Evolutionary Applications最新文献

{"title":"The Evolution of Knockdown Resistance: Genotypic and Phenotypic Insights Into Aedes aegypti Insecticide Resistance","authors":"Brook M. Jensen,&nbsp;Alden S. Estep,&nbsp;Silvie Huijben","doi":"10.1111/eva.70305","DOIUrl":"10.1111/eva.70305","url":null,"abstract":"<p>Insecticide resistance is a significant challenge for mosquito population control and disease prevention. This research investigated knockdown resistance (<i>kdr</i>) mutations V410L, V1016I, and F1534C in <i>Aedes aegypti</i> mosquitoes to address crucial gaps in understanding insecticide resistance evolution and management. Six common <i>kdr</i> genotypes were obtained through genetic crosses of three unique parental strains from the same location in Florida, USA. Through topical application of deltamethrin on both males and females, we quantified the resistance profiles of each genotype and sex. Triple homozygous mutants were over 52 times more resistant than the susceptible Rockefeller lab strain, with resistance ratios of the five other genotypes ranging from 8 to 19. We demonstrated that the resistant haplotypes <b>I</b>¹⁰¹⁶-<b>C</b>¹⁵³⁴ (on V410L mutant background) and <b>L</b>⁴¹⁰-<b>I</b>¹⁰¹⁶ (on F1534C mutant background) were incompletely recessive. Using these data in a simulation model, we show that the selective advantage is not constant but fluctuates within the window of selection. Selective advantage depended on the frequency of the resistance haplotype at the time of treatment, and both the level and dose of exposure. Finally, resistance profiles revealed that male mosquitoes had similar resistance profiles to females when sex and weight differences were accounted for, indicating that males could be used for resistance surveillance, which could enhance surveillance efforts. Overall, this study provides the first detailed quantification of dose–response curves and selection advantages for both sexes across multiple <i>kdr</i> genotypes. These results offer critical insights into the evolutionary dynamics of insecticide resistance and support the development of evidence-based strategies for more sustainable mosquito control.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13392631/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148576425","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":"Vegetative Propagation Preserves Genomic Diversity and Informs Translocation Strategies in a Rare Clonal Plant","authors":"Rob Massatti,&nbsp;Susan Bainbridge,&nbsp;Stella M. Copeland,&nbsp;Carter Crouch,&nbsp;Trevor M. Faske,&nbsp;Erik P. Hamerlynck,&nbsp;Brandon Palmer,&nbsp;Carla M. Roybal","doi":"10.1111/eva.70299","DOIUrl":"https://doi.org/10.1111/eva.70299","url":null,"abstract":"<p>Conservation translocations are widely used to increase population size and redundancy, yet their genetic consequences are often uncertain, particularly for clonal species with unknown rates of sexual reproduction. Propagation through asexual reproduction is frequently employed in these systems, but its effectiveness for preserving genomic diversity remains poorly evaluated. We used genome-wide single nucleotide polymorphism (SNP) data to assess the genetic outcomes of translocation efforts in <i>Pleuropogon oregonus</i>, a critically endangered grass endemic to eastern Oregon, USA. We quantified genetic diversity, relatedness, and population structure across natural and introduced sites and used coalescent simulations to infer the divergence history between disjunct populations. Genetic analyses identified two divergent lineages corresponding to northern and southern regions, with divergence predating the last glacial period and limited subsequent gene flow. Within regions, natural populations exhibited high clonality but retained genetically distinct individuals. Introductions that used vegetative propagules from the northern region maintained heterozygosity and allelic diversity comparable to sources and captured multiple distinct genotypes, including alleles likely originating from an unsampled source, thereby increasing population redundancy. In contrast, the introduction derived from a low-diversity, southern region source reflected similarly limited clonal diversity. Our results demonstrate that vegetative propagation can effectively preserve genomic diversity in clonal species when propagules are sampled representatively, but that evolutionary history may inform sourcing and mixing decisions. More broadly, this study provides an empirical framework for integrating genomic data into conservation translocations, highlighting conditions under which vegetative propagation maintains evolutionary potential and when it may pose risks to long-term persistence.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70299","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148467611","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":"Temporal Comparison Reveals Weakened Genotype–Phenotype Association at a Major-Effect Locus in Dworshak National Fish Hatchery Steelhead","authors":"Audrey C. Harris,&nbsp;Stuart C. Willis,&nbsp;Shawn R. Narum,&nbsp;Matthew R. Campbell","doi":"10.1111/eva.70300","DOIUrl":"https://doi.org/10.1111/eva.70300","url":null,"abstract":"<p>Life history diversity in salmonids contributes to population resilience, yet the mechanisms driving contemporary life history change remain difficult to disentangle from demographic and environmental processes. We evaluated long-term changes in neutral genetic variation, adaptive haplotypes near the <i>six6</i> gene, and life history traits in the Dworshak National Fish Hatchery steelhead (<i>Oncorhynchus mykiss</i>) broodstock by comparing archived scale samples from the founding broodstock and subsequent returns (1969–1976) with contemporary samples (2014–2016; 2019–2022). Neutral genetic diversity and population structure remained stable through time, consistent with prior evidence that observed life history shifts were not associated with erosion of neutral genetic diversity. In contrast, we detected pronounced temporal shifts in adaptive variation near the <i>six6</i> gene on chromosome 25, including a decline in the long haplotype historically associated with extended years in the ocean and larger body size. Ocean age composition also shifted over time, with an increased proportion of 2-ocean fish and altered age distributions within <i>six6</i> genotype classes. Although <i>six6</i> remained significantly associated with length-at-age, the magnitude of phenotypic differences among genotypes was substantially reduced in contemporary samples, indicating a weakening of the genotype–phenotype relationship. These results suggest that environmental conditions increasingly constrain, or otherwise alter, the expression of genetically based life history variation. Our findings demonstrate that life history change can occur without loss of neutral genetic diversity and highlight the importance of integrating genetic and demographic data to understand eco-evolutionary responses of salmonids under changing ocean conditions.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70300","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148467179","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":"Outpaced by Drought: Weak Local Adaptation and Limited Potential for Drought Adaptation in a Deciduous Conifer","authors":"Beth A. Roskilly,&nbsp;Martin R. Henry,&nbsp;Brandon M. Lind,&nbsp;Sally N. Aitken","doi":"10.1111/eva.70291","DOIUrl":"https://doi.org/10.1111/eva.70291","url":null,"abstract":"<p>As drought impacts on forests intensify, evaluating the potential for adaptation is critical for predicting forest responses and the impacts of management strategies. We assessed phenotypic and genomic variation in western larch (<i>Larix occidentalis</i> Nutt.) populations to evaluate the potential for drought adaptation across its range. First, we established a seedling common garden experiment outside the natural range with 52 populations subjected to two drought treatments. Second, we analyzed pooled targeted exome-sequence capture data from 44 populations of an adult provenance trial to evaluate the relative ability of climate, geography, and neutral genetic structure to predict landscape genomic variation. We found that population differentiation for drought resistance was low. Drought reduced population differentiation for growth and bud set, and weakened clinal associations for growth. We found no antagonistic correlations between drought resistance and growth or phenology, indicating that trade-offs are unlikely to constrain adaptation. Further, landscape genomic variation was primarily explained by neutral genetic structure, with little additional variation explained by climate or geography. Together, these findings demonstrate weak local adaptation to drought and reduced genetic variation in traits under drought indicate that natural populations of western larch may have limited potential to adapt to future drought conditions.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70291","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148467610","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":"Unravelling the Interplay Between Vairimorpha ceranae and Viruses in Geographically Isolated Honey Bee (Apis mellifera) Populations","authors":"Ana R. Lopes,&nbsp;Matthew Low,&nbsp;Raquel Martín-Hernández,&nbsp;Mariano Higes,&nbsp;Joachim R. de Miranda,&nbsp;M. Alice Pinto","doi":"10.1111/eva.70294","DOIUrl":"https://doi.org/10.1111/eva.70294","url":null,"abstract":"<p>Viral infections and the microsporidian <i>Vairimorpha ceranae</i> (‘vairimorpha’) have been involved in elevated honey bee (<i>Apis mellifera</i>) colony losses as a result of their individual or combined actions, with the ectoparasitic mite <i>Varroa destructor</i> (‘varroa’) often exacerbating these effects. This study investigates the relationship between vairimorpha and several common honey bee viruses within the unique ecological context of the remote mid-Atlantic Azores archipelago, which comprises three main islands where varroa is present and six islands where varroa is still absent. We sampled 494 colonies across these islands and employed RT-qPCR to detect and quantify vairimorpha and nine common honey bee viruses, of which seven were detected. The data were modelled using a Bayesian approach, which estimated the likelihood of an effect of the presence of vairimorpha on the loads of each of the viruses on varroa-infested and varroa<i>-</i>free islands. Both vairimorpha and the seven bee viruses were differentially distributed among the islands. An additive relationship was found between vairimorpha and both black queen cell virus (BQCV) and Lake Sinai virus (LSV), the latter driven almost exclusively by one strain (LSV-2), and this relationship was stronger on the varroa-infested islands (Pr = 96.2%) than on the varroa-free islands (Pr = 69.1%). No association was found between vairimorpha and the two main strains of DWV (DWV-A and DWV-B) across all islands, although an antagonistic relationship may exist between vairimorpha and the rare DWV-C strain, found only on varroa-free islands. This study supports previous findings and shows the importance of possible additive relationships among co-infecting honey bee pathogens and parasites.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70294","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148467252","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":"Phylogeny of Cutthroat Trout (Oncorhynchus clarkii) Based on Full Mitochondrial Genomes With Comments on Species Delimitation and Taxonomy","authors":"Tanner S. Van Orden,&nbsp;Kevin B. Rogers,&nbsp;Peter C. Searle,&nbsp;Andrea L. Kokkonen,&nbsp;Dennis K. Shiozawa,&nbsp;Richard Paul Evans","doi":"10.1111/eva.70304","DOIUrl":"https://doi.org/10.1111/eva.70304","url":null,"abstract":"<p>Despite the important role that species concepts and taxonomy play in understanding the evolution of species, taxonomists have struggled to describe the relationship between many organisms. Here, using Cutthroat Trout as a case study, we illustrate how full mitochondrial genomes and broad taxonomic sampling can provide further insight on disputed taxonomic relationships, and aid in management and conservation decisions of different species. Inconsistencies in the taxonomy of Cutthroat Trout inspired a special workshop at the 2015 annual meeting of the American Fisheries Society that emphasized the need for revision. To further resolve the relationship between different Cutthroat Trout groups, we sequenced and assembled full mitochondrial genomes from 123 Cutthroat Trout from across their native range. We used maximum likelihood and Bayesian phylogenetic approaches to examine the evolutionary relationships between all named Cutthroat Trout subspecies. Through these analyses, we find eight lineages of Cutthroat Trout that diverged more than one million years ago, and at least 12 lineages that diverged more than 790 thousand years ago, highlighting that despite the ancient split with Rainbow Trout at around ten million years ago, the modern diversity seen within the Cutthroat Trout Species Complex is much more recent. We do not find that Coastal, Westslope, or Lahontan Cutthroat Trout are substantially more different than the lineages in the Yellowstone complex. As such, we continue to recognize a single Cutthroat Trout species (<i>Oncorhynchus clarkii</i>) comprised of eleven distinct subspecies level clades, maintaining consistency with ongoing conservation efforts, management plans and ESA-related decisions, while also preserving stability associated with historical nomenclature. Overall, we highlight that using full mitochondrial genomes can increase phylogenetically informative information and that the consistent nature of mitochondrial genomes across the tree of life allows for a valuable and measurable comparison of different species concepts in closely related taxa.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70304","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148467251","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":"Local Thermal Adaptation in an Insect-Transmitted Plant Pathogen: The Role of Virulence Trade-Offs","authors":"Monica A. Donegan,&nbsp;Josephine Nuño,&nbsp;Ranlin Liu,&nbsp;Leonardo De La Fuente,&nbsp;Rodrigo P. P. Almeida","doi":"10.1111/eva.70303","DOIUrl":"https://doi.org/10.1111/eva.70303","url":null,"abstract":"<p>Little is known about local adaptation to temperature in bacterial pathogen populations in nature. For plant-pathogenic bacteria, local thermal adaptation may influence the evolution of virulence, which has strong implications for disease management and mitigation. <i>Xylella fastidiosa</i> (<i>Xf</i>) is an insect-transmitted bacterial pathogen that infects over 700 plant species globally and causes Pierce's disease of grapevines. Here, we compared in vitro growth and <i>in planta</i> virulence of multiple strains from two genetically distinct <i>Xf</i> populations from California regions having either a colder climate (Hopland) or warmer climate (Bakersfield). <i>Xf</i> strains from a warmer climate grew faster than cold-climate strains under suboptimal (20°C) temperatures, suggesting a lower thermal optimum. In reciprocal field experiments, infections of plants by <i>Xf</i> strains from a colder climate were more likely to survive the winter. After a mild winter in Bakersfield (warmer climate), there were severe symptoms and some vine mortality the following growing season in vines infected with the non-local, cold-climate (Hopland) strains, pointing to a potential trade-off between virulence and transmission due to vine mortality. Our data suggest that <i>Xf</i> populations in CA are locally adapted to temperature, with cold-climate strains exhibiting hypervirulence when transplanted to warmer climates, whereas warm-climate strains survive at lower rates when transplanted to colder climates. Thus, local thermal adaptation in bacterial pathogens may influence the optimum virulence phenotype across the landscape.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70303","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148467410","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":"Characterizing the Distribution of Oncorhynchus mykiss Genetic Diversity in the Klamath River Basin Before Dam Removal","authors":"Kathleen G. O'Malley,&nbsp;Mark E. Hereford,&nbsp;Kevin C. Olsen,&nbsp;Devon E. Pearse,&nbsp;William R. Tinniswood,&nbsp;Ben S. Ramirez,&nbsp;Jonathan B. Armstrong,&nbsp;Stanley J. Piotrowski","doi":"10.1111/eva.70297","DOIUrl":"10.1111/eva.70297","url":null,"abstract":"<p>Genetic assessments serve as powerful tools to evaluate the effects of anthropogenic habitat fragmentation on natural populations. In the Klamath River Basin, construction of four dams from 1912 to 1962 had a profound impact on the distribution of anadromous fishes, blocking access to over 751 river kilometers of critical habitat. To characterize the genetic diversity and connectivity among <i>Oncorhynchus mykiss</i> in the basin prior to the historic removal of the four dams in 2024, we genotyped 2466 samples at 193 presumably neutral and 105 putatively adaptive markers. Using complementary population genetic analyses, we found a clear division between coastal and inland <i>O. mykiss</i> lineages located primarily downstream and upstream of the outlet of Upper Klamath Lake, and little genetic structure associated with dams. Further, we detected distinct inland and coastal genetic lineages upstream of the lake outlet supporting the hypothesis that ancestral inland <i>O. mykiss</i> were secondarily invaded by a coastal lineage. We found that neutral genetic diversity was significantly greater in collections consisting primarily of anadromous <i>O. mykiss</i> compared to collections of adfluvial, fluvial, and resident fish while genetic diversity was significantly lower in adfluvial collections. Based on the chromosome <i>Omy5</i> markers associated with anadromous/resident phenotypes, we found that anadromous and heterozygous genotypes were more prevalent downstream of the lake outlet while resident genotypes were prevalent upstream of the outlet. Based on the chromosome <i>Omy28</i> markers associated with adult migration timing, we found that late-migration timing and heterozygous genotypes were numerous downstream of the lake outlet while early-migration timing genotypes were prevalent upstream of the outlet. The results of our population genetic analyses highlight the genetic diversity and structure of <i>O. mykiss</i> in the Klamath River Basin and will serve as a critical baseline for future assessments post dam removal.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13358376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148434522","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":"Genetic Analysis Reveals Climate Exposure and Conservation Opportunities for a Vulnerable Life History in Steelhead (Oncorhynchus mykiss)","authors":"Michelle Y. Pepping,&nbsp;Tasha Q. Thompson,&nbsp;Sean M. O'Rourke,&nbsp;Jonathan L. Hart,&nbsp;Michael R. Miller,&nbsp;Matthew R. Sloat","doi":"10.1111/eva.70293","DOIUrl":"10.1111/eva.70293","url":null,"abstract":"<p>The loss of intraspecific diversity is a hidden crisis that threatens to disrupt ecological processes and ecosystem services, diminishing economic, subsistence, and cultural benefits to human communities. Conserving this diversity requires a deeper understanding of its evolutionary underpinnings and the ecological conditions necessary for its persistence amid rapid environmental change. Here, we integrate evolutionary principles and empirical evidence from recently developed genetic assays to examine the maintenance of run timing diversity within steelhead (<i>Oncorhynchus mykiss</i>), a widely distributed anadromous salmonid with distinct summer and winter adult migration timings. Using a GREB1L-based genetic assay, we analyzed nearly 2000 juvenile samples from the North Umpqua River, Oregon, USA to map watershed-scale distributions of run timing genotypes alongside climate-driven stream warming patterns. We found that summer-run genotypes dominate only in habitats located above seasonally passable barriers, such as natural waterfalls, that restrict or prevent passage by adult winter-run steelhead. This pattern supports the hypothesis that exclusive access to habitat provides a critical fitness advantage that compensates for the costs associated with summer run timing. Temperature modeling further revealed that habitats currently exclusive to summer-run steelhead are already thermally stressful and are projected to become increasingly so under end-of-century climate scenarios, reducing the quality of critical summer-run steelhead habitat. Because the persistence of summer-run steelhead under climate change depends on access to exclusive habitat of sufficient quality, we propose strategies to establish or maintain habitat exclusivity in more climate-resilient areas within the basin while minimizing impacts on winter-run steelhead and other anadromous species. More broadly, our study demonstrates how understanding the genetic basis of run timing and the fitness trade-offs associated with different life histories can inform the conservation of intraspecific diversity in migratory fish.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13354926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148417191","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":"A Complete Telomere-To-Telomere Assembly of Plectropomus leopardus and Phylogenomic Insights Into Perciformes","authors":"Baojun Zhao,&nbsp;Chaofan Jin,&nbsp;Mingjian Liu,&nbsp;Haizhan Tang,&nbsp;Da Zheng,&nbsp;Mengya Wang,&nbsp;Bo Wang,&nbsp;Zhenmin Bao,&nbsp;Jingjie Hu","doi":"10.1111/eva.70296","DOIUrl":"10.1111/eva.70296","url":null,"abstract":"<p>The leopard coral grouper, <i>Plectropomus leopardus</i> Lacepède, 1802, is an ecologically and economically important species in the family Epinephelidae. However, the absence of a complete reference genome has impeded advanced genetic research on this species, and the phylogenetic position of Epinephelidae within Perciformes remains unresolved. Here, we generated a complete telomere-to-telomere (T2T) genome assembly (887.20 Mb; contig N50: 39.03 Mb; QV: 67) for <i>P. leopardus</i> with no need for gap-filling. Leveraging this genome combined with other available genome resources, we conducted a large-scale genomic re-annotation and reconstructed a robust genome-level phylogeny of the Perciformes. Our analysis revealed that Epinephelidae and Anthiadidae form a monophyletic clade situated at the base of the Perciformes, indicating that the traditional suborder Serranoidei is non-monophyletic. Comparative genomic analysis revealed that differential expansions of transposable elements represented the primary driver of genome size variation among <i>P. leopardus</i> and other groupers. Furthermore, we constructed a high-density haplotype reference panel using 110 individuals and annotated 1068 loss-of-function (LoF) mutations. Enrichment analysis indicated that genes with stop-gain LoF mutations are involved in the immune response and skin color variation. This study provides an essential genomic resource for <i>P. leopardus</i> and offers fundamental evolutionary insights into the Epinephelidae and, more broadly, the order Perciformes.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13351114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148417135","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}