Genome Biology And Evolution[JOURNAL]
Sun
200 papers
Genomic evidence for natural selection underlying high-altitude adaptive hemoglobin levels among Peruvian Andeans.
Zhu K, Jorgensen K, Weinstein J … +12 more , Kiyamu M, Elías G, Isherwood J, Breidenstein AM, Garcia O, Gerdes G, Pearson L, Lee FS, Rivera-Ch M, Leon-Velarde F, Brutsaert TD, Bigham AW
Genome Biol Evol · 2026 Jul · PMID 42402195 · Publisher ↗
High-altitude hypoxia presents an extreme environmental pressure that challenges human survival, growth, and reproduction. Despite this challenge, humans have thrived on the Andean Altiplano for millennia, displaying sev...
High-altitude hypoxia presents an extreme environmental pressure that challenges human survival, growth, and reproduction. Despite this challenge, humans have thrived on the Andean Altiplano for millennia, displaying several unique physiological responses to hypoxia such as elevated hemoglobin concentration ([Hb]). This trait closely resembles the acclimatization response observed among high-altitude sojourners but is distinct from the sea-level normative [Hb] that characterizes the Tibetan adaptive response. As recent candidate-gene efforts to understand the role of natural selection in shaping Andean [Hb] have produced conflicting results, it remains unclear what role natural selection may have played in shaping this unique hematopoietic response. Using genome-wide array data from Peruvian Andeans, we identified two genomic regions containing three genes, PDE1B, PPP1R1A, and RASGEF1B, that show evidence of recent positive selection and are associated with [Hb]. Importantly, Andean alleles within these regions are associated with lowered [Hb], suggesting that recent polygenic selection may be acting to reduce [Hb] within this population. We observe the greatest divergence of Andean allele frequencies from other global populations within the PDE1B/PPP1R1A region, and use WGS data and publicly available expression and Hi-C data to more closely identify how natural selection may be acting within this region to impact [Hb]. We identify a selective sweep that favors eleven PDE1B expression-decreasing alleles, and is located at the boundary of a topologically associating domain spanning several hemoglobin-linked genes. In sum, this study provides novel evidence that polygenic natural selection may be acting to lower Andean [Hb] in a manner phenotypically convergent with Tibetan populations.
Host Range Breadth Correlates with Genic Diversity in Honeybee Phages.
Robinson CRP, Dolezal AG, Liachko I … +1 more , Newton ILG
Genome Biol Evol · 2026 Jul · PMID 42398003 · Full text
Bacteriophages can evolve rapidly. Mutation and recombination via horizontal gene transfer allow them to counter adaptive responses by microbial hosts. However, little is known about the genomic processes underlying phag...
Bacteriophages can evolve rapidly. Mutation and recombination via horizontal gene transfer allow them to counter adaptive responses by microbial hosts. However, little is known about the genomic processes underlying phage evolution within an ecological context-especially within natural microbial communities. This is due in part to the difficulty in resolving aspects of phage ecology, such as host range. To better understand the interplay of phage ecology and evolution within natural microbial communities, we combined measures of phage host range in vivo with measures of genome evolution in order to infer the evolutionary pressures acting on phage genomes within individual honeybee worker microbiomes. We show that near-identical phage genomes, cooccurring across multiple honeybee colonies, exhibit large variation with respect to gene modules, despite retaining a highly similar core genome. Estimates of genic diversity suggest deviations from neutral evolutionary models and identify loci under putative diversifying selection. We then use HiC-resolved metagenomics and show that the honeybee gut contains a dense phage community that exhibits a wide degree of host range variation. This variation differed across individual metagenomes in both the number and phylogenetic distance of potential hosts. We show that common measures of genetic variation positively correlate with host range in bee-associated phages and that functional targets of diversifying selection are partitioned differently between broad or narrow host range phages. Our work underscores the high host range variation associated with phages within host-associated microbial communities and provides evidence that this variation impacts rates of phage evolution.
Genome-wide analysis of an endangered axolotl endemic to Mexico reveals genomic variation associated with body condition, environment and infection by a pathogenic fungus.
Soto-Cortés E, Basanta MD, Ávila-Akerberg V … +5 more , Castellanos-Morales G, Eguiarte LE, Gasca-Pineda J, González Martínez TM, Rebollar EA
Genome Biol Evol · 2026 Jul · PMID 42397068 · Publisher ↗
Amphibians are the most threatened group of vertebrates on the planet due to habitat loss, climate change and the emerging disease chytridiomycosis, caused by the pathogenic fungus Batrachochytrium dendrobatidis (Bd). Ax...
Amphibians are the most threatened group of vertebrates on the planet due to habitat loss, climate change and the emerging disease chytridiomycosis, caused by the pathogenic fungus Batrachochytrium dendrobatidis (Bd). Axolotls, species from the genus Ambystoma endemic to Mexico, are a highly vulnerable group of salamanders with restricted distributions and are severely affected by habitat fragmentation, invasive species, and pollution. In this context, population genomic studies are urgently needed to implement adequate conservation and management decisions. In this study, we identified abiotic and biotic factors associated with the genomic diversity and structure of Ambystoma altamirani through genome-wide single-nucleotide polymorphism (SNP) analyses. Based on 110,761 neutral SNPs from 99 individuals across five populations of A. altamirani, we found that genomic diversity of individuals was positively correlated with their body condition. Moreover, patterns of genetic structure identified three main genetic clusters which were correlated with habitat environmental differences. Specifically, elevation and temperature-associated variables significantly contributed to the genomic structuring of A. altamirani populations. Linear factor mixed models (LFMM) identified 1,670 SNPs associated with environmental variables as well as 80 and 47 SNPs associated with the biotic variables Bd infection intensity and body condition, respectively. We identified SNPs significantly associated with differences in Bd infection and body condition among homozygous or heterozygous genotypes. Overall, our study teases apart some of the factors likely influencing axolotl genetic diversity and population structuring, which should be considered for conservation strategies for this and other endangered amphibian species.
Conservation of IAMT preference for indole acetic acid methylation across 250 million years of seed plant divergence, with only one recent evolutionary switch in Ocimum.
Saadaie Jahromi B, Kostrzewa LM, Alhinaai T … +49 more , Al-Zadjali T, Amin A, Barth A, Bayne ME, Begeman GR, Bell WH, Bucko MG, Catania EM, Currie A, Fernanda de Lima Pereira G, Figueroa C, Galentine AB, Gambrell G, Garcia FD, Gauthier AE, Graber JR, Hagenbarth BJ, Hall A, Heemstra M, Huang R, Hunter J, Jaswa A, Karyadi N, Learman CJ, Lee KM, Lewis CT, McKenzie E, McKinney MF, McLean S, Mueller HM, Nadeem M, Nath S, Nusbaum VS, O'Connor B, Pasupathy N, Pathak E, Tahsin Raisa T, Ramirez K, Salazar B, Sander CE, Schneider E, Sedlacek K, Sirrine G, Spitsbergen JB, Garcia Torres L, Truong MH, Hernandez Velasco B, Woolfolk R, Barkman TJ
Genome Biol Evol · 2026 Jul · PMID 42391499 · Publisher ↗
Plant indole-3-acetic acid methyltransferase (IAMT) is an ancient SABATH enzyme that modulates auxin levels via S-adenosyl-L-Methionine (SAM)-dependent methylation. While most IAMTs studied previously prefer to methylate...
Plant indole-3-acetic acid methyltransferase (IAMT) is an ancient SABATH enzyme that modulates auxin levels via S-adenosyl-L-Methionine (SAM)-dependent methylation. While most IAMTs studied previously prefer to methylate indole-3-acetic acid (IAA), one orthologous enzyme prefers to methylate cinnamic acid (CA) and shows no activity towards IAA. To understand whether other closely related enzymes also show substrate preference switches, we combined molecular phylogenetic analyses with in-vitro enzyme assays. A maximum-likelihood tree of 704 IAMT-like enzymes shows pervasive retention of IAMT orthologs across nearly all angiosperms and gymnosperms. Our newly reported enzymatic assays of 59 orthologs spanning 52 species and 26 orders revealed strongly conserved methylation preference for IAA across all lineages. However, in the genus Ocimum (Lamiaceae), species appear to possess one copy of IAMT that encodes an IAA-preferring enzyme and a second copy that encodes an enzyme that prefers to methylate CA. Altogether, we experimentally investigated four lineages, Lamiales, Solanales, Fabales and Rosales, in which IAMT-type enzymes were duplicated but no others showed evidence for substrate preference switches. Alignments and computational modeling of Lamiaceae sequences highlighted M35, L325, and L363 as amino acid substitutions that may account for CA preference evolution in Ocimum enzymes. Yet, experimental mutation of those sites in either modern-day or ancestral sequences did not result in substrate preference changes in enzyme assays. Therefore, further studies are required to phylogenetically pinpoint the timing and structural basis for the shift towards cinnamic acid methylation preference and to deepen our understanding of molecular evolution of the SABATH enzyme family.
Regulatory logic and transposable element dynamics in Caenorhabditis genomes.
Eggers VK, Fierst JL
Genome Biol Evol · 2026 Jul · PMID 42389935 · Publisher ↗
Genome sequencing has revealed a tremendous diversity of transposable elements (TEs) in eukaryotes but there is little understanding of the evolutionary processes responsible for these patterns. Theoretical studies predi...
Genome sequencing has revealed a tremendous diversity of transposable elements (TEs) in eukaryotes but there is little understanding of the evolutionary processes responsible for these patterns. Theoretical studies predict interactions between elements can regulate TE proliferation but the narrow conditions are at odds with the abundance of TEs in natural populations. We implemented three models of TE regulation in stochastic simulations to analyze how regulatory logic interacted with population genetic factors including reproduction through outcrossing or self-fertility. We focused on autonomous TEs containing the recognition sequences and enzymes necessary for transposition and their non-autonomous relatives, elements that have lost this physical machinery. We found that large outcrossing populations evolving with either Negative Epistatic interactions between autonomous TEs or Asymmetric regulation between autonomous and non-autonomous elements stably maintained TEs. Small or self-fertile populations and those in which TEs moderately impacted fitness or inserted at high rates experienced TE proliferation to the point of population extinction, suggesting high selective pressure for mutational inactivation of TEs. We tested our model predictions in Caenorhabditis genomes by annotating TEs in two focal families, autonomous LINEs and their non-autonomous SINE relatives and the DNA transposon Mutator. We found variation in autonomous - non-autonomous relationships and rapid mutational decay in the sequences allowing TEs to transpose. Together, our results suggest that individual TE families evolve according to disparate regulatory rules relevant in the early, acute stages of TE invasion.
Interchromosomal translocations and large deletions drive the evolution of the outlier chromosome in the smallest photosynthetic eukaryote.
Bugnot C, Alioto T, Cruz Rodriguez F … +5 more , Manirakiza E, Gomez Garrido J, Gut M, Yau S, Piganeau G
Genome Biol Evol · 2026 Jul · PMID 42388146 · Publisher ↗
Marine microalgal populations can rapidly evolve resistance to viruses upon infection. In Ostreococcus mediterraneus resistance to the prasinovirus OmV2 emerged within five days in all virus-exposed populations. Whole-ge...
Marine microalgal populations can rapidly evolve resistance to viruses upon infection. In Ostreococcus mediterraneus resistance to the prasinovirus OmV2 emerged within five days in all virus-exposed populations. Whole-genome sequencing of pairs of resistant and susceptible cell lines revealed extensive structural genomic changes, particularly on the Small Outlier Chromosome (SOC). SOC alterations included large deletions, duplications, rearrangements, and whole chromosome duplication, yet no consistent structural variant or single nucleotide polymorphism was directly associated with resistance. Hybrid de novo assemblies confirmed the unique SOC assembly of each strain, with a highly polymorphic ∼2 kb tandem repeat region exhibiting an "accordion-like" pattern of expansion and contraction. No new viral insertions were found, though endogenous viral elements were conserved across lines. Two interchromosomal translocations between the SOC and chromosomes 2 and 17 offer novel insights into the mechanisms underlying the distinctive evolutionary path of this chromosome. Together, these findings demonstrate that resistance to OmV2 evolves rapidly and consistently but cannot yet be attributed to any specific structural variations, suggesting that transcriptional or post-transcriptional mechanisms underly the resistant phenotype. Instead, the high rate of localized genomic structural variations points to a distinct mechanism of chromosome evolution.
Chromosome-scale genome assemblies of duckweeds provide insights into genomic plasticity, aquatic adaptation and morphological reduction.
Tek MI, Boyle B, Normandeau E … +3 more , Lecomte L, Sabri M, Torkamaneh D
Genome Biol Evol · 2026 Jul · PMID 42381499 · Publisher ↗
Duckweeds (Lemnaceae) present a striking example of convergent genome evolution following the return from land to water. As the smallest and fastest-growing angiosperms, they exhibit extreme morphological reduction yet r...
Duckweeds (Lemnaceae) present a striking example of convergent genome evolution following the return from land to water. As the smallest and fastest-growing angiosperms, they exhibit extreme morphological reduction yet retain remarkable genomic plasticity through recurrent interspecific hybridisation, chromosomal rearrangements, and selective gene-family remodelling. The genomic mechanisms that distinguish this secondarily aquatic lifestyle from terrestrial ancestors, and whether these changes are convergent with other aquatic lineages such as seagrasses, have remained incompletely resolved. Here we report chromosome-scale genome assemblies for four duckweed species, Spirodela polyrhiza, Lemna minuta, Lemna japonica, and Lemna aequinoctialis, generated with PacBio HiFi long reads and Omni-C chromatin conformation capture. These assemblies include the first genomic characterisation of an unresolved hybrid lineage (L. aequinoctialis ×) that harbours a previously uncharacterised 3.5 Mb reciprocal translocation between subgenomes, as well as confirmation of the allodiploid origin of L. japonica. Comparative phylogenomics with land plants and the seagrass Zostera marina reveals a coherent, non-random programme of gene loss: effector-triggered immunity (ETI) components (EDS1 and PAD4) and the high-affinity nitrate transporter NRT2 are convergently absent across duckweeds and Z. marina, consistent with relaxed pathogen pressure and abundant dissolved nutrients in aquatic habitats. In contrast, secondary-metabolite biosynthesis pathways for flavonoids, anthocyanins, flavones and flavonols are retained or expanded despite overall genome compaction. These findings illustrate how the return to aquatic environments following terrestrialisation shaped duckweed genome evolution through convergent gene loss and selective pathway retention, and provide high-quality genomic resources to support future research in plant evolutionary biology and biotechnology.
Towards a functional genetics of adaptation: insights from microbial experimental evolution.
Kassen R
Genome Biol Evol · 2026 Jul · PMID 42379567 · Publisher ↗
A general theory of adaptation is one that accounts for both the quantitative and functional properties of adaptive evolution. To date, the field has focused more on the former and less on the latter. Here I build on the...
A general theory of adaptation is one that accounts for both the quantitative and functional properties of adaptive evolution. To date, the field has focused more on the former and less on the latter. Here I build on the results of adaptive laboratory evolution experiments in microbes to present a sketch for functional theory of adaptation built around the idea that the primary source of selection in the initial stages of adaptation often involves rapid re-growth in the presence of stress. Consequently, the genes targeted during adaptation are often those involved in the regulation of gene expression, including global regulators associated with managing the stress response. These mutations, especially those involving high level gene regulation, are often highly pleiotropic, in contrast to the expectation derived from the quantitative theory of adaptation. Whether this theory can be used to make sense of adaptation more generally beyond microbial evolution experiments remains an open issue.
Evidence for cryptic sex in Escovopsis, a mycoparasite in the fungus-growing ant symbiosis.
Young SE, Bryan CT, Gotting K … +1 more , Currie C
Genome Biol Evol · 2026 Jun · PMID 42377967 · Publisher ↗
The Red Queen hypothesis for the maintenance of sexual reproduction proposes that sex should be favored during parasite-host interactions. The presence of sexual reproduction in Escovopsis sensu lato (s.l.) (Hypocreaceae...
The Red Queen hypothesis for the maintenance of sexual reproduction proposes that sex should be favored during parasite-host interactions. The presence of sexual reproduction in Escovopsis sensu lato (s.l.) (Hypocreaceae, Ascomycota), obligate specialized parasites on the fungal gardens of fungus-growing ants, has been debated; previous analyses have concluded that sex is likely absent based on Escovopsis s.l. appearing to lack a complete mating-type (MAT) locus, which controls sexual compatibility in fungi. Using 39 previously sequenced genomes, we found that computational annotation of these loci was inconsistent. Through manual annotation, we show that all sequenced Escovopsis s.l. have a complete MAT1 locus. The MAT1 locus is found in the typical genomic context for Hypocreaceae fungi, contains the expected genes (one in the MAT1-2 idiomorph and three in the MAT1-1 idiomorph), are highly conserved at a structural and functional level, and are under strong purifying selection. Using a Phi test, we also find evidence for recombination in one closely related group of samples. Past phylogenomic analyses of Escovopsis s.l. have generated two distinct topologies, and we find that the MAT1 genes also have differing topologies. Further, phylogenetic network analyses show large-scale gene tree discordance between early diverging Escovopsis s.l. taxa and some outgroups, supporting a potential past hybridization event. Taken together, these data suggest that Escovopsis s.l. undergoes cryptic sex, changing our understanding of the ecology and evolution of the model fungus-growing ant symbiosis and opening many exciting research avenues on the dynamics of sex and infection in this system.
Experimental Evolution Under Biased Sex Ratios: Phenotypic and Genomic Responses in the Bulb Mite, Rhizoglyphus robini.
Chmielewski S, Parrett JM, Konczal M … +3 more , Szubert-Kruszyńska A, Łukasiewicz A, Radwan J
Genome Biol Evol · 2026 Jul · PMID 42377933 · Full text
Sexual selection may increase population fitness by favoring high-condition individuals and accelerating the purging of deleterious alleles. However, it can also reduce population fitness through intra- and interlocus se...
Sexual selection may increase population fitness by favoring high-condition individuals and accelerating the purging of deleterious alleles. However, it can also reduce population fitness through intra- and interlocus sexual conflict by promoting male-benefit traits that harm females and maintain polymorphism at sexually antagonistic loci. The balance between these opposing forces remains unresolved, yet it has major consequences for how sexual selection shapes population fitness and genome-wide variation. To explore the genomic and phenotypic effects of sexual selection and sexual conflict, we evolved replicated bulb mite (Rhizoglyphus robini) lines for 28 generations under male- versus female-biased sex ratios and combined phenotypic assays with whole-genome resequencing. Female fecundity and inbreeding depression did not differ between treatments, and genomic analyses revealed no treatment effect on the loss of rare, putatively deleterious SNPs. Contrary to expectations, males from male-biased lines were less harmful to stock females than males from female-biased lines. Genome-wide nucleotide diversity declined similarly across generations in both treatments, although synonymous exonic diversity declined more slowly in male-biased lines. While only a few SNPs diverged consistently between treatments, we identified large treatment-specific haplotype blocks, indicating that multiple genomic regions were involved in response to sex-ratio manipulation. Overall, our results indicate that sex ratio manipulation drives evolution of male harm to females and widespread haplotype frequency changes without clear evidence for enhanced purging or maintenance of genetic diversity. The response thus appears to reflect adaptation to an altered level of reproductive competition, but without measurable consequences for population fitness and genetic diversity.
Optimal organelle inheritance strategies under different changing environments and mutational pressures.
García-Pascual B, Nordbotten JM, Johnston IG
Genome Biol Evol · 2026 Jun · PMID 42363700 · Publisher ↗
Mitochondrial and chloroplast DNA (mtDNA and cpDNA) encode essential cellular apparatus. This organelle DNA (oDNA) exists at high copy number (ploidy) in eukaryotic cells, which must both mitigate mutational damage and a...
Mitochondrial and chloroplast DNA (mtDNA and cpDNA) encode essential cellular apparatus. This organelle DNA (oDNA) exists at high copy number (ploidy) in eukaryotic cells, which must both mitigate mutational damage and allow adaptation to changing demands. Across eukaryotes, oDNA is inherited and maintained by different classes of process. Inheritance is often maternal, but some species use paternal or doubly-uniparental (sex-dependent) inheritance (DUI), with different extents of "leakage" of oDNA from the non-primary parent. During development, genetic bottlenecks of different magnitudes and recombination-mediated repair are employed in different species. Here, we use modelling and simulation to investigate the fitness advantages, disadvantages, conflicts, and tradeoffs of these different strategies under different challenges of mutation and changes in selection imposed by the environment (in the absence of interactions with nuclear genes). We find a general tradeoff between maintaining heteroplasmy to support adaptation to environmental change, and supporting purifying selection against dysfunctional mutants. Different combinations of leakage and bottleneck size provide optimal resolutions to this tradeoff under different sets of challenges. We connect our findings to biologically observed behaviours, including the universality of non-minimal bottleneck sizes, a tradeoff between high ploidy for heteroplasmy and repair and tight bottlenecks for segregation, and environmental dependence of the benefits of leakage and DUI.
A reassessment of positive growth effects of expressed random sequence clones in E. coli suggests direct adaptive functions.
Künzel S, Borish C, Burghardt C … +2 more , Heidinger C, Tautz D
Genome Biol Evol · 2026 Jun · PMID 42360890 · Publisher ↗
De novo gene emergence from non-coding sequences is an important evolutionary mechanism, yet the functional potential of random sequences remains debated. Previous experiments suggested that expression of random sequence...
De novo gene emergence from non-coding sequences is an important evolutionary mechanism, yet the functional potential of random sequences remains debated. Previous experiments suggested that expression of random sequence clones in Escherichia coli can enhance growth of cells, i.e. they can provide a direct fitness advantage. However, these findings have been questioned, regarding potential confounding effects of the clone mixtures and a possibly negatively acting peptide expressed from the cloning vector. Here we performed controlled competitive growth assays using a defined subset of random sequence clones representing a spectrum of fitness effects. Experiments across multiple conditions, including two different growth cycle durations, induction states, and replicate sets, showed high technical reproducibility and consistent clone-specific growth trajectories for the majority of the clones, but for some also influences of genomic background and experimental conditions. While previous results for vector-derived control constructs could be confirmed, several random sequence clones exhibited higher positive selection coefficients then these vector constructs. These relative effects persisted even when negative clones were excluded, indicating that they are not driven by competition dynamics with negative clones. Our results demonstrate that positive growth effects of random sequence clones cannot be explained by clone mixture and vector artifacts alone. Instead, a subset of random sequences confers genuine fitness advantages comparable to beneficial mutations observed in experimental evolution studies. These findings provide experimental support for the capacity of random sequences to directly generate adaptive effects without the necessity to acquire additional adaptive mutations.
Genome Scanning Reveals the Genetic Basis of a Color Pattern Morphotype in an Island Population of the European Adder (Vipera berus).
Casillas N, Petersen B, Martin SLF … +11 more , Ophus KH, Bringsøe H, Brealey JC, Bieker VC, Morin-Lagos J, Dolmen D, Madsen T, Nielsen R, Allentoft ME, Cerca J, Martin MD
Genome Biol Evol · 2026 Jun · PMID 42360275 · Full text
Color polymorphism is an important trait due to its role in defense strategies, feeding habits, environmental responses such as temperature regulation, and overall fitness. While the genetic basis of color polymorphism i...
Color polymorphism is an important trait due to its role in defense strategies, feeding habits, environmental responses such as temperature regulation, and overall fitness. While the genetic basis of color polymorphism is well understood in mammals, it remains relatively understudied in nonavian reptiles. Vipera berus, the European adder, is the most widely distributed and northernmost terrestrial snake in the world. Similar to other European vipers, V. berus exhibits a range of dorsal color patterns spanning from zig-zag to complete melanism. However, a unique longitudinal dorsal stripe pattern was recently discovered in the isolated Gossa Island (∼45 km2) population of Norway, where ∼5% of snakes exhibit this distinct pattern instead of the common dorsal zig-zag pattern. In this study, we investigated the genetic basis of the unique phenotype observed on Gossa by combining low-depth whole-genome shotgun sequencing and pairwise FST genome scanning. We discovered a moderately sized, significantly differentiated genomic region containing five associated genes, including the premelanosome gene (PMEL) that encodes a well-known transmembrane glycoprotein that is a key component of melanosome organelles. We implicate a functionally relevant variant in the encoded premelanosome protein. Our results provide insight into the evolution and genetic basis of pigmentation of squamate reptiles using the unbiased approach of genome scanning, a method that has rarely been used in this context.
Exploring the determinants of polydnavirus chromosomal integration across host-parasitoid wasp systems.
Matrougui I, Savisaar R, Dias C … +8 more , Calatayud PA, Malusi P, Muller H, Mwangangi E, Obonyo J, Oukkal S, Charlat S, Gilbert C
Genome Biol Evol · 2026 Jun · PMID 42345440 · Publisher ↗
Polydnaviruses (PDV) are domesticated viruses integrated into the genome of parasitoid wasps. During oviposition, female wasps inject into their host both eggs and PDV particles containing wasp DNA circles. Circle-borne...
Polydnaviruses (PDV) are domesticated viruses integrated into the genome of parasitoid wasps. During oviposition, female wasps inject into their host both eggs and PDV particles containing wasp DNA circles. Circle-borne genes are expressed in the host and suppress its immune response, ensuring successful development of the wasp larvae. Several dozen distinct circles have been distinguished on the basis of their sequence and location within the wasp genome. Interestingly, these circles display very different propensities to integrate into the caterpillar genome but the factors influencing this variation remain poorly understood. Here, we experimentally quantified and modelled both the number of PDV integrations and the abundance of injected PDV circles in 8 distinct wasp-host systems. Integrations into the host genomes were observed at rates ranging across wasp species from 0.28 to 14.5 integrations per host haploid genome. Our analyses reveal that integration efficiency varies among circles. We particularly highlight a specific circle, referred to as circle 1, which we find to be both the most abundantly injected and the most efficiently integrated, even after controlling for the direct effects of the quantity injected on the total number of integrations. This pattern is compatible with the view that both the quantity and integration efficiency of injected circles may constitute key components of parasitism success. Finally, our analyses indicate that integration efficiency is reduced in non-suitable hosts, suggesting a possible contribution of host factors to the regulation of PDV circle integration.
Evidence that zymocin-like killer plasmids were present in the common ancestor of terrestrial fungi.
Heneghan PG, Salzberg LI, Wolfe KH
Genome Biol Evol · 2026 Jun · PMID 42342251 · Publisher ↗
Some budding yeasts secrete killer toxins made by linear dsDNA plasmids located in the cytosol. The best-known example is the Kluyveromyces lactis toxin zymocin, which is encoded by a 9-kb killer plasmid assisted by a 13...
Some budding yeasts secrete killer toxins made by linear dsDNA plasmids located in the cytosol. The best-known example is the Kluyveromyces lactis toxin zymocin, which is encoded by a 9-kb killer plasmid assisted by a 13-kb helper plasmid. These plasmids are distantly related to eukaryotic dsDNA viruses and have been called Virus-Like Elements (VLEs) but they do not produce virus particles. Their evolutionary origin is unclear because VLEs have been found only in budding yeasts (subphylum Saccharomycotina of phylum Ascomycota) and not in any other fungi. Here, we show that similar VLEs are present in two other phyla of terrestrial fungi, Zoopagomycota and Mucoromycota. In Zoopagomycota, some isolates of Coemansia harbor more than 20 different linear dsDNA plasmids simultaneously, many of which encode their own DNA polymerases (DNAPs). The chitinase genes present on some of the newly discovered VLEs are orthologs of the chitinase subunits of killer toxins encoded by Saccharomycotina VLEs, suggesting that some of the new VLEs may be killer plasmids. Phylogenetic analysis of DNAPs shows that the diversity of VLEs in Zoopagomycota greatly exceeds that in Saccharomycotina, and that Saccharomycotina killer and helper plasmids are related to two lineages of VLEs present in Zoopagomycota. Our results suggest that VLEs were present in the common ancestor of all terrestrial fungi about 650 Mya, and that they were already subdivided into killer and helper types by this time.
Ancient persistence and newfound diversity of CR1-group retrotransposons across vertebrates.
Stuart AJ, Du Z, Hassan NT … +1 more , Adelson DL
Genome Biol Evol · 2026 Jun · PMID 42340196 · Publisher ↗
Retrotransposons are mobile, repetitive DNA sequences that are ubiquitous across eukaryotes and widely recognised as key drivers of both gene and genome evolution. The CR1 group of retrotransposons is thought to have bee...
Retrotransposons are mobile, repetitive DNA sequences that are ubiquitous across eukaryotes and widely recognised as key drivers of both gene and genome evolution. The CR1 group of retrotransposons is thought to have been present in the most recent common ancestor of vertebrates ∼560 mya, and is the dominant retrotransposon in the majority of vertebrate species. The advent of long-read sequencing technologies has enabled the assembly of high-quality genomes from representatives of almost all major vertebrate orders, enabling comparative analysis with deeply divergent species. To better understand the composition of CR1-group elements (CGEs) in vertebrates, we systematically characterised transposable elements across representative species from every available extant order of vertebrate. Our analysis uncovered previously unknown phylogenetic relationships of CGEs within and between species and has pushed back the origin of certain CR1-group subclades by tens of millions of years. Additionally, entirely novel elements with no close relatives in existing databases were uncovered within several of the species analysed. We also detected numerous putative horizontal transfer events, many of which had not been previously documented. Overall, this investigation has provided the first vertebrate-wide analysis of an element that is historically understudied yet plays a pivotal role in genome biology and evolution.
Loss of MHC I and II function in the genome of glacier lanternfish provides insight into evolution of vertebrate immune systems.
Solbakken MH, Tørresen OK, Tooming-Klunderud A … +3 more , Skage M, Bakken T, Jakobsen KS
Genome Biol Evol · 2026 Jun · PMID 42340168 · Publisher ↗
Lanternfishes (Myctophidae) are one of the most abundant and species diverse orders inhabiting the mesopelagic zone. Exploitation of marine resources has recently attracted increased interest. It is therefore essential t...
Lanternfishes (Myctophidae) are one of the most abundant and species diverse orders inhabiting the mesopelagic zone. Exploitation of marine resources has recently attracted increased interest. It is therefore essential to improve our understanding of the meso- and deep-pelagic ecosystems with respect to conservation and management strategies. Genomic resources are paramount to enable in-depth studies of population structuring and understanding the inherent genetic diversity, but also to enable studies of processes such as local adaptation and selection. Here, we present a genome assembly of the glacier lanternfish (Benthosema glaciale) generated with long-read PacBio and Hi-C contact map data. By comparing additional available genomes from the Myctophiformes order we explore their adaptive immune strategies. Our findings reveal that multiple lineages within this order have lost a significant proportion of genes related to adaptive immunity (Electrona, Protomyctophum and Benthosema). We find simultaneous loss of both classical MHC class I and class II function coinciding with reduction in genetic diversity with respect to immunoglobulin and T-cell receptors. In contrast, the sister branch represented by Gymnoscopelus and Nannobrachium appears to have maintained the standard configuration of the jawed vertebrate adaptive immune system apart from large gene expansions in MHC class II. Our results demonstrate that the Benthosema-belonging lineage (Myctophinae) has completely lost the core functions of the adaptive immune system. How, when and why this occurred warrants further investigations.
High Rate of Mutation and Efficient Removal by Selection of Structural Variants From Natural Populations of Caenorhabditis Elegans.
Saxena AS, Baer CF
Genome Biol Evol · 2026 Jul · PMID 42340057 · Full text
The importance of genomic structural variants (SVs) is well-appreciated, but less is known about their mutational properties than of single-nucleotide variants (SNVs) and short indels. The reason is simple: the longer th...
The importance of genomic structural variants (SVs) is well-appreciated, but less is known about their mutational properties than of single-nucleotide variants (SNVs) and short indels. The reason is simple: the longer the variant, the less likely it will be covered by a single sequencing read, thus the harder it is to map unambiguously to a unique genomic location. Here we report SV mutation rate estimates from 6 mutation accumulation (MA) lines from 2 strains of C. elegans using long-read (PacBio) sequencing. The inferred SV mutation rate is ∼0.03/genome/generation, about 1/10 the SNV rate and 1/4 the short indel rate. We identified 40 SV mutations (12 insertions, 28 deletions, 0 inversions) and 52 false positive (FP) variants by manual inspection. Excluding one atypical line (5 mutations, 35 FPs), the signal (mutant) to noise (FP) ratio is approximately 2:1. False negative rates were determined by simulating variants in the reference genome and observing "recall." Recall rate ranges from >90% for short indels and declines as SV length increases. Small deletions have nearly the same recall rate as small insertions (∼100 bp), but deletions have higher recall rates than insertions as the size increases. The reported SV mutation rate is likely a lower bound. A quarter of identified SV mutations occur in SV hotspots that harbor pre-existing low complexity repeat variation. Comparison of the spectrum of spontaneous SVs to wild isolates implies that natural selection is not only efficient at removing SVs in exons but also effectively removes SVs in intergenic regions.
Evolutionary history of the α-Carbonic Anhydrase (αCA) gene family in the phylum Arthropoda, with comparisons to αCA in chordates.
Zhou YJ, Lee CE
Genome Biol Evol · 2026 Jun · PMID 42339777 · Publisher ↗
The α-Carbonic Anhydrase (αCA) gene family encodes an abundant and ancient metalloenzyme present in all animals. Found in both eukaryotes and prokaryotes, members of this gene family play vital roles in ionic regulation,...
The α-Carbonic Anhydrase (αCA) gene family encodes an abundant and ancient metalloenzyme present in all animals. Found in both eukaryotes and prokaryotes, members of this gene family play vital roles in ionic regulation, acid-base regulation, and respiration. However, little is known regarding the evolutionary history and patterns of molecular evolution of this gene family in the phylum Arthropoda, especially in relation to chordates. Through phylogenetic reconstruction and subcellular localization prediction, we discovered that arthropod αCA genes could be classified into three clades based on phylogenetic topology, as has been found in chordate αCA. Among the three distinct arthropod αCA clades, Clade III, enriched in predicted extracellular and cell membrane-bound subcellular localization, exhibited the highest rates of evolution and greatest number of homologs. Intriguingly, we found distinct patterns of gene family expansions and contractions between arthropods and chordates through gene tree-species tree reconciliation. Lastly, we found that αCA12, a member of Clade III αCA, showed signatures of positive selection (based on dN/dS) in two sibling species within the copepod Eurytemora affinis species complex (E. carolleeae and E. gulfia), compared to the general arthropod αCA background. In these populations, this particular paralog had previously shown contemporary signatures of selection during invasions into novel salinities. Overall, our results indicate that the αCA gene family shows signatures of selection both on macroevolutionary time scales across phyla, as well as between closely related sibling species within Arthropoda.
From Oak to Wine: Evolution, Admixture, and Adaptation of California and British Columbia Saccharomyces Cerevisiae Wine Strains.
Moore J, Marr RA, Montpetit R … +2 more , Montpetit B, Measday V
Genome Biol Evol · 2026 Jul · PMID 42329215 · Full text
Population admixture is a frequent outcome of range expansion among plants, animals, and fungi, and drives rapid genome diversification and adaptation. The globalization of winemaking has introduced domesticated European...
Population admixture is a frequent outcome of range expansion among plants, animals, and fungi, and drives rapid genome diversification and adaptation. The globalization of winemaking has introduced domesticated European Saccharomyces cerevisiae wine strains into North America, promoting admixture between distantly related lineages. However, the degree that admixture has shaped biological diversity and adaptation within S. cerevisiae remains unclear. Here, we integrate population genetics, high-throughput phenotyping, and gene-trait mapping to characterize the evolutionary impact of S. cerevisiae admixture in North American wine regions. Whole-genome surveys of wine and oak-associated S. cerevisiae strains isolated from California reveal regional diversification of wine strains, with a subset clustering within the Pacific West Coast Wine (PWCW) clade. The PWCW clade is an admixed population derived from Wine/European and North American oak strains first described in Canada. Phylogenetic analyses further suggest that admixture within the PWCW clade has been driven by recent east-west dispersal of a North American Oak lineage into California. Solid-agar phenotyping revealed key wine and oak-associated traits selected for within PWCW clade strains, including stress resistance, nitrogen utilization, and temperature tolerance, while high-throughput microvinifications showed strong association between phylogenetic placement, fermentation completeness, and metabolite production. Genome-wide association identified loci underlying adaptive phenotypes, including copy number variation and chromosomal rearrangements linked to key stress resistance traits. Collectively, these results uncover ongoing adaptation and admixing between North American S. cerevisiae strains, as driven by winemaking practices, and advance our understanding into how admixture influences genome evolution and adaptation.
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