The rapid and repeated emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, particularly within the Omicron lineage, highlights the virus's remarkable ability to adapt under shifting immune pressures. A central molecular battleground in this evolutionary arms race is the spike receptor-binding domain, which must simultaneously maintain high affinity for the human ACE2 receptor while evading recognition by neutralizing antibodies. In this study, we construct and analyze multiple combinatorial libraries of SARS-CoV-2 receptor-binding domain variants spanning major branches of Omicron evolution, including BA.1, BA.2, BA.5, XBB, and JN.1. Using high-throughput yeast display and binding assays, we map the effects of thousands of mutations and their combinations on ACE2 binding and antibody evasion. Our results reveal that while many receptor-binding domain mutations exhibit additive effects, several mutations interact epistatically in a background-dependent manner. In particular, we identify synergistic interactions between BA.1 and BA.5 mutations that enhance antibody evasion, likely facilitating the rise of recombinant variants and convergent evolution. Conversely, some mutations show lineage-restricted compatibility, suggesting potential constraints on future evolutionary trajectories. Our comprehensive genotype-to-phenotype maps uncover both rugged and smooth regions of the viral fitness landscape and underscore the importance of epistasis in shaping SARS-CoV-2 evolution. These findings improve our ability to anticipate future viral variants and provide a framework for understanding how host–pathogen coevolution unfolds at the molecular level.

Environmental genomics has led to the discovery of many new lineages of archaea, including "DPANN" (or Nanobdellati), comprising organisms with small genomes, reduced gene content, and potentially symbiotic or parasitic lifestyles. DPANN live in various environments, and several lineages have been identified that are adapted to extremely high salt concentrations, including the Nanohaloarchaeota. Since it was long thought that the Haloarchaea (within 'Euryarchaeota') were the only high salt-adapted archaea, the origins of these genome-reduced halophiles have been debated. Here we used phylogenetic, comparative genomic, and gene-tree/species-tree reconciliation approaches to resolve the evolution of halophily within DPANN, making use of recently-published genomes that help to inform the phylogenetic placement and genome evolution of salt-adapted lineages. Phylogenetic analysis placed Nanohaloarchaeota sister to a previously uncharacterised lineage, which we here refer to as Terrarchaeota. Terrarchaeota appear to be predominantly anaerobic thermophiles that are not adapted to high salt concentrations, indicating that adaptation to high salt evolved after their divergence from Nanohaloarchaeota. Furthermore, our analyses identified genomic hallmarks of salt adaptation in another recently discovered halophilic DPANN lineage within Aenigmatarchaeota, the Haloaenigmatarchaeaceae. We found that the Nanohaloarchaeota and Haloaenigmatarchaeaceae have distinct sets of proteins that enable life at high salt concentrations but share a common mechanism of evolutionary adaptation, in which niche-relevant genes were acquired horizontally from their halophilic hosts. This work provides the first detailed investigation into the enigmatic Terrarchaeota, and new insights into the convergent evolution of high salt adaptation within symbiotic clades of Archaea.

Archival specimens held in biorepositories (e.g. natural history collections) offer rare temporal snapshots of global biodiversity. These collections not only preserve species morphology and aspects of ecology, but increasingly provide access to historical molecular data, including insights into wildlife disease. As several pandemics have originated from animal viruses spilling over into the human population (i.e. SARS-CoV-2/COVID-19, 2009 H1N1 influenza, and HIV/AIDS), characterizing the diversity of viruses circulating in wildlife populations is essential for proactive pandemic preparedness. Yet, current surveillance remains biased toward contemporary viruses of economic importance. One solution to bridging spatiotemporal gaps in wildlife virus knowledge is retrospective screening of vouchered wildlife specimens. However, molecular analysis of specimens has been hindered by formalin fixation, which degrades and cross-links nucleic acids. Here, we demonstrate that formalin-fixed vouchered wildlife specimens retain both host and viral RNA fragments after being stored for up to 60 years. We recovered fragments of divergent strains of Rotavirus alphagastroenteritidis from two Australian species of order Chiroptera; Nyctophilus geoffroyi (lesser long-eared bat) and Rhinolophus megaphyllus (smaller horseshoe bat), representing the first characterization of R. alphagastroenteritidis (RVA) in Australian bats, and the oldest identification of the virus to date worldwide. Concurrently, we sequenced endogenous host RNA, providing a proof-of-concept for dual host–virus transcript recovery from vouchered specimens. This study highlights the role biorepositories can play in reconstructing unbiased historical viral landscapes from specimens, irrespective of the host disease status, and enabling spatiotemporal host–virus insight to advance both biodiversity science and global pandemic preparedness.

Protein function evolution provides a powerful lens to uncover biological complexity. Here, we introduce the concept of the pan-functionome-the full set of protein functions encoded by the proteome of individuals belonging to a taxonomic group-and explore its evolutionary implications. By analyzing over 1,000 annotated proteomes across major branches of life, we identify systematic differences in functional composition that reflect deep evolutionary patterns. The number of biological processes per protein increases non-linearly over time, with functional diversification rather than protein expansion driving organismal complexity. Distinct taxonomic divisions invest differently in biological processes, highlighting signatures of multicellularity, metabolism, and stress response. Phylogenetic analyses suggest that the evolution of protein functions follows a non-neutral model. Furthermore, functional profiles allow robust taxonomic classification and reveal unique adaptations in individual organisms. Our findings suggest that the functionome provides a complementary perspective on evolution, with potential applications in taxonomy, evolutionary biology, and comparative genomics.

Repeated (parallel or convergent) evolution is often taken as evidence of adaptation and is relevant to the predictability of evolution. However, much remains unknown about the genetic basis of repeated evolution. Here, we use genome editing to progressively knock out all the complete transposable elements (TEs), a rich source of mutations, in the fission yeast Schizosaccharomyces pombe. While progressive knockout has no apparent effect on the biology or fitness of S. pombe under normal conditions, certain TE knockout strains exhibit growth arrest under acid challenge. We next perform parallel replay experiments by evolving S. pombe strains with a single TE and without TE under acid stress. Adaptation occurs rapidly and repeatedly. We do not detect any new TE insertions at appreciable frequencies, indicating that the observed repeated adaptation is not driven by TE insertions. Instead, revival mutations in SPBC409.08, a pseudogene that encodes a putative transporter of the major facilitator superfamily, repeatedly undergo hard or soft selective sweeps and drive adaptation in all the replicates. Although the revival mutations exhibit a trend of diminishing returns, they also repeatedly become fixed in all evolved wild type populations. This work unveils the significance of pseudogene revival on repeated evolution and thus evolutionary predictability.

Recent discoveries reveal that many complex intraspecific polymorphisms are shaped by a single supergene that maintains coadapted genetic variants through suppressed recombination. Here we show that in the ant Temnothorax rugatulus, an extreme reproductive polymorphism is instead governed by two independent genomic rearrangements that arose sequentially on different chromosomes. Colonies of this species contain either a single large dispersing queen or multiple queens, including extremely miniaturized microgynes that cannot establish new colonies on their own and reproduce only by joining established multiple-queen colonies. Using chromosome-scale assemblies and population genomic data, we identify two genomic rearrangements, 9.3 Mb and 7.0 Mb in size, that jointly determine these strategies. Divergence dating shows that the supergene underlying colony social structure arose first, creating the conditions for the subsequent emergence of a miniaturization supergene. These findings demonstrate that complex adaptive strategies can be assembled stepwise through the sequential origin of multiple supergenes.

Orphan genes evolve rapidly, raising questions about whether their functions remain conserved or diverge across species. To address this, we investigated goddard (gdrd), an orphan gene essential for spermatogenesis in Drosophila melanogaster. Within the Drosophila genus, Gdrd proteins retain a conserved core structure but display substantial variation in length and primary sequence. Here we perform cross-species gene-swap assays in D. melanogaster testes to examine how these lineage-specific changes affect Gdrd function. Strikingly, the highly divergent D. mojavensis ortholog fully rescues fertility in gdrd null flies, suggesting that ancestral Gdrd acted within a conserved spermatogenesis pathway. By contrast, several orthologs, including one from a more closely related species, cannot substitute for the melanogaster gene. Cytological analysis shows that all divergent Gdrd orthologs retain some ability to interact with axonemes and ring centrioles, consistent with the protein's structural conservation, but many non-complementing orthologs display weaker axonemal binding. Furthermore, all tested orthologs exhibit divergent localizations to organellar structures. Using computational analyses and molecular dynamics simulations, we identified intrinsic protein qualities that may account for several observations made in the gene swap assays. Rescuing orthologs bear motifs with shared physicochemical properties in their intrinsically disordered regions, while non-rescuing variants exhibit structural instabilities. Taken together, these findings show that while Gdrd's ancestral structure and interactions are conserved, several orthologs have undergone lineage-specific evolutionary changes.

Genetic drift and gene flow can give rise to a complex population genetic structure. The inverse problem of estimating the genetic drift and gene flow in the past, based on the present-day genomic population structure, can be solved using an admixture graph. This describes differentiated local populations in terms of population splits and migrations between populations. The history and associated levels of genetic drift and admixture can be estimated based on the genome-wide SNP allele frequency data. Here, we present a set of statistical methods based on the admixture graph. Applying a prior on the stochastic variation of the effective population size decomposes the genetic drift values that are associated with the non-migration edges into the timings of the population splits and the effective population sizes at those times. This decomposition facilitates downstream analyses such as reconstruction of ancestral allele frequencies via a Brownian motion model with admixture. To trace changes in allele frequencies on a world map, we estimated the geographic locations of the ancestral populations using Brownian motion, the rate of which depends on the genetic drift values. Mapping the history of putative adaptations onto a world map can illuminate factors responsible for regional population heterogeneity. We investigated the effectiveness of detecting adaptations with a numerical simulation that mimics human population history, and by analyzing the eQTLs of the MC1R gene, which is involved in regulation of skin and hair pigmentation.

The transition from terrestrial to marine environments represents one of the most fundamental evolutionary shifts in vertebrate history, requiring radical physiological and genomic remodeling. We investigated the genomic signatures of saltwater adaptation in the green sea turtle (Chelonia mydas), the leatherback turtle (Dermochelys coriacea), and the independently evolved estuarine diamondback terrapin (Malaclemys terrapin). Our analyses reveal that the marine transition is characterized by rapid evolution and expansion in gene families linked to iron metabolism, organ morphogenesis, and sensory perception-patterns that mirror those seen in other secondarily marine tetrapods. Notably, while we identified shared targets of positive selection across these independent lineages, we found no evidence of repeated evolution at the nucleotide level, reinforcing that functional convergence often arises through distinct molecular trajectories. Furthermore, demographic reconstructions reveal that saltwater-adapted turtles share a history of deep-time population declines; however, the delayed recovery of M. terrapin underscores the specific susceptibility of estuarine specialists to Pleistocene sea-level volatility. By bridging comparative genomics and historical demography, this study provides new insights into the genomic basis of marine adaptations in turtles and a comprehensive framework for understanding the molecular and ecological mechanisms that facilitate major vertebrate transitions into the marine realm.