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The testis produces gametes through spermatogenesis and evolves rapidly at both the morphological and molecular level in mammals1-6, probably owing to the evolutionary pressure on males to be reproductively successful7. However, the molecular evolution of individual spermatogenic cell types across mammals remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from 11 species that cover the three main mammalian lineages (eutherians, marsupials and monotremes) and birds (the evolutionary outgroup), and include seven primates. We find that the rapid evolution of the testis was driven by accelerated fixation rates of gene expression changes, amino acid substitutions and new genes in late spermatogenic stages, probably facilitated by reduced pleiotropic constraints, haploid selection and transcriptionally permissive chromatin. We identify temporal expression changes of individual genes across species and conserved expression programs controlling ancestral spermatogenic processes. Genes predominantly expressed in spermatogonia (germ cells fuelling spermatogenesis) and Sertoli (somatic support) cells accumulated on X chromosomes during evolution, presumably owing to male-beneficial selective forces. Further work identified transcriptomal differences between X- and Y-bearing spermatids and uncovered that meiotic sex-chromosome inactivation (MSCI) also occurs in monotremes and hence is common to mammalian sex-chromosome systems. Thus, the mechanism of meiotic silencing of unsynapsed chromatin, which underlies MSCI, is an ancestral mammalian feature. Our study illuminates the molecular evolution of spermatogenesis and associated selective forces, and provides a resource for investigating the biology of the testis across mammals. We thank all members of the Kaessmann group, S. Tirier for discussions and N. Trost for the administration of the Kaessmann laboratory server. Computations were performed on the Kaessmann laboratory server and the bwForCluster from the Heidelberg University Computational Center (supported by the state of Baden-Württemberg through bwHPC and the German Research Foundation grant no. INST 35/1134-1 FUGG). This research was supported by grants from the ERC (grant no. 615253, OntoTransEvol) and German Research Council (DFG, grant nos. SFB 873 and KA 1710/4-1) to H.K., by the CellNetworks Postdoc Fellowship and EMBO Long-Term Fellowship to F.M. (grant no. ALTF 591-2017), and by the Australian Research Council (grant no. FT160100267) to F.G. and by the Novo Nordisk Foundation (grant no. NNF21OC0069913) to K.A. and (grant no. NNF18OC0031004) to M.H.S. The use of all other mammalian samples for the type of work described in this study was approved by ERC ethics screening panels (ERC starting grant no. 242597, SexGenTransEvolution and ERC consolidator grant no. 615253, OntoTransEvol).

Many biological membranes are asymmetric and exhibit complex lipid composition, comprising hundreds of distinct chemical species. Identifying the biological function and advantage of this complexity is a central goal of membrane biology. Here, we study how membrane complexity controls the energetics of the first steps of membrane fusions, that is, the formation of a stalk. We first present a computationally efficient method for simulating thermodynamically reversible pathways of stalk formation at coarse-grained resolution. The method reveals that the inner leaflet of a typical plasma membrane is far more fusogenic than the outer leaflet, which is likely an adaptation to evolutionary pressure. To rationalize these findings by the distinct lipid compositions, we computed ~200 free energies of stalk formation in membranes with different lipid head groups, tail lengths, tail unsaturations, and sterol content. In summary, the simulations reveal a drastic influence of the lipid composition on stalk formation and a comprehensive fusogenicity map of many biologically relevant lipid classes., Fusion of cellular membranes begins with the formation of a stalk. Here, the authors develop a computationally efficient method for coarse-grained simulations of stalk formation and apply this approach to comprehensively analyse how stalk formation is influenced by the membrane lipid composition.

The anoxygenic phototrophic bacterium Heliobacterium modesticaldum contains a photochemical reaction center protein complex (called the HbRC) consisting of a homodimer of the PshA polypeptide and two copies of a newly discovered polypeptide called PshX, which is a single transmembrane helix that binds two bacteriochlorophyll g molecules. To assess the function of PshX, we produced a ∆pshX strain of Hbt. modesticaldum by leveraging the endogenous Hbt. modesticaldum Type I-A CRISPR-Cas system to aid in mutant selection. We optimized this system by separating the homologous recombination and CRISPR-based selection steps into two plasmid transformations, allowing for markerless gene replacement. Fluorescence and low-temperature absorbance of the purified HbRC from the wild-type and ∆pshX strains showed that the bacteriochlorophylls bound by PshX have the lowest site energies in the entire HbRC. This indicates that PshX acts as a low-energy antenna subunit, participating in entropy-assisted uphill energy transfer toward the P800 special bacteriochlorophyll g pair. We further discuss the role that PshX may play in stability of the HbRC, its conservation in other heliobacterial species, and the evolutionary pressure to produce and maintain single-TMH subunits in similar locations in other reaction centers.

Ecology is complex and while there is a modern drive towards a holistic or “ecosystem approach” for managing marine systems, we are still a long way from fully understanding the interactions between the various components of different ecosystems and fully valuing their contributions. Microphytobenthos (MPB), and diatom biofilms, are an excellent example. While they are relatively widespread, their role was often overlooked in favor of more charismatic species or assemblages. However, the understanding of their ecological importance has increased with a growing body of evidence outlining their important role in system functions ranging from biogeochemical cycles, trophic interactions and a direct influence of sediment dynamics. The latter effect is related to the secretion of extracellular polymeric substances (EPS) which have a number of roles in ecosystem dynamics including the mediation of sediment erosion. Therefore, it is understandable that characterization of MPB assemblages as ecosystems engineers is becoming more widespread. A more recent development is the debate surrounding the evolutionary impact of ecosystem engineering and whether this is sufficiently distinct and important that it should be considered a separate evolutionary pressure, as described in the “niche construction” theory. MPB have already been cited in this debate and this chapter briefly introduces the range of functionality of MPB and discusses their role as ecosystem engineers and their potential place in niche construction theory.

Of Chargaff's four "rules" on DNA base frequencies, the functional interpretation of his second parity rule (PR2) is the most contentious. Thermophile base compositions (GC%) were taken by Galtier and Lobry (1997) as favoring Sueoka's neutral PR2 hypothesis over Forsdyke's selective PR2 hypothesis, namely that mutations improving local within-species recombination efficiency had generated a genome-wide potential for the strands of duplex DNA to separate and initiate recombination through the "kissing" of the tips of stem-loops. However, following Chargaff's GC rule, base composition mainly reflects a species-specific, genome-wide, evolutionary pressure. GC% could not have consistently followed the dictates of temperature, since it plays fundamental roles in both sustaining species integrity and, through primarily neutral genome-wide mutation, fostering speciation. Evidence for a local within-species recombination-initiating role of base order was obtained with a novel technology that masked the contribution of base composition to nucleic acid folding energy. Forsdyke's results were consistent with his PR2 hypothesis, appeared to resolve some root problems in biology and provided a theoretical underpinning for alignment-free taxonomic analyses using relative oligonucleotide frequencies (k-mer analysis). Moreover, consistent with Chargaff's cluster rule, discovery of the thermoadaptive role of the "purine-loading" of open reading frames made less tenable the Galtier-Lobry anti-selectionist arguments. Supplementary Information The online version contains supplementary material available at 10.1007/s10709-021-00119-5.

The high-specific-activity factor IX (FIX) variant Padua (R338L) is the most promising transgene for hemophilia B (HB) gene therapy. Although R338 is strongly conserved in mammalian evolution, amino acid substitutions at this position are underrepresented in HB databases. We therefore undertook a complete 20 amino acid scan and determined the specific activity of human (h) and canine (c) FIX variants with every amino acid substituted at position 338. Notably, we observe that hFIX-R338L is the most active variant and cFIX-R338L is sevenfold higher than wild-type (WT) cFIX. This is consistent with the previous identification of hFIX-R338L as a cause of a rare X-linked thrombophilia risk factor. Moreover, WT hFIX and cFIX are some of the least active variants. We confirmed the increased specific activity relative to FIX-WT in vivo of a new variant, cFIX-R338I, after gene therapy in an HB dog. Last, we screened 232 pediatric subjects with thromboembolic disease without identifying F9 R338 variants. Together these observations suggest a surprising evolutionary pressure to limit FIX activity with WT FIX rather than maximize FIX activity.

Desde sus orígenes, las plantas terrestres vasculares han coexistido con una amplia variedad de bacterias y hongos. Con la aparición de los insectos, de igual forma mantuvieron una estrecha relación con estos, tomando un carácter especial con la llegada de las plantas con flores en el período Cretácico temprano. Los diferentes procesos evolutivos han propiciado el desarrollo de una serie de relaciones interespecíficas, algunas de ellas beneficiosas para ambas partes como pudieran ser los variados mecanismos de polinización por medio de insectos en muchas especies de plantas y al mismo tiempo han surgido otros tipos de interacciones con especies capaces de producir enfermedades serias en las diferentes partes de las plantas. Esta presión de selección, unido a la imposibilidad de defensa que ofrece la locomoción, así como la carencia de un sistema de defensa basado en anticuerpos, han sido las principales responsables de la aparición en las plantas de complejos mecanismos de defensa, muchas veces rápidos y eficaces frente a las especies agresoras y otras veces no. La manifestación de las patologías en las plantas depende de complejas interacciones entre el huésped y el patógeno, lo que es un indicador de su evolución conjunta. De aquí la exquisita regulación de los mecanismos de agresión/defensa y la correspondiente selectividad en el reconocimiento de agentes agresores externos, lo que puede explicar la diferente sensibilidad de distintas especies o incluso diferentes variedades dentro de la misma especie. Desde hace un tiempo a la fecha, los investigadores han mostrado mucho interés en ciertas proteínas sintetizadas por la planta cuando es atacada por un microorganismo patógeno. Dado que aparecen en condiciones patológicas, han sido nombradas proteínas relacionadas con la patogenicidad o PR.

Differences in elemental stoichiometry among consumers can regulate fundamental ecological processes such as animal production or nutrient cycling within ecosystems. Research to date has established that consumer stoichiometry differs within and across taxa, but the degree to which organismal stoichiometry ranges ontogenetically across life stages or body sizes is poorly understood. To understand patterns of variation in organismal C:N:P stoichiometry, we analyzed the elemental carbon (C), nitrogen (N) and phosphorus (P) composition of 436 aquatic macroinvertebrates across the ontogeny of 13 taxa representing different life history strategies and developmental modes in a high mountain stream. Our results showed that C:N:P stoichiometry varied among taxonomic groups, macroinvertebrate taxa, but not among functional feeding groups. However, stoichiometric variability within taxa was comparable or exceeded those among taxa and was primarily caused by changes in P content. We found undocumented positive relationships between P content and body mass in hemimetabolous taxa, with %P increments ranging from five to eightfold across ontogeny. Overall, findings lend evidence to the idea that phylogenetic relationships may be an important but secondary determinant of C:N:P stoichiometry relative to ontogeny. Elucidating the mechanistic basis for the positive relationship between body mass and P content in hemimetabolous taxa may reveal fundamental differences in the ecology and evolutionary pressure behind hemi- versus holometabolous developmental modes in nature.

Allostery is a fundamental regulatory mechanism of protein function. Despite notable advances, understanding the molecular determinants of allostery remains an elusive goal. Our current knowledge of allostery is principally shaped by a structure-centric view which makes it difficult to understand the decentralized character of allostery. We present a function-centric approach using deep mutational scanning to elucidate the molecular basis and underlying functional landscape of allostery. We show that allosteric signaling exhibits a high-degree of functional plasticity and redundancy through myriad mutational pathways. Residues critical for allosteric signaling are surprisingly poorly conserved while those required for structural integrity are highly conserved, suggesting evolutionary pressure to preserve fold over function. Our results suggest multiple solutions to the thermodynamic conditions of cooperativity, in contrast to the common view of a finely-tuned allosteric residue network maintained under selection.

Cancer has proven to be an extremely difficult challenge to treat. Several fundamental issues currently underlie cancer treatment, including differentiating self from nonself, functional coupling of the recognition and therapeutic components of various therapies, and the propensity of cancerous cells to develop resistance to common treatment modalities via evolutionary pressure. Given these limitations, there is an increasing need to develop an all-encompassing therapeutic that can uniquely target malignant cells, decouple recognition from treatment, and overcome evolutionarily driven cancer resistance. We describe herein a new class of programmable self-assembling double-stranded RNA (dsRNA)-based cancer therapeutics that uniquely targets aberrant genetic sequences and in a functionally decoupled manner, undergoes oncogenic RNA-activated displacement (ORAD), initiating a therapeutic cascade that induces apoptosis and immune activation. As a proof of concept, we show that RNA strands targeting the EWS/Fli1 fusion gene in Ewing sarcoma cells that are end blocked with phosphorothioate bonds and additionally sealed with a 2′-deoxyuridine (2′-U)-modified DNA protector can be used to induce specific and potent killing of cells containing the target oncogenic sequence but not wild type., Graphical Abstract, The authors describe a new class of programmable self-assembling dsRNA-based cancer therapeutics that uniquely targets cancerous genetic sequences and in a functionally decoupled manner, undergoes oncogenic RNA-activated displacement (ORAD), initiating a therapeutic cascade that induces apoptosis and immune activation in cancer cells.

After 300 million years of evolution, the first land-living mammals reentered the marine environment some 50 million years ago. The driving forces for this dramatic lifestyle change are still a matter of discussion but the struggle for food resources and the opportunity to escape predators probably contributed. Reentering the oceans requires metabolic adaption putting evolutionary pressure on a number of genes. To explore whether eicosanoid signaling has been part of this adaptive response, we first explored whether the genomes of marine mammals involve functional genes encoding for key enzymes of eicosanoid biosynthesis. Cyclooxygenase (COX) and lipoxygenase (ALOX) genes are present in the genome of all marine mammals tested. Interestingly, ALOX12B, which has been implicated in skin development of land-living mammals, is lacking in whales and dolphins and genes encoding for its sister enzyme (ALOXE3) involve premature stop codons and/or frameshifting point mutations, which interrupt the open reading frames. ALOX15 orthologs have been detected in all marine mammals, and the recombinant enzymes exhibit similar catalytic properties as those of land-living species. All marine mammals express arachidonic acid 12-lipoxygenating ALOX15 orthologs, and these data are consistent with the Evolutionary Hypothesis of ALOX15 specificity. These enzymes exhibit membrane oxygenase activity and introduction of big amino acids at the triad positions altered the reaction specificity in favor of arachidonic acid 15-lipoxygenation. Thus, the ALOX15 orthologs of marine mammals follow the Triad concept explaining their catalytic specificity.

The advertisement call contains important spectral and temporal information for species-specific recognition and is generally related to sexual attraction. On the other hand, the territorial call i...

Lower Miocene outcrops from Patagonia (Gaiman Formation, Burdigalian) may reveal more clues for the yet unknown aspects for this period in the evolution of odontocetes. Here, we present the first toothless platanistoid dolphin from the lower Miocene of Patagonia, Dolgopolis kinchikafiforo, gen. et sp. nov. The specimen includes an incomplete skull, with no mandibles or earbones, but sufficiently different from other named odontocetes to propose a new genus and species. Phylogenetic analyses indicated it is a platanistoid of uncertain position within the group, and that it shares some homoplastic characters with physeteroids and ziphioids. Given the absence of defined alveoli and teeth and an inferred moderately short and wide rostrum, we interpreted this new species as most likely a capture suction feeder. Based on our phylogenetic hypothesis, the optimization of feeding strategies recovered raptorial feeding as the plesiomorphic method, and convergent evolution of capture suction feeders in at least four lineages. Platanistoids recorded all feeding strategies during the late Oligocene-early Miocene, although raptorial is the predominant method. This suggests a partitioning of the ecological niches in the early phases of platanistoid evolution, as well as a high diversification of feeding methods previously underestimated for this period. Thus, ecological adaptations have a strong evolutionary pressure in odontocetes communities and should be further explored Fil: Viglino, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Geología y Paleontología; Argentina Fil: Gaetán, Carlos Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Geología y Paleontología; Argentina Fil: Cuitiño, José Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Geología y Paleontología; Argentina Fil: Buono, Mónica Romina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Geología y Paleontología; Argentina

The neuropancreatic polypeptide hormone amylin forms pancreatic islet amyloid in type-2 diabetes. Islet amyloid formation contributes to β-cell death in the disease and to the failure of islet transplants, but the features which influence amylin amyloidogenicity are not understood. We constructed an amino acid sequence alignment of 202 sequences of amylin and used the alignment to design consensus sequences of vertebrate amylins, mammalian amylins, and primate amylins. Amylin is highly conserved, but there are differences between human amylin and each consensus sequence, ranging from one to six substitutions. Biophysical analysis shows that all of the consensus sequences form amyloid but do so more slowly than human amylin in vitro. The rate of amyloid formation by the primate consensus sequence is 3- to 4-fold slower than human amylin; the mammalian consensus sequence is approximately 20- to 25-fold slower, and the vertebrate consensus sequence is approximately 6-fold slower. All of the consensus sequences are moderately less toxic than human amylin toward a cultured β-cell line, with the vertebrate consensus sequence displaying the largest reduction in toxicity of 3- to 4-fold. All of the consensus sequences activate a human amylin receptor and exhibit only modest reductions in activity, ranging from 3- to 4-fold as judged by a cAMP production assay. The analysis argues that there is no strong selective evolutionary pressure to avoid the formation of islet amyloid and provides information relevant to the design of less amyloidogenic amylin variants.

Achlorophyllous, mycoheterotrophic plants depend on their mycorrhizal fungi for 100% of their carbon supply. Hence, there is strong evolutionary pressure towards a well-organized functioning of the association from the plant’s perspective. Members of the mycoheterotrophic genus Afrothismia have evolved elaborate fungal colonization patterns allowing a sustained benefit from external fungal penetration events. On the basis of anatomical details of the root-shoot systems of A. korupensis and A. hydra, we elucidate an evolutionary progression between the comparatively simple mycorrhizal pattern in A. gesnerioides and the so far most complex mycorrhiza in A. saingei. We detected two major advancements: (1) two species, A. korupensis and A. saingei, use the fungus itself as energy storage, replacing starch depositions used by A. gesnerioides and A. hydra, and (2) the morphological complexity of hyphal forms in plant tissue compartments increases from A. gesnerioides to A. saingei. We discuss the omitting of starch metabolism as well as the morpho-anatomical differences as an evolutionary fine-tuning of the compartmented mycorrhizal organization in Afrothismia. Our results support the idea of a taxonomic distinction between Afrothismia and other Thismiaceae.

Variants in genes encoding synaptic adhesion proteins of the neuroligin family, most notably neuroligin-4, are a significant cause of autism spectrum disorders in humans. Although human neuroligin-4 is encoded by two genes, NLGN4X and NLGN4Y, that are localized on the X-specific and male-specific regions of the two sex chromosomes, the chromosomal localization and full genomic sequence of the mouse Nlgn4 gene remain elusive. Here, we analyzed the neuroligin-4 genes of numerous rodent species by direct sequencing and bioinformatics, generated complete drafts of multiple rodent neuroligin-4 genes, and examined their evolution. Surprisingly, we find that the murine Nlgn4 gene is localized to the pseudoautosomal region (PAR) of the sex chromosomes, different from its human orthologs. We show that the sequence differences between various neuroligin-4 proteins are restricted to hotspots in which rodent neuroligin-4 proteins contain short repetitive sequence insertions compared with neuroligin-4 proteins from other species, whereas all other protein sequences are highly conserved. Evolutionarily, these sequence insertions initiate in the clade eumuroidea of the infraorder myomorpha and are additionally associated with dramatic changes in noncoding sequences and gene size. Importantly, these changes are not exclusively restricted to neuroligin-4 genes but reflect major evolutionary changes that substantially altered or even deleted genes from the PARs of both sex chromosomes. Our results show that despite the fact that the PAR in rodents and the neuroligin-4 genes within the rodent PAR underwent massive evolutionary changes, neuroligin-4 proteins maintained a highly conserved core structure, consistent with a substantial evolutionary pressure preserving its physiological function.

Bacteria are under immense evolutionary pressure from their viral invaders-bacteriophages. Bacteria have evolved numerous immune mechanisms, both innate and adaptive, to cope with this pressure. The discovery and exploitation of CRISPR-Cas systems have stimulated a resurgence in the identification and characterization of anti-phage mechanisms. Bacteriophages use an extensive battery of counter-defence strategies to co-exist in the presence of these diverse phage defence mechanisms. Understanding the dynamics of the interactions between these microorganisms has implications for phage-based therapies, microbial ecology and evolution, and the development of new biotechnological tools. Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriophages.

Coral reefs are under extreme threat due to a number of stressors, but temperature increases due to changing climate are the most severe. Rising ocean temperatures coupled with local extremes lead to extensive bleaching, where the coral-algal symbiosis breaks down and corals may die, compromising the structure and function of reefs. Although the symbiotic nature of the coral colony has historically been a focus of research on coral resilience, the host itself is a foundational component in the response to thermal stress. Fixed effects in the coral host set trait baselines through evolutionary processes, acting on many loci of small effect to create mosaics of thermal tolerance across latitudes and individual coral reefs. These genomic differences can be strongly heritable, producing wide variation among clones of different genotypes or families of a specific larval cross. Phenotypic plasticity is overlaid on these baselines and a growing body of knowledge demonstrates the potential for acclimatization of reef-building corals through a variety of mechanisms that promote resilience and stress tolerance. The long-term persistence of coral reefs will require many of these mechanisms to adjust to warmer temperatures within a generation, bridging the gap to reproductive events that allow recombination of standing diversity and adaptive change. Business-as-usual climate scenarios will probably lead to the loss of some coral populations or species in the future, so the interaction between intragenerational effects and evolutionary pressure is critical for the survival of reefs.

The generation of large immune gene families is often driven by evolutionary pressure exerted on host genomes by their pathogens, which has been described as the immunological arms race. The SpTransformer (SpTrf) gene family from the California purple sea urchin, Strongylocentrotus purpuratus, is upregulated upon immune challenge and encodes the SpTrf proteins that interact with pathogens during an immune response. Native SpTrf proteins bind both bacteria and yeast, and augment phagocytosis of a marine Vibrio, while a recombinant SpTrf protein (rSpTrf-E1) binds a subset of pathogens and a range of pathogen associated molecular patterns. In the sequenced sea urchin genome, there are four SpTrf gene clusters for a total of 17 genes. Here, we report an in-depth analysis of these genes to understand the sequence complexities of this family, its genomic structure, and to derive a putative evolutionary history for the formation of the gene clusters. We report a detailed characterization of gene structure including the intron type and UTRs with conserved transcriptional start sites, the start codon and multiple stop codons, and locations of polyadenylation signals. Phylogenetic and percent mismatch analyses of the genes and the intergenic regions allowed us to predict the last common ancestral SpTrf gene and a theoretical evolutionary history of the gene family. The appearance of the gene clusters from the theoretical ancestral gene may have been driven by multiple duplication and deletion events of regions containing SpTrf genes. Duplications and ectopic insertion events, indels, and point mutations in the exons likely resulted in the extant genes and family structure. This theoretical evolutionary history is consistent with the involvement of these genes in the arms race in responses to pathogens and suggests that the diversification of these genes and their encoded proteins have been selected for based on the survival benefits of pathogen binding and host protection.

Since the start of the pandemic, SARS-CoV-2 has infected almost 200 million human hosts and is set to encounter and gain entry in many more in the coming months. As the coronavirus flourish, the evolutionary pressure selects those variants that can complete the infection cycle faster and reproduce in large numbers compared to others. This increase in infectivity and transmissibility coupled with the immune response from high viral load may cause moderate to severe disease. Whether this leads to enhanced virulence in the prevalent Alpha and Delta variants is still not clear. This review describes the different types of SARS-CoV-2 variants that are now prevalent, their emergence, the mutations responsible for their growth advantages, and how they affect vaccine efficacy and increase chances of reinfection. Finally, we have also summarized the efforts made to recognize and predict the mutations, which can cause immune escape and track their emergence through impactful genomic surveillance.

SARS-CoV-2 infects humans and causes Coronavirus disease 2019 (COVID-19). The S1 domain of the spike glycoprotein of SARS-CoV-2 binds to human angiotensin-converting enzyme 2 (hACE2) via its receptor-binding domain, while the S2 domain facilitates fusion between the virus and the host cell membrane for entry. The spike glycoprotein of circulating SARS-CoV-2 genomes is a mutation hotspot. Some mutations may affect the binding affinity for hACE2, while others may modulate S-glycoprotein expression, or they could result in a virus that can escape from antibodies generated by infection with the original variant or by vaccination. Since a large number of variants are emerging, it is of vital importance to be able to rapidly assess their characteristics: while changes of binding affinity alone do not always cause direct advantages for the virus, they still can provide important insights on where the evolutionary pressure is directed. Here, we propose a simple and cost-effective computational protocol based on Molecular Dynamics simulations to rapidly screen the ability of mutated spike protein to bind to the hACE2 receptor and selected neutralizing biomolecules. Our results show that it is possible to achieve rapid and reliable predictions of binding affinities. A similar approach can be used to perform preliminary screenings of the potential effects of S-RBD mutations, helping to prioritize the more time-consuming and expensive experimental work.

Spiny mice (Acomys cahirinus) are terrestrial mammals that evolved unique scar-free regenerative wound healing properties. Myofibroblasts (MFs) are the major scar-forming cell type in skin. We found that following traumatic injury to ear pinnae, MFs appeared rapidly in both Acomys and mouse yet persisted only in mouse. The timing of MF loss in Acomys correlated with wound closure, blastema differentiation, and nuclear localization of the Hippo pathway target protein Yap. Experiments in vitro revealed an accelerated PP2A-dependent dephosphorylation activity that maintained nuclear Yap in Acomys dermal fibroblasts (DFs) and was not detected in mouse or human DFs. Treatment of Acomys in vivo with the nuclear Yap-TEAD inhibitor verteporfin prolonged MF persistence and converted tissue regeneration to fibrosis. Forced Yap activity prevented and rescued TGFβ1-induced human MF formation in vitro. These results suggest Acomys evolved modifications of Yap activity and MF fate important for scar-free regenerative wound healing in vivo.

The SAR116 clade within the class Alphaproteobacteria represents one of the most abundant groups of heterotrophic bacteria inhabiting the surface of the ocean. The small number of cultured representatives of SAR116 (only two to date) is a major bottleneck that has prevented an in-depth study at the genomic level to understand the relationship between genome diversity and its role in the marine environment. In this study, we use all publicly available genomes to provide a genomic overview of the phylogeny, metabolism, and biogeography within the SAR116 clade. This increased genomic diversity has led to the discovery of two subclades that, despite coexisting in the same environment, display different properties in their genomic makeup. One represents a novel subclade for which no pure cultures have been isolated and is composed mainly of single-amplified genomes (SAGs). Genomes within this subclade showed convergent evolutionary trajectories with more streamlined features, such as low GC content (ca. 30%), short intergenic spacers (

Background Mammalian genomes contain millions of putative regulatory sequences, which are delineated by binding of multiple transcription factors. The degree to which spacing and orientation constraints among transcription factor binding sites contribute to the recognition and identity of regulatory sequence is an unresolved but important question that impacts our understanding of genome function and evolution. Global mechanisms that underlie phenomena including the size of regulatory sequences, their uniqueness, and their evolutionary turnover remain poorly described. Results Here, we ask whether models incorporating different degrees of spacing and orientation constraints among transcription factor binding sites are broadly consistent with several global properties of regulatory sequence. These properties include length, sequence diversity, turnover rate, and dominance of specific TFs in regulatory site identity and cell type specification. Models with and without spacing and orientation constraints are generally consistent with all observed properties of regulatory sequence, and with regulatory sequences being fundamentally small (~ 1 nucleosome). Uniqueness of regulatory regions and their rapid evolutionary turnover are expected under all models examined. An intriguing issue we identify is that the complexity of eukaryotic regulatory sites must scale with the number of active transcription factors, in order to accomplish observed specificity. Conclusions Models of transcription factor binding with or without spacing and orientation constraints predict that regulatory sequences should be fundamentally short, unique, and turn over rapidly. We posit that the existence of master regulators may be, in part, a consequence of evolutionary pressure to limit the complexity and increase evolvability of regulatory sites.

Balancing selection occurs when different evolutionary pressures impact the fitness of multiple alleles, resulting in increased allelic diversity in the population. A new statistical method was developed to test for selection, improving inference by using efficient Bayesian techniques to test for density and strength of linkage disequilibrium. Evolutionary simulation studies showed that the method consistently outperformed existing methods. Using this methodology, we tested for novel signals of balancing selection genome wide in 500 samples from phased trios. Several novel signals of selection appeared in CYP2A7, GPC6, and CNR2 across multiple ancestries. Additionally, tests in SIRPA demonstrate dramatically strong selection signal, significantly higher than previously observed. Well-known signals around olfactory genes and the MHC, containing HLA genes associated with the immune response, also demonstrated strong signatures of selection. So, utilizing data from the 17th IHIW, a follow up analysis was then performed by leveraging over seven thousand HLA typed samples by NGS; in contrast, the genome wide scan did not include a detailed characterization of the HLA genes. The strongest signals observed in the IHIW samples were in DQA1 and DQB1 in or around exon 2, the portion of the gene responsible for antigen presentation and most likely to be under environmental and evolutionary pressure. Our new statistical approach and analysis suggest novel evolutionary pressure in new regions and additionally highlight the importance of improved sequencing and characterization of variation across the extended MHC and other critical regions.

The SARS-CoV-2 ancestral strain has caused pronounced super-spreading events, reflecting a disease characterized by overdispersion, where about 10% of infected people causes 80% of infections. New variants of the disease have different person-to-person variations in viral load, suggesting for example that the Alpha (B.1.1.7) variant is more infectious but relatively less prone to superspreading. Meanwhile, mitigation of the pandemic has focused on limiting social contacts (lockdowns, regulations on gatherings) and decreasing transmission risk through mask wearing and social distancing. Using a mathematical model, we show that the competitive advantage of disease variants may heavily depend on the restrictions imposed. In particular, we find that lockdowns exert an evolutionary pressure which favours variants with lower levels of overdispersion. We find that overdispersion is an evolutionarily unstable trait, with a tendency for more homogeneously spreading variants to eventually dominate.SignificanceOne of the most important and complex properties of viral pathogens is their ability to mutate. The SARS-CoV-2 pandemic has been characterized by overdispersion – a propensity for superspreading, which means that around 10% of those who become infected cause 80% of infections. However, evidence is mounting that this is not a stable property of the virus and that the Alpha variant spreads more homogeneously. We use a mathematical model to show that lockdowns exert a selection pressure, driving the pathogen towards more homogeneous transmission. In general, we highlight the importance of understanding how non-pharmaceutical interventions exert evolutionary pressure on pathogens. Our results imply that overdispersion should be taken into account when assessing the transmissibility of emerging variants.

Deep mutational scanning is a powerful method to explore the mutational fitness landscape of proteins. Its adaptation to anti-CRISPR proteins, which are natural CRISPR-Cas inhibitors and key players in the co-evolution of microbes and phages, would facilitate their in-depth characterization and optimization. Here, we developed a robust anti-CRISPR deep mutational scanning pipeline in Escherichia coli combining synthetic gene circuits based on CRISPR interference with flow cytometry-coupled sequencing and mathematical modeling. Using this pipeline, we created and characterized comprehensive single point mutation libraries for AcrIIA4 and AcrIIA5, two potent inhibitors of Streptococcus pyogenes Cas9. The resulting mutational fitness landscapes revealed that both Acrs possess a considerable mutational tolerance as well as an intrinsic redundancy with respect to Cas9 inhibitory features, suggesting evolutionary pressure towards high plasticity and robustness. Finally, to demonstrate that our pipeline can inform the optimization and fine-tuning of Acrs for genome editing applications, we cross-validated a subset of AcrIIA4 mutants via gene editing assays in mammalian cells and in vitro affinity measurements. Together, our work establishes deep mutational scanning as powerful method for anti-CRISPR protein characterization and optimization.

Long-term evolution experiments (LTEEs) reveal the dynamics of clonal compositions in an evolving bacterial population over time. Accurately inferring the haplotypes - the set of mutations that identify each clone, as well as the clonal frequencies and evolutionary history in a bacterial population is useful for the characterization of the evolutionary pressure on multiple correlated mutations instead of that on individual mutations. Here, we study the computational problem of reconstructing the haplotypes of bacterial clones from the variant allele frequencies (VAFs) observed during a time course in a LTEE. Previously, we formulated the problem using a maximum likelihood approach under the assumption that mutations occur spontaneously, and thus the likelihood of a mutation occurring in a specific clone is proportional to the frequency of the clone in the population when the mutation occurs. We also developed several heuristic greedy algorithms to solve the problem, which were shown to report accurate results of clonal reconstruction on simulated and real time course genomic sequencing data in LTEE. However, these algorithms are too slow to handle sparse time course data when the number of novel mutations occurring during the time course are much greater than the number of time points sampled. In this paper, we present a novel scalable algorithm for clonal reconstruction from sparse time course data. We employed a statistical method to estimate the sampling variance of VAFs derived from low coverage sequencing data and incorporated it into the maximum likelihood framework for clonal reconstruction on noisy sequencing data. We implemented the algorithm (named ClonalTREE2) and tested it using simulated and real sparse time course genomic sequencing data. The results showed that the algorithm was fast and achieved near-optimal accuracy under the maximum likelihood framework for the time course data involving hundreds of novel mutations at each time point. The source code of ClonalTREE2 is available at https://github.com/COL-IU/ClonalTREE2.

The mammalian suprachiasmatic nucleus (SCN) comprises about 20,000 interconnected oscillatory neurons that create and maintain a robust circadian signal which matches to external light cues. Here, we use an evolutionary game theoretic framework to explore how evolutionary constraints can influence the synchronization of the system under various assumptions on the connection topology, contributing to the understanding of the structure of interneuron connectivity. Our basic model represents the SCN as a network of agents each with two properties—a phase and a flag that determines if it communicates with its neighbors or not. Communication comes at a cost to the agent, but synchronization of phases with its neighbors bears a benefit. Earlier work shows that when we have “all-to-all” connectivity, where every agent potentially communicates with every other agent, there is often a simple trade-off that leads to complete communication and synchronization of the system: the benefit must be greater than twice the cost. This trade-off for all-to-all connectivity gives us a baseline to compare to when looking at other topologies. Using simulations, we compare three plausible topologies to the all-to-all case, finding that convergence to synchronous dynamics occurs in all considered topologies under similar benefit and cost trade-offs. Consequently, sparser, less biologically costly topologies are reasonable evolutionary outcomes for organisms that develop a synchronizable oscillatory network. Our simulations also shed light on constraints imposed by the time scale on which we observe the SCN to arise in mammals. We find two conditions that allow for a synchronizable system to arise in relatively few generations. First, the benefits of connectivity must outweigh the cost of facilitating the connectivity in the network. Second, the game at the core of the model needs to be more cooperative than antagonistic games such as the Prisoner’s Dilemma. These results again imply that evolutionary pressure may have driven the system towards sparser topologies, as they are less costly to create and maintain. Last, our simulations indicate that models based on the mutualism game fare the best in uptake of communication and synchronization compared to more antagonistic games such as the Prisoner’s Dilemma.

Draft genome sequences of non-bilaterian species have provided important insights into the evolution of the metazoan gene repertoire. However, there is little information about the evolution of gene clusters, genome architectures and karyotypes during animal evolution. Here we report chromosome-level genome assemblies of two related anthozoan cnidarians, the sea anemones, Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence of the chromosomes between the two species. We show that, in contrast to Bilateria, Hox and NK clusters of investigated cnidarians are disintegrated, indicating that microsynteny conservation is largely lost. In line with that, we find no evidence for topologically associated domains, suggesting fundamental difference in long-range gene regulation compared to vertebrates. However, both sea anemone genomes show remarkable chromosomal conservation with other cnidarians, several bilaterians and the sponge Ephydatia muelleri, allowing us to reconstruct the putative cnidarian and metazoan chromosomes, consisting of 19 and 16 ancestral linkage groups, respectively. These data suggest that large parts of the ancestral metazoan genome have been retained in chromosomes of some extant lineages, yet, higher order gene regulation may have evolved only after the cnidarian-bilaterian split.

Bivalve molluscs comprise 20,000 species occupying a wide diversity of marine habitats. As filter feeders and detritivores they act as ecosystem engineers clarifying water, creating reefs, and protecting coastlines. The global decline of natural oyster reefs has led to increased restoration efforts in recent years. Bivalves also play an important role in global food security contributing to >20% of worldwide aquaculture production. Despite this importance, relatively little is known about bivalve evolutionary adaptation strategies. Difficulties previously associated with highly heterozygous and repetitive regions of bivalve genomes have been overcome by long-read sequencing, enabling the generation of accurate bivalve assemblies. With these resources we have analyzed the genomes of 32 species representing each molluscan class, including 15 bivalve species, to identify gene families that have undergone expansion during bivalve evolution. Gene family expansions across bivalve genomes occur at the point of evolutionary pressures. We uncovered two key factors that shape bivalve evolutionary history: expansion of bivalvia into environmental niches with high stress followed by later exposure to specific pathogenic pressures. The conserved expansion of protein recycling gene families we found across bivalvia is mirrored by adaptations to a sedentary lifestyle seen in plants. These results reflect the ability of bivalves to tolerate high levels of environmental stress and constant exposure to pathogens as filter feeders. The increasing availability of accurate genome assemblies will provide greater resolution to these analyses allowing further points of evolutionary pressure to become clear in other understudied taxa and potentially different populations of a single species.

Gene duplication enables the emergence of new functions by lowering the general evolutionary pressure. Previous studies have highlighted the role of specific paralog genes during cell differentiation, e.g., in chromatin remodeling complexes. It remains unexplored whether similar mechanisms extend to other biological functions and whether the regulation of paralog genes is conserved across species. Here, we analyze the expression of paralogs across human tissues, during development and neuronal differentiation in fish, rodents and humans. While ~80% of paralog genes are co-regulated, a subset of paralogs shows divergent expression profiles, contributing to variability of protein complexes. We identify 78 substitutions of paralog pairs that occur during neuronal differentiation and are conserved across species. Among these, we highlight a substitution between the paralogs SEC23A and SEC23B subunits of the COPII complex. Altering the ratio between these two proteins via RNAi-mediated knockdown is sufficient to influence neuron differentiation. We propose that remodeling of the vesicular transport system via paralog substitutions is an evolutionary conserved mechanism enabling neuronal differentiation.

Bacteria colonise virtually all ecological niches on earth. To interact with their surroundings, they evolved sophisticated multi-protein secretion systems that transport proteins, called effectors, from the bacterial cytoplasm into the extracellular space or directly into target bacteria or eukaryotic cells. Secretion systems therefore perform critical roles in inter-bacterial competition and the pathogenesis of many clinically important opportunistic and professional human pathogens. Generically numbered type I, type II, etc. secretion systems (T1SSs, T2SSs, …), the complex multi-protein architecture of each type is remarkably conserved in different bacteria (Costa et al., 2015). In contrast, the effector repertoires are diverse in numbers and composition reflecting adaptation to specific lifestyles. Environmental, broad host range pathogens like Legionella pneumophila encode more than 300 effectors (Qiu and Luo, 2017). These effectors, whilst not selected under evolutionary pressure by the human immune system, still allow L. pneumophila to cause opportunistic infections. In contrast, pathogens with a more restricted mammalian host range, such as Salmonella enterica, have a considerably smaller (~20-40) arsenal of effectors (Jennings et al., 2017). This Frontiers Research Topic comprises a series of reviews and original research articles highlighting common and pathogen-specific findings and approaches to dissect the function of effectors in bacterial pathogenesis.