Molecular biology and evolution最新文献

{"title":"Regulatory plasticity of the human genome.","authors":"Jaya Srivastava, Ivan Ovcharenko","doi":"10.1093/molbev/msaf050","DOIUrl":"10.1093/molbev/msaf050","url":null,"abstract":"<p><p>Evolutionary turnover in non-coding regions has driven phenotypic divergence during past speciation events and continues to facilitate environmental adaptation through variants. We used a deep learning model to identify the substrates of regulatory turnover using genome wide mutations mimicking three evolutionary pathways: recent history (human-chimp substitutions), modern population (human population variation), and mutational susceptibility (random mutations). We observed enhancer turnover in approximately 6% of the whole genome, with more than 80% of the novel activity arising from repurposing of enhancers between cell-types. Frequency of turnover in a cell-type is remarkably similar across the three pathways, despite only ∼19% overlap in the source regions. The majority of turnover loci were found to be localized within 100kb of a gene, with the highest turnover occurring near neurodevelopmental genes including CNTNAP2, NPAS3, and AUTS2. Flanking enhancers of these genes undergo high turnover irrespective of the mutational model pathway, suggesting a high plasticity in neurocognitive evolution. Based on susceptibility to random mutations, these enhancers were identified as vulnerable by nature and feature a higher abundance of cell type-specific transcription factor binding sites (TFBSs). Our findings suggest that enhancer repurposing within vulnerable loci drives regulatory innovation while keeping the core regulatory networks intact.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582326","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}

{"title":"Misspecification Strikes: ASTRAL can Mislead in the Presence of Hybridization, even for Non-Anomalous Scenarios.","authors":"Vu Dinh, Hector Baños","doi":"10.1093/molbev/msaf049","DOIUrl":"https://doi.org/10.1093/molbev/msaf049","url":null,"abstract":"<p><p>ASTRAL is a powerful and widely used tool for species tree inference, known for its computational speed and robustness under incomplete lineage sorting. The method has often been used as an initial step in species network inference to provide a backbone tree structure upon which hybridization events are later added to such a tree via other methods. However, we show empirically and theoretically, that this methodology can yield flawed results. Specifically, we demonstrate that under the Network Multispecies Coalescent model - including non-anomalous scenarios - ASTRAL can produce a tree that does not correspond to any topology displayed by the true underlying network. This finding highlights the need for caution when using ASTRAL-based inferences in suspected hybridization cases.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573151","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}

{"title":"Lineage-Specific Class-A GPCR Dynamics Reflect Diverse Chemosensory Adaptations in Lophotrochozoa.","authors":"Rohan Nath, Biswajit Panda, Siuli Rakesh, Arunkumar Krishnan","doi":"10.1093/molbev/msaf042","DOIUrl":"10.1093/molbev/msaf042","url":null,"abstract":"<p><p>Sensing external chemosensory cues via Class-A G protein-coupled receptors (GPCRs) is crucial for a multitude of behavioral and biological functions, influencing animal evolution and ecological adaptations. While extensively studied in vertebrates and echinoderms, the role of GPCR-mediated chemoreception in major protostome clades like Lophotrochozoa remains obscure despite their remarkable ecological adaptations across diverse aquatic and terrestrial environments. Utilizing 238 lophotrochozoan genomes across eight phyla, we conducted a large-scale comparative genomics analysis to identify lineage-specific expansions of Class-A GPCR subsets that are likely adapted for chemoreception. Using phylogeny and orthology-inference-based clustering, we distinguished these expansions from conserved orthogroups of prospective endogenous ligand-binding Class-A GPCR subsets. Across phyla, lineage-specific expansions correlated with adaptations to various habitats, ecological niches, and lifestyles, while the influence of whole-genome duplications in driving these lineage-specific expansions appeared to be less significant. Species adapted to various coastal, freshwater, and terrestrial habitats across several classes of Mollusca, Annelida, and other analyzed phyla exhibit large and diverse lineage-specific expansions, while adaptations to extreme deep-sea environments, parasitic lifestyles, sessile behaviors, or alternative chemosensory mechanisms consistently exhibit reductions. Sequence heterogeneity, signatures of positive selection, and conformational flexibility in ligand-binding pockets further highlighted adaptations to environmental signals. In summary, the evolutionary dynamics of Class-A GPCRs in lophotrochozoans reveal a widespread pattern of lineage-specific expansions driven by adaptations for chemoreception across diverse environmental niches, mirroring the trends and prominent roles seen in deuterostome lineages. The comprehensive datasets spanning numerous genomes offer a valuable foundation for advancing GPCR-mediated chemoreception studies in Lophotrochozoa.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11886862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143409180","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}

{"title":"k-mer-based approaches to bridging pangenomics and population genetics.","authors":"Miles D Roberts, Olivia Davis, Emily B Josephs, Robert J Williamson","doi":"10.1093/molbev/msaf047","DOIUrl":"https://doi.org/10.1093/molbev/msaf047","url":null,"abstract":"<p><p>Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still lack multiple reference genomes and correctly aligning references to build pangenomes can be challenging for many species, limiting our ability to study this missing genomic variation in population genetics. Here, we argue that k-mers are a very useful but underutilized tool for bridging the reference-focused paradigms of population genetics with the reference-free paradigms of pangenomics. We review current literature on the uses of k-mers for performing three core components of most population genetics analyses: identifying, measuring, and explaining patterns of genetic variation. We also demonstrate how different k-mer-based measures of genetic variation behave in population genetic simulations according to the choice of k, depth of sequencing coverage, and degree of data compression. Overall, we find that k-mer-based measures of genetic diversity scale consistently with pairwise nucleotide diversity (π) up to values of about π = 0.025 (R2 = 0.97) for neutrally evolving populations. For populations with even more variation, using shorter k-mers will maintain the scalability up to at least π = 0.1. Furthermore, in our simulated populations, k-mer dissimilarity values can be reliably approximated from counting bloom filters, highlighting a potential avenue to decreasing the memory burden of k-mer based genomic dissimilarity analyses. For future studies, there is a great opportunity to further develop methods to identifying selected loci using k-mers.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557259","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}

{"title":"Widespread and Convergent Evolution of Cone Monochromacy in Galeomorph Sharks.","authors":"Nathan S Hart, Maria Pozo-Montoro, Olivia Seeger, Laura A Ryan, Louise Tosetto, Charlie Huveneers, Victor M Peddemors, Jane E Williamson, Troy F Gaston","doi":"10.1093/molbev/msaf043","DOIUrl":"10.1093/molbev/msaf043","url":null,"abstract":"<p><p>Color vision is widespread in marine vertebrates but is notably lacking in whales, dolphins, seals, and apparently also sharks. All sharks studied to date possess only a single spectral class of cone and are thus potentially totally color blind. The reason why sharks lack color vision is unclear, but as the visual pigments of only a handful of this large and ecologically diverse taxon have been studied, more data are required to address this question. Here, we assembled the retinal transcriptomes of 9 species from 7 families and 3 orders within the superorder Galeomorphii to screen for visual opsin and phototransduction genes. We reveal that cone monochromacy is widespread in galeomorph sharks, but the type of cone opsin expressed varies, with lamniform and orectolobiform sharks expressing a long-wavelength-sensitive (LWS) opsin, and carcharhiniform and heterodontiform sharks expressing a rhodopsin-like 2 (RH2) opsin. Cone monochromacy has evolved from a dichromatic ancestral state at least 4 times, implying strong selection pressure to prioritize achromatic over chromatic vision. While all species express the GRK1A and GRK7 isoforms of G protein-coupled receptor kinase, only sharks with the LWS cone opsin express the GRK1B isoform, which suggests that nonspectral functions of photoreception may have influenced, or result from, the opsin complement in the shark retina. Finally, we show that the shark rod (RH1) opsin gene shows evidence of positive selection at sites known to influence pigment kinetics (i.e. metarhodopsin II stability) and that the rate of retinal release likely differs substantially between species in ways that reflect their physiology and ecology.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11886822/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143409181","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}

{"title":"What Do We Gain When Tolerating Loss? The Information Bottleneck Wrings Out Recombination.","authors":"Apurva Narechania, Dean Bobo, Rob DeSalle, Barun Mathema, Barry Kreiswirth, Paul J Planet","doi":"10.1093/molbev/msaf029","DOIUrl":"10.1093/molbev/msaf029","url":null,"abstract":"<p><p>Most microbes have the capacity to acquire genetic material from their environment. Recombination of foreign DNA yields genomes that are, at least in part, incongruent with the vertical history of their species. Dominant approaches for detecting these transfers are phylogenetic, requiring a painstaking series of analyses including alignment and tree reconstruction. But these methods do not scale. Here, we propose an unsupervised, alignment-free, and tree-free technique based on the sequential information bottleneck, an optimization procedure designed to extract some portion of relevant information from 1 random variable conditioned on another. In our case, this joint probability distribution tabulates occurrence counts of k-mers against their genomes of origin with the expectation that recombination will create a strong signal that unifies certain sets of co-occurring k-mers. We conceptualize the technique as a rate-distortion problem, measuring distortion in the relevance information as k-mers are compressed into clusters based on their co-occurrence in the source genomes. The result is fast, model-free, lossy compression of k-mers into learned groups of shared genome sequence, differentiating recombined elements from the vertically inherited core. We show that the technique yields a new recombination measure based purely on information, divorced from any biases and limitations inherent to alignment and phylogeny.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080484","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}

{"title":"A Tale of Too Many Trees: A Conundrum for Phylogenetic Regression.","authors":"Richard Adams, Jenniffer Roa Lozano, Mataya Duncan, Jack Green, Raquel Assis, Michael DeGiorgio","doi":"10.1093/molbev/msaf032","DOIUrl":"10.1093/molbev/msaf032","url":null,"abstract":"<p><p>Just exactly which tree(s) should we assume when testing evolutionary hypotheses? This question has plagued comparative biologists for decades. Though all phylogenetic comparative methods require input trees, we seldom know with certainty whether even a perfectly estimated tree (if this is possible in practice) is appropriate for our studied traits. Yet, we also know that phylogenetic conflict is ubiquitous in modern comparative biology, and we are still learning about its dangers when testing evolutionary hypotheses. Here, we investigate the consequences of tree-trait mismatch for phylogenetic regression in the presence of gene tree-species tree conflict. Our simulation experiments reveal excessively high false positive rates for mismatched models with both small and large trees, simple and complex traits, and known and estimated phylogenies. In some cases, we find evidence of a directionality of error: assuming a species tree for traits that evolved according to a gene tree sometimes fares worse than the opposite. We also explored the impacts of tree choice using an expansive, cross-species gene expression dataset as an arguably \"best-case\" scenario in which one may have a better chance of matching tree with trait. Offering a potential path forward, we found promise in the application of a robust estimator as a potential, albeit imperfect, solution to some issues raised by tree mismatch. Collectively, our results emphasize the importance of careful study design for comparative methods, highlighting the need to fully appreciate the role of accurate and thoughtful phylogenetic modeling.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11884811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143391376","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}

{"title":"Repeatable Selection on Large Ancestry Blocks in an Avian Hybrid Zone.","authors":"Stephanie A Blain, Hannah C Justen, Quinn K Langdon, Kira E Delmore","doi":"10.1093/molbev/msaf044","DOIUrl":"10.1093/molbev/msaf044","url":null,"abstract":"<p><p>Hybrid zones create natural tests of genetic incompatibilities by combining loci from 2 species in the same genetic background in the wild, making them useful for identifying loci involved in both intrinsic and ecological (extrinsic) isolation. Two Swainson's thrush subspecies form a hybrid zone in western North America. These coastal and inland subspecies exhibit dramatic differences in migration routes; their hybrids exhibit poor migratory survival, suggesting that ecological incompatibilities maintain this zone. We used a panel of ancestry informative markers to identify repeated patterns of selection and introgression across 4 hybrid populations that span the entire length of the Swainson's thrush hybrid zone. Two repeatable patterns consistent with selection against incompatibilities-steep genomic clines and few transitions between ancestry states-were found in large genetic blocks on chromosomes 1 and 5. The block on chromosome 1 showed evidence for inland subspecies introgression while the block on chromosome 5 exhibited coastal subspecies introgression. Some regions previously associated with migratory phenotypes, including migratory orientation, or exhibiting misexpression between the subspecies exhibited signatures of selection in the hybrid zone. Both selection and introgression across the genome were shaped by genomic structural features and evolutionary history, with stronger selection and reduced introgression in regions of low recombination, high subspecies differentiation, positive selection within the subspecies, and on macrochromosomes. Cumulatively, these results suggest that linkage among loci interacts with divergent selection and past divergent evolution between species to strengthen barriers to gene flow within hybrid zones.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11886783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483537","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}

{"title":"Characterizing the Rates and Patterns of De Novo Germline Mutations in the Aye-Aye (Daubentonia madagascariensis).","authors":"Cyril J Versoza, Erin E Ehmke, Jeffrey D Jensen, Susanne P Pfeifer","doi":"10.1093/molbev/msaf034","DOIUrl":"10.1093/molbev/msaf034","url":null,"abstract":"<p><p>Given the many levels of biological variation in mutation rates observed to date in primates-spanning from species to individuals to genomic regions-future steps in our understanding of mutation rate evolution will not only be aided by a greater breadth of species coverage across the primate clade but also by a greater depth as afforded by an evaluation of multiple trios within individual species. In order to help bridge these gaps, we here present an analysis of a species representing one of the most basal splits on the primate tree (aye-ayes), combining whole-genome sequencing of seven parent-offspring trios from a three-generation pedigree with a novel computational pipeline that takes advantage of recently developed pan-genome graphs, thereby circumventing the application of (highly subjective) quality metrics that has previously been shown to result in notable differences in the detection of de novo mutations and ultimately estimates of mutation rates. This deep sampling has enabled both a detailed picture of parental age effects and sex dependency in mutation rates, which we here compare with previously studied primates, but has also provided unique insights into the nature of genetic variation in one of the most endangered primates on the planet.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 3","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11884812/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573214","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}

{"title":"Avian Migration-Mediated Transmission and Recombination Driving the Diversity of Gammacoronaviruses and Deltacoronaviruses.","authors":"Yuting Xu, Yelin Han, Panpan Xu, Siyu Zhou, Peng Zhao, Yuyang Wang, Jie Hu, Min Ma, Zirong Li, Shunqi Bo, Chenyao Zhao, Lei Ji, Yue Yuan, Wenliang Zhao, Jianwei Wang, Qi Jin, Guimei He, Zhiqiang Wu","doi":"10.1093/molbev/msaf045","DOIUrl":"10.1093/molbev/msaf045","url":null,"abstract":"<p><p>In the wake of pandemics like COVID-19, which have zoonotic origins, the role of wildlife as reservoirs for emerging infectious diseases has garnered heightened attention. Migratory birds, traversing continents, represent a potent but under-researched vector for the spread of infectious diseases, including novel coronaviruses. This study delves into the genetic diversity and transmission dynamics of coronaviruses in migratory birds, presenting pivotal findings. From April 2019 to April 2023, we screened 5,263 migratory bird samples collected from Shanghai, China, identifying 372 coronavirus-positive samples belonging to five avian-related coronavirus subgenera and subsequently obtaining 120 complete genome sequences. To facilitate further research with a global perspective, the study curated all available 19,000 avian-associated coronaviruses and expanded the original 12 species to 16, including three novel coronavirus species identified in our study and one re-classified species from the public domain. The study illuminates the intricate genetic evolution and transmission dynamics of birds-related coronaviruses on a global scale. A notable aspect of our research is the identification of complex recombination patterns within the spike protein across different virus species and subgenera, highlighting migratory birds as a reservoir of coronavirus. Notably, the coronaviruses found in migratory birds, predominantly from the orders Anseriformes, Charadriiformes, and Pelecaniformes, with domestic ducks from Anseriformes playing a key role in bridging the transmission of coronaviruses between migratory and non-migratory birds. These findings reveal the genetic and recombination characteristics of coronaviruses in migratory birds, emphasizing the critical role of ecologically pivotal bird species in coronavirus transmission and genetic diversity shaping.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11886833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441505","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}