial genome is apparent, although perhaps not widespread. Global samples of D. pulex reveal remarkably low mitochondrial effective population sizes, <3% of those for the nuclear genome. In addition, levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, suggesting an idiosyncratic evolutionary history of mitochondria in D. pulex. These population-genetic features appear to be a consequence of background selection associated with highly deleterious mutations arising in the strongly linked mitochondrial genome, which is consistent with polymorphism and divergence data suggesting a predominance of strong purifying selection. Nonetheless, the fixation of mildly deleterious mutations in the mitochondrial genome also appears to be driving positive selection on genes encoded in the nuclear genome whose products are deployed in the mitochondrion. 

Understanding why various organisms evolve alternative ways of living requires information on both the fitness advantages of phenotypic modifications and the costs of constructing and operating cellular features. Although the former has been the subject of a myriad of ecological studies, almost no attention has been given to how organisms allocate resources to alternative structures and functions. We address these matters by capitalizing on an array of observations on diverse ciliate species and from the emerging field of evolutionary bioenergetics. A relatively robust and general estimator for the total cost of a cell per cell cycle (in units of ATP equivalents) is provided, and this is then used to understand how the magnitudes of various investments scale with cell size. Among other things, we examine the costs associated with the large macronuclear genomes of ciliates, as well as ribosomes, various internal membranes, osmoregulation, cilia, and swimming activities. Although a number of uncertainties remain, the general approach taken may serve as blueprint for expanding this line of work to additional traits and phylogenetic lineages.

 

Fast diffusing Li isotopes provide important insights into the “recent” transient events or processes for both modern and ancient times, but questions remain concerning the large Li isotopic variations of mantle peridotites, which greatly hampers their usage as a geochemical tracer. This study investigates in situ Li content and isotopic profiles of the constituent minerals of abyssal peridotites from the Gakkel Ridge and Southwest Indian Ridge. The complicated and large variations of Li isotopic profiles in Clinopyroxene (Cpx) and Orthopyroxene (Opx) indicate Li isotopic disequilibrium at millimeter scale. The negative correlations of a wide range of Li contents (0.5 to 6.5 ppm) and δ⁷Li values (−10 to +20‰) of olivine, Opx and Cpx grains/relicts, trace element zoning of Cpx, the occurrence of plagioclase, olivine serpentinization along cracks, together with numerical modeling demonstrate the observed Li characteristics to be a manifestation of high‐temperature mineral‐melt Li diffusion during melt impregnation overprinted by low‐temperature mineral‐fluid Li diffusion during dissolution and serpentinization. The preservation of the Li isotopic diffusion profiles requires rapid cooling of 0.3–5°C/year after final‐stage melt impregnation at the Moho boundary, which is consistent with the low temperature at very slow spreadin g ridges caused by conductive cooling. Compared with the well‐studied melt‐rock interaction process, our study indicates that low‐temperature fluid‐rock interaction can induce Li diffusion even in the visibly unaltered mineral relicts of partially altered rocks.

 

Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication.

In order to test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties ofBrassica rapa. Like all ‘diploid’ flowering plants,B. rapahas a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivatedB. rapaaccessions.

Using a combination of approaches, we identified > 3000 candidate genes associated with the domestication of four majorB. rapacrop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non‐paleologs.

Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication ofB. rapaand provide support for its importance in the success of modern agriculture.

 

2D materials exhibit strong excitonic effects due to low dimensionality and enhanced Coulomb interactions, resulting in fascinating many‐particle phenomena like excitons. Though perovskite is a classical type of material hosting abundant correlated electronic phases, freestanding 2D perovskite oxides are not easy to fabricate and yet to be extensively studied. Here the realization of large size (1 × 1 cm²) freestanding perovskite SrTiO₃films, which show unexpected excitonic photoluminescence (PL) spectra and carrier dynamics, is reported. Two pronounced broad PL peaks emerge in 2D freestanding SrTiO₃films at 2.34–2.4 and 1.8–1.9 eV, of which the 2.34–2.4 eV emission originates from self‐trapped excitons localized within TiO₆octahedra, and the 1.8–1.9 eV peak from Ti vacancies. The time‐resolved PL shows a remarkable enhancement of nonradiative Auger recombination through three‐particle process, in which electron–hole excitons transfer their kinetic energy to other free electrons or holes. The results demonstrate unique excitonic properties in 2D perovskite SrTiO₃films and unravel their potential for high‐performance optoelectronic devices.