Journal of Molecular Evolution最新文献

{"title":"Horizontal Gene Transfer from Fungi to Myxozoa: Genomic Evidence and Evolutionary Implications.","authors":"Amr G A Ibrahim, Edson A Adriano","doi":"10.1007/s00239-026-10363-y","DOIUrl":"https://doi.org/10.1007/s00239-026-10363-y","url":null,"abstract":"<p><p>Horizontal gene transfer (HGT) is increasingly recognized as an important mechanism driving evolutionary innovation in eukaryotes, yet its functional significance in parasitic lineages remains poorly understood. Myxozoans are obligate cnidarian parasites characterized by extreme genome reduction and complex two-host life cycles, making them an intriguing system for investigating the evolutionary role of HGT. We conducted a comparative genomic and transcriptomic analysis to identify and characterize candidate genes putatively transferred from fungi to myxozoans. Phylogenetic reconstruction, sequence composition analyses, and functional annotation provided multiple lines of evidence supporting ancient HGT events retained across diverse myxozoan species. Candidate transferred genes encode proteins putatively involved in carbohydrate metabolism, defense, and regulatory processes. Exploratory codon-usage analysis revealed compositional differences between candidate genes and the sampled reference sets, a pattern that may be consistent with partial amelioration following ancient transfer, although broader quantitative comparisons will be required to evaluate codon adaptation more rigorously. Molecular clock analyses place the inferred fungi-to-myxozoan HGT events within a time interval that overlaps with the major diversification of myxozoans, around 300 Ma. Collectively, these findings suggest that candidate horizontally acquired genes may have contributed to functional innovation during myxozoan evolution, expanding our understanding of the evolutionary impact of HGT in these highly reduced parasites.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149357570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary Intelligence: How Coevolution Opened the Way to the AlphaFold Revolution.","authors":"Ugo Bastolla, Erik Aurell, Simona Cocco, David A Liberles, Cristian Micheletti, Laura Orellana, Ana Rojas, David Talavera, Alfonso Valencia","doi":"10.1007/s00239-026-10354-z","DOIUrl":"https://doi.org/10.1007/s00239-026-10354-z","url":null,"abstract":"<p><p>The sequences and structures of proteins that exist in nature are a joint product of physical mechanisms and evolutionary processes that are deeply interconnected. It was proposed that physical interactions between amino acids at different protein sites induce evolutionary correlations (co-evolution) between these sites. The inference of these correlations, first as mutual information, then as parameters of a statistical model that describes protein families (direct couplings) and, finally, through the deep neural networks of AlphaFold, produced very powerful developments that revolutionized the field of protein structure and function prediction, providing unprecedented advances in the understanding of proteins and even cells. To discuss the evolutionary mechanisms that produce the correlations exploited by AlphaFold, some of us organized the symposium \"Evolutionary intelligence: How coevolution opened the way to the AlphaFold revolution\" (Madrid, August 2025), sponsored by the Journal of Molecular Evolution and by the Computational Biology and Bioinformatics (BCB) Hub of the Spanish Research Council (CSIC). The symposium gathered a collection of researchers who contributed to the development and the advancement of the approach based on evolution-induced correlations. This paper represents a collective discussion of part of this community.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149334166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Pivot Study of 2-Hydroxyisoflavanone Dehydratase in Quercus lobata.","authors":"Matúš Kyseľ","doi":"10.1007/s00239-026-10361-0","DOIUrl":"https://doi.org/10.1007/s00239-026-10361-0","url":null,"abstract":"<p><p>This study proposes a methodological framework for investigating the regulatory architecture and evolutionary stability of the HIDH gene in Valley oak (Quercus lobata), reflecting the new ValleyOak3.0 assembly. The core of the methodology lies in distinguishing true biological divergence, such as frameshifts and alternative coding sequences, from computational artifacts by integrating an alignment modulator into the analytical workflow. The research systematically evaluates two primary architectures across Multiple Sequence Alignment effectors: sequence length expansion of the entire coding sequence (three categories), non-homologous segments associated with alignment modulation (six categories), enrichment patterns linked to sequence preference (four categories), and a density-based two MSA-independent metrics (four categories in total). By integrating an alignment modulator and incorporating reading frame analysis as a critical parameter, the methodology focuses on distinguishing true biological divergence, such as frameshifts and alternative coding sequences, from computational artifacts. While the application of the alignment modulator increased analytical precision from 42% to 71%, the findings reveal that reference motifs are inconsistently distributed across all effector categories, suggesting that their presence does not inherently guarantee transcriptional activity. Ultimately, this methodological transition from digital reconstruction to biological function provides a high-precision tool for discriminating between functional binding sites and background noise. This transition offers deeper insights into the advanced genomic characterization of Quercus lobata, serving as a valuable reference for ecotypic fitness changes in heterogeneously distributed oak species.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149322159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Weak Evolutionary Conservation of RNA-Protein Dispersion across Human and Arabidopsis Orthologs.","authors":"Yanying An, Ran Wang","doi":"10.1007/s00239-026-10362-z","DOIUrl":"https://doi.org/10.1007/s00239-026-10362-z","url":null,"abstract":"<p><p>Gene-specific relative RNA-protein dispersion, the difference between RNA and protein variation across tissues, may be conserved over evolutionary distance if particular genes experience consistent post-transcriptional regulatory constraints. We tested this in human and Arabidopsis thaliana by comparing a scale-invariant dispersion phenotype, B_disp, across 855 prespecified one-to-one orthologs, using tissue-resolved transcriptomic and proteomic atlases. Human and Arabidopsis B_disp showed a weak positive association (Spearman's ρ = 0.173, P < 0.001). Adjusting for protein detectability, RNA and protein abundance, and sequence conservation reduced it to ρ = 0.068 (bootstrap 95% confidence interval [CI] - 0.0003 to 0.136), although its direction was stable across four prespecified cohorts (ρ = 0.063-0.088). Masking 89 orthologs in four prespecified ancient systems (ribosome, proteasome, chaperone complexes and respiratory chain) lowered the adjusted association (Δρ = - 0.019, 95% CI -0.038 to -0.001) but did not change two alternative RNA-protein metrics. Exploratory analyses added after the primary analysis showed that this reduction was no larger than that from removing 89 random orthologs (two-sided P = 0.11) and was attributable to the respiratory-chain complex alone (24 pairs; Δρ = - 0.022; P = 0.00025). Among 447 sufficiently represented Gene Ontology (GO) terms, 119 unadjusted correlations, but no covariate-adjusted correlations, passed Benjamini-Hochberg correction. Genome-wide conservation of RNA-protein dispersion between human and Arabidopsis is therefore weak once abundance and detectability are considered, the residual signal is not localized to ancient core systems as a class, and the data do not identify a mode of natural selection.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149322160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasticity of Expression of Immunoregulatory Genes in Two Allopatric Populations of Drosophila ananassae: Novel Insight into Molecular Process Under Selection.","authors":"Pallab Paul, Sayarneel Mandal, Ishita Dutta, Papiya Ghosh, Sujay Ghosh","doi":"10.1007/s00239-026-10357-w","DOIUrl":"https://doi.org/10.1007/s00239-026-10357-w","url":null,"abstract":"<p><p>Evolutionary responses to persistent pathogen exposure can involve changes in immune regulation that vary among populations, sexes, and immune-related genes. We investigated the transcriptional response to long-term bacterial selection in two allopatric populations of Drosophila ananassae from the Indian subcontinent. Flies were subjected to continuous selection with Pseudomonas aeruginosa for 55 generations, while a separate relaxed-selection regime was initiated after generation 45 and maintained for a further 10 generations in the absence of bacterial challenge. The expression of nine immune-regulatory genes involved in melanization, immune signalling, and antimicrobial defence was quantified using RT-qPCR across generations, populations, and sexes. Continuous bacterial selection resulted in progressive changes in the expression of immune-related genes, although the magnitude and temporal pattern differed among genes, populations, and sexes. Different genes exhibited population specific trends in their changing expression level. Females generally showed greater transcriptional responses than males for several genes. Following removal of bacterial selection, expression of most genes declined toward control levels, although residual elevation persisted for several genes after ten generations of relaxed selection and the extent of reversion differed among genes and populations. These findings demonstrate that prolonged bacterial selection is associated with coordinated but gene-specific changes in immune gene expression in D. ananassae, together with population- and sex-dependent variation in transcriptional responses. The persistence and subsequent reversion of expression after removal of selection highlight the dynamic nature of immune regulation, while the underlying genetic, physiological, and epigenetic mechanisms remain to be determined. This study provides a molecular framework for investigating the evolution and regulation of immune responses under prolonged pathogen exposure and subsequent relaxation of selection.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149216124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene Observability Limits Comparative Genomic Inference of Vertebrate Lifespan Evolution.","authors":"Si Li, Yanyan Huang","doi":"10.1007/s00239-026-10359-8","DOIUrl":"https://doi.org/10.1007/s00239-026-10359-8","url":null,"abstract":"<p><p>Genes missing from a comparative matrix may be absent from the annotation rather than from the genome. We examined how incomplete gene records affect the interpretation of associations between gene representation and maximum lifespan in 68 amniotes. We grouped 200 genome maintenance genes into six modules and calculated the confidence-weighted fraction recovered in each species. Separate phylogenetic generalized least squares models found positive associations between all six scores and lifespan after accounting for body mass and clade. A separate principal component analysis showed that one component explained 99.01% of variation in the standardized scores, indicating redundancy among predictors. For the transposon/repeat module, adding two research-effort proxies reduced the score coefficient in the lifespan model. Genome completeness analyses, limited to 49 species, yielded less precise estimates. In simulations, we masked gene records in 31 genomes and generated responses with known score effects. Random masking weakened an imposed association. When research effort affected both the response and gene recovery, regressions omitting effort frequently detected a score association despite no direct score effect in the generating model. Including the generating effort variable reduced this detection rate to approximately 5%. Sequence comparisons for 140 avian species-gene combinations distinguished supported ortholog assignments from ambiguous or unresolved records. These results show that incomplete records can weaken or distort gene-score associations, depending on how records are lost. In this panel, the empirical lifespan associations cannot be separated into biological and observation components. Accounting for gene recovery and verifying ortholog identity are therefore necessary for biological interpretation.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recombination and Incomplete Lineage Sorting Resolve the Enigma of Lysozyme Evolution.","authors":"Dawson Houghtaling, Edward L Braun, Rebecca T Kimball","doi":"10.1007/s00239-026-10356-x","DOIUrl":"https://doi.org/10.1007/s00239-026-10356-x","url":null,"abstract":"<p><p>Lysozyme has long been a model for understanding enzyme structure, function, and evolution. Early studies revealed a conflict between organismal phylogeny and the distribution of three functionally important amino acid residues in galliform birds. Lysozymes differing at all three amino acids appear functionally equivalent, but intermediates exhibit reduced thermostability and have not been observed in nature. However, the phylogeny suggests two independent occurrences of the three mutations, requiring two separate transitions through putatively low fitness intermediates. We reexamined this apparent paradox using phylogenomic methods, accounting for incomplete lineage sorting and intralocus recombination. The lysozyme locus tree conflicts with an estimated species tree, but the conflict involves a short branch in coalescent units, consistent with incomplete lineage sorting. We also found evidence for recombination, with different parts of the lysozyme locus supporting alternative relationships. The three amino acids are encoded by exons located in different recombination-defined segments with different evolutionary histories. These results support a model where ancestral polymorphism, coupled with recombination between independently arising mutations, allowed rapid transitions between peaks in the fitness landscape without fixation of deleterious intermediates. Our findings resolve this long-standing question in lysozyme evolution and highlight the importance of considering complex genealogical processes such as incomplete lineage sorting and recombination when reconstructing ancestral proteins and interpreting apparent cases of molecular convergence.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149182672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversification of Cellulose Synthase (CESA) Genes in Mosses Suggests Both Ancient and Recent Gene duplications.","authors":"Alyssa Hartmann, Corinna Breusing, Alexandra Walling, Kerrina Whelan, Alison Roberts, Rachel S Schwartz","doi":"10.1007/s00239-026-10342-3","DOIUrl":"10.1007/s00239-026-10342-3","url":null,"abstract":"<p><p>Cellulose is an important polysaccharide that constitutes all plant cell walls, giving them strength and stability. The plant cellulose synthase (CESA) gene family, which encodes the catalytic subunits of cellulose synthesis complexes (CSCs), has diversified independently in several plant lineages, providing an interesting model for understanding selection for gene duplication. Here we quantified the presence of CESA genes across mosses to understand how the process of gene family diversification occurred in this group and how it parallels diversification in other groups. We first examined the CESA gene family in eight species of mosses across seven families for which whole genome assemblies were available. We then identified CESA genes from additional species, for which only short-read sequence data was available, by using BLAST searches and targeted gene assemblies. We validated this approach by comparing the assembled paralogs from the short-read data to the genes identified from whole genome assemblies in the eight reference species. This approach allowed us to identify paralogs directly from short-read data and greatly expand our sample set. Results from the combined empirical data support the hypothesis that CESA genes diversified within the moss lineage at least as early as the mesozoic period, during or possibly even prior to the onset of moss diversification, but also continue to diversify within modern species. In addition, we found evidence for purifying selection as the dominant force shaping these genes and observed that different lineages experienced different levels of evolutionary constraint. Lastly, our approach to assemble paralogs has the potential to allow researchers to improve analyses of gene duplication events.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"907-921"},"PeriodicalIF":2.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13672439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148982878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-mutation Based Genetic Networks to Infer Temporal Mutation Dynamics in Ancient Human Mitochondrial Genomes.","authors":"Rahul K Verma, Jesualdo A Fuentes-González, Jason Pienaar, Janna Fierst","doi":"10.1007/s00239-026-10347-y","DOIUrl":"10.1007/s00239-026-10347-y","url":null,"abstract":"<p><p>The evolutionary history of Homo sapiens is marked by complex interactions between environmental, cultural, and genetic factors. To investigate the molecular signatures of these processes, we analyzed ancient mitochondrial DNA (mtDNA) across temporal and geographic contexts using principles of co-occurrence of minor alleles defined as co-mutation, through spatiotemporal co-mutation networks of variable sites. Haplogroup-based assessments of variable sites revealed a major transition from foraging to agrarian lifestyles during the Copper-Bronze Age. Genetic network analyses demonstrated that COX and CYB loci exhibited distinct temporal dynamics, with their interactions modulated by NADH dehydrogenase genes in a geological age-dependent manner. To complement the network approach, we constructed phylogeny-based gene interaction networks and assessed polymorphism-to-divergence from chimpanzee ratios. The tree-based networks displayed topologies consistent with co-mutation analyses but showed reduced gene-gene connectivity. Polymorphism/divergence analysis further indicated that the CYB gene has been under long-term purifying selection, whereas ATP6, COX, and NADH dehydrogenase genes experienced episodic purifying selection aligned with distinct historical phases. Collectively, our findings demonstrate that network-based analysis of ancient mtDNA provides insights into early human lifestyle transitions and haplogroup diversification, contributing to the evolutionary foundations of modern human populations.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"922-936"},"PeriodicalIF":2.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13629412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148956181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and Structural Analysis of Gamete Recognition Proteins in a Broadcast Spawning Echinoderm Mesocentrotus franciscanus.","authors":"Pearl R Rivers Key, Yueling Hao, Darin R Rokyta, Don R Levitan","doi":"10.1007/s00239-026-10346-z","DOIUrl":"10.1007/s00239-026-10346-z","url":null,"abstract":"<p><p>Gamete recognition proteins are expressed on the surfaces of sperm and eggs, where they mediate interactions between gametes. The genetic basis for gamete recognition proteins, as well as their structure and interactions, have yet to be fully resolved. Using a new high-quality de novo genome assembly for the sea urchin Mesocentrotus franciscanus, we investigated the genomic structure, expression, and protein forms of several gamete recognition proteins: sperm bindin, egg receptor for sperm (HSP110), and egg bindin receptor (EBR1), as well as the receptor for egg jelly (REJ) and its paralogs. To inform future population genetic and evolutionary studies, we resolve the genomic structure of the large EBR1 protein, identifying fewer tandem CUB-TSP1 repeats in EBR1 compared to the initial characterization of this protein. As expected for an egg receptor for sperm, EBR1 is highly expressed in female reproductive tissues (eggs and female gonad), compared to other tissues. In contrast, HSP110 shows similar levels of expression across male and female reproductive tissues, as well as across non-reproductive tissues and development stages. HSP110 might be a pleiotropic gene that in part influences fertilization. Using protein structural modeling and functional domain predictions, we propose hypotheses about potential interactions among EBR1, bindin, and HSP110 proteins that may provide insight into sperm-egg interactions in sea urchins. Resolving the genomic structure of genes encoding gamete recognition proteins, in combination with functional annotations and protein structural modeling, enables deeper investigation into the consequences of variation in gamete recognition proteins and the evolution of reproductive isolation.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"953-977"},"PeriodicalIF":2.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13672419/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148944747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}