Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears.

Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans.

Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome.

Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic backgrounds of the recipients mean that postacquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the Escherichia coli pangenome based on complex patterns of the presence or absence of other accessory genes within a genome. Our analysis leverages the repeated transfer of genes through the E. coli pangenome to observe patterns of repeated evolution following similar events. We find that the presence or absence of a substantial set of genes is highly predictable from other genes alone, indicating that selection potentiates and maintains gene-gene co-occurrence and avoidance relationships deterministically over long-term bacterial evolution and is robust to differences in host evolutionary history. We propose that at least part of the pangenome can be understood as a set of genes with relationships that govern their likely cohabitants, analogous to an ecosystem's set of interacting organisms. Our findings indicate that intragenomic gene fitness effects may be key drivers of prokaryotic evolution, influencing the repeated emergence of complex gene-gene relationships across the pangenome.

Rigidity percolation in a random tensegrity via analytic graph theory.

Functional structures from across the engineered and biological world combine rigid elements such as bones and columns with flexible ones such as cables, fibers, and membranes. These structures are known loosely as tensegrities, since these cable-like elements have the highly nonlinear property of supporting only extensile tension. Marginally rigid systems are of particular interest because the number of structural constraints permits both flexible deformation and the support of external loads. We present a model system in which tensegrity elements are added at random to a regular backbone. This system can be solved analytically via a directed graph theory, revealing a mechanical critical point generalizing that of Maxwell. We show that even the addition of a few cable-like elements fundamentally modifies the nature of this transition point, as well as the later transition to a fully rigid structure. Moreover, the tensegrity network displays a collective avalanche behavior, in which the addition of a single cable leads to the elimination of multiple floppy modes, a phenomenon that becomes dominant at the transition point. These phenomena have implications for systems with nonlinear mechanical constraints, from biopolymer networks to soft robots to jammed packings to origami sheets.

Discrete symmetries control geometric mechanics in parallelogram-based origami.

Geometric compatibility constraints dictate the mechanical response of soft systems that can be utilized for the design of mechanical metamaterials such as the negative Poisson's ratio Miura-ori origami crease pattern. Here, we develop a formalism for linear compatibility that enables explicit investigation of the interplay between geometric symmetries and functionality in origami crease patterns. We apply this formalism to a particular class of periodic crease patterns with unit cells composed of four arbitrary parallelogram faces and establish that their mechanical response is characterized by an anticommuting symmetry. In particular, we show that the modes are eigenstates of this symmetry operator and that these modes are simultaneously diagonalizable with the symmetric strain operator and the antisymmetric curvature operator. This feature reveals that the anticommuting symmetry defines an equivalence class of crease pattern geometries that possess equal and opposite in-plane and out-of-plane Poisson's ratios. Finally, we show that such Poisson's ratios generically change sign as the crease pattern rigidly folds between degenerate ground states and we determine subfamilies that possess strictly negative in-plane or out-of-plane Poisson's ratios throughout all configurations.

Omnimodal topological polarization of bilayer networks: Analysis in the Maxwell limit and experiments on a 3D-printed prototype.

Periodic networks on the verge of mechanical instability, called Maxwell lattices, are known to exhibit zero-frequency modes localized to their boundaries. Topologically polarized Maxwell lattices, in particular, focus these zero modes to one of their boundaries in a manner that is protected against disorder by the reciprocal-space topology of the lattice's band structure. Here, we introduce a class of mechanical bilayers as a model system for designing topologically protected edge modes that couple in-plane dilational and shearing modes to out-of-plane flexural modes, a paradigm that we refer to as "omnimodal polarization." While these structures exhibit a high-dimensional design space that makes it difficult to predict the topological polarization of generic geometries, we are able to identify a family of mirror-symmetric bilayers that inherit the in-plane modal localization of their constitutive monolayers, whose topological polarization can be determined analytically. Importantly, the coupling between the layers results in the emergence of omnimodal polarization, whereby in-plane and out-of-plane edge modes localize on the same edge. We demonstrate these theoretical results by fabricating a mirror-symmetric, topologically polarized kagome bilayer consisting of a network of elastic beams via additive manufacturing and confirm this finite-frequency polarization via finite element analysis and laser-vibrometry experiments.

Robotic swimming in curved space via geometric phase.

Locomotion by shape changes or gas expulsion is assumed to require environmental interaction, due to conservation of momentum. However, as first noted in [J. Wisdom, Science 299, 1865-1869 (2003)] and later in [E. Guéron, Sci. Am. 301, 38-45 (2009)] and [J. Avron, O. Kenneth, New J. Phys, 8, 68 (2006)], the noncommutativity of translations permits translation without momentum exchange in either gravitationally curved spacetime or the curved surfaces encountered by locomotors in real-world environments. To realize this idea which remained unvalidated in experiments for almost 20 y, we show that a precision robophysical apparatus consisting of motors driven on curved tracks (and thereby confined to a spherical surface without a solid substrate) can self-propel without environmental momentum exchange. It produces shape changes comparable to the environment's inverse curvatures and generates movement of [Formula: see text] cm per gait. While this simple geometric effect predominates over short time, eventually the dissipative (frictional) and conservative forces, ubiquitous in real systems, couple to it to generate an emergent dynamics in which the swimming motion produces a force that is counter-balanced against residual gravitational forces. In this way, the robot both swims forward without momentum and becomes fixed in place with a finite momentum that can be released by ceasing the swimming motion. We envision that our work will be of use in a broad variety of contexts, such as active matter in curved space and robots navigating real-world environments with curved surfaces.

Prokaryotic Pangenomes Act as Evolving Ecosystems.

Understanding adaptation to the local environment is a central tenet and a major focus of evolutionary biology. But this is only part of the adaptionist story. In addition to the external environment, one of the main drivers of genome composition is genetic background. In this perspective, I argue that there is a growing body of evidence that intra-genomic selective pressures play a significant part in the composition of prokaryotic genomes and play a significant role in the origin, maintenance and structuring of prokaryotic pangenomes.

Outcome Evaluation of Repeat Stereotactic Radiosurgery for Cerebral Arteriovenous Malformations.

BACKGROUND: Repeat stereotactic radiosurgery (SRS) for persistent cerebral arteriovenous malformation (AVM) has generally favorable patient outcomes. However, reporting studies are limited by small patient numbers and single-institution biases. The purpose of this study was to provide the combined experience of multiple centers, in an effort to fully define the role of repeat SRS for patients with arteriovenous malformation. METHODS: This multicenter, retrospective cohort study included patients treated with repeat, single-fraction SRS between 1987 and 2022. Follow-up began at repeat SRS. The primary outcome was a favorable patient outcome, defined as a composite of nidus obliteration in the absence of hemorrhage or radiation-induced neurological deterioration. Secondary outcomes were obliteration, hemorrhage risk, and symptomatic radiation-induced changes. Competing risk analysis was performed to compute yearly rates and identify predictors for each outcome. RESULTS: The cohort comprised 505 patients (254 [50.3%] males; median [interquartile range] age, 34 [15] years) from 14 centers. The median clinical and magnetic resonance imaging follow-up was 52 (interquartile range, 61) and 47 (interquartile range, 52) months, respectively. At last follow-up, favorable outcome was achieved by 268 (53.1%) patients (5-year probability, 50% [95% CI, 45%-55%]) and obliteration by 300 (59.4%) patients (5-year probability, 56% [95% CI, 51%-61%]). Twenty-eight patients (5.6%) experienced post-SRS hemorrhage with an annual incidence rate of 1.38 per 100 patient-years. Symptomatic radiation-induced changes were evident in 28 (5.6%) patients, with most occurring in the first 3 years. Larger nidus volumes (between 2 and 4 cm3, subdistribution hazard, 0.61 [95% CI, 0.44-0.86]; P=0.005; >4 cm3, subdistribution hazard, 0.47 [95% CI, 0.32-0.7]; P<0.001) and brainstem/basal ganglia involvement (subdistribution hazard, 0.6 [95% CI, 0.45-0.81]; P<0.001) were associated with reduced probability of favorable outcome. CONCLUSIONS: Repeat SRS confers reasonable obliteration rates with a low complication risk. With most complications occurring in the first 3 years, extending the latency period to 5 years generally increases the rate of favorable patient outcomes and reduces the necessity of a third intervention.

Hidden symmetries generate rigid folding mechanisms in periodic origami.

We consider the zero-energy deformations of periodic origami sheets with generic crease patterns. Using a mapping from the linear folding motions of such sheets to force-bearing modes in conjunction with the Maxwell-Calladine index theorem we derive a relation between the number of linear folding motions and the number of rigid body modes that depends only on the average coordination number of the origami's vertices. This supports the recent result by Tachi [T. Tachi, Origami 6, 97-108 (2015)] which shows periodic origami sheets with triangular faces exhibit two-dimensional spaces of rigidly foldable cylindrical configurations. We also find, through analytical calculation and numerical simulation, branching of this configuration space from the flat state due to geometric compatibility constraints that prohibit finite Gaussian curvature. The same counting argument leads to pairing of spatially varying modes at opposite wavenumber in triangulated origami, preventing topological polarization but permitting a family of zero-energy deformations in the bulk that may be used to reconfigure the origami sheet.

Hemorrhage and Recurrence of Obliterated Brain Arteriovenous Malformations Treated With Stereotactic Radiosurgery.

BACKGROUND: Although complete nidal obliteration of brain arteriovenous malformations (AVM) is generally presumed to represent durable cure, postobliteration hemorrhage, and AVM recurrence have become increasingly recognized phenomena. The goal of the study was to define hemorrhage and nidal recurrence risks of obliterated AVMs treated with stereotactic radiosurgery (SRS). METHODS: This is a retrospective cohort study from the International Radiosurgery Research Foundation comprising AVM patients treated between 1987 and 2020. Patients with AVM obliteration on digital subtraction angiography (DSA) were included. Outcomes were (1) hemorrhage and (2) AVM recurrence. Follow-up duration began at the time of AVM obliteration and was censored at subsequent hemorrhage, AVM recurrence, additional AVM treatment, or loss to follow-up. Annualized risk and survival analyses were performed. A sensitivity analysis comprising patients with AVM obliteration on magnetic resonance imaging or DSA was also performed for postobliteration hemorrhage. RESULTS: The study cohort comprised 1632 SRS-treated patients with AVM obliteration on DSA. Pediatric patients comprised 15% of the cohort, and 42% of AVMs were previously ruptured. The mean imaging follow-up after AVM obliteration was 22 months. Among 1607 patients with DSA-confirmed AVM obliteration, 16 hemorrhages (1.0%) occurred over 2223 patient-years of follow-up (0.72%/y). Of the 1543 patients with DSA-confirmed AVM obliteration, 5 AVM recurrences (0.32%) occurred over 2071 patient-years of follow-up (0.24%/y). Of the 16 patients with postobliteration hemorrhage, AVM recurrence was identified in 2 (12.5%). In the sensitivity analysis comprising 1939 patients with post-SRS AVM obliteration on magnetic resonance imaging or DSA, 16 hemorrhages (0.83%) occurred over 2560 patient-years of follow-up (0.63%/y). CONCLUSIONS: Intracranial hemorrhage and recurrent arteriovenous shunting after complete nidal obliteration are rare in AVM patients treated with SRS, and each phenomenon harbors an annual risk of <1%. Although routine postobliteration DSA cannot be recommended to SRS-treated AVM patients, long-term neuroimaging may be advisable in these patients.

Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome.

A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome's accessory gene content is structured and maintained by selection. To test this hypothesis, we interrogated the genomes of 40 Pseudomonas species for statistically significant coincident (i.e., co-occurring/avoiding) gene patterns. We found that 86.7% of common accessory genes are involved in ≥1 coincident relationship. Further, genes that co-occur and/or avoid each other-but are not vertically inherited-are more likely to share functional categories, are more likely to be simultaneously transcribed, and are more likely to produce interacting proteins, than would be expected by chance. These results are not due to coincident genes being adjacent to one another on the chromosome. Together, these findings suggest that the accessory genome is structured into sets of genes that function together within a given strain. Given the similarity of the Pseudomonas pangenome with open pangenomes of other prokaryotic species, we speculate that these results are generalizable.

Band Theory and Boundary Modes of High-Dimensional Representations of Infinite Hyperbolic Lattices.

Periodic lattices in hyperbolic space are characterized by symmetries beyond Euclidean crystallographic groups, offering a new platform for classical and quantum waves, demonstrating great potential for a new class of topological metamaterials. One important feature of hyperbolic lattices is that their translation group is nonabelian, permitting high-dimensional irreducible representations (irreps), in contrast to abelian translation groups in Euclidean lattices. Here we introduce a general framework to construct wave eigenstates of high-dimensional irreps of infinite hyperbolic lattices, thereby generalizing Bloch's theorem, and discuss its implications on unusual mode counting and degeneracy, as well as bulk-edge correspondence in hyperbolic lattices. We apply this method to a mechanical hyperbolic lattice, and characterize its band structure and zero modes of high-dimensional irreps.

Local failure after stereotactic radiosurgery (SRS) for intracranial metastasis: analysis from a cooperative, prospective national registry.

INTRODUCTION: Stereotactic radiosurgery (SRS) has been increasingly employed to treat patients with intracranial metastasis, both as a salvage treatment after failed whole brain radiation therapy (WBRT) and as an initial treatment. "Several studies have shown that SRS may be as effective as WBRT with the added benefit of preserving neuro-cognition". However, some patients may have local failure following SRS for intracranial metastasis, defined as increase in total lesion volume by 25% after at least 3 months of follow up. METHODS: The SRS registry, established by the Neuro point alliance (NPA) under the auspices of the American Association of Neurological Surgeons (AANS), was queried for patients with intracranial metastasis receiving SRS at the participating sites. Demographic, clinical symptoms, tumor, and treatment characteristics as well as follow up status were summarized for the cohort. A multivariable explanatory cox- regression was performed to evaluate the impact of each of the factors on time to local failure.at last follow-up. RESULTS: A total of 441 patients with 1255 intracranial metastatic lesions undergoing SRS were identified. The most common primary cancer histology was non-small cell lung cancer (43.8%, n = 193). More than half of the cohort had more than 1 metastatic lesion (2-3 lesions: 29.5%, n = 130; more than 3 lesions: 25.2% (n = 111). The average duration of follow-up for the cohort was found to be 8.4 months (SD = 7.61). The mean clinical treatment volume (CTV), after adding together the volume of each lesion for each patient was 5.39 cc (SD = 7.6) at baseline. A total of 20.2% (n = 89) had local failure (increase in volume by > 25%) with a mean time to progression of 7.719 months (SD = 6.09). The progression free survival (PFS) for the cohort at 3, 6 and 12 months were found to be 94.9%, 84.3%, and 69.4%, respectively. On multivariable cox regression analysis, factors associated with increased hazard of local failure included male gender (HR 1.65, 95% CI 1.03-2.66, p = 0.037), chemotherapy at or before SRS (HR = 2.39, 95% CI 1.41-4.05, p = 0.001), WBRT at or before SRS (HR = 2.21, 95% CI 1.16- 4.22, p = 0.017), while surgical resection (HR 0.45, 95% CI 0.21-0. 97, p = 0.04) and immunotherapy (0.34, 95% CI 0.16-0.50, p = 0.014) were associated with lower hazard of local failure. CONCLUSION: Factors found to be predictive of local failure included higher RPA score and those receiving chemotherapy, while patients undergoing surgical resection and those with occipital lobe lesions were less likely to experience local failure. Our analyses not only corroborate those previously reported but also demonstrate the utility of a multi-institutional registry to advance real-world SRS research for patients with intracranial metastatic lesions.

Origins of major archaeal clades correspond to gene acquisitions from bacteria.

The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa.

Endosymbiotic origin and differential loss of eukaryotic genes.

Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes.

Repeat Gamma Knife Radiosurgery for Recurrent Glossopharyngeal Neuralgia: A Systematic Review and Our Initial Experience.

BACKGROUND: Glossopharyngeal neuralgia (GPN) is a rare facial pain syndrome with debilitating symptoms. For medication-resistant GPN, stereotactic radiosurgery (SRS) is an emerging treatment option with a promising role; however, recurrence rates after SRS are fairly high. We present a patient who underwent repeat SRS for recurrent GPN and subsequently maintained over 3 years of complete pain relief. For the first time, we present a systematic review of repeat SRS for recurrent GPN. SUMMARY: Twelve cases of repeat SRS for GPN have previously been reported in the literature (13 studies including ours). Among patients with follow-up, initial pain relief was achieved in 83% (n = 10) of cases a median of 5 weeks after repeat SRS; 2 patients failed to obtain any pain relief. A favorable pain response (BNI I-IIIb) was achieved in 67 and 58% of cases at 6 and 12 months, respectively. All 13 were targeted to the glossopharyngeal meatus. Three patients (23%) experienced adverse radiation effects. Five patients (50%) experienced recurrence a median of 14 months after repeat SRS. Two patients (17%) required additional surgical intervention. At the final follow-up, 75% (n = 9) of the patients had a favorable pain outcome. Key Messages: Repeat SRS may be a viable alternative to open surgery for the treatment of recurrent GPN, albeit with an increased risk of adverse radiation effects. Though limited by a small cohort of patients, the best predictors of an effective second treatment may be a response to initial SRS for >5 months, a maximum dose >75 Gy, and a target at the glossopharyngeal meatus. Larger prospective studies are needed to better define its role.

Bipartite Network Analysis of Gene Sharings in the Microbial World.

Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification, and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8,217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny. Homologous genes are recycled by lateral gene transfer, and multiple copies of homologous genes are carried by otherwise completely unrelated (and possibly nested) genomes, that is, viruses, plasmids and prokaryotes. When a homologous gene is present on at least one plasmid or virus and at least one chromosome, a process of "gene externalization," affected by a postprocessed selected functional bias, takes place, especially in Bacteria. Bipartite graphs give us a view of vertical and horizontal gene flow beyond classic taxonomy on a single very large, analytically tractable, graph that goes beyond the cellular Web of Life.

Curved boundaries and chiral instabilities - two sources of twist in homeotropic nematic tori.

Many liquid crystalline systems display spontaneous breaking of achiral symmetry, as achiral molecules aggregate into large chiral domains. In confined cylinders with homeotropic boundary conditions, chromonic liquid crystals - which have a twist elastic modulus which is at least an order of magnitude less than their splay and bend counter parts - adopt a twisted escaped radial texture (TER) to minimize their free energy, whilst 5CB - which has all three elastic constants roughly comparable - does not. In a recent series of experiments, we have shown that 5CB confined to tori and bent cylindrical capillaries with homeotropic boundary conditions also adopts a TER structure resulting from the curved nature of the confining boundaries [P. W. Ellis et al., Phys. Rev. Lett., 2018, 247803]. We shall call this microscopic twist, as the twisted director organization not only depends on the confinement geometry but also on the values of elastic moduli. Additionally, we demonstrate theoretically that the curved geometry of the boundary induces a twist in the escaped radial (ER) texture. Moving the escaped core of the structure towards the center of the torus not only lowers the splay and bend energies, but lowers the energetic cost of this distinct source for twist that we shall call geometric twist. As the torus becomes more curved, the ideal location for the escaped core approaches the inner radius of the torus.

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.

The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug-resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.

Formation of chimeric genes with essential functions at the origin of eukaryotes.

BACKGROUND: Eukaryotes evolved from the symbiotic association of at least two prokaryotic partners, and a good deal is known about the timings, mechanisms, and dynamics of these evolutionary steps. Recently, it was shown that a new class of nuclear genes, symbiogenetic genes (S-genes), was formed concomitant with endosymbiosis and the subsequent evolution of eukaryotic photosynthetic lineages. Understanding their origins and contributions to eukaryogenesis would provide insights into the ways in which cellular complexity has evolved. RESULTS: Here, we show that chimeric nuclear genes (S-genes), built from prokaryotic domains, are critical for explaining the leap forward in cellular complexity achieved during eukaryogenesis. A total of 282 S-gene families contributed solutions to many of the challenges faced by early eukaryotes, including enhancing the informational machinery, processing spliceosomal introns, tackling genotoxicity within the cell, and ensuring functional protein interactions in a larger, more compartmentalized cell. For hundreds of S-genes, we confirmed the origins of their components (bacterial, archaeal, or generally prokaryotic) by maximum likelihood phylogenies. Remarkably, Bacteria contributed nine-fold more S-genes than Archaea, including a two-fold greater contribution to informational functions. Therefore, there is an additional, large bacterial contribution to the evolution of eukaryotes, implying that fundamental eukaryotic properties do not strictly follow the traditional informational/operational divide for archaeal/bacterial contributions to eukaryogenesis. CONCLUSION: This study demonstrates the extent and process through which prokaryotic fragments from bacterial and archaeal genes inherited during eukaryogenesis underly the creation of novel chimeric genes with important functions.