Molecular biology and evolution最新文献_第2页

Localized Tissue-Specific Gene Expression and Gene Duplications are Important Sources of Social Morph Differences in a Social Bumblebee.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-01 DOI: 10.1093/molbev/msaf063

Hongfei Xu, Thomas J Colgan

{"title":"Localized Tissue-Specific Gene Expression and Gene Duplications are Important Sources of Social Morph Differences in a Social Bumblebee.","authors":"Hongfei Xu, Thomas J Colgan","doi":"10.1093/molbev/msaf063","DOIUrl":"10.1093/molbev/msaf063","url":null,"abstract":"Understanding the expression of multiple behaviorally and morphologically distinct phenotypes from a single genome represents a fundamental topic in evolutionary biology. Central to the complication of expressing phenotypes, which may differ in their optima, is the sharing of largely the same genome, which is predicted to manifest in conflict at the genomic level. This is particularly true for social insects where molecular mechanisms, such as differential gene expression, contribute to observed phenotypic differences between reproductive and nonreproductive morphs. In comparison, other mechanisms, such as tissue-specific expression and gene duplications, have been posited as contributing to social morph differences yet formal investigations are limited. Here, using a combination of transcriptomics for multiple tissues and comparative genomics, we show that in a social bumblebee, the strongest differences in gene expression are found in reproductive tissues, such as the spermatheca, an organ previously believed as vestigial in workers but recently shown as functional. In comparison, we find modest expression differences in genes between queens and workers for the brain, fat body, and ovary, which are traditionally investigated in social evolution. Interestingly, morph-biased genes in these three tissues display higher tissue-specificity suggesting that while social morphs may express a shared core transcriptome, localized expression profiles may contribute to phenotypic differences. We also find evidence of differential usage of duplicated genes by queens and workers, highlighting structural variants as a contributing factor to morph differences. Collectively, our findings highlight how social insects can utilize tissue-specific gene regulation and structural variants to contribute to phenotypic differences.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730731","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

Phyloformer: Fast, Accurate, and Versatile Phylogenetic Reconstruction with Deep Neural Networks.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-01 DOI: 10.1093/molbev/msaf051

Luca Nesterenko, Luc Blassel, Philippe Veber, Bastien Boussau, Laurent Jacob

{"title":"Phyloformer: Fast, Accurate, and Versatile Phylogenetic Reconstruction with Deep Neural Networks.","authors":"Luca Nesterenko, Luc Blassel, Philippe Veber, Bastien Boussau, Laurent Jacob","doi":"10.1093/molbev/msaf051","DOIUrl":"10.1093/molbev/msaf051","url":null,"abstract":"Phylogenetic inference aims at reconstructing the tree describing the evolution of a set of sequences descending from a common ancestor. The high computational cost of state-of-the-art maximum likelihood and Bayesian inference methods limits their usability under realistic evolutionary models. Harnessing recent advances in likelihood-free inference and geometric deep learning, we introduce Phyloformer, a fast and accurate method for evolutionary distance estimation and phylogenetic reconstruction. Sampling many trees and sequences under an evolutionary model, we train the network to learn a function that enables predicting a tree from a multiple sequence alignment. On simulated data, we compare Phyloformer to FastME-a distance method-and two maximum likelihood methods: FastTree and IQTree. Under a commonly used model of protein sequence evolution and exploiting graphics processing unit (GPU) acceleration, Phyloformer outpaces all other approaches and exceeds their accuracy in the Kuhner-Felsenstein metric that accounts for both the topology and branch lengths. In terms of topological accuracy alone, Phyloformer outperforms FastME, but falls behind maximum likelihood approaches, especially as the number of sequences increases. When a model of sequence evolution that includes dependencies between sites is used, Phyloformer outperforms all other methods across all metrics on alignments with fewer than 80 sequences. On 3,801 empirical gene alignments from five different datasets, Phyloformer matches the topological accuracy of the two maximum likelihood implementations. Our results pave the way for the adoption of sophisticated realistic models for phylogenetic inference.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11965795/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605713","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

Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-01 DOI: 10.1093/molbev/msaf055

Andrey O Demkiv, Saacnicteh Toledo-Patiño, Encarnación Medina-Carmona, Andrej Berg, Gaspar P Pinto, Antonietta Parracino, Jose M Sanchez-Ruiz, Alvan C Hengge, Paola Laurino, Liam M Longo, Shina Caroline Lynn Kamerlin

{"title":"Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases.","authors":"Andrey O Demkiv, Saacnicteh Toledo-Patiño, Encarnación Medina-Carmona, Andrej Berg, Gaspar P Pinto, Antonietta Parracino, Jose M Sanchez-Ruiz, Alvan C Hengge, Paola Laurino, Liam M Longo, Shina Caroline Lynn Kamerlin","doi":"10.1093/molbev/msaf055","DOIUrl":"10.1093/molbev/msaf055","url":null,"abstract":"At the heart of many nucleoside triphosphatases is a conserved phosphate-binding sequence motif. A current model of early enzyme evolution proposes that this six to eight residue motif could have sparked the emergence of the very first nucleoside triphosphatases-a striking example of evolutionary continuity from simple beginnings, if true. To test this provocative model, seven disembodied Walker A-derived peptides were extensively computationally characterized. Although dynamic flickers of nest-like conformations were observed, significant structural similarity between the situated peptide and its disembodied counterpart was not detected. Simulations suggest that phosphate binding is nonspecific, with a preference for GTP over orthophosphate. Control peptides with the same amino acid composition but different sequences and situated conformations behaved similarly to the Walker A peptides, revealing no indication that the Walker A sequence is privileged as a disembodied peptide. We conclude that the evolutionary history of the P-loop NTPase family is unlikely to have started with a disembodied Walker A peptide in an aqueous environment. The limits of evolutionary continuity for this protein family must be reconsidered. Finally, we argue that motifs such as the Walker A motif may represent incomplete or fragmentary molecular fossils-the true nature of which has been eroded by time.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959459/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605714","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

A Segregating Structural Variant Defines Novel Venom Phenotypes in the Eastern Diamondback Rattlesnake.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-01 DOI: 10.1093/molbev/msaf058

Pedro G Nachtigall, Gunnar S Nystrom, Emilie M Broussard, Kenneth P Wray, Inácio L M Junqueira-de-Azevedo, Christopher L Parkinson, Mark J Margres, Darin R Rokyta

{"title":"A Segregating Structural Variant Defines Novel Venom Phenotypes in the Eastern Diamondback Rattlesnake.","authors":"Pedro G Nachtigall, Gunnar S Nystrom, Emilie M Broussard, Kenneth P Wray, Inácio L M Junqueira-de-Azevedo, Christopher L Parkinson, Mark J Margres, Darin R Rokyta","doi":"10.1093/molbev/msaf058","DOIUrl":"10.1093/molbev/msaf058","url":null,"abstract":"Of all mutational mechanisms contributing to phenotypic variation, structural variants are both among the most capable of causing major effects as well as the most technically challenging to identify. Intraspecific variation in snake venoms is widely reported, and one of the most dramatic patterns described is the parallel evolution of streamlined neurotoxic rattlesnake venoms from hemorrhagic ancestors by means of deletion of snake venom metalloproteinase (SVMP) toxins and recruitment of neurotoxic dimeric phospholipase A2 (PLA2) toxins. While generating a haplotype-resolved, chromosome-level genome assembly for the eastern diamondback rattlesnake (Crotalus adamanteus), we discovered that our genome animal was heterozygous for a ∼225 Kb deletion containing six SVMP genes, paralleling one of the two steps involved in the origin of neurotoxic rattlesnake venoms. Range-wide population-genomic analysis revealed that, although this deletion is rare overall, it is the dominant homozygous genotype near the northwestern periphery of the species' range, where this species is vulnerable to extirpation. Although major SVMP deletions have been described in at least five other rattlesnake species, C. adamanteus is unique in not additionally gaining neurotoxic PLA2s. Previous work established a superficially complementary north-south gradient in myotoxin (MYO) expression based on copy number variation with high expression in the north and low in the south, yet we found that the SVMP and MYO genotypes vary independently, giving rise to an array of diverse, novel venom phenotypes across the range. Structural variation, therefore, forms the basis for the major axes of geographic venom variation for C. adamanteus.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11965796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657665","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

Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-01 DOI: 10.1093/molbev/msaf067

Niels Holtgrefe, Katharina T Huber, Leo van Iersel, Mark Jones, Samuel Martin, Vincent Moulton

{"title":"Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments.","authors":"Niels Holtgrefe, Katharina T Huber, Leo van Iersel, Mark Jones, Samuel Martin, Vincent Moulton","doi":"10.1093/molbev/msaf067","DOIUrl":"10.1093/molbev/msaf067","url":null,"abstract":"With the increasing availability of genomic data, biologists aim to find more accurate descriptions of evolutionary histories influenced by secondary contact, where diverging lineages reconnect before diverging again. Such reticulate evolutionary events can be more accurately represented in phylogenetic networks than in phylogenetic trees. Since the root location of phylogenetic networks cannot be inferred from biological data under several evolutionary models, we consider semi-directed (phylogenetic) networks: partially directed graphs without a root in which the directed edges represent reticulate evolutionary events. By specifying a known outgroup, the rooted topology can be recovered from such networks. We introduce the algorithm Squirrel (Semi-directed Quarnet-based Inference to Reconstruct Level-1 Networks) which constructs a semi-directed level-1 network from a full set of quarnets (four-leaf semi-directed networks). Our method also includes a heuristic to construct such a quarnet set directly from sequence alignments. We demonstrate Squirrel's performance through simulations and on real sequence data sets, the largest of which contains 29 aligned sequences close to 1.7 Mb long. The resulting networks are obtained on a standard laptop within a few minutes. Lastly, we prove that Squirrel is combinatorially consistent: given a full set of quarnets coming from a triangle-free semi-directed level-1 network, it is guaranteed to reconstruct the original network. Squirrel is implemented in Python, has an easy-to-use graphical user interface that takes sequence alignments or quarnets as input, and is freely available at https://github.com/nholtgrefe/squirrel.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

A Phylogenetic Method Identifies Candidate Drivers of the Evolution of the SARS-CoV-2 Mutation Spectrum.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-01 DOI: 10.1093/molbev/msaf059

Russ Corbett-Detig

引用次数: 0

Temporal patterns of haplotypic and allelic diversity reflect the changing selection landscape of the malaria parasite Plasmodium falciparum. 单倍型和等位基因多样性的时间模式反映了恶性疟原虫不断变化的选择景观。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-01 DOI: 10.1093/molbev/msaf075

Angela M Early, Stéphane Pelleau, Lise Musset, Daniel E Neafsey

{"title":"Temporal patterns of haplotypic and allelic diversity reflect the changing selection landscape of the malaria parasite Plasmodium falciparum.","authors":"Angela M Early, Stéphane Pelleau, Lise Musset, Daniel E Neafsey","doi":"10.1093/molbev/msaf075","DOIUrl":"https://doi.org/10.1093/molbev/msaf075","url":null,"abstract":"The malaria parasite Plasmodium falciparum regularly confronts orchestrated changes in frontline drug treatment that drastically alter its selection landscape. When this has occurred, the parasite has successfully adapted to new drugs through novel resistance mutations. These novel mutations, however, emerge in a genetic background already shaped by prior drug selection. In some instances, selection imposed by different drugs target the same loci in either synergistic or antagonistic ways, which may leave genomic signatures that are hard to attribute to a specific agent. Here, we use two approaches for detecting sequential bouts of drug adaptation: haplotype-based selection testing and temporal changes in allele frequencies. Using a set of longitudinal samples from French Guiana, we determine that since the official introduction of artemisinin combination therapy in 2007 there have been rapid hard selective sweeps at both known and novel loci. At four high-profile genes with demonstrated involvement in drug resistance (pfcrt, pfmdr1, pfaat1, and pfgch1), we see selection signals both before and after drug regime change; however, selection favored different haplotypes in the two time periods. Similarly, allele frequency analysis identified coding variants whose frequency trajectory changed sign under the new drug pressure. These selected alleles were enriched for genes implicated in artemisinin or partner drug resistance in other global populations. Overall, these results suggest that drug resistance in P. falciparum is governed by known alleles of large effect along with a polygenic architecture of potentially more subtle variants, any of which can experience fitness reversals under distinct drug regimes.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143753507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

A New Comparative Framework for Estimating Selection on Synonymous Substitutions.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-01 DOI: 10.1093/molbev/msaf068

Hannah Verdonk, Alyssa Pivirotto, Vitor Pavinato, Jody Hey, Sergei L K Pond

{"title":"A New Comparative Framework for Estimating Selection on Synonymous Substitutions.","authors":"Hannah Verdonk, Alyssa Pivirotto, Vitor Pavinato, Jody Hey, Sergei L K Pond","doi":"10.1093/molbev/msaf068","DOIUrl":"10.1093/molbev/msaf068","url":null,"abstract":"Selection on synonymous codon usage is a well-known and widespread phenomenon, yet existing models often do not account for it or its effect on synonymous substitution rates. In this article, we develop and expand the capabilities of multiclass synonymous substitution (MSS) models, which account for such selection by partitioning synonymous substitutions into 2 or more classes and estimating a relative substitution rate for each class, while accounting for important confounders like mutation bias. We identify extensive heterogeneity among relative synonymous substitution rates in an empirical dataset of ∼12,000 gene alignments from 12 Drosophila species. We validate model performance using data simulated under a forward population genetic simulation, demonstrating that MSS models are robust to model misspecification. MSS rates are significantly correlated with other covariates of selection on codon usage (population-level polymorphism data and tRNA abundance data), suggesting that models can detect weak signatures of selection on codon usage. With the MSS model, we can now study selection on synonymous substitutions in diverse taxa, independent of any a priori assumptions about the forces driving that selection.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143701060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

On the Probability of Reaching High Peaks in Fitness Landscapes by Adaptive Walks. 关于自适应行走在适应度景观中达到高峰的概率

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-01 DOI: 10.1093/molbev/msaf066

Yang Li, Jianzhi Zhang

{"title":"On the Probability of Reaching High Peaks in Fitness Landscapes by Adaptive Walks.","authors":"Yang Li, Jianzhi Zhang","doi":"10.1093/molbev/msaf066","DOIUrl":"10.1093/molbev/msaf066","url":null,"abstract":"Adaptive evolution can be described by an uphill walk in a fitness landscape. However, climbing the global peak in a multipeak landscape is improbable because of the high chance of being trapped at a local peak. Nonetheless, over three-quarters of simulated adaptive walks in the fitness landscape of the Escherichia coli dihydrofolate reductase (DHFR) gene were reported to end at the highest 14% of peaks, suggesting that biological systems may be substantially more evolvable than commonly thought. To investigate the cause and generality of this observation, we estimate in empirical and theoretical fitness landscapes the probability of reaching high peaks by adaptive walks (PHP), where high peaks refer to the highest 1, 5, 14, or 25% of all peaks. We find that (i) PHP varies substantially among landscapes, (ii) PHP in empirical landscapes is generally comparable to or smaller than that in same-size Rough Mount Fuji landscapes of similar ruggedness, and (iii) lowering landscape ruggedness boosts PHP. As observed in DHFR, we find in every examined landscape a positive correlation between the fitness of a peak and its basin size, which is the number of genotypes that can reach the peak through adaptive walks. Yet, this correlation does not guarantee a large PHP because of the influences of other factors. We conclude that evolvability depends on the specific fitness landscape and that the large PHP in the DHFR landscape is not a general property of empirical or theoretical fitness landscapes.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Estimates of the Mutation Rate per Year Can Explain Why the Molecular Clock Depends on Generation Time. 对每年突变率的估计可以解释为什么分子钟取决于世代时间。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-01 DOI: 10.1093/molbev/msaf069

Loveday Lewin, Adam Eyre-Walker

引用次数: 0