Journal of Molecular Evolution最新文献_第4页

Correction: Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays. 更正：Fit-Seq2.0：一个改进的软件，用于高通量适应度测量使用池竞争分析。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 DOI: 10.1007/s00239-025-10232-0

Fangfei Li, Jason Tarkington, Gavin Sherlock

引用次数: 0

Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities. Id位点的共同祖先：染色体重排和多基因可能性。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2025-01-17 DOI: 10.1007/s00239-025-10233-z

Ashutosh Sharma, Nagarjun Vijay

{"title":"Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities.","authors":"Ashutosh Sharma, Nagarjun Vijay","doi":"10.1007/s00239-025-10233-z","DOIUrl":"10.1007/s00239-025-10233-z","url":null,"abstract":"The diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait is driven by a complex chromosomal rearrangement on chromosome 20 at the Fm locus, resulting in the overexpression of the EDN3 (a gene central to melanocyte regulation). In contrast, the inhibition of dermal pigmentation is regulated by the Id locus. Although prior studies using genetic crosses, GWAS, and gene expression analysis have investigated the genetic underpinnings of the Id locus, its precise location and functional details remain elusive. Our study aims to precisely locate the Id locus, identify associated chromosomal rearrangements and candidate genes influencing dermal pigmentation, and examine the ancestral status of the Id locus in BBC breeds. Using public genomic data from BBC and non-BBC breeds, we refined the Id locus to a ~1.6 Mb region that co-localizes with Z amplicon repeat units at the distal end of the q-arm of chromosome Z within a 10.36 Mb inversion in Silkie BBC. Phylogenetic and population structure analyses reveal that the Id locus shares a common ancestry across all BBC breeds, much like the Fm locus. Selection signatures and highly differentiated BBC-specific SNPs within the MTAP gene position it as the prime candidate for the Id locus with CCDC112 and additional genes, suggesting a possible polygenic nature. Our results suggest that the Id locus is shared among BBC breeds and may function as a supergene cluster in shank and dermal pigmentation variation.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"163-180"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143006920","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

Positive Selection Shapes Breast Cancer Tumor Suppressor Genes: Unveiling Insights into BRCA1, BRCA2, and MDC1 Stability. 正向选择塑造乳腺癌抑癌基因：揭示 BRCA1、BRCA2 和 MDC1 稳定性的奥秘。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2024-12-16 DOI: 10.1007/s00239-024-10222-8

Youssef M Fadel, Marwan Khaled, Mohamed Emam, Nour H Marzouk, Sief El-Din Sobih, Habiba Abd-Elaty, Wafaa M Elrashedy, Gehad Mostafa, Salma Alm Eldeen, Mohaned Bador, Agostinho Antunes, Mohamed El Hadidi

{"title":"Positive Selection Shapes Breast Cancer Tumor Suppressor Genes: Unveiling Insights into BRCA1, BRCA2, and MDC1 Stability.","authors":"Youssef M Fadel, Marwan Khaled, Mohamed Emam, Nour H Marzouk, Sief El-Din Sobih, Habiba Abd-Elaty, Wafaa M Elrashedy, Gehad Mostafa, Salma Alm Eldeen, Mohaned Bador, Agostinho Antunes, Mohamed El Hadidi","doi":"10.1007/s00239-024-10222-8","DOIUrl":"10.1007/s00239-024-10222-8","url":null,"abstract":"Worldwide, breast cancer is the leading cause of death in women with cancers. Given this situation, new approaches to treatment are urgently needed. Tumor Suppressor Genes (TSGs) defects play a crucial role in tumor development, and recent studies propose their reactivation as a promising way for clinical intervention in breast cancer. Here, we performed detailed evolutionary analyses of 241 breast cancer TSGs across 25 mammalian genomes, revealing 28 genes under strong positive selection. These genes exhibit elevated molecular pressure in codons corresponding to amino acids located in crucial protein domains and motifs. Notably, one positively selected site in the BRCA1 C-terminal domain is known for its role in DNA damage response, suggesting potential interference with DNA repair mechanisms. Moreover, the substitution of some other sites found in important key motifs, namely two codons in BRCA2 (752 and 939) localized within the phosphoinositide-3-OH-kinase-related and playing a crucial role in the DNA repair and the DNA damage checkpoints. Our findings could be inspirational to foster future recommendations for drug-targeting sites and further illuminate the function of these proteins. Finally, the code developed in our study is delivered in the Automated tool for positive selection (ATPs) ( https://github.com/APS-P/Automated-Tool-for-Positive-Selection-ATPS-/wiki ) to assist the easy reproducibility and support future evolutionary genomics analyses.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"100-110"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142836947","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

2024 Zuckerkandl Prize. “2024年糖Candl奖”。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-01-22 DOI: 10.1007/s00239-025-10234-y

Ugo Bastolla, Kerry Geiler-Samerotte, Maeva Perez, David A Liberles

引用次数: 0

Putative MutS2 Homologs in Algae: More Goods in Shopping Bag? 藻类中的推定 MutS2 同源物：购物袋里还有更多商品？

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-10-04 DOI: 10.1007/s00239-024-10210-y

Mariia Berdieva, Vera Kalinina, Olga Palii, Sergei Skarlato

{"title":"Putative MutS2 Homologs in Algae: More Goods in Shopping Bag?","authors":"Mariia Berdieva, Vera Kalinina, Olga Palii, Sergei Skarlato","doi":"10.1007/s00239-024-10210-y","DOIUrl":"10.1007/s00239-024-10210-y","url":null,"abstract":"MutS2 proteins are presumably involved in either control of recombination or translation quality control in bacteria. MutS2 homologs have been found in plants and some algae; however, their actual diversity in eukaryotes remains unknown. We found putative MutS2 homologs in various species of photosynthetic eukaryotes and performed a detailed analysis of the revealed amino acid sequences. Three groups of homologs were distinguished depending on their domain composition: MutS2 homologs with full set of specific domains, MutS2-like sequences without endonuclease Smr domain, and MutS2-like homologs lacking Smr and clamp in domain IV, the extreme form of which are proteins with only a complete ATPase domain. We clarified the information about amino acid composition and set of specific motifs in the conserved domains in MutS2 and MutS2-like sequences. The models of the predicted tertiary structure were obtained for each group of homologs. The phylogenetic analysis demonstrated that all eukaryotic sequences split into two large groups. The first group included homologs belonging to species of Archaeplastida and a subset of haptophyte homologs, while the second-sequences of organisms from CASH groups (cryptophytes, alveolates, stramenopiles, haptophytes) and chlorarachniophytes. The cyanobacterial MutS2 clustered together with the first group, and proteins belonging to Deltaproteobacteria (orders Myxococcales and Bradymonadales) showed phylogenetic affinity to the CASH-including group with strong support. The observed tree pattern did not support a clear differentiation of eukaryotes into lineages with red and green algae-derived plastids. The results are discussed in the context of current conceptions of serial endosymbioses and genetic mosaicism in algae with complex plastids.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"815-833"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372076","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

Structural Insights into Cold-Active Lipase from Glaciozyma antarctica PI12: Alphafold2 Prediction and Molecular Dynamics Simulation. 冷活性脂肪酶（Glaciozyma antarctica PI12）的结构洞察：Alphafold2 预测与分子动力学模拟。

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/s00239-024-10219-3

Adamu Idris Matinja, Nor Hafizah Ahmad Kamarudin, Adam Thean Chor Leow, Siti Nurbaya Oslan, Mohd Shukuri Mohamad Ali

{"title":"Structural Insights into Cold-Active Lipase from Glaciozyma antarctica PI12: Alphafold2 Prediction and Molecular Dynamics Simulation.","authors":"Adamu Idris Matinja, Nor Hafizah Ahmad Kamarudin, Adam Thean Chor Leow, Siti Nurbaya Oslan, Mohd Shukuri Mohamad Ali","doi":"10.1007/s00239-024-10219-3","DOIUrl":"10.1007/s00239-024-10219-3","url":null,"abstract":"Cold-active enzymes have recently gained popularity because of their high activity at lower temperatures than their mesophilic and thermophilic counterparts, enabling them to withstand harsh reaction conditions and enhance industrial processes. Cold-active lipases are enzymes produced by psychrophiles that live and thrive in extremely cold conditions. Cold-active lipase applications are now growing in the detergency, synthesis of fine chemicals, food processing, bioremediation, and pharmaceutical industries. The cold adaptation mechanisms exhibited by these enzymes are yet to be fully understood. Using phylogenetic analysis, and advanced deep learning-based protein structure prediction tool Alphafold2, we identified an evolutionary processes in which a conserved cold-active-like motif is presence in a distinct subclade of the tree and further predicted and simulated the three-dimensional structure of a putative cold-active lipase with the cold active motif, Glalip03, from Glaciozyma antarctica PI12. Molecular dynamics at low temperatures have revealed global stability over a wide range of temperatures, flexibility, and the ability to cope with changes in water and solvent entropy. Therefore, the knowledge we uncover here will be crucial for future research into how these low-temperature-adapted enzymes maintain their overall flexibility and function at lower temperatures.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"944-963"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644389","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

Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning. 分子进化原理：多层次学习理论的非平衡热力学概念》。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-08-29 DOI: 10.1007/s00239-024-10195-8

Jens Smiatek

引用次数: 0

Stress-Induced Constraint on Expression Noise of Essential Genes in E. coli. 压力对大肠杆菌重要基因表达噪音的限制

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-10-11 DOI: 10.1007/s00239-024-10211-x

Perry A LaBoone, Raquel Assis

{"title":"Stress-Induced Constraint on Expression Noise of Essential Genes in E. coli.","authors":"Perry A LaBoone, Raquel Assis","doi":"10.1007/s00239-024-10211-x","DOIUrl":"10.1007/s00239-024-10211-x","url":null,"abstract":"Gene expression is an inherently noisy process that is constrained by natural selection. Yet the condition dependence of constraint on expression noise remains unclear. Here, we address this problem by studying constraint on expression noise of E. coli genes in eight diverse growth conditions. In particular, we use variation in expression noise as an analog for constraint, examining its relationships to expression level and to the number of regulatory inputs from transcription factors across and within conditions. We show that variation in expression noise is negatively associated with expression level, implicating constraint to minimize expression noise of highly expressed genes. However, this relationship is condition dependent, with the strongest constraint observed when E. coli are grown in the presence of glycerol or ciprofloxacin, which result in carbon or antibiotic stress, respectively. In contrast, we do not observe evidence of constraint on expression noise of highly regulated genes, suggesting that highly expressed and highly regulated genes represent distinct classes of genes. Indeed, we find that essential genes are often highly expressed but not highly regulated, with elevated expression noise in glycerol and ciprofloxacin conditions. Thus, our findings support the hypothesis that selective constraint on expression noise is condition dependent in E. coli, illustrating how it may play a critical role in ensuring expression stability of essential genes in unstable environments.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"834-841"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11646277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406432","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

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