Molecular biology and evolution最新文献

Taking a BREATH (Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories) to simultaneously infer phylogenetic and transmission trees for partially sampled outbreaks. 呼吸（传播历史的贝叶斯重建和进化分析），同时推断部分抽样暴发的系统发育和传播树。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-10 DOI: 10.1093/molbev/msag257

Caroline Colijn, Matthew Hall, Remco Bouckaert

{"title":"Taking a BREATH (Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories) to simultaneously infer phylogenetic and transmission trees for partially sampled outbreaks.","authors":"Caroline Colijn, Matthew Hall, Remco Bouckaert","doi":"10.1093/molbev/msag257","DOIUrl":"https://doi.org/10.1093/molbev/msag257","url":null,"abstract":"We introduce and apply Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories (BREATH), a method to simultaneously construct phylogenetic trees and transmission trees using sequence data for a host-to-host outbreak. BREATH's transmission process that accounts for a flexible natural history of infection (including a latent period if desired) and a separate process for sampling. It allows for unsampled individuals and within-host evolution. It also accounts for the fact that an outbreak may still be ongoing at the time of analysis, using right truncation adjustment. We perform a simulation study to verify our implementation and explore sensitivity to unknown or misspecified parameters. We then apply BREATH to a previously-described 13-year outbreak of tuberculosis. We find that using a transmission process to inform the phylogenetic reconstruction results in better resolution of the phylogeny (in topology, branch length and tree height) and a more precise estimate of the time of origin of the outbreak. Considerable uncertainty remains about transmission events in the outbreak, but our reconstructed transmission network resolves two major waves of transmission consistent with the previously-described epidemiology, estimates the numbers of unsampled individuals, and describes some high-probability transmission pairs. An open source implementation of BREATH is available from https://github.com/rbouckaert/BREATH as the BREATH package to BEAST 2.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149168318","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

Integrative genotype-environment association and single-cell transcriptomic analyses identify candidate mechanisms of environmental adaptation in pigs. 综合基因型-环境关联和单细胞转录组学分析确定了猪环境适应的候选机制。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-09 DOI: 10.1093/molbev/msag260

Dong Li, Tiantian Yuan, Xiang Li, Yu Quan, Xuekai Tian, Ye Cheng, Yulong Wang, Xinglong Wu, Boyuan Sun, Wansheng Liu, Yu Jiang, Rongrong Ding, Martien A M Groenen, Martijn F L Derks, Taiyong Yu

{"title":"Integrative genotype-environment association and single-cell transcriptomic analyses identify candidate mechanisms of environmental adaptation in pigs.","authors":"Dong Li, Tiantian Yuan, Xiang Li, Yu Quan, Xuekai Tian, Ye Cheng, Yulong Wang, Xinglong Wu, Boyuan Sun, Wansheng Liu, Yu Jiang, Rongrong Ding, Martien A M Groenen, Martijn F L Derks, Taiyong Yu","doi":"10.1093/molbev/msag260","DOIUrl":"https://doi.org/10.1093/molbev/msag260","url":null,"abstract":"As one of the earliest domesticated and most globally ubiquitous livestock, pigs (Sus scrofa) have undergone profound environmental adaptation while following human expansion across diverse bioclimatic zones. Despite their evolutionary significance, the genomic mechanisms enabling pigs to thrive in disparate ecological settings remain poorly understood. Here, we present a comprehensive global analysis using a dataset of 1,151 pig genome sequences representing 146 distinct populations. By integrating three complementary genotype-environment association (GEA) frameworks including Redundancy Analysis (RDA), BayPass, and Latent Factor Mixed Models (LFMM), we identified genomic regions and candidate genes associated with environmental variation. Our analysis detected several candidate genes associated with high-altitude adaptation, particularly those involved in ultraviolet radiation response. By integrating lung single-cell RNA sequencing analysis (scRNA) from high-altitude and commercial breeds, we identified ASXL1 as a candidate gene potentially involved in high-altitude adaptation. Meanwhile, scRNA revealed candidate regulatory pathways, including the NOTCH signaling pathway, that were overlooked by traditional GEA methods, suggested the complex regulatory landscape of physiological adaptation. Together, this study integrates large-scale population genomics and scRNA to provide insights into the genetic associations and regulatory landscapes potentially contributing to environmental adaptation in domestic pigs, advancing our understanding of livestock evolutionary responses to diverse ecological conditions.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149137465","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

Comparative population genomics reveals evolutionary potential and conservation priorities in three Procapra species. 比较种群基因组学揭示了三种原葵物种的进化潜力和保护优先级。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-07 DOI: 10.1093/molbev/msag258

Haoyang Wang, Xiaofan Ma, Xin Huang, Xiaoyu Hu, Chao Zhang, Huayao Gao, Ming Lu, Yalun Wang, Tongzuo Zhang, Zexuan Gao, Yonggang Nie

{"title":"Comparative population genomics reveals evolutionary potential and conservation priorities in three Procapra species.","authors":"Haoyang Wang, Xiaofan Ma, Xin Huang, Xiaoyu Hu, Chao Zhang, Huayao Gao, Ming Lu, Yalun Wang, Tongzuo Zhang, Zexuan Gao, Yonggang Nie","doi":"10.1093/molbev/msag258","DOIUrl":"https://doi.org/10.1093/molbev/msag258","url":null,"abstract":"The genus Procapra, comprising the Mongolian gazelle (P. gutturosa; MG), Przewalski's gazelle (P. przewalskii; PG), and Tibetan gazelle (P. picticaudata; TG), has experienced substantial range contractions and population declines due to anthropogenic disturbance and habitat degradation. Effective conservation of these species requires a clearer understanding of how distinct demographic histories have shaped their current evolutionary potential and genetic risks. Here, we assembled chromosome-level genomes for all three Procapra species and conducted population genomic analyses using whole-genome resequencing data from 93 individuals. Our findings show that MG underwent substantial historical population expansion and retained the highest genetic diversity and lowest levels of inbreeding. In contrast, TG currently has a relatively large census size, but its historically small effective population size may have contributed to elevated inbreeding and reduced genetic diversity. Despite having the smallest census size among the three species, PG retained intermediate genetic diversity, consistent with its historically larger effective population size, whereas severe contemporary habitat fragmentation is associated with elevated inbreeding and a pronounced demographic decline. Collectively, our results demonstrate that census size alone does not reliably predict genetic risk in closely related Procapra species and highlight the importance of demographic history in shaping evolutionary potential and species-specific conservation needs. Given the escalating anthropogenic fragmentation affecting PG, targeted conservation actions are urgently needed to limit further inbreeding and erosion of genetic diversity and to safeguard its long-term viability.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112222","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

Interpreting Convolutional Neural Networks in Population Genetics. 解读群体遗传学中的卷积神经网络。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-05 DOI: 10.1093/molbev/msag256

Huiting Xu, Leon Zong, Dylan D Ray, Lei Lei, Daniel R Schrider, Franz Baumdicker, Sara Mathieson

{"title":"Interpreting Convolutional Neural Networks in Population Genetics.","authors":"Huiting Xu, Leon Zong, Dylan D Ray, Lei Lei, Daniel R Schrider, Franz Baumdicker, Sara Mathieson","doi":"10.1093/molbev/msag256","DOIUrl":"https://doi.org/10.1093/molbev/msag256","url":null,"abstract":"Machine learning approaches have become a powerful alternative to traditional methods in population genetics. Convolutional neural networks (CNNs) in particular have been successful in inferring natural selection, recombination rates, introgression, dispersal distances, and effective population size changes. One limitation of CNNs and other deep learning methods is that they can be difficult to interpret. When they have been shown to be as or more successful than summary-statistic-based methods, what are they learning? Here we investigate CNNs from two different methods: the pg-gan discriminator for identifying real vs.∼simulated data, and two networks trained to detect selective sweeps. We first compute correlations between learned network features and traditional summary statistics, then assess whether summary statistics can be predicted from the learned features. To understand the learned features, we compute feature importance through SHAP values and feature groupings through dimensionality reduction. Finally we use decision trees and random forests to build an interpretable \"model-of-the-model\". Our results reveal that some CNN architectures can implicitly compute summary statistics such as pairwise heterozygosity, while statistics such as the site frequency spectrum are less similar to the network's learned features. We find that long-range linkage disequilibrium is readily approximated by the networks and may be more efficiently computed by CNNs than traditional methods (which are quadratic in the number of sites). Overall, this work contributes to the interpretability of deep learning methods in population genetics by clarifying the relationships between model architecture, learned network features, established summary statistics, and predicted evolutionary parameters.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149111858","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

Characterizing the detectable and invisible fractions of genomic loci under balancing selection. 在平衡选择下描述基因组位点的可检测和不可见部分。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag228

Débora Y C Brandt, Aida M Andrés, Tim Connallon, Max Reuter

{"title":"Characterizing the detectable and invisible fractions of genomic loci under balancing selection.","authors":"Débora Y C Brandt, Aida M Andrés, Tim Connallon, Max Reuter","doi":"10.1093/molbev/msag228","DOIUrl":"https://doi.org/10.1093/molbev/msag228","url":null,"abstract":"Balancing selection refers to scenarios where selection maintains genetic polymorphisms affecting fitness and its components. Empirical studies have documented specific cases of balancing selection, yet the general prevalence of balanced polymorphisms within genomes remains a topic of longstanding debate. Although genome-wide scans for signals of balancing selection suggest that it is rare, current methods are notoriously conservative and may identify only a small and unrepresentative fraction of loci evolving under balancing selection. What, then, are the proportions of loci under balancing selection that are detectable versus invisible to genome scans? Here, we address this question using a combination of analytical modeling and population genetic simulations. Our results provide quantitative support for the intuition that a large fraction of loci under balancing selection will be invisible to standard tests for balancing selection, with the detectable loci representing a biased subset with large and symmetrical fitness effects on different fitness components. Quantifying power across parameters that vary between species also shows that the detectable and invisible fractions of genomic loci under balancing selection are likely to differ substantially between organisms. For example, a Drosophila melanogaster-like ratio of mutation to recombination rates (∼0.1) reduces detection power by roughly a quarter of the power expected with a human-like ratio (∼1). This, combined with other evidence suggesting that balancing selection could be common in D. melanogaster, showcases how our appreciation of the prevalence of balancing selection is limited by our ability to detect its genomic signals, especially in those species where it might be common.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"43 10","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13635458/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149111854","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

Using gene topologies to partition sex chromosomes into regions with distinct histories. 使用基因拓扑将性染色体划分为具有不同历史的区域。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag249

Suzie Tallon, Lila Maladesky, Roula Jabbour-Zahab, Aline Muyle, Thomas Lenormand

{"title":"Using gene topologies to partition sex chromosomes into regions with distinct histories.","authors":"Suzie Tallon, Lila Maladesky, Roula Jabbour-Zahab, Aline Muyle, Thomas Lenormand","doi":"10.1093/molbev/msag249","DOIUrl":"10.1093/molbev/msag249","url":null,"abstract":"Sex chromosomes often evolve through successive recombination arrests, forming evolutionary strata. Accurately describing these strata, their boundaries and history is crucial for studying sex chromosome evolution, but this can be very challenging, particularly in young sex chromosomes where X-Y or Z-W divergence is low or in highly rearranged sex chromosomes where strata are divided into pieces. Standard approaches to distinguish recently evolved strata involve combining signals from dS, Fst and gene-by-gene phylogenies, all of which can be noisy. Here, we propose a new method that uses the proportion of allele topologies observed on sex-linked genes between at least a pair of sister species, obtained from reconstructed X and Y sequences aligned to the same reference, along with an outgroup to infer ancestral alleles, with flexibility in the reconstruction pipeline. We implement a change-point analysis to objectively identify transitions in these proportions. Our method both delimitates strata and infers whether their evolutionary history is shared or convergent between species. We illustrate and test this method on Silene and Artemia species. Our new method is reliable and robust, globally confirming previous findings known for some of these species. The method is also sensitive, refining those previous findings and identifying regions that were not previously reported. We finally illustrate how this approach can inform scenarios that retrace the history of sex chromosomes in these species. Overall, this approach presents a tool that can be widely used and that complement existing methods to study sex chromosomes.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"43 10","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13673985/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207263","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

Multiscale structural evolution of proline-rich protein genes shapes primate salivary defenses. 富含脯氨酸的蛋白质基因的多尺度结构进化塑造了灵长类动物的唾液防御。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag224

William D Aguado, Charikleia Karageorgiou, Sarah Kassem, Raquel Hernández Rojas, Carrie C Veilleux, Amanda D Melin, Erin R Vogel, Stefan Ruhl, Omer Gokcumen, Petar Pajic

{"title":"Multiscale structural evolution of proline-rich protein genes shapes primate salivary defenses.","authors":"William D Aguado, Charikleia Karageorgiou, Sarah Kassem, Raquel Hernández Rojas, Carrie C Veilleux, Amanda D Melin, Erin R Vogel, Stefan Ruhl, Omer Gokcumen, Petar Pajic","doi":"10.1093/molbev/msag224","DOIUrl":"10.1093/molbev/msag224","url":null,"abstract":"Saliva forms the first biochemical interface with the environment, mediating dietary exposure and oral defense. Proline-rich proteins in saliva protect plant-eating mammals from the harmful effects of consuming tannins. Yet the evolution of the genes encoding these proteins remains poorly resolved. Here, integrating long-read genome assemblies with comparative genomics, phylogenetics, transcriptomics, and dietary data, we investigate the salivary proline-rich protein gene family across 27 primate species to test whether dietary ecology has shaped the evolution of this locus. We find that the proline-rich protein locus is dynamic, shaped by recurrent lineage-specific gene duplications and inversions. Despite pervasive structural variation, proline-rich protein genes consistently rank among the top five most highly expressed transcripts in nonhuman primate parotid glands, indicating constraint on maintaining high expression in saliva. Humans retain abundant proline-rich protein expression, but at reduced levels relative to other primates, potentially reflecting a lineage-specific regulatory shift. We further identify widespread exonic tandem repeats that provide a flexible mechanism for modulating protein composition. Notably, colobine PRH genes independently evolved trinucleotide repeats encoding histidine-rich peptides, coinciding with folivory and suggesting a lineage-specific adaptation. Together, our results position proline-rich proteins as a model for understanding how large-scale structural rearrangements and fine-scale repeat expansions jointly shape the diversity and evolution of proteins in saliva.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148865745","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

Ancient nuclear genome duplication events in vertebrates facilitated the functional diversification of ohnologous cytochrome c: insights from Buergeria frogs. 脊椎动物古老的核基因组重复事件促进了同源细胞色素c的功能多样化：来自布氏蛙的见解。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag243

Yuka Asaeda, Sotaro Fujii, Hajime Ogino, Michael A Hough, Takeshi Igawa, Yoshihiro Sambongi

{"title":"Ancient nuclear genome duplication events in vertebrates facilitated the functional diversification of ohnologous cytochrome c: insights from Buergeria frogs.","authors":"Yuka Asaeda, Sotaro Fujii, Hajime Ogino, Michael A Hough, Takeshi Igawa, Yoshihiro Sambongi","doi":"10.1093/molbev/msag243","DOIUrl":"10.1093/molbev/msag243","url":null,"abstract":"In vertebrates, a nuclear gene encoding mitochondrial cytochrome c (CYC) was duplicated and diverged into one with ubiquitous expression (somatic-type) and the other with testis-preferred expression (testis-type). In this study, synteny-based phylogenetic analyses suggest that cyc ohnologs originated through whole-genome duplication events in the common ancestor of vertebrates and have been conserved for approximately 450 to 540 million years. Molecular evolutionary analyses revealed pervasive purifying selection and an approximate Phe/Tyr dichotomy at position 46 between somatic- and testis-type CYC proteins. This was the case in 2 closely related amphibians, Buergeria buergeri and its hot-spring-dwelling species, Buergeria japonica. The recombinant testis-type CYC proteins from B. buergeri (Bb-CYCT) and B. japonica (Bj-CYCT) exhibited significantly higher resistance to hydrogen peroxide (H2O2) than somatic-type counterpart proteins (Bb-CYCS and Bj-CYCS). Structural analysis showed that the Tyr-46 residues in the testis-type CYC proteins face the heme, suggesting a protective role against H2O2 through oxidation of its hydroxyl group compared to the spatially corresponding Phe-46 residue in the somatic-type counterparts. When the Tyr-46 residue in Bj-CYCT was replaced with the Phe residue, the H2O2 resistance was significantly reduced, confirming the functional importance of Tyr-46. These results demonstrate that functional divergence between somatic- and testis-type Buergeria CYC proteins is at least partly attributable to the Phe-to-Tyr substitution, suggesting that ancient nuclear genome duplication contributed to tissue-specific divergence of mitochondrial function.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13655612/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149040055","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

Widespread male-female expression imbalance of X-linked genes across phrynosomatid lizards. 横毛蜥中广泛存在的x连锁基因的雌雄表达不平衡。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag232

Matthew D Hale, Pietro L H de Mello, Daniel T Nondorf, Christopher D Robinson, Henry B John-Alder, Christian L Cox, Robert M Cox

{"title":"Widespread male-female expression imbalance of X-linked genes across phrynosomatid lizards.","authors":"Matthew D Hale, Pietro L H de Mello, Daniel T Nondorf, Christopher D Robinson, Henry B John-Alder, Christian L Cox, Robert M Cox","doi":"10.1093/molbev/msag232","DOIUrl":"10.1093/molbev/msag232","url":null,"abstract":"Classic theory on sex chromosome evolution predicts that selection should restore ancestral diploid expression for hemizygous X-linked genes in males. However, this dosage compensation is often incomplete, leaving the X chromosome enriched for genes with female-biased expression. In this context, iguanian lizards are noteworthy among vertebrates because several species from separate families appear to exhibit both near-complete dosage compensation and male-female expression balance across their ancient, homologous X chromosomes. We tested for similar expression balance in a phrynosomatid iguanian, Sceloporus undulatus (Eastern Fence Lizard), and instead found that both ancient and more recently sex-linked regions of the X chromosome are enriched for genes with female-biased expression, regardless of age (neonate, maturing, adult) or tissue (brain, liver, muscle). By expanding our analysis across ten phrynosomatid species spanning four genera, we found that male-female expression imbalance on the ancestral region of X is phylogenetically conserved in this family. We also found that an inferred chromosomal rearrangement in Sceloporus jarrovii has resulted in the evolution of female-biased expression by a formerly autosomal region. Whereas sex-biased expression of the ancestral region of X is primarily due to females overexpressing X-linked genes relative to autosomal genes, sex-biased expression of these formerly autosomal genes in S. jarrovii is primarily due to males underexpressing genes in this putative neo-X region. We conclude that male-female expression imbalance on X is widespread across phrynosomatids, potentially reflecting both overexpression in females for ancestral regions that have evolved dosage compensation and underexpression in males for neo-X regions in which dosage compensation has yet to evolve.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13642048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148912942","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

kamino: fast proteome-wide variant calling for amino acid phylogenomics. 卡米诺：需要氨基酸系统基因组学的快速蛋白质组变异。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag250

Romain Derelle, John Lees, Leonid Chindelevitch

{"title":"kamino: fast proteome-wide variant calling for amino acid phylogenomics.","authors":"Romain Derelle, John Lees, Leonid Chindelevitch","doi":"10.1093/molbev/msag250","DOIUrl":"10.1093/molbev/msag250","url":null,"abstract":"Amino acid-based phylogenetics usually relies on first clustering and aligning orthologous proteins. This approach is powerful but computationally demanding. Here, we present kamino, a reference- and alignment-free method that rapidly builds amino acid phylogenomic alignments directly from proteomes. As with similar algorithms, homologous regions are identified through shared sequences flanking variable regions. The method uses local changes in recoded k-mer occupancy to efficiently identify variable positions within these homologous regions and extract the corresponding pseudo-aligned sequences. It generates phylogenetically informative alignments across diverse prokaryotic and eukaryotic datasets. Phylogenetic analyses show that it accurately recovers Mycobacterium tuberculosis lineages, most curated GTDB taxa, and relationships consistent with published Drosophila and mammalian phylogenies, while producing signals broadly similar to BUSCO-based approaches. Runtimes are comparable to genome-based alignment-free methods and several orders of magnitude faster than classical marker-based pipelines, with moderate memory requirements. The method performs well across a broad range of divergence levels, from within-species comparisons to family-level prokaryotic and phylum-level eukaryotic datasets. kamino therefore provides a fast and simple route from proteomes to phylogenomic alignments across a broad range of evolutionary scales. The program is implemented in Rust and freely available at https://github.com/rderelle/kamino.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13650691/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069781","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