Genome Biology and Evolution最新文献_第4页

The Gender and Geographic Location of Authors Impact Citation Rates of GBE Papers. 作者的性别和地理位置影响GBE论文的被引率。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-01 DOI: 10.1093/gbe/evag090

David Alvarez-Ponce

引用次数: 0

Editorial 2026. 2026年社论。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-01 DOI: 10.1093/gbe/evag091

Maud I Tenaillon, Laura A Katz

引用次数: 0

Haplotype-Resolved Genome of the Critically Endangered, Paleo-endemic Tree, Eidothea hardeniana. 极度濒危的古特有树硬叶杉的单倍型解析基因组。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-01 DOI: 10.1093/gbe/evag071

Abhishek Soni, Agnelo Furtado, Maurizio Rossetto, Robert J Henry

{"title":"Haplotype-Resolved Genome of the Critically Endangered, Paleo-endemic Tree, Eidothea hardeniana.","authors":"Abhishek Soni, Agnelo Furtado, Maurizio Rossetto, Robert J Henry","doi":"10.1093/gbe/evag071","DOIUrl":"10.1093/gbe/evag071","url":null,"abstract":"A fully phased, chromosome-level reference genome assembly for an IUCN-declared critically endangered and paleo-endemic tree, Eidothea hardeniana (Nightcap Oak) was assembled de novo using long-read PacBio HiFi, Oxford Nanopore (ONT) and Hi-C sequencing technologies. Consensus assembly represented high contiguity (N50 ∼ 49 Mb), (BUSCO 99.2%), assembly size in accordance with flow cytometry derived genome size estimate, and the presence of telomeric and centromeric repeats on pseudochromosomes. Haplotype 1 (598 Mb) achieved an N50 of 45.8 Mb and 99.1% BUSCO completeness, while Haplotype 2 (596 Mb) showed similar quality (N50: 47.3 Mb; BUSCO: 98.4%). Repeat content comprised approximately 54% of the genome. Gene annotation confirmed approximately 30120 protein coding genes with BUSCO completeness of 99.5%. Comparative orthology with other assembled Proteaceae genomes identified ∼13,000 shared ortholog clusters and 227 Eidothea-specific orthologs clusters. Heterozygosity in E. hardeniana was estimated at 1.17 SNVs per kilobase (0.12%), which is approximately one-third of the level reported for the other sequenced critically endangered Proteaceae species, Macadamia jansenii. This genome represents the first assembled genome from the Australian lineage of the Proteoideae subfamily within Proteaceae. As a high-quality reference for conservation genomics, it provides a foundation for SNP genotyping, population structure analyses, and the development of informed genetic rescue strategies for E. hardeniana and related species.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13080361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147480518","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

Identifying Adaptive Footprints in the Presence of Demographic Uncertainty. 在人口不确定性存在的情况下识别适应性足迹。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-01 DOI: 10.1093/gbe/evag075

Sandipan Paul Arnab, Mohammad Khan, Andre Luiz Campelo Dos Santos, Matteo Fumagalli, Michael DeGiorgio

{"title":"Identifying Adaptive Footprints in the Presence of Demographic Uncertainty.","authors":"Sandipan Paul Arnab, Mohammad Khan, Andre Luiz Campelo Dos Santos, Matteo Fumagalli, Michael DeGiorgio","doi":"10.1093/gbe/evag075","DOIUrl":"10.1093/gbe/evag075","url":null,"abstract":"Identifying genomic regions shaped by natural selection is a central goal in evolutionary genomics. Existing machine learning methods for this task are typically trained on labeled data simulated according to specific evolutionary scenarios. While effective in controlled settings, these models are limited by their reliance on explicit class labels, detecting only the processes they were trained to recognize. This limitation makes it difficult to interpret predictions for regions shaped by other evolutionary forces, a problem especially acute when analyzing genomes influenced by mixtures of adaptive and demographic factors. One-vs-rest strategies offer a potential alternative but suffer from the complexity of modeling processes as a catch-all \"rest\" class. Here, we explore positive-unlabeled learning as a flexible framework for detecting adaptive events. This semi-supervised approach permits identification of a target class using only positive labels and an unlabeled background, without requiring explicit modeling of negatives. To assess its utility, we focus on a binary classification setting for detecting selective sweeps against a mixed background of unlabeled sweeps and neutrally evolving regions. We introduce PULSe, a method that trains only on labeled sweep observations while treating remaining data as unlabeled. By avoiding assumptions about background composition, PULSe enables robust sweep discovery in realistic genomic landscapes. We evaluate performance across demographic, adaptive, and confounding contexts, including domain shift from misspecified models, and find that PULSe delivers strong generalizability. Finally, analyzing European and Bengali genomes, we recapitulate known sweep candidates, demonstrating PULSe as a versatile tool for detecting adaptive regions across diverse genomic landscapes.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13049369/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147503644","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

Complex Patterns of Hitchhiking Mutation Load Among Stickleback Populations. 棘鱼种群搭便车突变负荷的复杂模式。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-01 DOI: 10.1093/gbe/evag088

Jana Nickel, Jan Laine, Andrew D Foote

{"title":"Complex Patterns of Hitchhiking Mutation Load Among Stickleback Populations.","authors":"Jana Nickel, Jan Laine, Andrew D Foote","doi":"10.1093/gbe/evag088","DOIUrl":"10.1093/gbe/evag088","url":null,"abstract":"Positive selection causes beneficial alleles to rise to high frequency in a population. This can cause linked genetic variation to \"hitchhike,\" and thereby also rise in frequency. This linked variation may include deleterious recessive alleles, previously neutrally harbored at low frequency and in heterozygous genotypes. Modeling studies have shown that local effective population size and reduced recombination rate should contribute to the probability of deleterious mutations being swept to high frequency by being linked to beneficial alleles in selective sweeps or selection on inversion karyotypes. Marine sticklebacks have repeatedly adapted to thousands of freshwater habitats that became available after the last ice age, resulting in the formation of distinct marine and freshwater ecotypes. Selection acts on ancient standing genetic variation present in marine populations, causing freshwater-adaptive alleles to increase rapidly over tens of generations. These genomic regions play a key role in the repeated freshwater adaptation of morphological, physiological, and behavioral traits, and evolve under strong selection. Thus, threespine stickleback is an ideal system for investigating the impact of hitchhiking mutation load. We estimate the mutation load in regions of low recombination, including inversions and the Eda haplotype. We find some evidence for increased accumulation of deleterious alleles in one inversion, while this is not the case for two other inversions. Inversions deviated from Hardy-Weinberg equilibrium in several populations due to an excess of homozygotes.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13081801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147616034","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

Genome Scans Reveal Species-Specific Selection in the Genus Lynx. 基因组扫描揭示了猞猁属的物种特异性选择。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-01 DOI: 10.1093/gbe/evag086

Lorena Lorenzo-Fernández, Enrico Bazzicalupo, Erin L Koen, Jan E Janecka, William J Murphy, Krzysztof Schmidt, José A Godoy

{"title":"Genome Scans Reveal Species-Specific Selection in the Genus Lynx.","authors":"Lorena Lorenzo-Fernández, Enrico Bazzicalupo, Erin L Koen, Jan E Janecka, William J Murphy, Krzysztof Schmidt, José A Godoy","doi":"10.1093/gbe/evag086","DOIUrl":"10.1093/gbe/evag086","url":null,"abstract":"Understanding the genetic basis of adaptation is essential for reconstructing evolutionary processes, and this can be accomplished particularly by studying closely related species occupying diverse ecological niches. In this study, we performed genome-wide scans for recent selective sweeps in the four extant species of the Lynx genus-Lynx canadensis (Canada lynx), Lynx rufus (bobcat), Lynx lynx (Eurasian lynx), and Lynx pardinus (Iberian lynx)-using a composite likelihood ratio test based on genotype frequency spectrum. Analyzing whole-genome sequences from 80 individuals, we identified species-specific selective sweeps and conducted functional enrichment analyses to explore biological processes under selection. Results revealed distinct adaptive mechanisms shaped by ecological specialization and demographic histories of different species. In Canada lynx, enriched functions include olfactory signaling and pigmentation-related processes; the Eurasian lynx showed signals related to cardiac and neural development; the Iberian lynx exhibited enrichment in immune-related pathways, potentially reflecting pathogen-mediated selection under strong genetic drift; and the bobcat displayed functional signals in reproductive and metabolic regulation. Our study revealed the species-specific nature of recent signatures of ecological differentiation in the genomes of closely related species of the genus Lynx, with minimal overlap, illustrating their diverse evolutionary trajectories and shedding light into the mechanism of adaptation among highly specialized carnivores.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13092354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147689535","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

Snakes (Colubridae: Erythrolamprus) With a Complex Toxic Diet Show Convergent yet Highly Heterogeneous Voltage-gated Sodium Channel Evolution. 具有复杂毒性饮食的蛇（蛇科：赤蛇科）表现出收敛但高度异质的电压门控钠通道进化。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-01 DOI: 10.1093/gbe/evag092

Valeria Ramírez-Castañeda, Rebecca D Tarvin, Roberto Márquez

{"title":"Snakes (Colubridae: Erythrolamprus) With a Complex Toxic Diet Show Convergent yet Highly Heterogeneous Voltage-gated Sodium Channel Evolution.","authors":"Valeria Ramírez-Castañeda, Rebecca D Tarvin, Roberto Márquez","doi":"10.1093/gbe/evag092","DOIUrl":"10.1093/gbe/evag092","url":null,"abstract":"Chemical defense has evolved convergently across multiple lineages and plays a crucial role in shaping ecological communities through selection for toxin resistance. Research on toxin resistance has been pivotal in understanding the genetic basis of trait evolution, as resistance can evolve through mutations in a few target genes, resulting in target-site resistance (TSR). However, in tropical ecosystems, multiple selective pressures from prey with different toxins create complex chemical scenarios for predators that require multiple resistance mechanisms. Royal ground snakes (Erythrolamprus spp.) are significant but understudied predators of poisonous frogs (families Bufonidae and Dendrobatidae), whose toxins affect voltage-gated sodium channels (VGSCs) and other neuromuscular system proteins. In this study, we investigated the evolution of TSR in VGSC genes in relation to toxic frog predation in Erythrolamprus snakes, tracing the phylogenetic origin and geographic distribution of TSR-conferring genotypes across six species in this group. Our findings reveal convergent yet highly heterogeneous TSR evolution in at least two species that evolved to predate poisonous frogs, and possibly in a third one. Amino acid changes at nine resistance-related positions across eight VGSC genes were identified, suggesting a shared evolutionary path across this gene family. Four of these changes are known to provide tetrodotoxin resistance in other animals. We observed polymorphism in resistance-related sites across species and VGSC paralogs, hinting at a complex evolutionary history of alleles at these loci. These findings offer new insights into adaptive mechanisms in predators with complex toxic diets and introduce Erythrolamprus as a model to understand variation in toxin resistance mechanisms.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147672553","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: Before the East African radiation: sex chromosome systems in basal haplotilapiine cichlids. 校正：东非辐射前：基类单罗非鱼的性染色体系统。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-01 DOI: 10.1093/gbe/evag076

引用次数: 0

Dynamics of Expression Variability Contribute to Retention of Small-Scale vs. Whole-Genome Duplicates. 表达变异性的动态有助于保留小规模与全基因组重复。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-01 DOI: 10.1093/gbe/evag077

Haoran Cai, David L Des Marais

引用次数: 0

Patterns of Conservation and Loss of Hox Genes in Xenacoelomorph Lineage Since Divergence From Last Common Bilaterian Ancestor. 自最后一个共同的双边祖先分化以来，异种形态谱系中Hox基因的保存和丢失模式。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-01 DOI: 10.1093/gbe/evag094

Ariane Buckenmeyer, Samuel Abalde, Joseph F Ryan, Ulf Jondelius

{"title":"Patterns of Conservation and Loss of Hox Genes in Xenacoelomorph Lineage Since Divergence From Last Common Bilaterian Ancestor.","authors":"Ariane Buckenmeyer, Samuel Abalde, Joseph F Ryan, Ulf Jondelius","doi":"10.1093/gbe/evag094","DOIUrl":"10.1093/gbe/evag094","url":null,"abstract":"The explosion of body forms found in bilaterians is thought to be tied to the diversification of Hox transcription factors, which play a critical role in development along the anterior-posterior axis for most bilaterians. However, the evolutionary history of Hox genes in Bilateria's early branches remains unclear. Xenacoelomorpha, a clade of marine worms including Xenoturbella and the acoelomorphs Acoela and Nemertodermatida, have a simple Hox complement and are a particular group of interest. Past surveys of Hox in Xenacoelomorpha have been taxonomically limited. To address this, we analyze the homeodomains and surrounding amino acid motifs coded by Hox, ParaHox, and extended Hox genes across 40 xenacoelomorph transcriptomes and four genomes, along with representatives of other major bilaterian groups and the anthozoan Nematostella vectensis. We show that several motif annotations previously proposed to be synapomorphies of Acoela are ubiquitous across both Xenacoelomorpha and the rest of Bilateria and found new Hox content specific to Acoela and Xenoturbella. Our results reveal homology between xenacoelomorph antHox and other bilaterian Hox1 genes, though the relationships of centHox and postHox genes remain unresolved either due to rapid sequence evolution or extensive birth-death processes. Our analyses suggest that diversification of bilaterian Hox involved both extensive retention and loss of ancestral content. Hox variability between xenacoelomorphs and other bilaterians reflects selective retention of ancestral Hox content rather than affinity to either deuterostomes or protostomes and does not remove support from a monophyletic Xenacoelomorpha sister group to all other Bilateria.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147672542","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