Molecular biology and evolution最新文献_第4页

From neuropeptides to toxins: illuminating the origins of venom complexity in cone snails. 从神经肽到毒素：阐明锥螺毒液复杂性的起源。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-09-01 DOI: 10.1093/molbev/msag206

Thomas Lund Koch, Giada Ferrari, Sunita B Sumanam, Paula Flórez Salcedo, Maren Watkins, Kevin Chase, Ave Tooming-Klunderud, Arturo O Lluisma, Angel Yanagihara, Neil D Young, Baldomero M Olivera, Eivind A B Undheim, Helena Safavi-Hemami

{"title":"From neuropeptides to toxins: illuminating the origins of venom complexity in cone snails.","authors":"Thomas Lund Koch, Giada Ferrari, Sunita B Sumanam, Paula Flórez Salcedo, Maren Watkins, Kevin Chase, Ave Tooming-Klunderud, Arturo O Lluisma, Angel Yanagihara, Neil D Young, Baldomero M Olivera, Eivind A B Undheim, Helena Safavi-Hemami","doi":"10.1093/molbev/msag206","DOIUrl":"10.1093/molbev/msag206","url":null,"abstract":"New genes and gene functions are key drivers of evolutionary innovation. Venomous animals, such as cone snails, provide striking examples of gene innovation, yet the mechanisms by which toxins arise remain poorly understood. Using the Conus textile genome, we uncover how neuropeptide genes were recruited into the venom and neofunctionalized as doppelgänger toxins. We identify over 20 independent recruitment events that evolved dynamically across the Conus lineage. Rather than arising from ohnologs of a whole-genome duplication event ∼200 mya, these toxins evolved through diverse mechanisms, including exon shuffling, alternative splicing, and ectopic recombination, often facilitated by lineage-specific transposable elements. Our findings reveal a dynamic interplay between genome architecture and molecular innovation, offering broad insight into the evolution of complex gene repertoires in venoms and beyond.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13542836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148766246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Questioning the evidence for host-symbiont codiversification in mycorrhizal symbioses. 菌根共生中宿主-共生体共多样化证据的质疑。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-09-01 DOI: 10.1093/molbev/msag207

Fantine Bodin, Hélène Morlon, Benoît Perez-Lamarque

{"title":"Questioning the evidence for host-symbiont codiversification in mycorrhizal symbioses.","authors":"Fantine Bodin, Hélène Morlon, Benoît Perez-Lamarque","doi":"10.1093/molbev/msag207","DOIUrl":"10.1093/molbev/msag207","url":null,"abstract":"The vast majority of plants form mycorrhizal symbioses. The ecological importance of these mutualistic interactions has sparked interest in their long evolutionary history. By examining interaction networks and phylogenetic trees, several studies have suggested that plants codiversify with their associated mycorrhizal fungi. However, recent research has demonstrated that phylogenetic congruence (interpreted as codiversification when divergence times match) is often conflated with another pattern called cophylogenetic signal (ie closely related plants interacting with closely related fungi and vice versa), which may arise from different biological processes. We performed cophylogenetic analyses on 29 diverse mycorrhizal networks to reevaluate the evidence for codiversification in mycorrhizal symbioses. We found a significant cophylogenetic signal but no phylogenetic congruence: Closely related plants often interact with closely related fungi, but their phylogenies do not match. Instead of codiversification, this finding is consistent with trait matching between plants and mycorrhizal fungi, where compatible, evolutionarily conserved plant and fungal traits govern their interactions. Our work highlights the importance of appropriately interpreting the cophylogenetic methods used to study the macroevolution of plants and their mycorrhizal fungi. It suggests that previous evidence of codiversification in mycorrhizal symbioses actually detected cophylogenetic signal, since, across the multiple and diverse networks analyzed here, there is no evidence that codiversification occurred during the evolution of mycorrhizal symbioses.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13533336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148759794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gene-level complexity explains genome-wide variation in the distribution of fitness effects. 基因水平的复杂性解释了适应度效应分布的全基因组变异。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-09-01 DOI: 10.1093/molbev/msag216

Burçin Yıldırım, Jennifer E James

{"title":"Gene-level complexity explains genome-wide variation in the distribution of fitness effects.","authors":"Burçin Yıldırım, Jennifer E James","doi":"10.1093/molbev/msag216","DOIUrl":"10.1093/molbev/msag216","url":null,"abstract":"The distribution of fitness effects (DFE)-describing how harmful, neutral, or beneficial new mutations are-is central to understanding how populations evolve. Although the DFE varies across genomes and species, it remains unclear which aspects of genomic organization drive this variation. Here, we inferred gene-level selective constraints across the genomes of Mus musculus castaneus, Drosophila melanogaster and Saccharomyces cerevisiae using a combination of population genetics and machine learning trained on diverse gene features. Many gene features were predictive of selective constraint, with conservation, gene structure, and expression being the most informative. These selective constraints delineated gene classes with distinct DFEs. Genes with higher connectivity and expression-features reflecting how many traits a gene influences-experienced stronger and less dispersed deleterious effects with increasing selective constraint. Between species, the rate of adaptation decreased with increasing organismal complexity, whereas across the genome it did not decrease monotonically with selective constraint, but tended to be higher at intermediate levels. While between-species comparisons of DFE parameters were less consistent with predictions of Fisher's geometric model (FGM) based on organismal complexity, variation in DFE parameters across the genome aligned more closely with FGM when complexity was considered at the gene level. Our results suggest that gene-level complexity, captured by genomic feature proxies, provides a more informative definition of complexity for DFE variation than organism-level labels, and highlight the value of using gene features collectively to link genomic architecture, fitness landscapes, and patterns of molecular evolution.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13537021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148851327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolutionary diversification of invertase paralogs couples carbon metabolism and sexual reproduction in fission yeasts. 裂变酵母中转化酶的进化多样化与碳代谢和有性生殖有关。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-09-01 DOI: 10.1093/molbev/msag233

Ambre Noly, Céline Faux, Maria Shaldaeva, Louison Bois-Naegelin, Philippe Fort, Dominique Helmlinger

{"title":"Evolutionary diversification of invertase paralogs couples carbon metabolism and sexual reproduction in fission yeasts.","authors":"Ambre Noly, Céline Faux, Maria Shaldaeva, Louison Bois-Naegelin, Philippe Fort, Dominique Helmlinger","doi":"10.1093/molbev/msag233","DOIUrl":"10.1093/molbev/msag233","url":null,"abstract":"Dynamic patterns of gene gain and loss play a major role in the diversification of eukaryotes, reflecting adaptation to a broad range of ecological contexts. Reconstructing the evolutionary history of genes provides a powerful framework for understanding how functional innovation shapes life-history traits. Here, we report a comprehensive analysis of gene gain and loss across the fission yeast clade, whose evolutionary trajectory remains elusive. Reductive evolution of metabolic genes is a major contributor to species diversification, as observed in other fungal taxa. Notably, we uncovered an evolutionary scenario in which an ancestral gene duplication was followed by lineage-specific loss of one or the other paralog, except in Schizosaccharomyces pombe, which retained both. We demonstrate that these paralogs encode catalytically active invertases, named Inv1 and Inv2, with distinct enzymatic properties, localization, regulation, and physiological roles. Inv1 is a secreted enzyme subject to glucose-catabolite repression and is the sole invertase required for sucrose assimilation, resembling canonical yeast invertases. In contrast, Inv2 is intracellular, constitutively expressed, and required for inducing sexual differentiation in response to nutrient availability. Overall, these findings reveal an unexpected role for carbon metabolism in modulating the haploid-diploid cycle of fission yeasts, suggesting that diversification of core metabolic functions may contribute to adaptation to environments with distinct sugar compositions.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148912935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to: Deep learning reveals genomic regions introgressed between two recurrently hybridizing lynx species. 更正：深度学习揭示了两个经常杂交的猞猁物种之间的基因组区域渐渗。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-09-01 DOI: 10.1093/molbev/msag234

引用次数: 0

Acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes. 细菌染色体中毒素-抗毒素系统的获取和侵蚀。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-09-01 DOI: 10.1093/molbev/msag230

Ludovic Belot, Amaury Payelleville, Dukas Jurėnas, Eduardo P C Rocha, Laurence Van Melderen

{"title":"Acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes.","authors":"Ludovic Belot, Amaury Payelleville, Dukas Jurėnas, Eduardo P C Rocha, Laurence Van Melderen","doi":"10.1093/molbev/msag230","DOIUrl":"10.1093/molbev/msag230","url":null,"abstract":"Toxin-antitoxin systems are widespread in bacterial genomes. Yet, their integration, persistence, and impact on chromosome dynamics remain unclear. Here, we identified 80 type II toxin-antitoxin systems in the single chromosome of Photorhabdus laumondii TT01, 50 of which were experimentally validated. Comparative analysis across the Photorhabdus genus revealed a highly heterogeneous distribution, with toxin-antitoxin systems frequently clustering within discrete genomic regions, either alone or associated with cointegrate-forming transposases and integrases. Toxin-antitoxin systems rarely clustered with other putative defense systems and are preferentially associated with different types of recombinases, suggesting distinct pathways of acquisition for the two types of functions. Functional analyses showed that most validated toxin-antitoxin systems display addictive properties and stabilize plasmids. These addictive toxin-antitoxin systems are preferentially located in genomic regions characterized by high gene turnover, consistent with recent acquisition events. Despite their plasmid-stabilizing capacity, toxin-antitoxin systems do not promote long-term conservation of their immediate chromosomal neighborhoods. Instead, we observed frequent toxin-antitoxin loss, either through complete deletion or toxin pseudogenization, indicating relaxed selection for their persistence in bacterial lineages. We propose a stepwise model for toxin-antitoxin evolution in bacterial chromosomes: initial acquisition mediated by mobile genetic elements, preferential integration into permissive genomic regions, subsequent genetic streamlining of linked loci, and progressive gene loss. The short-lasting linkage between toxin-antitoxin systems and their genomic neighborhoods is consistent with the view that toxin-antitoxin modules can behave as autonomous, selfish genetic elements.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148912862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data. 从PacBio HiFi长读测序数据推断中国和印度恒河猴（Macaca mulatta）种群的人口统计学历史。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-09-01 DOI: 10.1093/molbev/msag237

Erangi J Heenkenda, Cyril J Versoza, John W Terbot, Vivak Soni, Gabriella J Spatola, Susanne P Pfeifer, Jeffrey D Jensen

{"title":"Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data.","authors":"Erangi J Heenkenda, Cyril J Versoza, John W Terbot, Vivak Soni, Gabriella J Spatola, Susanne P Pfeifer, Jeffrey D Jensen","doi":"10.1093/molbev/msag237","DOIUrl":"10.1093/molbev/msag237","url":null,"abstract":"The rhesus macaque (Macaca mulatta) is one of the most widely used animal models in biomedical research, both as it resembles humans in key biological aspects and as it is characterized by a broad geographic range. Most of the individuals housed in U.S. research colonies have been sampled from either China or India, though notably the source population of these animals has significantly shifted over time. Given the substantial genetic and immunological differences between these populations, a deeper understanding of the underlying population structure is critically important for biomedical interpretation. Despite this, the demographic histories of these two populations remain poorly resolved. Here, we present an analysis of whole-genome PacBio HiFi long-read sequencing data from ten unrelated individuals of each population, applying four related model- and nonmodel based demographic inference approaches, in order to reconstruct their ancestral history. We evaluated the fit of the subsequently estimated models against the empirical data and incorporated underlying uncertainty in the mutation rates used for scaling. We inferred a well-fitting population history characterized by substantial structure between Chinese and Indian populations, with a split time of ∼140,000 generations ago from an ancestral population of ∼65,000 individuals. We additionally inferred the subsequent history of size change within, and gene flow between, these populations, reaching the current estimated sizes of ∼220,000 individuals in the Chinese population and ∼14,000 individuals in the Indian population. The robust baseline demographic model established in this study will serve as a valuable resource for future research on this species, including for improved fine-scale recombination mapping, selection inference, and association studies.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617669/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Signatures of nonsense-mediated mRNA decay but no evidence for transcriptional adaptation associated with protein-truncating variants in wild yeast diploids. 无义介导的mRNA衰变的特征，但没有证据表明转录适应与野生酵母二倍体中蛋白质截断变异相关。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-09-01 DOI: 10.1093/molbev/msag219

Marzena Marszałek, Wiesław Babik, Ryszard Korona, Katarzyna Tomala

{"title":"Signatures of nonsense-mediated mRNA decay but no evidence for transcriptional adaptation associated with protein-truncating variants in wild yeast diploids.","authors":"Marzena Marszałek, Wiesław Babik, Ryszard Korona, Katarzyna Tomala","doi":"10.1093/molbev/msag219","DOIUrl":"10.1093/molbev/msag219","url":null,"abstract":"Transcriptional adaptation (TA) is a regulatory process in which loss or disruption of gene function caused by protein-truncating variants (PTVs) triggers compensatory changes in expression of the healthy allele or in expression of related genes. Nonsense-mediated mRNA decay (NMD), a conserved RNA surveillance pathway that degrades transcripts containing premature termination codons, is required to initiate this process. In natural yeast populations, PTV mutations occur relatively frequently, raising the question of whether and how their effects are mitigated. In this study, we investigated TA and NMD among PTVs occurring in natural yeast populations. We observed a strong reduction in the abundance of PTV-containing transcripts, suggesting efficient recognition and degradation of transcripts containing premature stop codons. However, despite evidence of this mRNA surveillance activity, we did not detect a clear signature of transcriptional adaptation. While compensation may still occur in specific contexts, particularly for dosage-sensitive genes, it does not appear to represent a general response to PTVs in yeast. The transcriptional deregulation caused by PTVs in natural isolates may be causing too little harm to favor the evolution or maintenance of complex mechanisms required for adequate compensation. The ability to resist specific transcriptomic ruptures would thus rely mostly on the general robustness of genetic networks. Overall, our findings suggest that TA is not a universal response to loss-of-function mutations in yeast.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13537020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Redesign of energetically frustrated regions rescues function in defective T4 clamp loaders. 重新设计能量受挫区域挽救功能有缺陷的T4钳装载机。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-09-01 DOI: 10.1093/molbev/msag204

Siddharth Nimkar, Thu Nguyen, Deepti Karandur, Subu Subramanian, Michael E O'Donnell, John Kuriyan

{"title":"Redesign of energetically frustrated regions rescues function in defective T4 clamp loaders.","authors":"Siddharth Nimkar, Thu Nguyen, Deepti Karandur, Subu Subramanian, Michael E O'Donnell, John Kuriyan","doi":"10.1093/molbev/msag204","DOIUrl":"10.1093/molbev/msag204","url":null,"abstract":"DNA polymerase clamp loaders are AAA + ATPases that load sliding clamps on DNA for high-speed replication. Using a platform for high-throughput mutagenesis of replication proteins in T4 bacteriophage, we carried out saturation mutagenesis of the AAA + ATPase module of the T4 clamp loader bearing a mutation, Gln 118→Asn (Q118N), that reduces fitness. We identified residues for which different mutations improve the fitness of the Q118N variant but are neutral in the wild-type background. These conditionally neutral \"rescue hotspots\" overlap with those identified earlier in another defective variant (D110C). These rescue hotspots localize to regions where the sequence is not optimal for the structure, as determined by energetic frustration analysis. We designed new sequences for three of these regions, using the protein-design algorithm ProteinMPNN. In two helical regions, several designed sequences increased the fitness of both wild-type and mutant proteins, likely due to enhanced stability. An inter-domain hinge in the AAA + module changes conformation during activation, and designs for the hinge lead to loss of fitness in the wild-type background. However, when using the active conformation as the template, designs for the hinge increase the fitness of defective variants. In contrast, designs templated on the inactive conformation lead to loss of fitness, suggesting that a proper conformational balance is crucial. Thus, adaptive capacity in the clamp loader resides in a network of conditionally neutral sites that enable functional tuning through shifts in stability and conformational equilibria.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13533335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148761565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolutionary persistence of a highly prevalent multicopy mitochondrial-derived nuclear insertion (Mega-NUMT) in Neotropical Drosophila flies. 在新热带果蝇中高度流行的多拷贝线粒体衍生核插入（Mega-NUMT）的进化持久性。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-09-01 DOI: 10.1093/molbev/msag227

Merce Montoliu-Nerin, Anton Strunov, Eleanor Heyworth, Daniela I Schneider, Julia Thoma, Aurélie Hua-Van, Cécile Courret, Lisa Klasson, Wolfgang J Miller

{"title":"Evolutionary persistence of a highly prevalent multicopy mitochondrial-derived nuclear insertion (Mega-NUMT) in Neotropical Drosophila flies.","authors":"Merce Montoliu-Nerin, Anton Strunov, Eleanor Heyworth, Daniela I Schneider, Julia Thoma, Aurélie Hua-Van, Cécile Courret, Lisa Klasson, Wolfgang J Miller","doi":"10.1093/molbev/msag227","DOIUrl":"10.1093/molbev/msag227","url":null,"abstract":"Although strict maternal transmission of mitochondria is a general feature of animals for ensuring homogeneity in mitochondrial DNA (mtDNA) across generations, exceptions were reported in the recent past. For example, some extremely rare but spectacular cases of heteroplasmy and paternal transmission in humans have questioned the universal evolutionary principle. Hence, as an alternative, the Mega-NUMT concept was coined to explain this discovery and was thereafter partly proven to exist. This concept expands on the quite common transfer of mtDNA fragments to the nucleus (NUMTs) by considering the existence of multicopy mitochondrial nuclear insertions. Mega-NUMT reports are currently restricted to a few cases in animals, including humans. However, their detailed genomic organization, natural prevalence, and potential biological functions remain unclear. Here, we discovered that up to 60 full-sized mitochondrial genomes are integrated into the nuclear genome of the neotropical Drosophila paulistorum using long-read sequencing and in situ hybridization. The copies are organized in one cluster on chromosome 3, which we designated the \"Dpau Mega-NUMT\". Contrary to the rarity in humans, this Mega-NUMT is found at high prevalence (40%) in both laboratory lines and natural D. paulistorum populations of different semispecies. Additionally, the Mega-NUMT copies are phylogenetically separated from the current mitotypes of D. paulistorum. Together, these observations suggest long-term maintenance of the Mega-NUMT in nature. Hence, we propose that the Dpau Mega-NUMT may have been transferred to the nuclear genome before the D. paulistorum semispecies radiation and speculate based on these findings that it possibly is maintained at relatively high prevalence in nature by balancing selection or due to a yet undetermined function.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13565137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148874747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0