Journal of Molecular Evolution最新文献

{"title":"The evolutionary path of widespread IR heteroplasmy of chloroplast genomes in the context of Rhodophyta phylogeny.","authors":"Yang Li, Xiaomei Huang, Yuanhao Li, Ting Wang, Yuhui Xing, Jingjing Guo, Xiaoya Ma, Bojian Zhong","doi":"10.1007/s00239-026-10306-7","DOIUrl":"10.1007/s00239-026-10306-7","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"340-352"},"PeriodicalIF":1.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147443833","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":"Experimental and Computational Simulation of the Prebiotic Peptide Bond Formation Driven by Wet-Dry Cycles and Gamma Ionizing Radiation: An Insight into Molecular Evolution.","authors":"E Fonseca-González, C A Fuentes-Carreon, A Heredia-Barbero","doi":"10.1007/s00239-026-10309-4","DOIUrl":"10.1007/s00239-026-10309-4","url":null,"abstract":"<p><p>The origin of life through prebiotic chemistry and molecular evolution processes is a significant and unresolved issue in science. A key part of this process is how simple molecules, such as amino acids, transition into functional polymers, like peptides, which can store information and facilitate reactions. During this transition, wet-dry cycles and the interaction with ionizing radiation are essential mechanisms for increasing molecular complexity. This process involves the repeated hydration and dehydration of organic compounds, promoting the formation of peptide bonds that connect amino acids into longer chains. On a faster-spinning ancient Earth, these cycles might have been more relevant for the shorter days. In this scenario, a faster rotation rate affected the climate, tidal forces, and evaporation rates. The transition from simple amino acids to functional peptides remains a central question in understanding the complexation of molecules that led to life's origins. This work investigates how hydration-dehydration cycles impact solid-state gamma irradiated (40 kGy) DL-glutamic acid oligomerization. Infrared spectroscopy analysis confirms the presence of the characteristic amide I and II bands (approximately 1700 -1500 cm⁻¹), indicating an apparent change in peptide bond formation in gamma-irradiated samples. DSC and TGA thermal analysis reveal a contrasting difference in the thermograms from the control and gamma-irradiated samples. Thermal analyses demonstrate enhanced thermal stability in irradiated samples, agreeing with HyperChem computer simulations. The increase in stability in the oligomerization process. These findings support the model where cosmic ionizing radiation synergized with more frequent wet-dry cycles to promote prebiotic peptide synthesis. Our preliminary results substantiate the possibility that dry-wet cycles and ionizing irradiation on ancient Earth might have had planetary conditions to drive the molecular evolution towards abiotic synthesis of peptides.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"369-382"},"PeriodicalIF":1.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13076372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147623262","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":"Structural Features of Algal and Fungal GATA Transcription Factors may Play a Role in Symbiosis.","authors":"Pavel Virolainen, Viktoria Pankova, Alexey Nerezenko, Elena Chekunova","doi":"10.1007/s00239-026-10310-x","DOIUrl":"10.1007/s00239-026-10310-x","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"383-404"},"PeriodicalIF":1.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147530016","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":"Replication Rate-Information Storage Trade-Off Shapes Genome Architecture Across Domains.","authors":"Parthasarathi Sahu, Sashikanta Barik, Koushik Ghosh, Hemachander Subramanian","doi":"10.1007/s00239-026-10311-w","DOIUrl":"https://doi.org/10.1007/s00239-026-10311-w","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147574277","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":"Mapping Patterns of G-Quadruplex-Forming Sequence Conservation in Primates.","authors":"Emilyane de Oliveira Santana Amaral, Manuel Jara-Espejo, Sergio Roberto Peres Line","doi":"10.1007/s00239-026-10312-9","DOIUrl":"https://doi.org/10.1007/s00239-026-10312-9","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147574362","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":"Clay Minerals, Panacea or Parameter in RNA Oligomerization?","authors":"Saúl A Villafañe-Barajas, Alberto Vázquez-Salazar","doi":"10.1007/s00239-025-10295-z","DOIUrl":"10.1007/s00239-025-10295-z","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"24-27"},"PeriodicalIF":1.8,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145850322","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":"MEGA 12.1: Cross-Platform Release for macOS and Linux Operating Systems.","authors":"Glen Stecher, Michael Suleski, Qiqing Tao, Koichiro Tamura, Sudhir Kumar","doi":"10.1007/s00239-025-10287-z","DOIUrl":"10.1007/s00239-025-10287-z","url":null,"abstract":"<p><p>The Molecular Evolutionary Genetics Analysis (MEGA) software is widely used for molecular evolutionary and phylogenetic analyses. We present MEGA version 12.1, a cross-platform release that operates natively on macOS (Intel and Apple M-series processors) and modern Linux distributions. This version incorporates all the methodological and computational improvements of MEGA 12 for Microsoft Windows, including techniques that markedly reduce computational time during maximum likelihood (ML) analyses. These features include a filtered best-fit ML model test that bypasses evaluating derivative models unlikely to be optimal, an adaptive bootstrap test of phylogeny that automatically determines the necessary number of replicates, and fine-grained parallelization of ML algorithms for better multi-core performance. MEGA 12.1 has an enhanced graphical user interface, supporting high-resolution displays and improving analysis progress reporting and result visualization. A significant addition in MEGA 12.1 is an improved Calibration Editor that integrates seamlessly with the TimeTree database of molecular divergence times for easy retrieval of calibration points for molecular dating. This version also supports full cross-platform session file compatibility, allowing seamless sharing of analysis sessions across macOS, Linux, and Windows. These updates enhance accessibility, computational efficiency, and usability of MEGA across diverse computing environments. MEGA 12.1 is available for free at https://www.megasoftware.net.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"14-18"},"PeriodicalIF":1.8,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145540072","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":"Correction: Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.","authors":"Garance Sarton-Lohéac, Nikolai Romashchenko, Clément Marie Train, Sina Majidian, Natasha Glover","doi":"10.1007/s00239-025-10298-w","DOIUrl":"10.1007/s00239-025-10298-w","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"275-278"},"PeriodicalIF":1.8,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12920328/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145846717","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":"Molecular Evolution of the Green-Sensitive Opsins (RH2) in Sulawesi Oryzias Species with a Single Origin.","authors":"Nobuyuki Inomata, Yohey Terai, Junko Kusumi, Kosuke M Teshima, Ixchel F Mandagi, Sjamsu A Lawelle, Kawilarang W A Masengi, Sayaka Mitsumoto, Saki Hashizume","doi":"10.1007/s00239-025-10288-y","DOIUrl":"10.1007/s00239-025-10288-y","url":null,"abstract":"<p><p>The green-sensitive opsin (RH2) family has experienced considerably more gene duplication and loss events than other opsin families during evolution of teleost fishes. Although evolutionary patterns of RH2 genes in Oryzias species, which belong to the three major species groups, inhabiting various areas have been previously investigated, the evolutionary mechanisms underlying the diversification of the endemic species on Sulawesi Island, whose common ancestor colonized the region ~ 20 million years ago, remain unclear. In this study, we determined nucleotide sequences of RH2 genes from 21 individuals of nineteen Oryzias species (Adrianichthyidae) on Sulawesi. In RH2-A, we identified four amino acid sites (positions 94, 112, 166, and 198) with ω values over 5.3, indicating strong positive selection. Notably, substitutions at three of these sites are known to affect the absorption spectra and occurred independently on separate phylogenetic branches during species divergence. In RH2‑B and RH2‑C genes, identical amino acid residues were shared within an individual and among species, suggesting parallel mutations and/or gene conversion events. Moreover, five amino acid substitutions between RH2‑B and RH2‑C genes were fixed before colonization on Sulawesi, and four of these substitutions were associated with fine spectral tuning. While RH2‑B and RH2‑C have undergone concerted evolution in the species outside of Sulawesi, on Sulawesi the paralogs have divergently evolved. This divergence appeared to result from newly arisen mutations in either the RH2-B or RH2-C during speciation. In the RH2 genes, a number of amino acid substitutions at distinct sites led to shifts in the absorption spectrum. In particular, RH2‑A contains positively selected residues involved in spectral tuning, suggesting that these substitutions may have contributed to adaptive evolution. Our findings provide new insights into the evolutionary dynamics of RH2 gene diversification.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"127-135"},"PeriodicalIF":1.8,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145540588","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":"Comparative Analysis of AlphaFold2 Models and Intrinsic Disorder Illuminates Structural Divergence as a Symptom of Functional Divergence Across the Calmodulin Superfamily.","authors":"Kyoko Nakamura, Jessica Siltberg-Liberles","doi":"10.1007/s00239-025-10293-1","DOIUrl":"10.1007/s00239-025-10293-1","url":null,"abstract":"<p><p>Protein structure enables function. Eukaryotic genomes contain paralogous genes often encoding functionally diverse proteins forming superfamilies. As protein sequences evolve, their function may change but identifying functional divergence from sequence alone is difficult. With AlphaFold2, large-scale evolutionary analyses of protein 3D structures to identify structural divergence as a symptom of functional divergence may be possible. We investigated the structural features of 448 proteins in the calmodulin superfamily that includes many functionally divergent paralogs with conformational heterogeneity. Phylogenetic reconstruction yielded 18 main clades. Across the phylogeny, most residues in the AlphaFold2 models were predicted with high model confidence. Further, conformationally flexible clades were more disordered based on IUPred2A prediction. Clustering based on pairwise similarity of structural properties including 3D structure, and secondary structure and disorder mapped to the alignment context revealed a similar agreement with the sequence-based phylogeny except for the clades with numerous recent gene duplications. Clustering based on model confidence was less similar to the sequence-based phylogeny. Notably, AlphaFold2 frequently modeled functionally similar proteins from the same main clade into highly similar structures while the models differ more between functionally divergent main clades and within clades with extensive gene duplications, which may yield rapidly diverging sequences with unexpected co-evolutionary patterns. These results suggest that by comparing the evolutionary signals from sequence, AlphaFold2 models, and disorder across protein families, we can expand our perspective on protein structure evolution including identifying functional divergence.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":"94 1","pages":"149-163"},"PeriodicalIF":1.8,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146220120","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}