Genome Biology And Evolution[JOURNAL]
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200 papers
Tachinid Endoparasitoid Flies do not Rely on Domesticated Viruses, Unlike Multiple Hymenopteran Lineages.
Oukkal S, Guinet B, Hebert PDN … +5 more , Janzen D, Hallwachs W, Fleming AJ, Charlat S, Varaldi J
Genome Biol Evol · 2026 Mar · PMID 41630380 · Full text
Viral domestication, the co-option of integrated viral genes for host functions, has been repeatedly documented in endoparasitoid Hymenoptera. Whether this phenomenon extends to other parasitoid insects remains to be ass...
Viral domestication, the co-option of integrated viral genes for host functions, has been repeatedly documented in endoparasitoid Hymenoptera. Whether this phenomenon extends to other parasitoid insects remains to be assessed. Here, we tested this hypothesis in tachinid flies, the largest group of non-hymenopteran parasitoids. To this end, we investigated patterns of viral endogenization in 52 genomes, including 37 newly sequenced species. Similarly to hymenopteran endoparasitoids, tachinid genomes were found to display numerous endogenous viral elements (EVEs), primarily derived from insect-infecting viruses with either DNA or RNA genomes. However, the majority of integrated sequences were species-specific, with no evidence of major ancient gene domestication events. In addition, the EVE content did not differ between dipteran parasitoids and their free-living Diptera counterparts. These findings contrast with the recurrent viral domestication observed in endoparasitoid Hymenoptera. This pattern is discussed in light of important attributes of tachinid flies including their lack of venom and perforating ovipositor, and their avoidance of the host immune system.
Assessing Ancient DNA Sampling Strategies for Natural Selection Inference in Humans Using Allele Frequency Time Series Data.
Anchieri L, G Amorim CE, Neuenschwander S … +1 more , Malaspinas AS
Genome Biol Evol · 2026 Jan · PMID 41626877 · Full text
The increased availability of genomic data from ancient humans allows estimating the strength of natural selection at a given locus using time series data. Several methods have been developed for this purpose and were or...
The increased availability of genomic data from ancient humans allows estimating the strength of natural selection at a given locus using time series data. Several methods have been developed for this purpose and were originally validated through simulations using mostly large sample sizes. However, human ancient DNA (aDNA) data typically have high missingness and include only a small uneven number of individuals per time point, making estimations of selection challenging. Here, we benchmark the inference of selection with aDNA-like time series datasets using extensive simulations and four methods: ApproxWF, BMWS, Slattice, and Sr. We test several sampling schemes of time series data and selection coefficients (s) and focus on whether one can infer selection using time series datasets with sparse data and small sample sizes. We show that detecting selection with aDNA data is possible for strong s with a sample size of ~100 when assuming constant Ne. While ApproxWF performs best across simulations, the other methods present more variable results and do not perform well for typical aDNA datasets. Importantly, generally low false positive rates (<6%) highlight low risks to falsely detect selection when the loci are evolving neutrally. Moreover, relatively high power (>90%) for s ≥ 0.02 (Nes ≥ 200) shows that strong selection can generally be detected with confidence. We also show that more homogenous sampling improves the accuracy of the estimations. Finally, we provide recommendations for future research aiming to estimate selection with aDNA, noting the importance of spreading data evenly across time and avoiding time points with extremely small sample sizes.
ERGA-BGE Genomes of Culex laticinctus, Culex modestus, Culex perexiguus, and Culex theileri: Unveiling the Genomes of the Key Vectors of West Nile Virus in the Mediterranean Basin.
Ruiz-López MJ, Cebrián-Camisón S, Irisarri I … +10 more , Magallanes S, Martínez-de la Puente J, Figuerola J, Waterhouse RM, Wellcome Sanger Institute Tree Of Life Management Samples And Laboratory Team, Wellcome Sanger Institute Scientific Operations Sequencing Operations, Wellcome Sanger Institute Tree Of Life Core Informatics Team, Haggerty L, Martin F, Brown T
Genome Biol Evol · 2026 Jan · PMID 41626876 · Full text
The reference genomes of Culex laticinctus, Culex modestus, Culex perexiguus, and Culex theileri offer crucial resources for exploring the genetic basis of vector competence for different pathogens, including the emergin...
The reference genomes of Culex laticinctus, Culex modestus, Culex perexiguus, and Culex theileri offer crucial resources for exploring the genetic basis of vector competence for different pathogens, including the emerging West Nile virus. Each genome was assembled into three contiguous chromosomal pseudomolecules. These chromosome-level assemblies encompass 834, 698, 436, and 934 Mb, respectively. They are composed of 3,284, 4,220, 1,917, and 2,704 contigs and 312, 979, 475, and 709 scaffolds, with contig N50 values of 434, 313, 473, and 770 kb, and scaffold N50 values of 292, 246, 150, and 281 Mb, respectively. These genomes offer an essential genomic resource for advancing our understanding of Culex evolution and population genomic analyses, which will help to implement sustainable mosquito control efforts and disease prevention.
Parallel Erosion of a Testis-Specific Na+/K+ ATPase in Three Mammalian Lineages Sheds Light into the Evolution of Spermatozoa Energetics.
Valente R, Machado AM, Pericuesta E … +9 more , García-Párraga D, Artilheiro N, Alves F, Sousa-Pinto I, Pinto B, Cordeiro JM, Ruivo R, Gutiérrez-Adán A, Castro LFC
Genome Biol Evol · 2026 Jan · PMID 41626717 · Full text
Understanding how extant physiological landscapes arise from novel genetic interactions is key to elucidating phenotypic evolution. Sperm cells exemplify a striking case of functional compartmentalization shaped by molec...
Understanding how extant physiological landscapes arise from novel genetic interactions is key to elucidating phenotypic evolution. Sperm cells exemplify a striking case of functional compartmentalization shaped by molecular adjustments, notably regarding energy metabolism. Here, we examine the impact of gene duplication and loss on the evolution of sperm energetics in mammals. Our findings reveal that the acquisition of an exclusive mechanism controlling the sperm plasma membrane Na+ gradient, critical for glucose uptake, emerged in the ancestor of mammals through gene duplication, which originated the Na+/K+ ATPase transporting subunit alpha 4 transporter (Atp1a4). Furthermore, we demonstrate that testis-specific expression of Atp1a4 was acquired after the divergence from monotremes. Notably, we identify three independent pseudogenization events of Atp1a4, including in pangolins, the naked mole-rat (Heterocephalus glaber) and toothed whales. The recurrent loss of function in Atp1a4 coincides with the erosion of the testis-specific glycolytic pathway in these lineages. Furthermore, enrichment analysis of striped dolphin (Stenella coeruleoalba) and naked mole-rat testis transcriptomes also suggests significant alterations in sperm capacitation processes. Overall, we show that the elaboration of a sodium-dependent glucose uptake wiring was a key innovation in the energetic landscape governing mammalian spermatozoa, with secondary gene loss in three separate lineages pointing to drastic alterations in motility and capacitation processes. Our findings illustrate how metabolic pathways co-shaped by gene duplication and erosion define extant physiological phenotypes.
Increased Genetic Load in Breed Chickens and Reduced Coding Content in Long ROH.
Huang R, Zhen Y
Genome Biol Evol · 2026 Jan · PMID 41615280 · Full text
Domestic organisms provide valuable models for studying the impact of population bottlenecks, inbreeding, and artificial selection on the accumulation of deleterious variants. While previous studies largely focused on co...
Domestic organisms provide valuable models for studying the impact of population bottlenecks, inbreeding, and artificial selection on the accumulation of deleterious variants. While previous studies largely focused on coding variants, our study investigated both coding and noncoding contributions to genetic load in diverse chicken breeds, revealing the consequences of inbreeding and artificial selection on genome-wide patterns of deleterious variation. Using representative chicken populations with different selection histories, we show that domestication processes significantly impact the genetic load in chicken populations. Village chickens, which have experienced only the initial domestication, exhibit comparable levels of neutral heterozygosity and realized load to their wild progenitor, the Red Jungle Fowl. In contrast, breed chickens that have undergone more intense artificial selection show a significant decrease in neutral heterozygosity, an increase in the ratio of 0-fold to 4-fold heterozygosity, and a higher realized genetic load in both coding and noncoding regions. However, signals of purging of loss-of-function and noncoding deleterious variants were also detected in domestic chicken. Inbreeding is a major contributor to the increase in genome-wide realized load. We found selection against recently inbred individuals carrying long ROHs covering more coding regions, and an enrichment of homozygous noncoding deleterious variants in ROHs of no less than 2 Mb. Additionally, we found that artificial selection drastically elevated the relative allele frequency of deleterious variants within sweep regions. These findings have implications for the importance of genetic background evaluation of breeding flocks and strategic management to maintain long-term health in domestic populations.
Sign Epistasis Can be Absent in Multi-peaked Landscapes With Neutral Mutations.
Ivankov DN, Zorin EM
Genome Biol Evol · 2026 Jan · PMID 41611468 · Full text
Fitness landscapes provide a rigorous mathematical framework for analyzing evolutionary dynamics, including the study of epistasis, the main obstacle to predicting phenotype from genotype. In 2011, Poelwijk et al. formul...
Fitness landscapes provide a rigorous mathematical framework for analyzing evolutionary dynamics, including the study of epistasis, the main obstacle to predicting phenotype from genotype. In 2011, Poelwijk et al. formulated a foundational theorem stating that in any multi-peaked fitness landscape, "at least two mutations exhibit reciprocal sign epistasis" (Poelwijk et al., J. Theor. Biol., 272:141). The proof relied on the implicit assumption that neutral mutations are absent, commonly accepted in theoretical studies in evolutionary biology. In this study, we extend Poelwijk et al.'s analysis by incorporating genotypes with equal fitness, specifically, accounting for neutral mutations. We demonstrate that when neutral mutations are considered, conventional pairwise reciprocal sign epistasis (RSE) may be entirely absent from a multi-peaked landscape. Instead, RSE is guaranteed only when considering "distant" RSE defined through composite mutations, wherein groups of mutations are treated collectively across all their possible combinations. Applying these concepts to empirical fitness landscapes faces a practical limitation: phenotypic measurements contain experimental noise, making some mutational effects statistically indistinguishable from zero. Under such conditions, statistically significant detection of RSE in multi-peaked landscapes may be impossible even when composite mutations are considered. Theoretically, our findings imply that in the presence of neutral mutations, compensatory mutations in a multi-peaked fitness landscape need not be adjacent; rather, compensation can occur following one or more neutral steps along an evolutionary path. Practically, in real-world scenarios where fitness measurements contain uncertainty, there may be a fundamental technical limitation to detecting RSE in a statistically significant manner within multi-peaked landscapes.
Chromosome-Level Sex-Specific Genome Assemblies of Onthophagus binodis Provide Insight into Scarab Sex Chromosomes.
Nadolski EM, Choi Y, Jones JA … +2 more , Moczek AP, Davidson PL
Genome Biol Evol · 2026 Jan · PMID 41608851 · Full text
Onthophagus binodis is a coprophagous scarab beetle native to southern Africa. This species and many others in the tribe Onthophagini have been introduced to farms across multiple continents in the context of cattle past...
Onthophagus binodis is a coprophagous scarab beetle native to southern Africa. This species and many others in the tribe Onthophagini have been introduced to farms across multiple continents in the context of cattle pasture management efforts. The ecosystem services provided by this species, along with the amenability of comparative developmental and evolutionary studies in this clade, contribute to its role as an emerging insect model system. Here, we present sex-specific chromosomal-level genome assemblies for O. binodis generated from a combination of PacBio long reads and HiC chromatin conformation sequencing. The completeness of the 950.5 Mb female assembly and the 880.5 Mb male assembly is indicated by a contig length N50 of at least 58.6 Mb. BUSCO single-copy and duplicated completeness scores were 99.0% and 0.9% for the female assembly and 97.4% and 2.1% for the male assembly. Gene modeling identified at least 15,403 gene models in each genome with an average transcript length of 1.6 kb. Comparative analyses with other Onthophagini genomes indicated a dramatic expansion of repetitive sequences, which now comprise over 75% of this species' genome and have driven the expansion of overall genome size to nearly twice that of close relatives. We combined the best-assembled chromosome-scale scaffolds from each sex to generate a hybrid reference assembly for this species. Comparative genomic analyses show that the nine autosomes and the X chromosome identified here in O. binodis are likely conserved throughout Onthophagini. Our sex-specific sequencing approach allowed us to identify putative Y chromosome sequences in the male assembly via coverage mapping and k-mer abundance comparisons. These genomes will be of great value to the scientific community as resources for studying insect genome evolution, development, and ecology.
Recombination and Retroprocessing in Broomrapes Reveal RNA-Mediated Gene Transfer Mechanism and a Generalizable Model for Mitochondrial Evolution in Heterotrophic Plants.
Cai L, Havird JC, Jansen RK
Genome Biol Evol · 2026 Jan · PMID 41601402 · Full text
The altered life history strategies of heterotrophic organisms often leave a profound genetic footprint on energy metabolism related functions. In parasitic plants, the reliance on host-derived nutrients and loss of phot...
The altered life history strategies of heterotrophic organisms often leave a profound genetic footprint on energy metabolism related functions. In parasitic plants, the reliance on host-derived nutrients and loss of photosynthesis in holoparasites have led to highly degraded to absent plastid genomes, but its impact on mitochondrial genome (mitogenome) evolution has remained controversial. By examining mitogenomes from 45 Orobanchaceae species including three independent transitions to holoparasitism and key evolutionary intermediates, we identified measurable and predictable genetic alterations in genomic shuffling, RNA editing, and intracellular (IGT) and horizontal gene transfer (HGT) en route to a nonphotosynthetic lifestyle. In-depth comparative analyses revealed DNA recombination and repair processes, especially conversion of RNA-mediated retroprocessing, as significant drivers for genome structure evolution. In particular, we identified a novel RNA-mediated IGT and HGT mechanism, which has not been demonstrated previously in cross-species and inter-organelle transfers. We propose a dosage effect mechanism to explain the biased transferability of plastid DNA to mitochondria across green plants, especially in heterotrophic lineages like parasites and mycoheterotrophs. Evolutionary rates scaled with these genomic changes, but the direction and strength of selection varied substantially among genes and clades, resulting in high contingency in mitochondrial genome evolution. Finally, we summarize mitochondrial evolutionary trends in Orobanchaceae that are potentially generalizable to other heterotrophic plants: increased recombination and repair activities, rather than relaxed selection alone, lead to differentiated genome structure compared to free-living species.
Spontaneous Mutations Occur More in Highly Transcribed Regions in Daphnia.
Coate JE, Ho EKH, Schaack S
Genome Biol Evol · 2026 Jan · PMID 41588656 · Full text
Many molecular processes (eg replication, recombination, and transcription) use DNA as a template molecule, which may lead to an increase or decrease in the likelihood of spontaneous mutation and/or repair of mutations t...
Many molecular processes (eg replication, recombination, and transcription) use DNA as a template molecule, which may lead to an increase or decrease in the likelihood of spontaneous mutation and/or repair of mutations to this key information storage molecule. In the case of transcription, both positive and negative correlations with the likelihood of mutation have been observed across species, which have formed the basis of two proposed mechanistic models: transcription-associated mutagenesis and transcription-coupled repair. Here, we examine the patterns of spontaneous mutations in regions of low and high transcription in two species of the aquatic microcrustacean, Daphnia. By mapping events from a long-term mutation accumulation study (n = 66 lineages derived from nine different genotypes from three populations) with multiple, large-scale publicly available RNA-seq datasets, we find that mutations are more frequently observed in regions of high transcription in D. magna, as well as in the congener, D. pulex. The results are robust across mutation types (base substitutions, insertions, and deletions) and among transcriptional profiles (across developmental stages and environmental conditions). Overall, the positive correlation was robust to different methodological approaches and when controlling for other genomic features (like GC-content). Based on our observations, transcription-associated mutagenesis provides a more likely explanation for the positive relationship between mutation accumulation and transcription levels observed in Daphnia. Characterizing such patterns is important for understanding the evolution of genes, differentially expressed regions of the genome, and the mutation rate.
Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria.
Martinez-Gutierrez CA, Huang Y, Bobay LM
Genome Biol Evol · 2026 Jan · PMID 41575375 · Full text
The genetic material of bacteria and archaea is organized into various structures and setups, attesting that genome architecture is dynamic in these organisms. However, strong selective pressures are also acting to prese...
The genetic material of bacteria and archaea is organized into various structures and setups, attesting that genome architecture is dynamic in these organisms. However, strong selective pressures are also acting to preserve genome organization, and it remains unclear how frequently genomes experience rearrangements and what mechanisms lead to these processes. Here, we assessed the dynamics and the drivers of genomic rearrangements across 121 microbial species. We show that synteny is highly conserved within most species, although several species present exceptionally flexible genomic layouts. Our results show that genomic rearrangements occur at a variable pace across bacteria and archaea, pointing to different selective constraints driving the accumulation of genomic changes across species. Importantly, we found that not only inversions but also translocations are highly enriched near the origin of replication (Ori), which suggests that many rearrangements may confer an adaptive advantage to the cell through the relocation of genes that benefit from gene dosage effects. Finally, our results confirm the view that mobile genetic elements-in particular transposable elements-are the main drivers of genomic translocations and inversions. Overall, our study shows that microbial species present largely stable genomic layouts and identifies key patterns and drivers of genome rearrangements in prokaryotes.
Major Histocompatibility Complex Immunogenetic Diversity Differs Substantially Across Sea Turtle Species and Genomic Regions.
Martin KR, Adkins JL, Chea V … +7 more , Sarkis CM, Phillips KF, Forsman AM, Seney EE, Komoroske LM, Mansfield KL, Savage AE
Genome Biol Evol · 2026 Jan · PMID 41575191 · Full text
Major histocompatibility complex (MHC) immune loci illustrate how natural selection shapes functional genetic diversity in wild populations. Balancing selection favors high MHC diversity within individuals and population...
Major histocompatibility complex (MHC) immune loci illustrate how natural selection shapes functional genetic diversity in wild populations. Balancing selection favors high MHC diversity within individuals and populations that persists beyond speciation, leading to shared allelic lineages among taxa. However, some vertebrates show markedly lower allelic diversity and even the loss of entire MHC gene classes. Variation in life history and disease prevalence makes sea turtles an important group for studying interspecific MHC diversity, but this has been minimally explored. We sequenced class I and class II MHC genes in over 300 individuals from loggerhead (Caretta caretta), green (Chelonia mydas), leatherback (Dermochelys coriacea), and Kemp's ridley (Lepidochelys kempii) sea turtles. We recovered 162 class I and 308 class II functionally distinct alleles, many of which were shared among species. Codon usage analyses suggest that the shared alleles have been maintained through speciation. High allele counts and evidence of diversifying and positive selection suggest balancing selection maintains considerable MHC diversity in sea turtles. However, we found two notable exceptions: (i) D. coriacea had extremely low nucleotide and allelic diversity across all MHC loci and (ii) one MHC class II gene copy on a different chromosome from the core MHC genomic region showed little evidence of positive selection and almost no genetic variability among all four species, suggesting an atypical and potentially functionally distinct gene. Our study finds notably high allelic and nucleotide diversity in sea turtle MHC promoted by balancing selection, yet evolutionary pressures vary considerably between species and gene copies.
Draft Genome of Entamoeba marina Provides Insights Into the Attenuation of Pathogenicity and Adaptation to the Marine Environment.
Kawano-Sugaya T, Izumiyama S, Nozaki T
Genome Biol Evol · 2026 Jan · PMID 41572473 · Full text
Entamoeba is the amoebozoan parasite commonly found in the intestines of animals. E. marina is the first exception isolated from marine sediments, possibly adapting from animal intestines to the sea. However, the evoluti...
Entamoeba is the amoebozoan parasite commonly found in the intestines of animals. E. marina is the first exception isolated from marine sediments, possibly adapting from animal intestines to the sea. However, the evolutionary process of E. marina remains uncertain due to the lack of a genome sequence. Here, we present the de novo genome and transcriptome of E. marina using Oxford Nanopore MinION and Illumina HiSeq/MiSeq. The genome of E. marina is approximately 37.5 Mbp in length and consists of 202 contigs, which is the second longest, next to E. invadens. E. marina showed a significant reduction in the major virulence-associated gene families, including cysteine proteases, lysosomal enzyme transporters, and surface galactose/N-acetylglucosamine-specific lectins, suggesting diversification, more specifically, reduction of pathogenicity-related genes. Genome and RNA-seq analyses also indicated genes either conserved throughout eukaryotes or laterally transferred from prokaryotes, and potentially responsible for salt tolerance. Our study provides insights into the mechanisms underlying the lifestyle changes in the evolution of parasitic eukaryotes.
Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism.
Dauphin B, Baril T, Morin E … +8 more , Oggenfuss U, Pfister S, De Freitas Pereira M, Grigoriev IV, Kohler A, Martin F, Croll D, Peter M
Genome Biol Evol · 2026 Jan · PMID 41566997 · Full text
Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal species remain poorly understood. Cenococcum geophilum, the most widespread ect...
Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal species remain poorly understood. Cenococcum geophilum, the most widespread ectomycorrhizal fungus in boreal and temperate forests with its large, repeat-rich genome, represents an ideal system to investigate TE-mediated adaptation to the physical environment and symbiotic lifestyle. However, previous studies have been limited by fragmented genome assemblies that prevented the resolution of repeat-rich regions. We assembled a telomere-to-telomere reference genome of C. geophilum strain 1.58 using PacBio HiFi and Hi-C datasets, resulting in a 178.54 Mbp genome with seven contiguous chromosomes. We identified 14,145 genes and over 78% of the genome consists of transposable elements (TEs). Of these, 94% are affected by repeat-induced point mutations (RIP), a genome defense mechanism that acts during the sexual reproduction phase, indicating cryptic or ancient sexual reproduction in this putatively asexual fungus. Long terminal repeat retrotransposons, LINEs, and DNA transposons dominate, with three TE families (Ty3, Ty1, and Tad1) contributing over 60% of the genome size, indicating recent transposition bursts. Screening of 15 additional C. geophilum strains revealed recent and lineage-specific TE expansions, implying that several TEs escaped the RIP machinery and retained potential activity. Supporting TE activity in the context of symbiosis, we found 56 TEs differentially transcribed between ectomycorrhizal and free-living mycelium tissues. An even higher number (n = 66) of TEs were differentially expressed between stress resistance morphology (i.e. sclerotia) and free-living mycelium. This supports that TEs are differentially regulated as a response to symbiotic and stress-related conditions. Our results demonstrate that the C. geophilum genome expansion was driven by a few lineage-specific TE families in recent history, with high RIP activity attesting to sexual reproduction. We also provide insights how TEs could respond to lifestyle transitions and traits associated with desiccation resistance.
Origin and Evolution of Very Large Extracellular Proteins in Fructophilic Lactic Acid Bacteria.
Pedersen JE, Mota-Merlo M, Garcia-Montaner A … +2 more , Selmer M, Andersson SGE
Genome Biol Evol · 2026 Jan · PMID 41566947 · Full text
Large surface proteins in bacteria serve important functions in aggregation, biofilm formation, and cell interaction processes. In Apilactobacillus kunkeei, a defensive symbiont of the honeybee Apis mellifera, as much as...
Large surface proteins in bacteria serve important functions in aggregation, biofilm formation, and cell interaction processes. In Apilactobacillus kunkeei, a defensive symbiont of the honeybee Apis mellifera, as much as 6% of the 1.5 Mb genome consists of 5 consecutive genes for extracellular surface proteins of 3,000 to 8,000 amino acids, named Giant1-5. Here, we predict the structures of these proteins and provide a study of their origin and evolution. The structure predictions suggest that the Giant1-4 proteins contain a β-solenoid domain at their N-terminal ends with similarity to the β-solenoid domain in serine-rich repeat proteins, which mediates binding to glycoproteins, polysaccharides, and epithelial cells. Phylogenetic analyses based on the β-solenoid domains of the Giant1-3 proteins indicate sequence exchange between 2 genera of otherwise distantly related obligate fructophilic lactic acid bacteria, while the diversification of the positional homologs of the giant1-3 genes in the A. kunkeei population is mostly due to short, intra-genic recombination events. Genes for the Giant4-5 proteins were only identified in A. kunkeei and 2 closely related bacterial species, suggesting that they were added to the giant gene cluster more recently. The phylogenetic analyses indicate co-evolution of the giant4-5 genes in A. kunkeei, and the near sequence identity of one of the 2 giant4-5 subtypes correlates with predicted recombination events that span across both genes. Our findings provide new insights into the evolution of very large surface proteins in the bacterial ecosystem adapted to the carbohydrate-rich growth niches provided by bees, their food sources, and food products.
Molecular Complexity Constrained Early Amino Acid Recruitment into the Genetic Code.
Hashmi SA, Chok H, Cabrera R … +1 more , Blanco C
Genome Biol Evol · 2026 Mar · PMID 41555552 · Full text
Previously proposed chronologies of amino acid incorporation into the genetic code rely on consensus rankings derived from prebiotic synthesis experiments, biosynthetic pathways, or genomic trends. However, the role of i...
Previously proposed chronologies of amino acid incorporation into the genetic code rely on consensus rankings derived from prebiotic synthesis experiments, biosynthetic pathways, or genomic trends. However, the role of intrinsic molecular properties in shaping amino acid recruitment remains largely underexplored. In this study, we reconstruct a complexity-based amino acid chronology by integrating 16 molecular complexity metrics from chemical graph and information theory. Unlike approaches influenced by environmental variability, detection biases, or the evolutionary constraints of genome-based chronologies, our method provides a perspective on amino acid incorporation independent of these factors. Instead of imposing a linear ranking, we derive a minimum spanning tree capturing complexity-based relationships between amino acids. The resulting hierarchy places structurally simple amino acids in basal positions, while biosynthetically complex residues appear later, aligning with existing prebiotic and genomic chronologies. Furthermore, amino acids positioned closer in the complexity space exhibit significantly greater mutational connectivity than expected by chance, suggesting that molecular complexity reflects underlying structural considerations that constrained the genetic code's evolutionary pathways. This supports the idea that the code evolved not only to maintain biochemical stability but also to facilitate complexity-preserving substitutions, ensuring smooth adaptive transitions while minimizing energetic cost differences. Additionally, molecular complexity significantly correlates with amino acid enrichment in LUCA's inferred proteome, reinforcing its role as a fundamental constraint on early protein evolution. Our approach, rooted in intrinsic molecular properties rather than external contingencies, offers new insights into the constraints shaping the genetic code and expands the scope for identifying universal principles of biochemical evolution.
Correction to: Divergence and Selection in a Cryptic Species Complex (Geonoma undata: Arecaceae) in the Northern Andes of Colombia.
Genome Biol Evol · 2026 Jan · PMID 41554030 · Full text
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Degradation Determinants Are Abundant in Human Noncanonical Proteins and Minor Annotated Isoforms.
Casola C, Owoyemi A, Vakirlis N
Genome Biol Evol · 2026 Jan · PMID 41549067 · Full text
The comprehensive characterization of human proteins, a key objective in contemporary biology, has been revolutionized by the identification of thousands of potential novel proteins through ribosome profiling and proteom...
The comprehensive characterization of human proteins, a key objective in contemporary biology, has been revolutionized by the identification of thousands of potential novel proteins through ribosome profiling and proteomics. Determining the physiological activity of these noncanonical proteins has proven difficult, because they are encoded by different types of coding regions and tend to share no sequence similarity with canonical polypeptides. Evidence from immunopeptidomic assays combined with a better understanding of the quality control of protein synthesis suggest that many noncanonical proteins may possess low stability in the cellular environment. Here, we tested this hypothesis by analyzing the frequency of multiple sequence features eliciting either proteasomal degradation or autophagy across 91,003 canonical (annotated) protein isoforms and 11,499 noncanonical proteins. Overall, noncanonical proteins were enriched for degradation-related features compared to all canonical proteins. Notably, degradation determinants were also enriched in canonical protein isoforms starting with a non-methionine amino acid. Analyses of original and shuffled sequences showed evidence of selective pressure either against or toward the accumulation of specific degradation signatures only in major isoforms of canonical proteins. However, stability was significantly higher in noncanonical proteins with evidence of phenotypic effects upon knock-out in cell lines. Notably, we found that the C-terminal tail hydrophobicity represents a reliable proxy for degradation propensity with potential applications in identifying functional noncanonical proteins. These findings underscore the critical role of degradation processes in regulating the half-life of noncanonical proteins and demonstrate the power of degradation-associated signatures in discriminating noncanonical genes likely to encode biologically functional molecules.
Imagin: An Integrase-Like Gene Conserved Across Malacostracan Crustaceans Derived From a Ginger1 DNA Transposon.
Hao L, Kawato S, Nozaki R … +3 more , Furukawa M, Kondo H, Hirono I
Genome Biol Evol · 2026 Jan · PMID 41542995 · Full text
Domestication of transposable elements has been extensively documented in vertebrates, but few examples have been reported in nonmodel organisms, particularly crustaceans. Here, we present Imagin (Integrase-like gene in...
Domestication of transposable elements has been extensively documented in vertebrates, but few examples have been reported in nonmodel organisms, particularly crustaceans. Here, we present Imagin (Integrase-like gene in MAlacostracans derived from GINger1), a gene family derived from a Ginger1 DNA transposon domesticated in the common ancestor of malacostracan crustaceans over 400 million years ago. We discovered Imagin in the kuruma shrimp Penaeus japonicus as a single-copy, multiexon gene residing within a conserved intron of the methylmalonyl-CoA mutase (MMUT) gene. Comprehensive phylogenetic and structural analyses demonstrate that while Imagin orthologs are under strong purifying selection and retain the conserved H2C2 zinc-finger domain and integrase core, they have ubiquitously lost the catalytic DDE triad essential for endonuclease activity. These structural features indicate that Imagin has undergone molecular exaptation, abandoning its ancestral mobility for a host function. Consistent with this loss of enzymatic capacity, PjImagin protein accumulates predominantly in the cytosol of oocytes during early development, rather than the nucleus. This localization pattern implies that the gene has been co-opted for a noncatalytic role, potentially involving nucleic acid binding, during female gonadal development in penaeid shrimp. Furthermore, transcriptome data revealed divergent expression profiles across lineages, where Imagin is enriched in the ovaries of penaeid shrimp but predominantly in the testes of other decapods, such as crabs and lobsters. Imagin thus represents a novel case of TE evolution, illustrating a complex history of ancient domestication followed by structural remodeling and regulatory subfunctionalization.
Genome Shows no Recent Inbreeding in Near-Extinction Woolly Rhinoceros Sample Found in Ancient Wolf's Stomach.
Guðjónsdóttir SM, Lord E, Pochon Z … +7 more , Lemež Š, Dussex N, Stanton DWG, Sinding MS, Fedorov S, Dalén L, Chacón-Duque JC
Genome Biol Evol · 2026 Jan · PMID 41530912 · Full text
Using temporarily spaced high-coverage ancient genomes, we can assess population decline prior to extinction. However, finding suitable ancient remains for recovering this type of data is challenging. Here, we sequenced...
Using temporarily spaced high-coverage ancient genomes, we can assess population decline prior to extinction. However, finding suitable ancient remains for recovering this type of data is challenging. Here, we sequenced a high-coverage genome from muscle tissue of a 14,400-year-old woolly rhinoceros (Coelodonta antiquitatis)-a cold-adapted herbivore that went extinct ∼14,000-years ago-found inside a permafrost-preserved wolf's stomach. We compared genome-wide diversity, inbreeding, genetic load, and population size changes in this sample with two other Late Pleistocene Siberian woolly rhinoceros. We found no evidence of population size decline, nor any genomic erosion, shortly prior to the species' demise. Given the few long homozygous segments, typically indicative of recent inbreeding, we infer a stable population size only a few centuries before extinction. Thus, the woolly rhinoceros' extinction likely happened rapidly, during the Bølling-Allerød interstadial. This study demonstrates the ability to recover high-quality DNA from unlikely sources to elucidate species' extinction dynamics.
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments.
Malik AJ, Mao S, Hugenholtz P … +1 more , Ascher DB
Genome Biol Evol · 2026 Jan · PMID 41527918 · Full text
Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-based approaches. Encoding three-dimensional protein structures using a simplif...
Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-based approaches. Encoding three-dimensional protein structures using a simplified structure-aware alphabet can lead to compact, comparable strings that retain key spatial relationships. Although this enables comparison, structure-aware alignments can experience misaligned regions, particularly when comparing proteins with substantial divergence in fold architecture. To address this, a web-based resource, Structome-AlignViewer, is introduced in this work for evaluating the quality of structure-aware alignments through both spatial mapping of alignment columns to protein structures and quantitative confidence scoring. Confidence is computed from pairwise structural substitutions between adjacent inputs and normalized within each alignment to highlight relatively well-supported columns. To provide broader context, thousands of alignments from established structural classification systems were analyzed, allowing for an empirical comparative statistic to be derived to assess alignment quality. The option to exclude gap-rich regions enables users to refine alignments and focus on conserved structural cores. This approach provides an interpretable method for assessing structural alignment quality and supports more robust comparative and evolutionary analyses. Structome-AlignViewer is freely available at https://biosig.lab.uq.edu.au/structome_alignviewer/.
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