Genome Biology and Evolution最新文献

{"title":"Optimal Organelle Inheritance Strategies Under Different Changing Environments and Mutational Pressures.","authors":"Belén García-Pascual, Jan M Nordbotten, Iain G Johnston","doi":"10.1093/gbe/evag161","DOIUrl":"10.1093/gbe/evag161","url":null,"abstract":"<p><p>Mitochondrial and chloroplast DNA encode essential cellular apparatus. This organelle DNA exists at high copy number (ploidy) in eukaryotic cells, which must both mitigate mutational damage and allow adaptation to changing demands. Across eukaryotes, organelle DNA is inherited and maintained by different classes of processes. Inheritance is often maternal, but some species use paternal or doubly uniparental (sex-dependent) inheritance, with different extents of \"leakage\" of organelle DNA from the non-primary parent. During development, genetic bottlenecks of different magnitudes and recombination-mediated repair are employed in different species. Here, we use modeling and simulation to investigate the fitness advantages, disadvantages, conflicts, and tradeoffs of these different strategies under different challenges of mutation and changes in selection imposed by the environment (in the absence of interactions with nuclear genes). We find a general tradeoff between maintaining heteroplasmy to support adaptation to environmental change and supporting purifying selection against dysfunctional mutants. Different combinations of leakage and bottleneck size provide optimal resolutions to this tradeoff under different sets of challenges. We connect our findings to biologically observed behaviors, including the universality of non-minimal bottleneck sizes, a tradeoff between high ploidy for heteroplasmy and repair and tight bottlenecks for segregation, and environmental dependence of the benefits of leakage and doubly uniparental inheritance.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13351738/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148338411","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}

{"title":"Toward a Functional Genetics of Adaptation: Insights From Microbial Experimental Evolution.","authors":"Rees Kassen","doi":"10.1093/gbe/evag158","DOIUrl":"10.1093/gbe/evag158","url":null,"abstract":"<p><p>A general theory of adaptation is one that accounts for both the quantitative and functional properties of adaptive evolution. To date, the field has focused more on the former and less on the latter. Here, I build on the results of adaptive laboratory evolution experiments in microbes to present a sketch for a functional theory of adaptation built around the idea that the primary source of selection in the initial stages of adaptation involves rapid re-growth in the presence of stress. Consequently, the genes targeted during adaptation are often those involved in the regulation of gene expression, including global regulators associated with managing the stress response. These mutations, especially those involving high level gene regulation, are often highly pleiotropic, in contrast to the expectation derived from the quantitative theory of adaptation. Whether this theory can be used to make sense of adaptation more generally beyond microbial evolution experiments remains an open issue.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13335803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148360594","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}

{"title":"Unique Tunicate Traits Possibly Encoded by Horizontally Transferred Genes.","authors":"Natsuko Tamura, Izumi Oda-Ishii, Yutaka Satou","doi":"10.1093/gbe/evag170","DOIUrl":"10.1093/gbe/evag170","url":null,"abstract":"<p><p>While horizontal gene transfer (HGT) is common among prokaryotes, its prevalence and impact among metazoans are debatable. A clear example of HGT in animals is the cellulose synthase gene in tunicates, invertebrate chordates that possess the unique ability to produce a cellulose-containing tunic, despite sharing a conserved larval body plan with vertebrates. To investigate evolutionary roles of HGT in animals, we surveyed the genome of a tunicate and identified eight groups of candidate genes that are unlikely to have been vertically transferred. Notably, these candidates encode proteins potentially associated with physiological and structural features unique to tunicates, suggesting that integration of foreign genetic material has contributed to emergence of adaptive traits unique to the tunicate lineage.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13390645/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148404562","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}

{"title":"Genotypic and Phenotypic Diversity of Maudiozyma humilis: The Multiple Evolutionary Trajectories of a Domesticated Yeast.","authors":"Manon Lebleux, Jess Rouïl, Diego Segond, Thérèse Marlin, Kate Howell, Pamela Bechara, Thibault Nidelet, Lucie Arnould, Delphine Sicard, Hugo Devillers","doi":"10.1093/gbe/evag176","DOIUrl":"10.1093/gbe/evag176","url":null,"abstract":"<p><p>Maudiozyma humilis is the second most frequently encountered yeast species in sourdough bread. Despite its ecological and food relevance, little is known about its evolutionary trajectories and phenotype traits of interest. Here we investigated the genomic and phenotypic diversity of a worldwide collection of 55 M. humilis strains by combining genomic analyses and high-throughput phenotyping of fermentation kinetics and fitness. Population genomic analysis revealed six distinct clades, three diploid and three triploid, with no geographical or substrate-specific structuring. Phylogenetic, loss of heterozygosity (LOH), and allele specific analyses indicated that triploid strains originated from both recent and more ancient hybridization events involving multiple lineages. The absence of the HO gene and mating-type silent cassettes revealed the inability of M. humilis to carry mating-type switching. In addition, high linkage disequilibrium and variable LOH accumulation were observed consistent with a predominantly clonal reproduction. Last, an exceptionally high level of heterozygosity was detected, suggesting that occasional hybridization is the major driver of genetic diversity. Phenotypic characterization in a synthetic sourdough medium revealed variation in fermentation kinetics and fitness statistically associated with the genetic clades. Interestingly, genetic distance between clades and strains better explains the phenotypic variation than difference in ploidy. Altogether, our findings highlight the complex evolutionary history of M. humilis, shaped by hybridization and ploidy variation, and reveal that historical contingency shapes the phenotypic landscape of this species. Beyond providing the first analysis of M. humilis evolution, our result challenges the hypothesis that increases in ploidy are necessarily beneficial in domesticated species.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13413579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148436427","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}

{"title":"Experimental Evolution Under Biased Sex Ratios: Phenotypic and Genomic Responses in the Bulb Mite, Rhizoglyphus robini.","authors":"Sebastian Chmielewski, Jonathan M Parrett, Mateusz Konczal, Agnieszka Szubert-Kruszyńska, Aleksandra Łukasiewicz, Jacek Radwan","doi":"10.1093/gbe/evag151","DOIUrl":"10.1093/gbe/evag151","url":null,"abstract":"<p><p>Sexual selection may increase population fitness by favoring high-condition individuals and accelerating the purging of deleterious alleles. However, it can also reduce population fitness through intra- and interlocus sexual conflict by promoting male-benefit traits that harm females and maintain polymorphism at sexually antagonistic loci. The balance between these opposing forces remains unresolved, yet it has major consequences for how sexual selection shapes population fitness and genome-wide variation. To explore the genomic and phenotypic effects of sexual selection and sexual conflict, we evolved replicated bulb mite (Rhizoglyphus robini) lines for 28 generations under male- versus female-biased sex ratios and combined phenotypic assays with whole-genome resequencing. Female fecundity and inbreeding depression did not differ between treatments, and genomic analyses revealed no treatment effect on the loss of rare, putatively deleterious SNPs. Contrary to expectations, males from male-biased lines were less harmful to stock females than males from female-biased lines. Genome-wide nucleotide diversity declined similarly across generations in both treatments, although synonymous exonic diversity declined more slowly in male-biased lines. While only a few SNPs diverged consistently between treatments, we identified large treatment-specific haplotype blocks, indicating that multiple genomic regions were involved in response to sex-ratio manipulation. Overall, our results indicate that sex ratio manipulation drives evolution of male harm to females and widespread haplotype frequency changes without clear evidence for enhanced purging or maintenance of genetic diversity. The response thus appears to reflect adaptation to an altered level of reproductive competition, but without measurable consequences for population fitness and genetic diversity.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13329799/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148351725","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}

{"title":"Evolutionary History of the α-Carbonic Anhydrase Gene Family in the Phylum Arthropoda, With Comparisons to αCA in Chordates.","authors":"Yifei Joye Zhou, Carol Eunmi Lee","doi":"10.1093/gbe/evag156","DOIUrl":"10.1093/gbe/evag156","url":null,"abstract":"<p><p>The α-carbonic anhydrase (αCA) gene family encodes an abundant and ancient metalloenzyme present in all animals. Found in both eukaryotes and prokaryotes, members of this gene family play vital roles in ionic regulation, acid-base regulation, and respiration. However, little is known regarding the evolutionary history and patterns of molecular evolution of this gene family in the phylum Arthropoda, especially in relation to chordates. Through phylogenetic reconstruction and subcellular localization prediction, we discovered that arthropod αCA genes could be classified into three clades based on phylogenetic topology, as has been found in chordate αCA. Among the three distinct arthropod αCA clades, Clade III, enriched in predicted extracellular and cell membrane-bound subcellular localization, exhibited the highest rates of evolution and greatest number of homologs. Intriguingly, we found distinct patterns of gene family expansions and contractions between arthropods and chordates through gene tree-species tree reconciliation. Lastly, we found that αCA12, a member of Clade III αCA, showed signatures of positive selection (based on dN/dS) in two sibling species within the copepod Eurytemora affinis species complex (E. carolleeae and E. gulfia), compared to the general arthropod αCA background. In these populations, this particular paralog had previously shown contemporary signatures of selection during invasions into novel salinities. Overall, our results indicate that the αCA gene family shows signatures of selection both on macroevolutionary time scales across phyla, as well as between closely related sibling species within Arthropoda.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13367328/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148308009","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}

{"title":"Correction to: Genomics of Sable (Martes zibellina) × Pine Marten (Martes martes) Hybridization.","authors":"","doi":"10.1093/gbe/evag189","DOIUrl":"10.1093/gbe/evag189","url":null,"abstract":"","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"18 7","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13403556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148591259","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}

{"title":"Conservation of IAMT Preference for Indole Acetic Acid Methylation Across 250 Million Years of Seed Plant Divergence, With Only One Recent Evolutionary Switch in Ocimum.","authors":"Bahar Saadaie Jahromi, Liberty M Kostrzewa, Turki Alhinaai, Tariq Al-Zadjali, Afrida Amin, Allyson Barth, McKenna E Bayne, Gregory R Begeman, William H Bell, Melanie G Bucko, Emily M Catania, Angel Currie, Glaucia Fernanda de Lima Pereira, Citlali Figueroa, Allexia B Galentine, Gedi Gambrell, Fernando D Garcia, Avery E Gauthier, Joseph R Graber, Brenna J Hagenbarth, Amethyst Hall, Madeline Heemstra, Ruiqi Huang, Johnathon Hunter, Ami Jaswa, Nathania Karyadi, Caleb J Learman, Kar Men Lee, Clayton T Lewis, Elizabeth McKenzie, Marie F McKinney, Samantha McLean, Haley M Mueller, Merub Nadeem, Sneha Nath, Vyctoria S Nusbaum, Bryan O'Connor, Nivetha Pasupathy, Enish Pathak, Tashfia Tahsin Raisa, Karina Ramirez, Bridget Salazar, Christian E Sander, Erin Schneider, Kevin Sedlacek, Gwenyth Sirrine, Jake B Spitsbergen, Leire Garcia Torres, My Hien Truong, Brisa Hernandez Velasco, Royal Woolfolk, Todd J Barkman","doi":"10.1093/gbe/evag167","DOIUrl":"10.1093/gbe/evag167","url":null,"abstract":"<p><p>Plant indole-3-acetic acid methyltransferase (IAMT) is an ancient SABATH enzyme that modulates auxin levels via S-adenosyl-L-methionine (SAM)-dependent methylation. While most IAMTs studied previously prefer to methylate indole-3-acetic acid (IAA), one orthologous enzyme prefers to methylate cinnamic acid (CA) and shows no activity toward IAA. To understand whether other closely related enzymes also show substrate preference switches, we combined molecular phylogenetic analyses with in vitro enzyme assays. A maximum likelihood tree of 704 IAMT-like enzymes shows pervasive retention of IAMT orthologs across nearly all angiosperms and gymnosperms. Our newly reported enzymatic assays of 59 orthologs spanning 52 species and 26 orders revealed strongly conserved methylation preference for IAA across all lineages. However, in the genus Ocimum (Lamiaceae), species appear to possess one copy of IAMT that encodes an IAA-preferring enzyme and a second copy that encodes an enzyme that prefers to methylate CA. Altogether, we experimentally investigated four lineages, Lamiales, Solanales, Fabales, and Rosales, in which IAMT-type enzymes were duplicated but no others showed evidence for substrate preference switches. Alignments and computational modeling of Lamiaceae sequences highlighted M35, L325, and L363 as amino acid substitutions that may account for CA preference evolution in Ocimum enzymes. Yet, experimental mutation of those sites in either modern-day or ancestral sequences did not result in substrate preference changes in enzyme assays. Therefore, further studies are required to phylogenetically pinpoint the timing and structural basis for the shift toward CA methylation preference and to deepen our understanding of molecular evolution of the SABATH enzyme family.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13376665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148375494","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}

{"title":"Ancient Persistence and Newfound Diversity of CR1-Group Retrotransposons Across Vertebrates.","authors":"Alexander J Stuart, Zhenglong Du, Nozhat T Hassan, David L Adelson","doi":"10.1093/gbe/evag155","DOIUrl":"10.1093/gbe/evag155","url":null,"abstract":"<p><p>Retrotransposons are mobile, repetitive DNA sequences that are ubiquitous across eukaryotes and widely recognized as key drivers of both gene and genome evolution. The CR1 group of retrotransposons is thought to have been present in the most recent common ancestor of vertebrates ∼560 Ma and is the dominant retrotransposon in the majority of vertebrate species. The advent of long-read sequencing technologies has enabled the assembly of high-quality genomes from representatives of almost all major vertebrate orders, enabling comparative analysis with deeply divergent species. To better understand the composition of CR1-group elements (CGEs) in vertebrates, we systematically characterized transposable elements across representative species from every available extant order of vertebrates. Our analysis uncovered previously unknown phylogenetic relationships of CGEs within and between species and has pushed back the origin of certain CR1-group subclades by tens of millions of years. Additionally, entirely novel elements with no close relatives in existing databases were uncovered within several of the species analyzed. We also detected numerous putative horizontal transfer events, many of which had not been previously documented. Overall, this investigation has provided the first vertebrate-wide analysis of an element that is historically understudied yet plays a pivotal role in genome biology and evolution.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13343379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148308020","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}

{"title":"Genome-Wide Diversity of Goats From Indonesia and the Philippines Reveals Local Ancestry With Different Levels of Cosmopolitan Admixture.","authors":"Ryo Masuko, Ayin, Maho Masaoka, Fuki Kawaguchi, Shinji Sasazaki, Muhammad I A Dagong, Sri R A Bugiwati, Joseph S Masangkay, Jiaqi Wu, Takahiro Yonezawa, Johannes A Lenstra, Hideyuki Mannen","doi":"10.1093/gbe/evag177","DOIUrl":"10.1093/gbe/evag177","url":null,"abstract":"<p><p>In order to investigate the genetic diversity, differentiation, gene flows, and propagation routes of Island Southeast Asian (ISEA) goats, we genotyped 50K genome-wide SNPs in 57 Philippine and 30 Indonesian Katjang goats. Correlations of the distance from the domestication center and the genetic diversities of 21 Asian populations were significantly negative. A relatively high diversity of the Philippine population (He = 0.363) against the distance from the domestication center suggests a history of admixture, notably without large effects on their Katjang phenotype. This was confirmed by supervised PCA (Principal Component Analysis), f3 coancestry and f4 admixture analyses, Treemix-inferred migrations and model-based clustering (Admixture program). The inferred differential admixture of ISEA goats agreed with previously reported fixation of mtDNA haplogroup B in Indonesia, but not in the Philippines, and with high frequencies of African or European Y-chromosomal haplogroups that were not observed in Mainland Southeast Asia. We propose that admixture of cosmopolitan European and African goats into ISEA was mediated by a unique feature of the domestic goat, the maritime transport of goats during the colonial period as a source of provisions. This was followed by more recent imports of popular breeds such as Boer, and other cosmopolitan breeds.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13403562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148470174","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}