Journal of Molecular Evolution最新文献_第5页

Models of Fluctuating Selection Between Generations: A Solution for the Theoretical Inconsistency. 代间波动选择模型：理论不一致性的解决方案》。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-11-16 DOI: 10.1007/s00239-024-10214-8

Xun Gu

{"title":"Models of Fluctuating Selection Between Generations: A Solution for the Theoretical Inconsistency.","authors":"Xun Gu","doi":"10.1007/s00239-024-10214-8","DOIUrl":"10.1007/s00239-024-10214-8","url":null,"abstract":"The theory of selection fluctuation between generations has been a topic with much activities in population genetics and molecular evolution in 1970's. Most studies suggested that, as the result of fluctuating selection between generations, the frequency of an (on average) neutral mutation may fluctuate around 0.5 during the long-term evolution before it was ultimately fixed or lost. However, this pattern can only be derived from a specific type Wright-Fisher additive model, coined by the Nei-Yokoyama puzzle. In this commentary, I revisited this issue and figured out a theoretical assumption that has never been claimed explicitly, the notion of reference phenotype. Consider one locus with two-alleles: A is the wildtype allele and A' is the mutation. The fluctuating selection model actually requires a constraint that one of three genotypes (AA, AA', or A'A') must maintain a constant fitness without fluctuating between generations. It appears that the balancing selection at a frequency of 0.5 emerges only when the heterozygote (AA') is the reference genotype. Because it is difficult to determine which genotype could be the reference genotype in a real population, a desirable population genetics model should take all three possibilities into account. To this end, I propose a mixture model, where each genotype has a certain chance to be the reference genotype. My analysis showed that the emergence of balancing selection depends on the relative proportions of three different reference genotypes.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"663-668"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644317","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}

引用次数: 0

PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization. PsiPartition：基于参数化排序指标和贝叶斯优化的基因组数据改进位点划分。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-12-05 DOI: 10.1007/s00239-024-10215-7

Shijie Xu, Akira Onoda

{"title":"PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization.","authors":"Shijie Xu, Akira Onoda","doi":"10.1007/s00239-024-10215-7","DOIUrl":"10.1007/s00239-024-10215-7","url":null,"abstract":"Phylogenetics has been widely used in molecular biology to infer the evolutionary relationships among species. With the rapid development of sequencing technology, genomic data with thousands of sites become increasingly common in phylogenetic analysis, while heterogeneity among sites arises as one of the major challenges. A single homogeneous model is not sufficient to describe the evolution of all sites and partitioned models are often employed to model the evolution of heterogeneous sites by partitioning them into distinct groups and utilizing distinct evolutionary models for each group. It is crucial to determine the best partitioning, which greatly affects the reconstruction correctness of phylogeny. However, the best partitioning is usually intractable to obtain in practice. Traditional partitioning methods rely on heuristic algorithms or greedy search to determine the best ones in their solution space, are usually time consuming, and with no guarantee of optimality. In this study, we propose a novel partitioning approach, termed PsiPartition, based on the parameterized sorting indices of sites and Bayesian optimization. We apply our method to empirical datasets, and it performs significantly better compared to existing methods, in terms of Bayesian information criterion (BIC) and the corrected Akaike information criterion (AICc). We test PsiPartition on the simulated datasets with different site heterogeneity, alignment lengths, and number of loci. It is demonstrated that PsiPartition evidently and stably outperforms other methods in terms of the Robinson-Foulds (RF) distance between the true simulated trees and the reconstructed trees, especially on the data with more site heterogeneity. More importantly, our proposed Bayesian optimization-based method, for the first time, provides a new general framework to efficiently determine the optimal number of partitions. The corresponding reproducible source code and data are available at http://github.com/xu-shi-jie/PsiPartition .","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"874-890"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785976","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}

引用次数: 0

High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity. 高核苷酸偏斜 Palindromic DNA 序列因其解压缩倾向而成为潜在的复制起源。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-09-23 DOI: 10.1007/s00239-024-10202-y

Parthasarathi Sahu, Sashikanta Barik, Koushik Ghosh, Hemachander Subramanian

引用次数: 0

Correction: Perspectives on the Origin of Biological Homochirality on Earth. 更正：地球上生物同性起源的视角》（Perspectives on the Origin of Biological Homochirality on Earth）。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 DOI: 10.1007/s00239-024-10206-8

Koji Tamura

引用次数: 0

Cryptic Diversity in Scorpaenodes xyris (Jordan & Gilbert 1882) (Scorpaeniformes: Scorpaenidae) Throughout the Tropical Eastern Pacific. Scorpaenodes xyris (Jordan & Gilbert 1882) (Scorpaeniformes: Scorpaenidae) 在整个东太平洋热带地区的隐秘多样性。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-11-16 DOI: 10.1007/s00239-024-10212-w

Moises Emanuel Bernal-Hernández, Rosa Gabriela Beltrán-López, D Ross Robertson, Carole C Baldwin, Eduardo Espinoza, Juan Esteban Martínez-Gómez, Enrique Barraza, Arturo Angulo, Jonathan Valdiviezo-Rivera, Adrian F González Acosta, Omar Domínguez-Domínguez

{"title":"Cryptic Diversity in Scorpaenodes xyris (Jordan & Gilbert 1882) (Scorpaeniformes: Scorpaenidae) Throughout the Tropical Eastern Pacific.","authors":"Moises Emanuel Bernal-Hernández, Rosa Gabriela Beltrán-López, D Ross Robertson, Carole C Baldwin, Eduardo Espinoza, Juan Esteban Martínez-Gómez, Enrique Barraza, Arturo Angulo, Jonathan Valdiviezo-Rivera, Adrian F González Acosta, Omar Domínguez-Domínguez","doi":"10.1007/s00239-024-10212-w","DOIUrl":"10.1007/s00239-024-10212-w","url":null,"abstract":"The tropical eastern Pacific (TEP) is a biogeographic region with a substantial set of isolated oceanic islands and mainland shoreline habitat barriers, as well as complex oceanographic dynamics due to major ocean currents, upwelling areas, eddies, and thermal instabilities. These characteristics have shaped spatial patterns of biodiversity between and within species of reef and shore fishes of the region, which has a very high rate of endemism. Scorpaenodes xyris, a small ecologically cryptic reef-dwelling scorpionfish, is widely distributed throughout the TEP, including all the mainland reef areas and all the oceanic islands. This wide distribution and its ecological characteristics make this species a good model to study the evolutionary history of this type of reef fish across the breadth of a tropical biogeographical region. Our evaluation of geographic patterns of genetic (mitochondrial and nuclear) variation shows that S. xyris comprises two highly differentiated clades (A and B), one of which contains four independent evolutionary subunits. Clade A includes four sub-clades: 1. The Cortez mainland Province; 2. The Revillagigedo Islands; 3. Clipperton Atoll; and 4. The Galapagos Islands. Clade B, in contrast, comprises a single unit that includes the Mexican and Panamic mainland provinces, plus Cocos Island. This geographical arrangement largely corresponds to previously indicated regionalization of the TEP. Oceanic distances isolating the islands have produced much of that evolutionary pattern, although oceanographic processes likely have also contributed.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"842-860"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644289","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}

引用次数: 0

Biothermodynamics of Hemoglobin and Red Blood Cells: Analysis of Structure and Evolution of Hemoglobin and Red Blood Cells, Based on Molecular and Empirical Formulas, Biosynthesis Reactions, and Thermodynamic Properties of Formation and Biosynthesis. 血红蛋白和红细胞的生物热力学：基于分子和经验公式、生物合成反应以及形成和生物合成的热力学性质，分析血红蛋白和红细胞的结构和演变。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-11-08 DOI: 10.1007/s00239-024-10205-9

Marko E Popović, Maja Stevanović, Marijana Pantović Pavlović

{"title":"Biothermodynamics of Hemoglobin and Red Blood Cells: Analysis of Structure and Evolution of Hemoglobin and Red Blood Cells, Based on Molecular and Empirical Formulas, Biosynthesis Reactions, and Thermodynamic Properties of Formation and Biosynthesis.","authors":"Marko E Popović, Maja Stevanović, Marijana Pantović Pavlović","doi":"10.1007/s00239-024-10205-9","DOIUrl":"10.1007/s00239-024-10205-9","url":null,"abstract":"Hemoglobin and red blood cells (erythrocytes) have been studied extensively from the perspective of life and biomedical sciences. However, no analysis of hemoglobin and red blood cells from the perspective of chemical thermodynamics has been reported in the literature. Such an analysis would provide an insight into their structure and turnover from the aspect of biothermodynamics and bioenergetics. In this paper, a biothermodynamic analysis was made of hemoglobin and red blood cells. Molecular formulas, empirical formulas, biosynthesis reactions, and thermodynamic properties of formation and biosynthesis were determined for the alpha chain, beta chain, heme B, hemoglobin and red blood cells. Empirical formulas and thermodynamic properties of hemoglobin were compared to those of other biological macromolecules, which include proteins and nucleic acids. Moreover, the energetic requirements of biosynthesis of hemoglobin and red blood cells were analyzed. Based on this, a discussion was made of the specific structure of red blood cells (i.e. no nuclei nor organelles) and its role as an evolutionary adaptation for more energetically efficient biosynthesis needed for the turnover of red blood cells.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"776-798"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142622144","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}

引用次数: 0

Correction: G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases. 更正：G:U-independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Syntheases.

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 DOI: 10.1007/s00239-024-10203-x

Misa Arutaki, Ryodai Kurihara, Toru Matsuoka, Ayako Inami, Kei Tokunaga, Tomomasa Ohno, Hiroki Takahashi, Haruka Takano, Tadashi Ando, Hiromi Mutsuro-Aoki, Takuya Umehara, Koji Tamura

引用次数: 0

In Silico Investigation of the Interactions Between Cotton Leaf Curl Multan Virus Proteins and the Transcriptional Gene Silencing Factors of Gossypium hirsutum L. 棉花卷叶 Multan 病毒蛋白质与 Gossypium hirsutum L.转录基因沉默因子之间相互作用的硅学研究

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-11-14 DOI: 10.1007/s00239-024-10216-6

Heena Jain, Ekta Rawal, Prabhat Kumar, Satish Kumar Sain, Priyanka Siwach

{"title":"In Silico Investigation of the Interactions Between Cotton Leaf Curl Multan Virus Proteins and the Transcriptional Gene Silencing Factors of Gossypium hirsutum L.","authors":"Heena Jain, Ekta Rawal, Prabhat Kumar, Satish Kumar Sain, Priyanka Siwach","doi":"10.1007/s00239-024-10216-6","DOIUrl":"10.1007/s00239-024-10216-6","url":null,"abstract":"The highly dynamic nature of the Cotton leaf curl virus (CLCuV) complex (causing Cotton leaf curl disease, a significant global threat to cotton) presents a formidable challenge in unraveling precise molecular mechanisms governing viral-host interactions. To address this challenge, the present study investigated the molecular interactions of 6 viral proteins (Rep, TrAP, C4, C5, V2, and βC1) with 18 cotton Transcriptional Gene Silencing (TGS) proteins. Protein-protein dockings conducted for different viral-host protein pairs using Clustered Protein Docking (ClusPro) and Global RAnge Molecular Matching (GRAMM) (216 docking runs), revealed variable binding energies. The interacting pairs with the highest binding affinities were further scrutinized using bioCOmplexes COntact MAPS (COCOMAPS) server, which revealed robust binding of three viral proteins- TrAP, C4, and C5 with 14 TGS proteins, identifying several novel interactions (not reported yet by earlier studies), such as TrAP targeting DCL3, HDA6, and SUVH6; C4 targeting RAV2, CMT2, and DMT1; and C5 targeting CLSY1, RDR1, RDR2, AGO4, SAMS, and SAHH. Visualizing these interactions in PyMol provided a detailed insight into interacting regions. Further assessment of the impact of 18 variants of the C4 protein on interaction with CMT2 revealed no correlation between sequence variation and docking energies. However, conserved residues in the C4 binding regions emerged as potential targets for disrupting viral integrity. Hence, this study provides valuable insights into the viral-host interplay, advancing our understanding of Cotton leaf curl Multan virus pathogenicity and opening novel avenues for devising various antiviral strategies by targeting the host-viral interacting regions after experimental validation.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"891-911"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142622146","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}

引用次数: 0

Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multifunctionality. 进化蛋白质多功能性的内在紊乱和其他可塑武库

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-08-30 DOI: 10.1007/s00239-024-10196-7

Asifa Aftab, Souradeep Sil, Seema Nath, Anirneya Basu, Sankar Basu

{"title":"Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multifunctionality.","authors":"Asifa Aftab, Souradeep Sil, Seema Nath, Anirneya Basu, Sankar Basu","doi":"10.1007/s00239-024-10196-7","DOIUrl":"10.1007/s00239-024-10196-7","url":null,"abstract":"Microscopic evolution at the functional biomolecular level is an ongoing process. Leveraging functional and high-throughput assays, along with computational data mining, has led to a remarkable expansion of our understanding of multifunctional protein (and gene) families over the past few decades. Various molecular and intermolecular mechanisms are now known that collectively meet the cumulative multifunctional demands in higher organisms along an evolutionary path. This multitasking ability is attributed to a certain degree of intrinsic or adapted flexibility at the structure-function level. Evolutionary diversification of structure-function relationships in proteins highlights the functional importance of intrinsically disordered proteins/regions (IDPs/IDRs) which are highly dynamic biological soft matter. Multifunctionality is favorably supported by the fluid-like shapes of IDPs/IDRs, enabling them to undergo disorder-to-order transitions upon binding to different molecular partners. Other new malleable members of the protein superfamily, such as those involved in fold-switching, also undergo structural transitions. This new insight diverges from all traditional notions of functional singularity in enzyme classes and emphasizes a far more complex, multi-layered diversification of protein functionality. However, a thorough review in this line, focusing on flexibility and function-driven structural transitions related to evolved multifunctionality in proteins, is currently missing. This review attempts to address this gap while broadening the scope of multifunctionality beyond single protein sequences. It argues that protein intrinsic disorder is likely the most striking mechanism for expressing multifunctionality in proteins. A phenomenological analogy has also been drawn to illustrate the increasingly complex nature of modern digital life, driven by the need for multitasking, particularly involving media.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"669-684"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108231","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}

引用次数: 0

Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates. 脊椎动物性别决定的随机表观遗传修饰与进化

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-11-20 DOI: 10.1007/s00239-024-10213-9

Sergio Branciamore, Andrei S Rodin, Arthur D Riggs

{"title":"Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates.","authors":"Sergio Branciamore, Andrei S Rodin, Arthur D Riggs","doi":"10.1007/s00239-024-10213-9","DOIUrl":"10.1007/s00239-024-10213-9","url":null,"abstract":"In this report, we propose a novel mathematical model of the origin and evolution of sex determination in vertebrates that is based on the stochastic epigenetic modification (SEM) mechanism. We have previously shown that SEM, with rates consistent with experimental observation, can both increase the rate of gene fixation and decrease pseudogenization, thus dramatically improving the efficacy of evolution. Here, we present a conjectural model of the origin and evolution of sex determination wherein the SEM mechanism alone is sufficient to parsimoniously trigger and guide the evolution of heteromorphic sex chromosomes from the initial homomorphic chromosome configuration, without presupposing any allele frequency differences. Under this theoretical model, the SEM mechanism (i) predated vertebrate sex determination origins and evolution, (ii) has been conveniently and parsimoniously co-opted by the vertebrate sex determination systems during the evolutionary transitioning to the extant vertebrate sex determination, likely acting \"on top\" of these systems, and (iii) continues existing, alongside all known vertebrate sex determination systems, as a universal pan-vertebrate sex determination modulation mechanism.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"861-873"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11646274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675959","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}

引用次数: 0