Genome Biology and Evolution最新文献_第2页

Genomic evidence for facultative selfing in the cichlid fish Cyphotilapia frontosa. 紫鳉鱼兼性自交的基因组证据。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-03 DOI: 10.1093/gbe/evag246

M Efe Uysal, Daniela Souza-Costa, Allison Marks, Adrian Indermaur, Wolfgang Gessl, Walter Salzburger, Julia M I Barth

{"title":"Genomic evidence for facultative selfing in the cichlid fish Cyphotilapia frontosa.","authors":"M Efe Uysal, Daniela Souza-Costa, Allison Marks, Adrian Indermaur, Wolfgang Gessl, Walter Salzburger, Julia M I Barth","doi":"10.1093/gbe/evag246","DOIUrl":"https://doi.org/10.1093/gbe/evag246","url":null,"abstract":"Organisms have evolved a remarkable diversity of reproductive strategies in response to environmental variations and selective pressures. Although most vertebrates do reproduce biparentally, rare alternative modes such as selfing (self-fertilization) and different forms of parthenogenesis exist, but remain poorly characterized. Here, we investigated an unusual reproductive event in the normally biparental cichlid fish Cyphotilapia frontosa, in which a female produced offspring in the absence of a male. Using whole-genome sequencing data, we analyzed whether reproduction occurred via selfing or parthenogenesis by comparing patterns of heterozygosity with those from a wild, genetically diverse C. frontosa family collected in Lake Tanganyika and a closely related inbred Ctenochromis benthicola family. The uniparental family exhibited reduced genetic diversity, elevated relatedness, and genome-wide patterns of homozygosity distinct from those expected under parthenogenesis or inbreeding, but consistent with self-fertilization. Our study provides rare genomic evidence of selfing in a vertebrate and suggests that such alternative reproductive modes may be overlooked rather than truly absent. These findings contribute to a broader understanding of how alternative reproductive strategies evolve in vertebrate lineages.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149108507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Genome Evolution in Social Insects. 社会性昆虫的基因组进化。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag221

Megan Barkdull, Corrie S Moreau

引用次数: 0

A Selective Sweep Likely Linked to Xenobiotic Detoxification Identified Along Altitudinal Gradients in the Pine Processionary Moth. 在松木行军蛾中，沿海拔梯度确定了可能与外源性解毒有关的选择性清除。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag239

Pierre Nouhaud, Mathieu Gautier, Alexandre Schifano, Laure Sauné, Carole Kerdelhué, Charles Perrier

{"title":"A Selective Sweep Likely Linked to Xenobiotic Detoxification Identified Along Altitudinal Gradients in the Pine Processionary Moth.","authors":"Pierre Nouhaud, Mathieu Gautier, Alexandre Schifano, Laure Sauné, Carole Kerdelhué, Charles Perrier","doi":"10.1093/gbe/evag239","DOIUrl":"10.1093/gbe/evag239","url":null,"abstract":"Understanding how natural populations adapt to complex environmental gradients is crucial for predicting evolutionary responses to global change. The pine processionary moth (Thaumetopoea pityocampa), a major forest pest expanding northward and upward in Europe, provides an ideal model to explore genomic adaptation along altitudinal and/or latitudinal gradients. We combined pooled and individual whole-genome resequencing of four pairs of low- and high-elevation populations from Spain, Italy, and France (mainland and Corsica) to detect signatures of local adaptation. Population structure analyses revealed strong differentiation among distant populations but limited divergence within altitude pairs. Genome scans identified a few candidate regions under selection, and we notably uncovered a large (∼1 Mbp) region showing reduced nucleotide diversity, negative Tajima's D, and fixed allele differences between high- and low-altitude populations, consistent with a recent selective sweep. This region includes a cluster of cytochrome P450 genes and the voltage-gated sodium channel gene para, both involved in detoxification and insecticide resistance. Although signatures of selection were observed at this locus in two distant population pairs, no definitive evidence of recent introgression was found between these distant populations, suggesting independent evolution. Altogether, our results do not show clear evidence for altitudinal adaptation in T. pityocampa but suggest that xenobiotic exposure could exert a strong selective pressure locally. Our study highlights candidate genes and regions for further investigation of resistance evolution in an insect species in the wild.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Active and Unusually Expanded PIF/Harbinger Transposable Elements in the Caenorhabditis inopinata Genome. 隐杆线虫基因组中活性的和异常扩增的PIF/Harbinger转座因子。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag240

Kazuki Sato, Xiaodan Jin, Shun Oomura, Kazuma Kawahara, Simo Sun, Akemi Yoshida, Nami Haruta, Asako Sugimoto, Taisei Kikuchi

{"title":"Active and Unusually Expanded PIF/Harbinger Transposable Elements in the Caenorhabditis inopinata Genome.","authors":"Kazuki Sato, Xiaodan Jin, Shun Oomura, Kazuma Kawahara, Simo Sun, Akemi Yoshida, Nami Haruta, Asako Sugimoto, Taisei Kikuchi","doi":"10.1093/gbe/evag240","DOIUrl":"10.1093/gbe/evag240","url":null,"abstract":"Understanding how transposable elements (TEs) transition from rapid amplification to functional decay is fundamental to unraveling the mechanisms of genome evolution and structural variation. How TE families evolve following expansion, specifically why distinct descendant lineages retain or lose mobilization competence, remains poorly understood. The PIF/Harbinger superfamily, whose canonical elements encode two distinct proteins required for mobilization-a DDE transposase and a MADF DNA-binding protein-provides a compelling model to address this question. In Caenorhabditis inopinata, the closest known relative of C. elegans, we identified a spontaneous dumpy mutant caused by insertion of a PIF/Harbinger element into the Cin-dpy-11 coding region. The inserted element, designated Harbinger-1M_cIno and belonging to the C. elegans Turmoil2 lineage, retains a MADF domain but lacks a recognizable DDE transposase open reading frame. Genome-wide curation recovered 258 related copies, revealing a strongly asymmetric family structure: noncoding and MADF-bearing derivatives expanded, whereas only a single locus retained an intact DDE gene. This demonstrates a novel functional partitioning where catalytic (DDE) and DNA-binding (MADF) roles are physically separated across distinct elements and supplied in trans. A second family, Harbinger-2M_cIno (1,376 copies), lacks a DDE source entirely and exhibits greater sequence divergence and terminal degradation. Together, these findings reveal that PIF/Harbinger lineages in C. inopinata differ in their timing of expansion and mobilization competence, illustrating how bipartite TEs maintain activity through functional division while limiting host toxicity.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13668399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149074484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 High-Quality Genome Assembly of Johnsongrass Illuminates Relationships Between Polyploidization, Crop-Wild Hybridization, and Reproductive Biology. 高质量的约翰逊草基因组组装草图阐明了多倍体化、作物-野生杂交和生殖生物学之间的关系。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag230

Melinda K Yerka, Julia N Wright, David Alvarez-Ponce, Deepti Nigam, Amit Jhala, John Lindquist, Juli Petereit, Hans Vasquez-Gross, Yinping Jiao

{"title":"A High-Quality Genome Assembly of Johnsongrass Illuminates Relationships Between Polyploidization, Crop-Wild Hybridization, and Reproductive Biology.","authors":"Melinda K Yerka, Julia N Wright, David Alvarez-Ponce, Deepti Nigam, Amit Jhala, John Lindquist, Juli Petereit, Hans Vasquez-Gross, Yinping Jiao","doi":"10.1093/gbe/evag230","DOIUrl":"10.1093/gbe/evag230","url":null,"abstract":"Johnsongrass [Sorghum halepense (L.) Pers.] is an allopolyploid, rhizomatous, perennial grass species and one of the most troublesome weeds in global agriculture. We assembled the first Johnsongrass genome to clarify poorly understood genetic factors influencing variable rates of crop-wild hybridization with cultivated sorghum [S. bicolor (L.) Moench]. The draft genome assembly has a total size of 3.26 Gb and BUSCO completeness of 95.3%. We also report the first evolutionary analysis of INHIBITION OF ALIEN POLLEN (IAP), the only known cross-(in)compatibility locus in the genus. Our results reveal an evolutionary history of genome instability, including the loss of distinct parental subgenomes, and suggest that Nebraska accession \"J-37,\" the genome donor, is a segmental allotetraploid that may function as a diploid or aneuploid during meiosis. Genome instability could explain observations of variable ploidies in Johnsongrass and facilitate ongoing hybridization with sorghum where gamete ploidies and IAP alleles match. Given this information, we provide a suggested research framework for studying evolution and gene expression in the Sorghum genus where crop-wild hybridization occurs and for predicting the potential for hybridization between specific crossing partners. Collectively, this work will bolster efforts to study and manage reproductive biology in other crop-wild polyploid complexes.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13629665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148982360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

The genomic basis of adaptation to profundal habitats across the Swiss Alpine whitefish radiation. 适应瑞士高山白鱼辐射的深层栖息地的基因组基础。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag242

David Frei, Ole Seehausen, Philine G D Feulner

{"title":"The genomic basis of adaptation to profundal habitats across the Swiss Alpine whitefish radiation.","authors":"David Frei, Ole Seehausen, Philine G D Feulner","doi":"10.1093/gbe/evag242","DOIUrl":"https://doi.org/10.1093/gbe/evag242","url":null,"abstract":"When populations experience heterogenous environments multifarious divergent selection may lead to ecological speciation or even adaptive radiation. The underlying genetic architecture of adaptation can be simple or complex and is relevant for predicting evolutionary responses. Whitefish have radiated across Swiss perialpine lakes and within the radiation, more than 30 species have been taxonomically described. Across Swiss lake systems, several phenotypically similar species (i.e, ecomorphs) have evolved independently and utilise distinct environmental niches. Profundal species, adapted to spawn in depths below 60m, have repeatedly evolved in lakes Thun, Constance, Lucerne, Zug, and Walen. We here analysed whole-genome resequencing data of all three to six whitefish species of four of these lakes (Thun, Constance, Lucerne, and Walen) to identify genomic signals of parallel profundal adaptation. The results indicate that a small but spread-out fraction of the genome shows signals of parallel differentiation across all four studied lakes, with pairwise tests revealing more genomic regions with evidence of parallel evolution between profundal species when both were pelagic. Consistent with previous work investigating parallel divergence between two different Alpine whitefish ecomorphs, these results suggest a polygenic basis of adaptation including genotypic redundancy, which makes repeated evolution more likely but results in little repeatability of its genetic basis.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149108653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Synthetic Approaches as Empirical Tools for Testing Evolutionary Theory. 综合方法作为检验进化论的经验工具。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag245

Xueying C Li, Paco Majic, Cauã Antunes Westmann

{"title":"Synthetic Approaches as Empirical Tools for Testing Evolutionary Theory.","authors":"Xueying C Li, Paco Majic, Cauã Antunes Westmann","doi":"10.1093/gbe/evag245","DOIUrl":"10.1093/gbe/evag245","url":null,"abstract":"Evolutionary biology has traditionally inferred process from patterns in extant organisms and the fossil record, leaving many foundational questions constrained by their historical nature. Over the past two decades, a growing family of synthetic approaches-high-throughput mapping such as deep mutational scanning, reconstructive experiments such as ancestral sequence reconstruction, controlled evolution, and synthetic biology in the narrower sense-have made it possible to test these questions directly by systematically exploring sequence space, reconstructing historical states, replaying evolution under defined conditions, and engineering biological systems. Here, we review how these approaches reshape several foundational questions: the distribution of mutational effects, the structure and navigability of fitness landscapes, the evolution of evolvability, developmental constraint, historical contingency, and the engineering of evolutionary systems. Across these domains, these experiments are exposing unexpected mechanistic detail that refines and extends classical theory-revealing, for example, how strongly mutational effects depend on environmental and genetic context, how ruggedness can coexist with broad accessibility on fitness landscapes, how genotype-phenotype maps are intrinsically biased and heterogeneous, and how random sequences carry latent functional potential that may serve as raw material for later innovation. As these technologies continue to expand the empirical reach of evolutionary biology, theory in turn sharpens the questions they are best suited to address-an iterative dialogue between experiment and theory that brings us closer to understanding how life evolves.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13669622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149108704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Lateralized Gene Splicing in the Brain is Associated With Lateralized Feeding Behavior in an Asymmetrical Scale-eating Cichlid Fish. 脑侧化基因剪接与不对称食鳞鱼侧化摄食行为有关。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag237

Xiaomeng Tian, Axel Meyer

{"title":"Lateralized Gene Splicing in the Brain is Associated With Lateralized Feeding Behavior in an Asymmetrical Scale-eating Cichlid Fish.","authors":"Xiaomeng Tian, Axel Meyer","doi":"10.1093/gbe/evag237","DOIUrl":"10.1093/gbe/evag237","url":null,"abstract":"Lateralized behavior (\"handedness\") is a trait observed across all vertebrates, including humans. As an adaptive trait involved in both intraspecific and interspecific interactions, it holds broad evolutionary significance. However, the molecular basis of its brain regulation-particularly post-transcriptional regulation-remains poorly understood. Perissodus microlepis, a textbook example in evolutionary biology and an endemic scale-eating cichlid fish from Lake Tanganyika, displays pronounced lateralized feeding behavior that is complemented by its asymmetric head, by which it bites the scales preferentially from only one side or the other side of its prey. Based on data from two previous studies, we investigated the patterns of alternative splicing-an important yet understudied regulatory mechanism-across multiple brain regions in both resting and predatory states of L-eft or the R-ight morphs of this species. We found that the telencephalon, the cognitive center of the vertebrate brain, shows enrichment in functions related to microtubule and neural development in both states. Compared to the resting state, brain regions in the predatory state exhibited more consistent functional profiles, exhibiting pronounced enrichment in the nervous system. We identified several genes whose proportion of alternatively spliced transcripts was strongly correlated with behavioral laterality, establishing a potentially causal link between alternative splicing and handedness. Our findings underscore the significant role of alternative splicing in important adaptive traits, such as lateralized behavior and present a set of candidate genes for further investigation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"18 10","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13646608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149136302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Comparative Genomics Reveals Signatures of Distinct Metabolic Strategies and Gene Loss Associated With Hydra Immortality. 比较基因组学揭示了与九头蛇不朽相关的不同代谢策略和基因丢失的特征。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag218

Kaoruko Nojiri, Koryu Kin, Akimasa Someya, Tetsuo Kon, Koto Kon-Nanjo, Hiroshi Shimizu, Kazuharu Arakawa, Etsuo A Susaki

{"title":"Comparative Genomics Reveals Signatures of Distinct Metabolic Strategies and Gene Loss Associated With Hydra Immortality.","authors":"Kaoruko Nojiri, Koryu Kin, Akimasa Someya, Tetsuo Kon, Koto Kon-Nanjo, Hiroshi Shimizu, Kazuharu Arakawa, Etsuo A Susaki","doi":"10.1093/gbe/evag218","DOIUrl":"10.1093/gbe/evag218","url":null,"abstract":"Hydra is a freshwater cnidarian genus that provides a unique comparative model for aging research, contrasting the immortal Hydra vulgaris with the aging-inducible Hydra oligactis. Here, we report a high-quality, chromosome-level genome assembly of H. vulgaris strain AEP.JNIG. Our assembly is comparable in quality to existing resources, facilitating the analysis of genomic diversity across laboratory strains. Epigenomic profiling revealed that gene-body hypermethylation correlates with transcriptional stability and the suppression of spurious transcription in evolutionary conserved genes, suggesting an epigenetic mechanism for genomic integrity. Furthermore, comparative genomics demonstrated that while Hydra conserves fundamental pathways associated with major biological processes implicated in aging, the immortal H. vulgaris paradoxically lacks canonical anti-aging genes (eg Klotho, nicotinamide phosphoribosyltransferase) found in the aging-inducible H. oligactis. Instead, H. vulgaris exhibits a distinct metabolic signature related to mitochondrial energy production and nucleoside triphosphate biosynthesis. Collectively, our comparative genomics results suggest multiple potential mechanisms associated with the H. vulgaris immortality and the aging traits of H. oligactis, providing novel targets for future functional studies.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13629666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148818306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Correction to: Signals of Ancestry-Specific Selection in Gentle Africanized Honey Bees. 修正：温和非洲化蜜蜂的祖先特异性选择信号。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag250

引用次数: 0