Genome Biology And Evolution[JOURNAL]
Sun
200 papers
Haplotype-Resolved Genome of the Critically Endangered, Paleo-endemic Tree, Eidothea hardeniana.
Soni A, Furtado A, Rossetto M … +1 more , Henry RJ
Genome Biol Evol · 2026 Apr · PMID 41851977 · Full text
A fully phased, chromosome-level reference genome assembly for an IUCN-declared critically endangered and paleo-endemic tree, Eidothea hardeniana (Nightcap Oak) was assembled de novo using long-read PacBio HiFi, Oxford N...
A fully phased, chromosome-level reference genome assembly for an IUCN-declared critically endangered and paleo-endemic tree, Eidothea hardeniana (Nightcap Oak) was assembled de novo using long-read PacBio HiFi, Oxford Nanopore (ONT) and Hi-C sequencing technologies. Consensus assembly represented high contiguity (N50 ∼ 49 Mb), (BUSCO 99.2%), assembly size in accordance with flow cytometry derived genome size estimate, and the presence of telomeric and centromeric repeats on pseudochromosomes. Haplotype 1 (598 Mb) achieved an N50 of 45.8 Mb and 99.1% BUSCO completeness, while Haplotype 2 (596 Mb) showed similar quality (N50: 47.3 Mb; BUSCO: 98.4%). Repeat content comprised approximately 54% of the genome. Gene annotation confirmed approximately 30120 protein coding genes with BUSCO completeness of 99.5%. Comparative orthology with other assembled Proteaceae genomes identified ∼13,000 shared ortholog clusters and 227 Eidothea-specific orthologs clusters. Heterozygosity in E. hardeniana was estimated at 1.17 SNVs per kilobase (0.12%), which is approximately one-third of the level reported for the other sequenced critically endangered Proteaceae species, Macadamia jansenii. This genome represents the first assembled genome from the Australian lineage of the Proteoideae subfamily within Proteaceae. As a high-quality reference for conservation genomics, it provides a foundation for SNP genotyping, population structure analyses, and the development of informed genetic rescue strategies for E. hardeniana and related species.
Lifespan Predicts Mitochondrial Substitution Rates across Vertebrates, but Methodology Matters.
Sterling JE, Zwonitzer KD, Havird JC
Genome Biol Evol · 2026 Mar · PMID 41837793 · Full text
Why do some species live for mere months, while others persist for centuries? A leading explanation implicates mitochondria. The mitochondrial theory of aging predicts that mitochondrial efficiency diminishes with age du...
Why do some species live for mere months, while others persist for centuries? A leading explanation implicates mitochondria. The mitochondrial theory of aging predicts that mitochondrial efficiency diminishes with age due to the accumulation of mutations within mitochondrial DNA (mtDNA). While experimental evidence for this theory is mixed, evolutionary analyses offer an ideal opportunity to determine if mitochondrial substitution rates are linked to longevity. Here, we explored the relationship between mtDNA evolution and species' lifespans across four clades-Aves, Actinopterygii, Bivalvia, and Sebastidae-using five normalization strategies. Across most methods, long-lived vertebrates showed reduced synonymous and nonsynonymous substitution rates, suggesting lower mtDNA mutation. However, we found that the strength and direction of these relationships varied drastically depending on the normalization approach used (ie correcting for divergence, generation time, and phylogeny). We also analyzed mtDNA mutation spectra and found similar patterns in long- and short-lived species, suggesting decreased rates of mtDNA mutations in long-lived species are not due to suppression of specific mutation processes, as predicted from the free radical theory of aging. We also find little evidence for a relationship between selection on mitochondrial protein-coding genes and lifespan. Our results align with the idea that decreased mutation rates may help preserve mitochondrial integrity in long-lived vertebrate species, but that these species have not been selected to have particularly efficient OXPHOS or protection against a specific mitochondrial mutation process. Together, these findings underscore the critical link between mitochondrial stability and lifespan, and highlight the power of natural systems in this field.
Pressure-tolerant Evolution in Rhodopsin of Deep-diving Whales.
Takeuchi H, Hayakawa T
Genome Biol Evol · 2026 Apr · PMID 41837783 · Full text
Life in the deep sea presents extreme challenges to protein structure and function, with hydrostatic pressure serving as a significant source of molecular stress. Although cetacean rhodopsins have been thoroughly examine...
Life in the deep sea presents extreme challenges to protein structure and function, with hydrostatic pressure serving as a significant source of molecular stress. Although cetacean rhodopsins have been thoroughly examined concerning their spectral tuning to the underwater light environment, their possible adaptations to pressure have yet to be explored. In this study, we investigated whether rhodopsin has undergone structural modifications that facilitate visual function during deep dives. Using a physicochemical property-based codon substitution model, we found that amino acid replacements associated with a radical shift in amino acid compressibility preferentially accumulated in deep-diving cetaceans belonging to the superfamily Physeteroidea and the family Ziphiidae. Molecular dynamics simulations further revealed that alanine at residue 2997.46a confers enhanced pressure tolerance of rhodopsin relative to serine, as evidenced by lower isothermal compressibility, diminished flexibility, and reduced free-energy costs under high pressure. These findings identify residue 2997.46a as a recurrent target for pressure adaptation in deep-diving cetaceans. More broadly, our study offers a novel perspective on cetacean visual adaptation, demonstrating that rhodopsins have evolved not only for spectral sensitivity but also for structural resilience under extreme hydrostatic pressure. This integrative framework, which combines evolutionary modeling with molecular dynamics simulations, advances our understanding of protein adaptation in the deep-sea environment.
Comparative Genomics Provide Insight Into the Evolution of European Aphanomyces euteiches Strains.
Kälin C, Piombo E, Manyara D … +3 more , Dubusc S, Dubey M, Karlsson M
Genome Biol Evol · 2026 Apr · PMID 41832745 · Full text
Aphanomyces euteiches is an oomycete pathogen causing root rot in pea and other legumes, leading to devastating yield losses in pea production. Previously, three genetic groups of A. euteiches were identified in Europe b...
Aphanomyces euteiches is an oomycete pathogen causing root rot in pea and other legumes, leading to devastating yield losses in pea production. Previously, three genetic groups of A. euteiches were identified in Europe based on simple sequence repeat markers. In this study, we determined the genome sequences of 68 European A. euteiches strains and performed a comparative genomic analysis with the aim to investigate the population genetic structure of A. euteiches, to delineate species boundaries and to identify gene families evolving under selection for gene gains or losses. Population genetic analysis based on genome-wide single nucleotide polymorphisms identified three genetic groups in Europe, where strains from Italy formed a distinct and genetically isolated group. Genealogical concordance phylogenetic species recognition analysis indicated that strains from Italy may represent a cryptic species. Aphanomyces strains differed in virulence on susceptible and partially resistant pea host genotypes, but virulence did not correlate with genetic groups. Analysis of virulence-related gene family evolution revealed a significant expansion of gene families acting in the detoxification of plant-derived secondary metabolites in plant-pathogenic Aphanomyces species. Moreover, the carbohydrate esterase family 1 (CE1) was significantly expanded in A. euteiches but not in the cryptic species represented by Italian strains. Modular structure analyses revealed exclusive presence of feruloyl esterase domains in CE1 homologs of plant-pathogenic Aphanomyces species, indicating a role in plant cell wall degradation.
Genomic Exaptation and Regulatory Landscape Shifts as Key Mechanisms Enabling Flatworm Terrestrialization.
Carbonetto B, Benítez-Álvarez L, García-Vernet R … +12 more , Eleftheriadi K, Vargas-Chávez C, Escudero N, Salces-Ortiz J, Rojo I, Fernández-Álvarez FÁ, Alwell C, Chiva C, Sabidó E, Mateos E, Carbayo F, Fernández R
Genome Biol Evol · 2026 Mar · PMID 41823257 · Full text
Understanding the genomic toolkit that enabled animal terrestrialization, the shift from aquatic to terrestrial habitats, is key to uncovering the evolutionary origins of land biodiversity. Yet, the genomic basis of the...
Understanding the genomic toolkit that enabled animal terrestrialization, the shift from aquatic to terrestrial habitats, is key to uncovering the evolutionary origins of land biodiversity. Yet, the genomic basis of the physiological and metabolic adaptations required for life on land remains poorly understood across most terrestrial animal phyla. Planarians (Platyhelminthes) offer a powerful model, as only one terrestrial lineage, the Geoplanidae (order Tricladida), is known. Here, we integrated genomics, transcriptomics, and proteomics to explore the genetic changes potentially supporting terrestrial adaptation. We identified a major burst of gene gain in the lineage leading to Tricladida, preceding the radiation of terrestrial planarians. Upon abiotic stress exposure, terrestrial and freshwater species exhibited distinct responses: most differentially expressed genes belonged to orthogroups gained in Tricladida, with over half under strong directional selection in terrestrial flatworms, suggesting their adaptive relevance. Transcriptomic profiles revealed divergent strategies: terrestrial species upregulated ancient genes, while freshwater species downregulated a separate set of ancestral genes. Across all datasets, the abiotic stress-response toolkit in terrestrial planarians was markedly different from freshwater relatives, with significant regulatory divergence. Our results highlight gene gain and co-option, rather than lineage-specific innovations, as key drivers of terrestrial flatworm evolution, emphasizing genomic exaptation and regulatory shifts as central to terrestrialization in Platyhelminthes. This study provides the first genome-wide view of the genetic basis of flatworm terrestrialization and sheds light on broader patterns of animal terrestrial adaptation.
A Deep Dive into the Globin Superfamily of Sharks, Skates, and Rays: Contrasting Patterns of Gene Loss and Retention Relative to Bony Vertebrates.
Walt HK, Hinton JA, Kuraku S … +3 more , Opazo JC, Storz JF, Hoffmann FG
Genome Biol Evol · 2026 Mar · PMID 41821395 · Full text
The globin gene superfamily encodes oxygen-binding proteins that are present in all domains of life. Hemoglobin and myoglobin of jawed vertebrates are among the most well-studied proteins in the context of structure-func...
The globin gene superfamily encodes oxygen-binding proteins that are present in all domains of life. Hemoglobin and myoglobin of jawed vertebrates are among the most well-studied proteins in the context of structure-function relationships and evolution after gene duplication. However, these studies have primarily focused on bony vertebrates, and research on the evolution of the globin gene family in cartilaginous fish has been limited by a lack of genomic resources. In this study, we leverage newly available cartilaginous fish genomes to investigate globin gene family evolution across skates, rays, sharks, and sawfish. We found that, when present, most globin genes are in a single copy, with androglobin, globin-Y, and myoglobin present in all cartilaginous fish, whereas the two globin-X paralogs of gnathostomes have been differentially retained by elasmobranchs (sharks, skates, and rays), which retained paralog 1, and the Holocephali, which retained paralog 2. Neuroglobin appears to have been lost at the common ancestor of all cartilaginous fish. The α- and β-globin gene subfamilies underwent independent expansions in different lineages of cartilaginous fish. Most cartilaginous fish globins have conserved synteny with other jawed vertebrates except myoglobin. Additionally, Nprl3, which directly flanks the hemoglobin clusters of other jawed and jawless vertebrates and regulates hemoglobin gene expression, is on a separate chromosome from the hemoglobin clusters of cartilaginous fish. When we examined globin gene expression patterns across cartilaginous fish tissues and developmental stages, we found that most globins are expressed as expected compared to other jawed vertebrates. However, hemoglobin paralogs are more widely expressed in embryonic tissues compared to later-stage tissues in cases where many copies exist. Our results reveal similar and contrasting patterns of globin gene evolution between cartilaginous and bony vertebrates and shed light on the early stages of globin gene evolution in gnathostomes.
Genome Assemblies of the Daisy Gorteria diffusa Elucidate the Molecular-Genomic Basis of Pollination by Sexual Deception.
Kellenberger RT, Delahaie B, Meier JI … +2 more , Ellis AG, Glover BJ
Genome Biol Evol · 2026 Mar · PMID 41818491 · Full text
Plant sexual deception, the floral mimicry of female insects to attract mate-searching males for pollination, is a long-studied reproductive strategy with a poorly understood genomic basis. Here, we assembled the genomes...
Plant sexual deception, the floral mimicry of female insects to attract mate-searching males for pollination, is a long-studied reproductive strategy with a poorly understood genomic basis. Here, we assembled the genomes of a sexually deceptive, a semi-deceptive, and a derived nondeceptive floral form of the South African daisy Gorteria diffusa to chromosome-scale and near-chromosome scale, respectively. We located several previously identified genes involved in the development of deceptive floral traits, including tandem duplications of GdbHLH and GdMYBSG6 transcription factors regulating the complex coloration of sexually deceptive floral structures. Using additional genotyping-by-sequencing data of six G. diffusa floral forms, we further identified several large inverted genomic segments with a high fixation index (FST), which seem to play a role in maintaining the distinct identity of some floral forms in zones of secondary contact. Finally, genome synteny analyses revealed that the genome of the derived nondeceptive floral form is contracted and shows signs of recent genome-wide deletion of long terminal repeat retrotransposons. Our results provide insight into the genomic elements underlying plant sexual deception as well as some of the structural genomic differences between sexually deceptive and nondeceptive floral forms.
Retrotransposition Events Shape the Evolution of the Ataxin-3 Gene Family in Primates.
Felício D, Martins IM, Pinto A … +5 more , Sequeiros J, Amorim A, Lopes AM, Seixas S, Martins S
Genome Biol Evol · 2026 Mar · PMID 41818480 · Full text
Evolutionary studies of disease-associated genes provide crucial insights into pathological mechanisms and potential therapeutic targets. Polyglutamine spinocerebellar ataxias (SCAs) are human neurodegenerative diseases...
Evolutionary studies of disease-associated genes provide crucial insights into pathological mechanisms and potential therapeutic targets. Polyglutamine spinocerebellar ataxias (SCAs) are human neurodegenerative diseases caused by toxic expanded CAG repeats. Studies on SCA1 have shown that a paralog of the causing-gene can partially rescue protein function and alleviate the neuropathology. The most common SCA, Machado-Joseph disease (MJD/SCA3), caused by mutated ataxin-3 gene (ATXN3), has no treatment currently available. Its paralog ataxin-3 like (ATXN3L) remains largely unexplored. Here, we identify three new retrotransposition events of ATXN3: ATXN3L0 in Euarchontoglires, ATXN3L2 in Simiformes, and ATXN3L3 in Cercopithecidae, in addition to ATXN3L (herein called ATXN3L1) originated in Haplorrhini. ATXN3 and ATXN3L1 are both under purifying selection throughout primate evolution, maintaining about 70% of amino acid identity. Also, the high conservation of ATXN3L1 Josephin domain hints at functional redundancy with the parental disease-associated ATXN3. ATXN3L2 presents a remarkable nucleotide similarity to ATXN3 (79%) in an interrupted reading frame, which may produce a regulatory RNA. Conversely, ATXN3L0 is likely a non-functional retrocopy and ATXN3L3 is absent in humans with no relevance for the disease. The comparison of (CAG)n interruption patterns of the different paralogs in several primates elucidates the process leading to the currently observed pure long tracts in human ATXN3, responsible for disease when expanded. This study intends to pioneer the identification of new paralogs of SCA-associated genes and the use of phylogenetic analyses to explore their potential role for targeted therapies.
Chromosome-Scale Reference Genome Assemblies for Two Anoplophora Longhorned Beetle Species (Coleoptera: Cerambycidae).
Kim S, Jung S, Farrell BD … +1 more , Shin S
Genome Biol Evol · 2026 Mar · PMID 41807107 · Full text
The Asian longhorned beetle, Anoplophora glabripennis (Motschulsky), and the citrus longhorned beetle, A. malasiaca (Thomson) (Coleoptera: Cerambycidae), represent two globally notorious forest pests whose introductions...
The Asian longhorned beetle, Anoplophora glabripennis (Motschulsky), and the citrus longhorned beetle, A. malasiaca (Thomson) (Coleoptera: Cerambycidae), represent two globally notorious forest pests whose introductions into North America and Europe have caused extensive damage to economically important temperate deciduous hardwood forests. Anoplophora glabripennis was the first longhorned beetle for which a reference genome was generated; however, the available assembly remains at the scaffold level, limiting chromosome-level analyses in a species that has emerged as a key model for investigating the genomic and ecological basis of plant-feeding evolution. Here, we present the first chromosome-scale genome assemblies for A. glabripennis and Anoplophora malasiaca, generated using PacBio HiFi long-read and Pore-C chromatin conformation capture sequencing. The assembled genomes span 730.1 and 708.0 Mbp for A. glabripennis and A. malasiaca, respectively, with scaffold N50 of 81.3 and 43.9 Mbp. A total of 96.7% and 95.2% of each assembly was anchored to 10 and 15 chromosome-level scaffolds, respectively, and the X chromosome was identified through synteny analysis. Repeat elements account for 66.5% and 65.5% of the genomes, and 14,624 and 13,814 protein-coding genes were functionally annotated. These reference-quality genomes provide a valuable comparative framework for elucidating the genomic basis of xylophagy and temperate adaptation in longhorned beetles and establish a foundation for devising targeted management strategies against invasive populations of both A. glabripennis and A. malasiaca in their introduced regions.
The Road so Far: Tracing the Molecular Evolution of Hexokinase Family in Metazoa.
Jardim-Messeder D, de Souza-Vieira Y, Oliveira GAP … +3 more , Margis R, Mello B, Sachetto-Martins G
Genome Biol Evol · 2026 Mar · PMID 41793121 · Full text
Hexokinases (HXKs) are key enzymes in glucose metabolism and play essential roles in energy homeostasis. In vertebrates, the HXK family has undergone extensive expansion and diversification, giving rise to multiple paral...
Hexokinases (HXKs) are key enzymes in glucose metabolism and play essential roles in energy homeostasis. In vertebrates, the HXK family has undergone extensive expansion and diversification, giving rise to multiple paralogs with distinct structural and regulatory features. Here, we present a comprehensive evolutionary analysis of the HXK gene family across Metazoa, integrating phylogenetic reconstruction, molecular dating, synteny analysis, structural comparisons, and selection pressure inference. Our results indicate that the 100 kDa hexokinase paralogs originated from domain duplication and fusion events in early vertebrates, followed by lineage-specific duplications giving rise to HXK1, HXK2, HXK3, HXK4, and HXK5. Structural analysis revealed that only HXK2 retains catalytic activity in both N- and C-terminal domains, while the other paralogs exhibit divergence and loss of N-terminal catalytic function. Selection analyses across 470 mammalian genomes revealed paralog- and lineage-specific signatures of episodic positive selection, particularly in HXK3, suggesting adaptive evolution in response to distinct metabolic demands. These findings provide new insights into the functional evolution and specialization of HXKs in vertebrate metabolism and highlight the interplay between gene duplication, structural adaptation, and selective pressures in shaping metabolic diversity.
The Evolutionary Flexibility of the Drosophila Circadian Clock: Network Constraints or Adaptive Freedom?
Creasey LD, Petrov PB, Tauber E
Genome Biol Evol · 2026 Mar · PMID 41793113 · Full text
The study of network evolution is critical to understanding how complex biological processes arise and adapt over time. Protein networks, composed of interacting components, can exhibit varying degrees of conservation an...
The study of network evolution is critical to understanding how complex biological processes arise and adapt over time. Protein networks, composed of interacting components, can exhibit varying degrees of conservation and flexibility, enabling organisms to fine-tune their responses to environmental changes. Using the circadian clock system in Drosophila as a case study, we explore how such networks evolve. We leverage the recently published 101 Drosophilidae genome project to analyze the evolution and co-evolution of 11 core clock proteins across 65 species spanning about 60 million years of evolution. A sliding window analysis of coding regions reveals substantial heterogeneity in nucleotide divergence, with Clk and per exhibiting high divergence, whereas Pdp1 and sgg show virtually no evolutionary change. Additionally, we assessed interdependent amino acid evolution across different proteins, identifying 67 co-evolving site pairs, primarily among CLK-PER, CLK-CWO, and SGG-PER. Using codon-based models of evolution, we found four genes (cwo, jet, per, and sgg) showing evidence of positive selection. Since several clock proteins are pleiotropic, we tested whether their multifunctionality influences their evolutionary constraints. Using alternative approaches to assess pleiotropy, we found no significant correlation between pleiotropy and the nonsynonymous substitution rate (Ka) in 440 Drosophila proteins, including circadian clock ones. Overall, our findings suggest that the circadian clock network does not impose strong constraints on the evolution of its components. This flexibility may facilitate species-specific adaptation of the clock and allow the pleiotropic functions of clock proteins.
Positive Selection Targeted Primate Genes that Encode Transposable Element Repressors.
Cagliani R, Forni D, Mozzi A … +4 more , Sarama R, Pozzoli U, Fumagalli M, Sironi M
Genome Biol Evol · 2026 Mar · PMID 41784387 · Full text
Transposable element (TE) mobilization poses a significant fitness challenge to host genomes. Consequently, a variety of systems have emerged to silence TE activity. Just like TEs, such systems are widespread and their e...
Transposable element (TE) mobilization poses a significant fitness challenge to host genomes. Consequently, a variety of systems have emerged to silence TE activity. Just like TEs, such systems are widespread and their evolution is expected to be shaped by intra-genomic conflicts. To test this hypothesis, we performed an evolutionary analysis of TE control systems across different timescales. We show that a substantial fraction of TE control genes were targets of positive selection during primate evolution, with several proteins of the piRNA-pathway showing a considerable number of positively selected sites. In these proteins, selection was strongest in intrinsically disordered regions (IDRs), particularly those with low conformational entropy. We suggest that positive selection modulates IDR properties by introducing changes in sequence patterns and ensemble features properties, which are in turn related to function. Analysis of genetic data from 54 human populations detected several signals of strong positive selection at TE control genes. In line with findings in primates, we identified as selection targets three genes (TEX15, GTSF1, and GTSF1L) that participate in the piRNA pathway. Additionally, 4 of the 13 genes with strong evidence of positive selection encode components of the NuRD complex, which plays central functions not only related to TE control but also to the maintenance of genome integrity and cell cycle control. Our data provide insight into the evolution of TE control systems in primates and human populations. Whereas the signatures we detected are consistent with a genomic conflict between TEs and their repressors, additional pressures may drive the evolution of the genes we analyzed.
Unraveling the Genome of Epidendrum Fulgens: Demographic History and Gene Family Dynamics in a Resilient Neotropical Orchid.
de Mattos JS, Aecyo P, Keepers K … +6 more , Tavares MM, Della-Rosa F, Palma-Silva C, Kane NC, Pinheiro F, Riaño-Pachon DM
Genome Biol Evol · 2026 Mar · PMID 41784355 · Full text
Epidendrum L. (Orchidaceae) is one of the largest plant genera in the neotropics, accounting for more than 1,500 species and a high variety of morphological, physiological, and ecological adaptations. However, addressing...
Epidendrum L. (Orchidaceae) is one of the largest plant genera in the neotropics, accounting for more than 1,500 species and a high variety of morphological, physiological, and ecological adaptations. However, addressing evolutionary and ecological questions in the genus is a challenge due to the lack of publicly available genomic resources. Here, we present the first chromosome-scale genome assembly from the orchid genus Epidendrum, E. fulgens (2n = 24, 2C = 2.4 pg), a perennial-terrestrial that occurs in coastal restingas and inland granitic rock outcrops along the Brazilian Atlantic Forest. The genome sequencing was performed using PacBio HiFi and Omni-C technologies, and the final assembly comprised 12 chromosome-scale scaffolds, representing the 12 pseudochromosomes expected for E. fulgens. The primary assembly pseudochromosomes captured 97.3% of BUSCO genes, with an N50 of 88.6 Mbp and L50 of 5; similar metrics were observed for both locally phased haplotypes. Approximately 77% of the genome consisted of transposable elements, and the annotation identified 30,830 protein-coding genes and 6,141 associated Gene Ontology (GO) terms. We also found two events of population expansion and retraction in E. fulgens demographic history, and many expanded and contracted gene families. GO enrichment analysis showed functional categorization for the expanded and contracted gene sets (cell cycle regulation, cell shape and morphology, osmoregulation, environmental plasticity, and stress response), evidencing the traits that are functionally important for this species' adaptation and persistence in nutrient-poor soils and extreme environments. With this study, we highlight the need to further explore the genomic space in the Orchidaceae family and in the Neotropical region, providing new resources for future studies aiming to investigate the origin and resilience of Neotropical flora.
Molecular evolution of a sex-linked inversion polymorphism in zebra finches.
Price PD, Pepper J, Rogers TF … +2 more , Wright AE, Slate J
Genome Biol Evol · 2026 Mar · PMID 41784315 · Publisher ↗
Recent years have seen an explosion in examples of supergenes, where recombination is suppressed between haplotypes, often via inversion polymorphisms, to control complex traits. However, an enduring problem in evolution...
Recent years have seen an explosion in examples of supergenes, where recombination is suppressed between haplotypes, often via inversion polymorphisms, to control complex traits. However, an enduring problem in evolutionary biology is understanding the molecular consequences of recombination suppression, especially when it has been present for long periods. Here, we explore the molecular evolution of the A and B haplotypes of a large, sex-linked inversion polymorphism in a passerine bird, the zebra finch (Taeniopygia guttata, ) responsible for most of the genetic variation in sperm morphology. We find evidence for reduced efficacy of purifying selection acting on the coding sequence of the Z-linked haplotypes and an increase in mutational load. However, we fail to find a positive association between expression and sequence divergence, consistent with an absence of any compensatory expression evolution for the accumulation of deleterious alleles.
How Does Transcription-Associated Mutagenesis Shape tRNA Microevolution?
Baños H, Wang L, Simonti C … +2 more , Paaby AB, Heitsch C
Genome Biol Evol · 2026 Mar · PMID 41784298 · Full text
Transfer RNAs (tRNAs) are among the most highly conserved and frequently transcribed genes. Recent studies have demonstrated that tRNAs experience exceptionally high rates of transcription-associated mutagenesis (TAM) as...
Transfer RNAs (tRNAs) are among the most highly conserved and frequently transcribed genes. Recent studies have demonstrated that tRNAs experience exceptionally high rates of transcription-associated mutagenesis (TAM) as well as strong purifying selection. How the mutational input of TAM, which induces a nonuniform distribution of nucleotide substitutions, affects the fitness of tRNA molecules is unclear. Secondary structure in tRNAs is strongly conserved over macroevolutionary time, suggesting that mutations that disrupt paired sites may be especially deleterious, and TAM-induced mutations primarily involve nucleotide transitions, which tend to preserve base-pairing stability. To examine how TAM affects tRNA molecule fitness and shapes tRNA evolution over short timescales, we analyzed tRNA allelic variation in contemporary Caenorhabditis elegans strains. We propose a model of tRNA microevolution driven by TAM and demonstrate that the observed secondary structure characteristics align with our predicted TAM-biased patterns. Furthermore, we developed a continuous Markov substitution model that incorporates TAM-specific mutational biases. This TAM-biased model fits the C. elegans tRNA data more effectively than standard models, such as the general time-reversible model. Based on these results, we conclude that tRNAs in natural populations carry substantial levels of structure-destabilizing mutations, which may be tolerated but nevertheless likely induce meaningful fitness costs. Our findings are consistent with recent experimental studies on tRNA fitness in yeast, but challenge prior theoretical and computational analyses that emphasize RNA base-pairing as a primary determinant in genotype-phenotype systems.
Genomics of Sable (Martes zibellina) × Pine Marten (Martes martes) Hybridization.
Tomarovsky AA, Totikov AA, Bulyonkova TM … +29 more , Perelman PL, Abramov AV, Serdyukova NA, Yakupova AR, Prokopov D, Beklemisheva VR, Sinding MS, Davletshina G, Pobedintseva M, Krasheninnikova K, Foerster DW, Mukhacheva AS, Mironova A, Sidorov M, Nie W, Wang J, Romanenko SA, Proskuryakova AA, Ferguson-Smith M, Yang F, Cherkasov N, Balanovskaya E, Gilbert MTP, Okhlopkov IM, Zhuk A, Graphodatsky AS, Powell R, Koepfli KP, Kliver S
Genome Biol Evol · 2026 Mar · PMID 41782206 · Full text
The sable (Martes zibellina) and pine marten (Martes martes) are two Palearctic mustelids with long-recognized hybrids (kidases), whose fertility was controversial for years. Early genetic studies confirmed the existence...
The sable (Martes zibellina) and pine marten (Martes martes) are two Palearctic mustelids with long-recognized hybrids (kidases), whose fertility was controversial for years. Early genetic studies confirmed the existence of hybrids beyond F1, but limited marker resolution prevented detailed characterization of hybrid ancestry. Both species were hunted for centuries, but anthropogenic pressures during the 20th-century caused severe bottlenecks in the sable. Hunting bans and large-scale reintroduction programs restored sable populations across much of its range, including the sympatric zone, potentially affecting hybridization. We resequenced 30 individuals from most of the sables' range and the Eastern part of pine marten's. Among samples, we found a broad spectrum of hybrid types with mosaic recombinant chromosomes that confirm hybrid fertility and indicate crossover is not suppressed in kidases. This necessitates re-evaluation of previous research, as we detected notable discrepancies between short tandem repeat-based ancestry and whole-genome analysis. We revealed mitochondrial DNA introgression from sables into most pine martens, indicating displacement of native pine marten mitochondrial sequences. Pine marten heterozygosity is relatively low (∼0.5 to 0.6 hetSNPs/kbp), while sable's diversity (∼1.5 to 1.8 hetSNPs/kbp) is unexpectedly high given its demographic history, likely reflecting successful reintroduction programs. We dated species divergence at 1.52 [confidence interval (CI): 1.05 to 2.06] Mya, and identified candidate genes potentially associated with hybrid fertility issues. This study is the first to elucidate marten hybridization at the whole-genome level, opening new research directions for understanding hybridization among Holarctic martens, the genetic consequences of reintroduction programs, and comparative adaptomics.
Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora).
Totikov AA, Tomarovsky AA, Perelman PL … +24 more , Bulyonkova TM, Serdyukova NA, Yakupova AR, Mohr D, Foerster DW, Grau Jipoulou JH, Beklemisheva VR, Sidorov M, Miranda I, Farelo L, Abramov AV, Krasheninnikova K, Mukhacheva AS, Panov VV, Balanovska E, Cherkasov N, Zub K, Scott AF, Melo-Ferreira J, Okhlopkov IM, Zhuk A, Koepfli KP, Graphodatsky AS, Kliver S
Genome Biol Evol · 2026 Mar · PMID 41782205 · Full text
Mustelinae are among the most diverse and taxonomically complex subfamilies within the Mustelidae, yet their evolutionary history and genetic diversity remain largely unexplored at the whole-genome level. Here, we presen...
Mustelinae are among the most diverse and taxonomically complex subfamilies within the Mustelidae, yet their evolutionary history and genetic diversity remain largely unexplored at the whole-genome level. Here, we present the first comprehensive comparative and phylogenomic study of this lineage, integrating nuclear and mitochondrial genomes from 10 species across the Holarctic and Indomalayan realms. Our dataset includes two novel genome assemblies (Mustela strigidorsa, M. sibirica) and an improved genome for M. nivalis, enabling robust cross-species analyses of genome size, chromosomal evolution, genetic diversity, and demographic history. We uncover striking inter- and intraspecific variation in genome-wide heterozygosity and genome size, with evidence of marked homozygosity in some Asian lineages (M. eversmanii, M. sibirica, M. strigidorsa) and remarkable genetic diversity in widespread species such as M. nivalis and M. erminea. Phylogenomic results support the previously suggested split of M. richardsonii from M. erminea, but we found no evidence for speciation within M. nivalis. Ancestral reconstruction of chromosomal rearrangements revealed key chromosomal fissions that shaped the Mustelinae radiation, including early events predating the divergence of modern Mustela species. The results confirmed the suggested ancestral karyotypes of Mustela (2n = 44) and Mustelinae (2n = 42). Finally, demographic reconstructions exposed species-specific responses to Quaternary climatic cycles, ranging from long-term resilience in M. nivalis to repeated population bottlenecks in M. putorius and M. sibirica. Collectively, our findings establish a genomic foundation for future evolutionary and conservation genomic research on this emblematic Mustelidae lineage.
Evidence of Relaxed Selection in the Mitochondrial Genomes of Phototrophic Paulinella Lineages.
Han S, Lhee D, Yang JH … +2 more , Bhattacharya D, Yoon HS
Genome Biol Evol · 2026 Mar · PMID 41777055 · Full text
Primary endosymbiosis, resulting in the establishment of a photosynthetic organelle in eukaryotes, has occurred twice: more than 1.5 billion years ago in the common ancestor of Archaeplastida and 90 to 140 million years...
Primary endosymbiosis, resulting in the establishment of a photosynthetic organelle in eukaryotes, has occurred twice: more than 1.5 billion years ago in the common ancestor of Archaeplastida and 90 to 140 million years ago in the Paulinella lineage. The relatively recent, independent event in phototrophic Paulinella provides opportunities for investigating the earlier stages of primary plastid establishment. In Archaeplastida, plastid origin is so ancient that little can be inferred about the eukaryotic host in which endosymbiosis occurred. By contrast, the genus Paulinella includes nine heterotrophic species that are closely related to the phototrophic lineage, which can be used to understand the impact of primary endosymbiosis on "host" cell evolution. Research on heterotrophic Paulinella is very limited, and analyses addressing the evolutionary impacts of primary endosymbiosis on the ancestral heterotrophic lineage have been lacking. In this study, we used long-read sequencing to determine the mitochondrial genome sequence from three taxa of heterotrophic Paulinella that formed a "bloom" in their native environment. We also determined the mitogenomes of two phototrophic Paulinella species. Along with two available mitogenomes, we conducted a comparative analysis of phototrophic and heterotrophic Paulinella mitogenomes and find that gene order rearrangements occurred more frequently in the phototrophic lineage. We detected signatures of relaxed selection in mitochondrial DNA from the phototrophic Paulinella clade. This pattern likely reflects reduced effective population size (Ne) associated with plastid primary endosymbiosis, in line with the endosymbiotic ratchet hypothesis. We propose that the reduced Ne in phototrophic Paulinella strongly impacted mitogenome evolution in these species.
Allelic Variation at tRNA Genes in Three Nematode Species Indicates Mutation Load Despite Strong Purifying Selection.
Bell AD, Simonti C, Baños H … +4 more , Wang L, Heitsch C, Lachance J, Paaby AB
Genome Biol Evol · 2026 Mar · PMID 41777052 · Full text
Cytosolic transfer RNAs (tRNAs), which are encoded as hundreds of genes in nuclear genomes, experience exceptionally high mutation rates and have been hypothesized to confer substantial mutational load in natural populat...
Cytosolic transfer RNAs (tRNAs), which are encoded as hundreds of genes in nuclear genomes, experience exceptionally high mutation rates and have been hypothesized to confer substantial mutational load in natural populations. Although this phenomenon appears universal across multicellular eukaryotes, a comprehensive characterization of standing variation in tRNA repertoires is still lacking in any system. Here, we resolve within-species allelic variation in nuclear-encoded tRNAs in three nematode species: Caenorhabditis elegans, C. briggsae, and C. tropicalis. We show that these genes carry signatures of high rates of historical transcription-associated mutagenesis and of purifying selection, resulting in allelic variation that includes pervasive instances of within-gene mismatches between the amino acid recognized by the tRNA backbone and that indicated by the anticodon. Furthermore, patterns of tRNA genomic organization and variation differ markedly from those of protein-coding regions. Individual genomes harbor distinct complements of tRNA genes with predicted functional differences, an observation that coincides with recent evidence that variation in tRNA expression and regulation contributes to human disease. Our findings offer an entry point for identifying the microevolutionary processes that act on tRNA repertoires and, in turn, connecting those processes to the macroevolutionary patterns that have more frequently been the focus of study.
Genome Evolution and the Enigmatic Axial Skeleton of the Hero Shew (Soricidae: Scutisorex Somereni).
Chipps AS, Hutter CR, Demos TC … +1 more , Esselstyn JA
Genome Biol Evol · 2026 Mar · PMID 41762126 · Full text
Linking genetic variation with traits of interest has been a longstanding challenge for evolutionary biologists. Here, we explore elements of genome evolution in the hero shrew (Soricidae: Scutisorex somereni): a small,...
Linking genetic variation with traits of interest has been a longstanding challenge for evolutionary biologists. Here, we explore elements of genome evolution in the hero shrew (Soricidae: Scutisorex somereni): a small, elusive mammal with the most distinctive vertebral column in the entire tree of life. We first assembled and annotated a draft genome from short-read, long-read, and chromosome-conformation-capture sequencing for S. somereni. We combined this genome with publicly available genomes from 30 other mammal species spanning millions of years of evolutionary history to search for genes potentially related to the evolution of the S. somereni axial skeleton. We first performed an orthology clustering analysis to identify gene duplications and single copy orthologs. With orthogroups, we tested for gene family expansion and contraction. The single copy orthologs that we identified were used to test for positive selection or changes in selective constraint in S. somereni compared to the other species considered. We found significant gene family size change in immune, sensory, and metabolic gene families, and identified multiple HOX genes under positive selection that might help explain the evolution of the hero shrew's extreme phenotype. Overall, our study is a critical first step that has highlighted candidate genes and gene families for further genomic exploration, underscoring the continuing challenge of understanding the genomic underpinnings of unusual phenotypes.
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