Genome Biology And Evolution[JOURNAL]
Sun
200 papers
Genomic Characterization of Dengue Virus in the Ningxia Hui Autonomous Region, China (2019 and 2023).
Li L, Zhan J, Yang D … +9 more , Li T, Sun X, Yuan F, Cao M, Zhang W, Mu T, Wang J, Pei J, Ma X
Genome Biol Evol · 2026 Mar · PMID 41762122 · Full text
Dengue virus (DENV) transmission has risen across China in recent years, but genomic data from inland regions remain scarce. We screened 9 clinical samples collected in Ningxia in 2019 and 2023, obtaining 5 near-complete...
Dengue virus (DENV) transmission has risen across China in recent years, but genomic data from inland regions remain scarce. We screened 9 clinical samples collected in Ningxia in 2019 and 2023, obtaining 5 near-complete DENV-1 genomes, and performed phylogenetic reconstruction and molecular clock analyses using a global dataset of 452 DENV-1 sequences to infer spatiotemporal origins; epitope divergence relative to vaccine strains and human monoclonal antibodies was also assessed. The 2019 Ningxia strains clustered within DENV-1 genotype I, clade E, and were closely related to viruses from Hebei Province, whereas the 2023 strain fell within genotype I, clade K, showing the highest similarity to sequences from Yunnan and Guangdong. The most recent common ancestor of the Ningxia strains was estimated to have existed around 1989 (95% highest posterior density: 1985-1993) and is shared with strains from Guangdong, Yunnan, and Southeast Asia. Comparative analysis of prM-E proteins identified 16 (2019) and 11 (2023) amino acid substitutions relative to the vaccine strain, and E-protein epitope mutation (N52D) is predicted to alter binding to the neutralizing antibody 1F4. These findings establish a molecular baseline for origin tracing and proactive surveillance in northwestern China.
Genome Assembly of Spinifex sericeus Provides Insights into Repetitive Content and Haplotype Variation in a Dioecious Coastal Grass.
Chen SH, Bragg JG, Jones A
Genome Biol Evol · 2026 Mar · PMID 41755646 · Full text
Spinifex sericeus (beach spinifex) is a perennial, dioecious grass native to the coastal ecosystem of Oceania that has an important role in dune stability. We present a near telomere-to-telomere, haplotype-resolved nucle...
Spinifex sericeus (beach spinifex) is a perennial, dioecious grass native to the coastal ecosystem of Oceania that has an important role in dune stability. We present a near telomere-to-telomere, haplotype-resolved nuclear genome and complete organelle genomes of S. sericeus. The nuclear genome is highly repeat-rich, dominated by long terminal repeat (LTR) retrotransposons. Comparative analysis of the two haplotypes reveals extensive structural variation and high levels of duplication that are suggestive of active and expanding LTRs that may drive genome evolution and expansion in this species. The chloroplast genome exhibits heteroplasmy, having two distinct circular configurations spanning 138 kbp each. The complex mitochondrial genome consists of a large linear component spanning 1.85 Mbp and a small circular 134 kbp component. These genomic resources provide a foundation for advancing research on sex determination and stress adaptation in grasses, as well as practical applications in crop improvement and genetically informed coastal dune restoration.
Genomes from 117 vertebrate species reveal rapidly evolving segmental-duplication landscapes.
Aqil A, Islam S, Hach F … +3 more , Numanagić I, Masuda N, Gokcumen O
Genome Biol Evol · 2026 Feb · PMID 41755628 · Publisher ↗
Segmental duplications are major drivers of evolutionary innovation, yet their dynamics across vertebrates remain poorly understood. Here, we identify segmental duplications from long-read-sequenced genomes of 117 verteb...
Segmental duplications are major drivers of evolutionary innovation, yet their dynamics across vertebrates remain poorly understood. Here, we identify segmental duplications from long-read-sequenced genomes of 117 vertebrates and one starfish, generating the largest multi-species dataset of its kind. We find that vertebrate genomes show a higher propensity for tandem duplications than for interspersed duplications. However, when focusing only on subtelomeric regions, avian and mammalian genomes show the opposite propensity toward interspersed duplications. We also observe that, across vertebrates, tandem duplications tend to be larger than interspersed duplications. Next, we construct a segmental-duplication network for each species and use network-derived metrics to quantify the duplication landscape for that species. We then compute interspecies distances for each metric and find that these distances show at most weak correlations with phylogenetic distance, indicating that segmental-duplication landscapes evolve rapidly. Functional enrichment analysis of hyper-duplicated genes reveals a strong enrichment in platypus for pheromone response, driven by the expansion of the vomeronasal pheromone receptor V1R gene family. Overall, our results uncover the general properties of vertebrate segmental duplications, demonstrate the lability of segmental-duplication landscapes, and highlight the utility of network-based approaches for studying genome evolution.
Assessing the Potential of Ancient Protein Sequences in the Study of Hominid Evolution.
Patramanis I, Skov L, Cappellini E … +1 more , Racimo F
Genome Biol Evol · 2026 Mar · PMID 41748326 · Full text
Palaeoproteomic data can provide invaluable insights into hominid evolution over long timescales. Yet, the potential and limitations of ancient protein sequences to resolve evolutionary relations between species remains...
Palaeoproteomic data can provide invaluable insights into hominid evolution over long timescales. Yet, the potential and limitations of ancient protein sequences to resolve evolutionary relations between species remains largely unexplored. In this study, we aim to quantify how much information about these relations can be obtained from limited ancient protein data, at the scale that is currently available or will be available in the near future. We harness sequence alignments of 12 enamel and collagen proteins that have been previously reported in fossil material that is at least 1 million years old. We utilize in silico translations of hominid DNA sequences of these proteins and highlight their differential sequence conservation, indicating some of them contain much larger amounts of information than others. We also evaluate the extent to which inferred topologies from protein data differ from inferred topologies from the more informationally dense DNA data. We show that the former may sometimes lead to inferences of the wrong tree topology due to the informational loss that comes when working with peptide data. Additionally, we determine the number of concatenated proteins necessary to confidently reconstruct the population/species tree summarizing the relations between humans, chimpanzees, and gorillas, as well as those between modern humans, Neanderthals, and Denisovans. As expected, increasing the number of proteins in a concatenation enhances resolution, but we note that trees inferred from the full set of collagen and enamel proteins do not necessarily correspond to population trees inferred from genome-wide data. We show this is especially the case in the closely related groups of our recent ancestors. We further demonstrate that while a number of proteins fall within archaic introgressed haplotypes of present day humans, ancient admixture is not the main source of the observed tree incongruence. Our study underscores the potential and limitations of utilizing palaeoproteomic data in deep time phylogenetic reconstructions, indicating that these will be aided not only by increased recovery of proteins in the future, but also by more careful modeling of evolutionary relations across the genome, beyond simply building single phylogenetic trees.
Substitution Spectrum and Selection at G-quadruplexes in Great Ape Telomere-to-Telomere Genomes.
Zhang X, Mohanty SK, Chiaromonte F … +1 more , Makova KD
Genome Biol Evol · 2026 Mar · PMID 41746207 · Full text
G-quadruplexes (G4s) are noncanonical DNA secondary structures formed by runs of guanines (stems) connected by other nucleotides (loops). These structures are enriched at regulatory regions such as promoters, CpG islands...
G-quadruplexes (G4s) are noncanonical DNA secondary structures formed by runs of guanines (stems) connected by other nucleotides (loops). These structures are enriched at regulatory regions such as promoters, CpG islands, untranslated regions (UTRs), enhancers, and replication origins, where they play key roles in transcription and replication. Although prior studies have demonstrated that G4s exhibit higher mutation rates than canonical DNA, little is known about the substitution patterns and selection acting specifically on G4 stems and loops. In this study, we utilized Telomere-to-Telomere (T2T) genome assemblies from human and two non-human great apes (chimpanzee and Bornean orangutan) to analyse substitution spectra and selective constraints within G4s, focusing on differences between stems and loops. We observed that fixed nucleotide substitutions leading to the gain or loss of G4 structures are more frequently located at stems, while those in G4s conserved across species are more often found at loops. On the other hand, single-nucleotide polymorphisms had similar frequencies between stems and loops. To evaluate selection, we employed two approaches: we computed the ratio of substitution to polymorphism frequencies at stems versus loops and performed phylogenetic modeling using PhyloFit. Both methods consistently revealed that stems of shared G4s experience stronger purifying selection than loops, particularly at promoters, enhancers, and UTRs. Our results provide novel insights into the sequence variation and selection of G4s, informing our understanding of their contributions to genome evolution and function.
Pervasive Transcription in the Human Genome Exceeds Background Noise.
Adey BN, Maddock DJ, Hermann-Le Denmat S … +4 more , Dinger ME, Gardner PP, Poole AM, Ganley ARD
Genome Biol Evol · 2026 May · PMID 41742398 · Full text
Large genomes such as the human genome are pervasively transcribed yet encode relatively few unambiguously functional elements. This has led to debate over whether pervasive transcription is indicative of large suites of...
Large genomes such as the human genome are pervasively transcribed yet encode relatively few unambiguously functional elements. This has led to debate over whether pervasive transcription is indicative of large suites of uncharacterized functional elements or is simply background noise. Here, we used a deep-learning model to estimate background transcription in the human genome as a way of distinguishing between these two hypotheses. We applied the model to randomized (reversed or shuffled) versions of the human genome and found that transcription is predicted to be sparse across all randomization methods, initiating with at least four-fold lower frequencies than in the native human genome. This relatively low level of background transcription from the human genome suggests that most transcription is not a consequence of background noise, thus it requires other explanations. We find that randomizing only interspersed repeats in human genome has little impact on predicted transcription, suggesting that transcription of mobile elements does not explain the excess transcription in the human genome. Instead, most transcriptional events may derive from functional noncoding RNA transcripts, some general requirement for extensive transcription initiation/elongation, and/or mutational biases leading to the frequent appearance of transcription initiation sites by chance.
Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.
Foquet B, Eccles LE, Markee A … +4 more , Triant DA, Frandsen PB, Stoppel WL, Kawahara AY
Genome Biol Evol · 2026 Mar · PMID 41738778 · Full text
Gene duplications are a major driver of molecular diversification and phenotypic evolution. Arthropod silk genes provide an excellent model for studying these processes due to their extensive internal repeats and rapid e...
Gene duplications are a major driver of molecular diversification and phenotypic evolution. Arthropod silk genes provide an excellent model for studying these processes due to their extensive internal repeats and rapid evolutionary rates. In Lepidoptera, the Fibroin heavy chain (fibH) gene encodes the primary structural protein for silk fibers, contributing largely to their mechanical strength. This inner fibroin core is surrounded by an outer coating composed primarily of sericins. Sericins are a group of highly repetitive, serine-rich proteins that modulate silk fiber properties. Although sericins in the domestic silkworm (Bombyx mori) have been associated with life stage-specific variation in silk characteristics, their evolution and function remain poorly understood. Here, we provide a detailed molecular characterization of sericin genes in the Luna moth (Actias luna) known for forming dense, robust, silk-woven cocoons. We identified eight sericin genes that (i) include two clusters of closely related paralogs, (ii) exhibit considerable variation in repeat number and amino acid composition, and (iii) display distinct gene expression patterns across life stages. A comparison of sericin genes between A. luna and three other moths of the superfamily Bombycoidea reveals evidence for convergent subfunctionalization. These findings suggest that sericin gene duplications enable dynamic shifts in silk composition both within and between species, potentially reflecting adaptive responses to ecological and functional demands.
A Chromosome-level Assembly and Functional Genomic Resources for the Model Annelid Capitella teleta.
Davies BE, Gonzalez P, Sur A … +16 more , Wei J, Frankish T, Montagne J, Carrillo-Baltodano AM, Guynes K, Liang Y, Donnellan RD, Travis Moreland R, Singh S, Zhang S, Yu R, Wolfsberg TG, Meyer NP, Seaver EC, Baxevanis AD, Martín-Durán JM
Genome Biol Evol · 2026 Mar · PMID 41732109 · Full text
The polychaete Capitella teleta is a primary model for evolutionary developmental biology, comparative genomics, conservation, and ecotoxicology. Although it was the first polychaete genome sequenced, the original assemb...
The polychaete Capitella teleta is a primary model for evolutionary developmental biology, comparative genomics, conservation, and ecotoxicology. Although it was the first polychaete genome sequenced, the original assembly is outdated by modern standards. Here, we combine long-read and short-read sequencing with Hi-C chromatin conformation capture to assemble chromosome-level nuclear and mitochondrial genomes of the laboratory strain of C. teleta. This reference assembly accurately reflects the expected genome size (∼243.6 Mb) and contains a highly complete, evolutionarily conserved gene repertoire. Notably, the nuclear and mitochondrial genomes are heavily rearranged, indicating a decoupling between gene family repertoire and chromosomal evolution. The analyses of developmental time courses of bulk and single-cell RNA-seq, ATAC-seq, and EM-seq data using the new reference assembly resulted in a significant improvement in quality, enabling the identification of new cell-type-specific gene markers. Finally, we generated a publicly available genome browser that ensures these resources comply with FAIR principles. Our study provides state-of-the-art genomic resources for C. teleta, addressing a pressing community need and opening new research opportunities in animal and genome evolution.
Metabolic resistance of the tiger mosquito to pyrethroid insecticides in La Réunion Island likely results from local adaptation.
Bacot T, Bonneville JM, Lacroix V … +10 more , Oberbach P, Gaude T, Nadalin L, Laporte F, Habchi-Hanriot N, Dupuy G, Czeher C, Fontaine MC, Boyer F, David JP
Genome Biol Evol · 2026 Mar · PMID 41718473 · Full text
The resistance of mosquitoes to insecticides is a valuable model system for studying the genetic bases of xenobiotic adaptation in insects. The spread of the Asian tiger mosquito Aedes albopictus, combined with the massi...
The resistance of mosquitoes to insecticides is a valuable model system for studying the genetic bases of xenobiotic adaptation in insects. The spread of the Asian tiger mosquito Aedes albopictus, combined with the massive use of pyrethroid insecticides to limit arbovirus transmission, resulted in the rise of resistance in various continents. Here, we investigated the genetic mechanisms underlying the recent adaptation of this mosquito to deltamethrin in La Réunion Island. Bioassays confirmed the presence of resistance alleles in field populations. The resistance phenotype was further enhanced in the laboratory following a few generations of controlled selection. Combining whole genome Pool-seq and RNA-seq revealed no evidence of target-site resistance mutations, but the over-expression and variant selection of detoxification enzymes associated with pyrethroid metabolism, including cytochrome P450s, transferases, and ABC-transporters. Among over-expressed detoxification genes, only one was linked to a gene duplication, while polymorphism data suggest most of them are trans-regulated. Genome-wide selection signatures revealed a 9 Mb inversion acting as a superlocus responding to controlled selection. Altogether, this study indicates that the multigenic metabolic resistance phenotype observed in this insular territory mainly results from local adaptation. From an applied perspective, this study provides a set of markers to track pyrethroid resistance in the tiger mosquito in the South-West Indian Ocean. As this region is subjected to recurrent arbovirus outbreaks, the additive resistance phenotype that may arise from the introduction of Kdr mutations from other territories also calls for improving resistance surveillance at the regional scale.
Decoding the Avian Missing Gene Mystery: Dot Chromosomes Unmask Extensive Gene Loss and Novel Genetic Instability.
Hron T, Miklík D, Pačes J … +5 more , Pajer P, Pečenka V, Hejnar J, Nehyba J, Elleder D
Genome Biol Evol · 2026 Mar · PMID 41700414 · Full text
The apparent absence of numerous conserved vertebrate genes from avian genomes has puzzled researchers for over a decade. In recent years, a subset of these genes has been identified; however, their sequences are unusual...
The apparent absence of numerous conserved vertebrate genes from avian genomes has puzzled researchers for over a decade. In recent years, a subset of these genes has been identified; however, their sequences are unusually problematic, often evading detection by standard sequencing technologies. This limitation has hindered detailed investigation of the phenomenon-until recent progress in long read technologies, which are more robust against sequencing biases. This enabled us to classify real gene losses extensively, which strikingly revealed that a large number of the genes residing on so-called dot chromosomes were indeed lost during avian evolution. We demonstrate that dot microchromosomes-small, repeat-dense avian chromosomes-harbor widespread gene attrition, with 29% of ohnologs (duplicates from ancestral genome doublings) eliminated, far exceeding rates on other chromosomes. Moreover, we reveal that genes retained on these dot chromosomes exhibit a previously undescribed form of dynamic genetic instability. This instability, which we term sequence stuttering, is characterized by a massive expansion of short sequences within intronic regions. Intriguingly, in some cases, the expanding sequences appear to originate from neighboring exons. As a result, intron lengths vary extensively among individual chickens, suggesting that these events are evolutionarily recent. Since this phenomenon has not been reported in any other vertebrate species, our findings lay the groundwork for future research into its underlying mechanisms, evolutionary implications, and potential identification of similar loci across vertebrate genomes.
Recurrent Chromosome Destabilization Through Repeat-Mediated Rearrangements in a Fungal Pathogen.
Fouché S, Oggenfuss U, McDonald BA … +1 more , Croll D
Genome Biol Evol · 2026 Mar · PMID 41693398 · Full text
Genomic instability caused by chromosomal rearrangements has severe consequences for organismal fitness and progression of cancerous cell lines. The triggers of destabilized chromosomes remain poorly understood but likel...
Genomic instability caused by chromosomal rearrangements has severe consequences for organismal fitness and progression of cancerous cell lines. The triggers of destabilized chromosomes remain poorly understood but likely co-locate with fragile sites. Here, we retrace a runaway chromosomal degeneration process observed in the fungal pathogen Zymoseptoria tritici using telomere-to-telomere assemblies across an experimental progeny. We show that the same fragile sites triggered reproducible, large-scale rearrangements through nonallelic recombination. Across our four-generation progeny, chromosomal rearrangements were accompanied by nondisjunction events leading to aneuploid progeny with up to four chromosomal copies. We identify a specific transposable element family co-locating with fragile sites, likely triggering ongoing repeated chromosomal degeneration. The element has recently been associated with lower virulence of the pathogen and has undergone an expansion of copy numbers across the genome. Chromosome sequences are also targeted by repeat-induced point mutation, a genome defense mechanism actively leading to hypermutation on duplicated sequences. Our work identifies the exact sequence triggers that initiate chromosome instability and perpetuate degenerative cycles. Dissecting proximate causes leading to runaway chromosomal degeneration could expand our understanding of chromosomal evolution beyond fungal pathogens.
Predictors of Protein Evolution in the drosophilid Immune System.
Dhakad P, Obbard DJ
Genome Biol Evol · 2026 Mar · PMID 41693166 · Full text
The evolutionary dynamics of immune genes are shaped by diverse selective pressures, yet the relative roles of gene-level traits, functional specialization, and pathway context remain poorly understood. Here, we applied...
The evolutionary dynamics of immune genes are shaped by diverse selective pressures, yet the relative roles of gene-level traits, functional specialization, and pathway context remain poorly understood. Here, we applied a meta-analytic mixed model approach to quantify how immune-pathway genes differ from other genes in their relative rate of protein sequence divergence (dN/dS), evidence for positive selection, and gene turnover rate (λ). We do this while simultaneously accounting for gene length, expression level, genetic and protein-protein interactions, and structural features such as relative solvent accessibility (RSA). In general, rates of sequence evolution were strongly and positively associated with RSA, and negatively associated with gene length, expression, and the number of genetic/protein-protein interactions, whereas gene turnover rate was largely unaffected by these factors. We find immune genes evolved significantly faster at the protein sequence level than nonimmune genes but, contrary to our expectation, exhibited lower gene turnover rates. Functional and pathway-level analyses revealed accelerated protein evolution in effectors, receptors, and antiviral genes, with the cGAS-STING and Toll pathways showing the highest dN/dS. Gene turnover rate was elevated only in effectors, whereas cellular defense genes were particularly conserved. We also found evidence for an elevated proportion of sites under episodic positive selection in immune genes, particularly in effectors, indicating ongoing adaptive diversification. These findings highlight how immune diversification in Drosophilidae arises from multiple, partly independent, evolutionary axes, shaped jointly by structural constraints, functional roles, and lineage-specific pathogen pressures.
Exploring the First Draft Genome of the Oribatid Mite, Oppia nitens: A Standardized Model Invertebrate in Soil Ecotoxicology.
Adedokun AA, Fajana HO, Jegede OO … +7 more , Hammond SA, Smith DDN, Kvas S, Hewavithana T, Jin L, Princz J, Siciliano SD
Genome Biol Evol · 2026 Jan · PMID 41684253 · Full text
Oribatid mites are among the most abundant groups of soil microarthropods. Oppia nitens (family Oppiidae), a member of one of the largest and most diverse oribatid mite families, has been developed as a standardized mode...
Oribatid mites are among the most abundant groups of soil microarthropods. Oppia nitens (family Oppiidae), a member of one of the largest and most diverse oribatid mite families, has been developed as a standardized model organism for assessing soil contamination. However, limited genomic resources for this species hinder our understanding of its physiological adaptations and sensitivities to chemical and environmental stressors. Here, we present the annotated O. nitens draft genome, generated through a de novo hybrid assembly combining Oxford Nanopore Technologies and Illumina sequencing data, providing a foundation for identifying genes associated with adaptation to environmental and chemical stress. The assembled genome consists of 65 scaffolds spanning 125.4 Mb, with a GC content of 24.5% and an N50 of 4.41 Mb. Genome completeness, assessed using arthropod Benchmarking Universal Single-Copy Orthologs (BUSCO), revealed 99.1% BUSCO completeness, 98.0% complete single copy, 1.1% duplicated, 0.5% fragmented, and 0.4% missing orthologs (arachnida_odb12, n = 1123). Using the National Center for Biotechnology Information Eukaryotic Genome Annotation Pipeline, we annotated 15,291 genes, 16,969 mRNAs, and 14,938 proteins. This high-quality draft genome represents the first comprehensive genomic resource for O. nitens and provides a valuable foundation for future investigations into the molecular mechanisms underlying environmental adaptation, particularly tolerance to metal stress.
Evolutionary Transitions in Social Behavior are Associated With Convergent and Partially Reversible Expansions of Transcription Factor Binding Sites.
Ploessl SG, Jones BM
Genome Biol Evol · 2026 Jan · PMID 41684252 · Full text
The evolution of sociality involves shifts in physiology and behavior, most notably the emergence of a reproductive division of labor. Within social colonies, these distinct behavioral phenotypes arise from differential...
The evolution of sociality involves shifts in physiology and behavior, most notably the emergence of a reproductive division of labor. Within social colonies, these distinct behavioral phenotypes arise from differential regulation of a shared genome. Changes in transcription factor (TF) binding motifs are one potential mechanism underpinning this plasticity, with prior studies suggesting that social species exhibit expansions in TF binding sites. However, it remains unclear whether motif expansions are reversed when sociality is lost. Here we analyze predicted TF motif occurrences across gene promoters in 42 bee species spanning millions of years of evolutionary divergence and multiple independent gains and losses of sociality. We compare motif presence across species to test whether motif expansions are a convergent feature of social evolution and whether their presence secondarily decreases when social behavior is lost. Our findings are consistent with previous research, demonstrating an expansion of TF motifs in lineages which have gained sociality. However, contrary to expectation, we do not observe genome-wide motif contractions in lineages which have secondarily lost social behavior. Despite this overall pattern, we still identify several motifs, promoter regions, and specific motif-promoter pairs which exhibit complementary changes with both gains and losses of sociality. These regulatory targets are enriched for similar organismal functions, providing strong candidates for further study. Our results lend additional support to the hypothesis that novel phenotypes may arise through modification of existing gene regulatory networks.
The Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes.
Wagner M, Resl P, Klar N … +7 more , Huie JM, Bista I, McCarthy S, Smith M, Durbin R, Koblmüller S, Svardal H
Genome Biol Evol · 2026 Mar · PMID 41671394 · Full text
Understanding the genetic basis of widespread phenotypic convergence, particularly for complex morphological traits, remains a major challenge in evolutionary biology. The Mediterranean gravel beach clingfishes of the ge...
Understanding the genetic basis of widespread phenotypic convergence, particularly for complex morphological traits, remains a major challenge in evolutionary biology. The Mediterranean gravel beach clingfishes of the genus Gouania provide an excellent system to study this phenomenon. Within this genus, two distinct morphotypes, "slender" and "stout," have repeatedly evolved, adapting to different microhabitats. These morphotypes differ in multiple complex traits, including body elongation, head compression, vertebral number, eye size, and the structure of the adhesive disc. First, to scrutinize phylogenetic convergence, we combined 3D morphometrics of the pelvic girdle and skull, with molecular species delimitation based on >660 DNA barcodes, and a phylogenomic framework based on more than 3,400 single-copy orthologs. Second, by employing whole-genome resequencing and a novel "convergence score" statistic, we examined genomic convergence across multiple levels: nucleotides, sequences, genes, and functional pathways. While we found no evidence of large-scale genomic or protein-level convergence, we identified promising candidate regions at the level of single variants, genes, and biological pathways. Notably, a longer shared (but interrupted) haplotype around the candidate gene adam12 was associated with convergent traits. The lack of simple genomic patterns may reflect the radiation's age and the complex genetic basis of the underlying morphological traits (eg eye size, neurocranium shape). Altogether, our findings highlight the importance of assessing genomic convergence at multiple molecular levels to uncover diagnostic signals across varying evolutionary processes and timescales.
Transcriptomic Adjustment to Decreasing Oxygen Reveals Novel Functional Strategies for Extreme Hypoxia Tolerance in the Copepod Tigriopus californicus.
Powers MJ, Barreto FS
Genome Biol Evol · 2026 Jan · PMID 41670122 · Full text
Hypoxia-induced regulatory changes are well understood across aquatic and terrestrial systems. These changes are normally initiated by elements belonging to hypoxia-inducible factor (HIF) pathway. These elements generate...
Hypoxia-induced regulatory changes are well understood across aquatic and terrestrial systems. These changes are normally initiated by elements belonging to hypoxia-inducible factor (HIF) pathway. These elements generate responses that help organisms survive hypoxia, such as protein stabilization, antioxidant activity, or the switch from aerobic to anaerobic metabolism. The HIF pathway is initiated by the transcription factor HIF-α via deactivation of its repressor EGLN. However, recent work revealed that many aquatic invertebrates do not possess HIF-α or EGLN. Among these is the intertidal copepod Tigriopus californicus. Although this copepod experiences daily bouts of hypoxia, T. californicus tolerates even extended anoxia with minimal mortality. Because T. californicus lacks HIF-α, it is unclear how the transcriptional response proceeds on a fine timescale in this species and which physiological strategies they use to cope with severe hypoxia. In this study, we captured gene expression over a species-typical course of hypoxia including normoxia, mild hypoxia (∼3.5 mg O2 L-1), at critical oxygen tension (Pcrit; ∼0.5 mg O2 L-1), anoxia (0 mg O2 L-1), and recovery. We identified and clustered genes affected by this hypoxia course and tested for enrichment of Gene Ontology and transcription factor binding site motifs. We identified genes with known responses to hypoxia, including genes with interactions with HIF-α in other systems. We also identified genes related to functions unique to T. californicus, including exoskeletal modifications that could represent a specialized response allowing T. californicus to persist in extreme hypoxic environments despite lacking HIF-α.
Recent Microbial Evolutionary Insights From Metagenomics.
Moguel B, Carrillo Olivas L, Guerrero-Osornio MG … +1 more , Herrera Paredes S
Genome Biol Evol · 2026 Mar · PMID 41668418 · Full text
Microorganisms have profoundly shaped Earth's biological and geological history, from the origins of oxygenic photosynthesis to present-day global biogeochemical cycles. Metagenomics-through its ability to recover genomi...
Microorganisms have profoundly shaped Earth's biological and geological history, from the origins of oxygenic photosynthesis to present-day global biogeochemical cycles. Metagenomics-through its ability to recover genomic information directly from environmental samples-has revolutionized our understanding of microbial evolution by uncovering unbeknownst lineages, revealing functional adaptations, and reshaping our view of the Tree of Life. By bypassing the need for cultivation, shotgun metagenomics and metabarcoding approaches have enabled researchers to investigate microbial diversity, ecology, and evolutionary processes across aquatic, terrestrial, extreme, and host-associated environments. This review highlights recent advances in evolutionary biology driven by metagenomics, including studies on deep evolutionary branching events, microbial adaptation to extreme environments, the evolution of host-associated microbiomes, and the emergence and spread of pathogens and antimicrobial resistance. The integration of ancient DNA has expanded our ability to reconstruct past ecosystems and disease dynamics, offering insights into long-term microbial evolution. In parallel, studies of microbial domestication and urban settings reveal how human practices have shaped microbial genomes over millennia. Despite significant progress, key challenges remain-including improving bioinformatic tools for degraded ancient DNA, resolving deep phylogenetic relationships, identifying adaptive variants, and linking genomic shifts to ecosystem-level processes. The future of microbial evolutionary research will depend on combining longitudinal metagenomic data, experimental evolution, functional assays, and predictive modeling to better understand microbial responses to climate change and anthropogenic pressures. Together, these approaches will deepen our understanding of microbial evolution and its consequences for life on Earth-past, present, and future.
Cryptocercus Genomes Expand Knowledge of Adaptations to Xylophagy and Termite Sociality.
Jones ARC, Mikhailova AA, Aumont C … +9 more , Berger J, Liu C, He S, Wang Z, Winkler S, Bornberg-Bauer E, Legendre F, McMahon DP, Harrison MC
Genome Biol Evol · 2026 Jan · PMID 41655980 · Full text
Subsociality and wood-eating or xylophagy are understood as key drivers in the evolution of eusociality in Blattodea (cockroaches and termites), two features observed in the cockroach genus Cryptocercus, the sister group...
Subsociality and wood-eating or xylophagy are understood as key drivers in the evolution of eusociality in Blattodea (cockroaches and termites), two features observed in the cockroach genus Cryptocercus, the sister group of all termites. We analyze two high-quality genomes from this genus, C. punctulatus from North America and C. meridianus from Southeast Asia, to explore the evolutionary transitions to xylophagy and subsociality within Blattodea. Our analyses reveal evidence of relaxed selection in both Cryptocercus and termites, indicating that a reduction in effective population size may have occurred in their subsocial ancestors. These findings challenge the expected positive correlation between dN/dS ratios and social complexity, as Cryptocercus exhibits elevated dN/dS values that may exceed those of eusocial termites. Additionally, we infer a reduction in the number of Ionotropic Receptors and a change from uni- to bimodal methylation signatures in protein coding genes in a common ancestor of Cryptocercus and termites, mechanisms previously thought to have evolved with the emergence of eusociality in termites. Future studies incorporating additional genomic data from diverse blattodean species can further build on these findings and provide deeper insights into the molecular mechanisms driving transitions to xylophagy and eusociality.
Evolutionary Dynamics of Dosage Compensation and Sex-biased Gene Expression in Morabine Grasshopper Vandiemenella viatica.
Jayaprasad S, Schielzeth H, Palacios-Gimenez OM
Genome Biol Evol · 2026 Jan · PMID 41635935 · Full text
Sex chromosome evolution and gene regulation are closely linked but remain understudied in many taxa. Young neo-sex chromosomes offer unique insights into these processes. We examine dosage compensation and sex-biased ge...
Sex chromosome evolution and gene regulation are closely linked but remain understudied in many taxa. Young neo-sex chromosomes offer unique insights into these processes. We examine dosage compensation and sex-biased gene expression in Vandiemenella viatica grasshoppers by comparing the ancestral X chromosome in the P24X0 race with derived neo-sex chromosomes in the P24XY race. The P24XY neo-XY arose via X-autosome fusion: the XL arm represents the ancestral X and the XR arm a former autosome (chromosome 1 in P24X0) now part of the neo-X and homologous to the neo-Y. We first assess dosage compensation via male and female gene expression. In somatic tissues, male P24X0 X-linked and P24XY XL-linked genes are upregulated to match both female expression and autosomal levels, indicating near-complete dosage compensation. In testes, expression of X-linked and the XL-linked genes is reduced nearly 4-fold reflecting absent dosage compensation and the presence of meiotic X chromosome inactivation. We then analyze sex-biased gene expression across tissues and chromosomes. Gonads show stronger sex-biased gene expression than somatic tissues. Female-biased genes are concentrated on the P24X0 X and P24XY XL, whereas male-biased genes are enriched on autosomes and the XR arm of the neo-X. Overall, the ancestral X in P24X0 and the XL arm of the P24XY neo-X are hypertranscribed, while the XR arm retains autosomal expression, male-biased enrichment, and lacks dosage compensation. These patterns show that dosage compensation is regulated at levels of chromosome arms and illustrate how chromosome structure, gene regulation, and reproduction interact, shedding light on sex chromosome evolution in V. viatica.
Trio-sequencing Reveals High Germline Mutation Rates in the Colorado Potato Beetle (Leptinotarsa decemlineata).
Xu S, Al-Madhagy S, Duchen P … +1 more , Edison A
Genome Biol Evol · 2026 Jan · PMID 41635933 · Full text
Germline mutation rates are fundamental to evolution, yet they remain unquantified for beetles (Coleoptera), the most speciose order including major pests. We sequenced genomes from 16 trios of the Colorado potato beetle...
Germline mutation rates are fundamental to evolution, yet they remain unquantified for beetles (Coleoptera), the most speciose order including major pests. We sequenced genomes from 16 trios of the Colorado potato beetle (Leptinotarsa decemlineata, CPB)-a pest that has evolved resistance to many insecticides. We estimated a germline mutation rate of 5.8 × 10-9 (95% CI: 4.7 × 10-9, 7.2 × 10-9) per site per generation in CPB, a rate 2-fold higher than the median for other insects. Across 13 insect species, mutation rate was positively associated with genome-wide GC content (PGLS). The increased mutation rate in CPB is also consistent with drift-barrier expectations. Based on this mutation rate and the beetle's fecundity, we estimate that the brood from just one CPB female can introduce nearly 141 new mutations into the coding regions each generation. These findings inform CPB's rapid pesticide resistance evolution and fill a key gap in arthropod genomics and evolution.
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