Journal of Heredity最新文献

{"title":"Retention of ancestral polymorphism, not recent introgression, best explains elevated levels of genetic variation in Gila Trout Oncorhynchus gilae.","authors":"David T Camak, Megan J Osborne, Thomas F Turner","doi":"10.1093/jhered/esaf110","DOIUrl":"10.1093/jhered/esaf110","url":null,"abstract":"<p><p>Introgressive hybridization is widespread in nature, often between native and introduced species. Closely related species also share ancestral genetic variation that mimics introgressive hybridization. In this study, we employed reduced-representation genome sequencing to test whether elevated levels of genetic variation in a protected fish species were best explained by hybridization or shared ancestry with an introduced nonnative fish. Gila Trout Oncorhynchus gilae is endemic to remote headwaters of the Gila River in the southwestern US. Its close relative, Rainbow Trout O. mykiss, was stocked into the Gila River from the late 1890s to the late 1960s. Shortly thereafter, Gila Trout was protected under the US Endangered Species Act. An isozyme study conducted in the late 1990s identified introgressed individuals in Iron Creek, a genetically distinct Gila Trout lineage. This finding was important for conservation because Iron Creek harbors unique genetic variants and is the 'wildest' Gila Trout lineage with no hatchery influence. We reassessed genetic variation in the Iron Creek lineage using nextRAD and contemporary samples and found little evidence of recent introgression with Rainbow Trout. We simulated Wright-Fisher evolution under different scenarios assuming that Iron Creek was previously hybridized to explore potential mechanisms responsible for loss of nonnative alleles. Though not fully conclusive, the preponderance of evidence indicates genetic variation shared with Rainbow Trout arises from retention of ancestral polymorphism in Iron Creek Gila Trout. Recent common ancestry of potentially hybridizing species poses an important challenge to wholesale application of structured decision frameworks to manage putatively introgressed populations.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"761-777"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145901652","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}

{"title":"Correction to: Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes.","authors":"","doi":"10.1093/jhered/esag038","DOIUrl":"10.1093/jhered/esag038","url":null,"abstract":"","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"957"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147935544","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}

{"title":"Genome assembly for the Sierra Nevada Parnassian (Parnassius behrii) and a brief review of butterfly genome sizes.","authors":"Zachary G MacDonald, Joseph N Curti, Robert Cooper, Sean D Schoville, Merly Escalona, Noravit Chumchim, Colin W Fairbairn, Erin Toffelmier, Courtney Miller, Mohan P A Marimuthu, Oanh Nguyen, William Seligmann, Thomas W Gillespie, H Bradley Shaffer","doi":"10.1093/jhered/esaf093","DOIUrl":"10.1093/jhered/esaf093","url":null,"abstract":"<p><p>The Sierra Nevada Parnassian (Parnassius behrii W.H. Edwards, 1870) (Lepidoptera: Papilionidae) is a high-elevation specialist butterfly endemic to the Sierra Nevada, California. We present a genome assembly for P. behrii, representing the first major genomic resource for the species and greater Parnassius phoebus species complex. The assembly consists of two haplotypes, 1.59 Gb and 1.46 Gb in length, with contig N50 values of 10.93 Mb and 11.84 Mb, scaffold N50 values of 52.56 Mb and 51.90 Mb, scaffold L50 values of 13 and 14, and BUSCO completeness scores of 98.7% and 94.4%, respectively. Both haplotypes are highly contiguous, with 31 chromosome-length scaffolds, including putative Z and W sex chromosomes. We annotated the genome with National Center for Biotechnology Information's (NCBI's) EGAPx pipeline, integrating database and novel transcript alignment with Hidden Markov Model-based gene predictions, yielding 17,191 genes with a BUSCO score of 98.1%. RepeatMasker identified that 26.68% (424.97 Mb) of the genome consists of repetitive elements. We also assembled a mitochondrial genome for P. behrii (15,391 bp) containing 2 rRNAs, 22 unique transfer RNAs, and 13 protein-coding genes. We finally reviewed 514 high-quality butterfly genomes available from the National Center for Biotechnology Information (NCBI). Parnassius species were observed to have the largest genomes, with P. behrii being the largest. This assembly provides a foundational resource for whole-genome research on P. behrii and the broader P. phoebus complex, enabling analyses of evolutionary differentiation, local adaptation, inbreeding, gene flow, taxonomy and conservation practices.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"888-900"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145764608","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":"The origin of the octoploid cloudberry (Rubus chamaemorus) genome is the result of multiple and complex polyploidization events.","authors":"Marius A Strand, Thu-Hien To, Ole K Tørresen, Sarah Fullmer, Giada Ferrari, Morten Skage, Ave Tooming-Klunderud, Simen Rød Sandve, Kjetill S Jakobsen","doi":"10.1093/jhered/esag028","DOIUrl":"10.1093/jhered/esag028","url":null,"abstract":"<p><p>We describe a chromosome-level genome assembly from an individual male plant of the cloudberry (Rubus chamaemorus). The haplotype-resolved assemblies contain 1 pseudo-haplotype spanning 1,198 megabases and 1 pseudo-haplotype spanning 1161 megabases. Most of these 2 assemblies, 93.57% and 96.55% respectively, are each scaffolded into 28 pseudo-chromosomes. Both assemblies show high completeness, with the same Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 99.2%. Most BUSCO genes are duplicated in both pseudo-haplotypes, in line with the polyploid nature of the cloudberry genome. The assemblies contain 74,132 and 70,692 predicted protein-coding genes, respectively. Analysis of repetitive sequences classified ~60% of each haplotype as repeats. Comparative synteny with red raspberry (Rubus idaeus) reveals a 4:1 chromosome correspondence, supporting an octoploid origin. Across k-mer composition, synonymous divergence, and genome-wide gene-tree analyses, 1 set of 7 chromosomes is consistently distinct (β), while the remaining 21 (3 × 7) chromosomes form an α set with no resolvable internal subdivision. These results are consistent with a complex polyploid origin of the cloudberry genome, involving a combination of allopolyploid and autopolyploid processes. Significance statement Cloudberry cultivation has lagged due to limited genomic resources and an unresolved polyploid history. We present a haplotype-resolved, chromosome-scale assembly that resolves 4 homologs per ancestral chromosome into 28 pseudo-chromosomes per haplotype and shows a 4:1 correspondence with red raspberry (Rubus idaeus). Genome-wide analyses support an octoploid architecture with 1 distinct 7-chromosome set (β) and a remaining α-set of 21 chromosomes with no resolvable internal subdivision. This reference provides a foundation for future work on polyploid origin, trait discovery, and breeding.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"822-833"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147517026","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 chromosome-level genome assembly for snowshoe hare (Lepus americanus).","authors":"Cynthia K S Ulbing, Nicole M Foley, Terje Raudsepp, L Scott Mills, William J Murphy, Jeffrey M Good","doi":"10.1093/jhered/esag020","DOIUrl":"10.1093/jhered/esag020","url":null,"abstract":"<p><p>The snowshoe hare (Lepus americanus) is considered a critical keystone species of the boreal and temperate forests of North America. Although their population ecology and evolutionary dynamics have been studied extensively, a lack of high-quality genomic resources has limited molecular insights into their biology. Here, we combined cytogenetic karyotype analysis, PacBio HiFi long-read sequencing (~33× coverage), and chromosome conformation capture (Hi-C) sequencing to generate a phased chromosome-level genome assembly from a male snowshoe hare specimen. The primary haploid assembly is 2.75 Gb, with the 24 largest scaffolds corresponding to individual chromosomes (2n = 48 chromosomes, scaffold N50 = 131 Mb) and containing only 213 gaps. Assembly completeness was high, with 99.6% of mammalian Benchmarking Universal Single-Copy Orthologs recovered. Comparative analysis of this genome with other Lepus species revealed conservation of chromosomal architecture within the genus, while alignment with the European rabbit (Oryctolagus cuniculus) genome identified chromosomal rearrangements consistent with known karyotypic divergence between hares and rabbits. This genome assembly establishes a critical reference for future genomic studies in snowshoe hares and related taxa.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"908-917"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147367230","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":"Chromosome-level genome of the Adriatic sturgeon, Acipenser naccarii: A resource for polyploid fish genomics.","authors":"Roberto Biello, Annalisa Scapolatiello, Sebastiano Fava, Victor Hugo Muñoz Mora, Stefano Dalle Palle, Patrícia Santos, Alessio Iannucci, Tatiana Tilley, Nivesh Jain, Jennifer Balacco, Brian O'Toole, Giulio Formenti, Erich D Jarvis, Claudio Ciofi, Emiliano Trucchi, Leonardo Congiu, Giorgio Bertorelle, Andrea Benazzo","doi":"10.1093/jhered/esag023","DOIUrl":"10.1093/jhered/esag023","url":null,"abstract":"<p><p>The Adriatic sturgeon, Acipenser naccarii, a tetraploid species endemic to the North Adriatic region, has experienced significant population declines, resulting in its classification as \"Critically Endangered\" by the International Union for Conservation of Nature (IUCN). Historically widespread in the Adriatic Sea's tributaries, the species is now at high risk of extinction with occasional reproductions occurring in the wild. Using long-read sequencing (PacBio HiFi) and chromatin conformation capture sequencing (Hi-C), we generated a phased reference genome for the tetraploid Adriatic sturgeon. The haploid assembly spans 1.94 Gb across 2,083 scaffolds, with a contig N50 of 1.024 Mb, a scaffold N50 of 39.6 Mb, and a scaffold L90 of 276. Approximately 80% of the genome is contained within the first 60 scaffolds, indicating a high degree of contiguity. The Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of the haploid assembly reached 88.9%, whereas combined metrics for all four haploid assemblies increased to 94.1%. This comprehensive genomic resource provides valuable insights into the genetic and evolutionary mechanisms of polyploidy and, more specifically, it will improve our understanding of the genetic diversity of the Adriatic sturgeon, thereby informing targeted conservation strategies for this critically endangered species.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"877-887"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147446052","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 genome assembly of the North American golden eagle, Aquila chrysaetos canadensis.","authors":"Samantha L R Capel, Robert N Fisher, Merly Escalona, Peter H Bloom, Noravit Chumchim, Colin W Fairbairn, Oanh H Nguyen, Ruta M Sahasrabudhe, William E Seligmann, Todd E Katzner, H Bradley Shaffer, Michael R Buchalski","doi":"10.1093/jhered/esag022","DOIUrl":"10.1093/jhered/esag022","url":null,"abstract":"<p><p>The golden eagle (Aquila chrysaetos) is an apex predator across its Holarctic range. Although chromosome-level reference genome assemblies are available for two of the six golden eagle subspecies (European and Japanese), current assemblies for the North American subspecies (A. c. canadensis) were generated using short-read sequencing technology, limiting completeness, contiguity, and accuracy. Here we present a chromosome-length de novo genome assembly for a male A. c. canadensis as part of the California Conservation Genomics Project. We used Pacific Biosciences HiFi reads and Omni-C chromatin-proximity sequencing to produce a high-quality assembly consistent with the standard California Conservation Genomics Project reference genome protocol. Our assembly spans 1.28 Gbp and comprises 316 scaffolds with a scaffold N50 of 47.3 Mbp, a contig N50 of 30.3 Mbp, and a benchmarking universal single-copy ortholog completeness score of 97.4%. This reference genome assembly offers a valuable resource for delineating genomic variation and assessing conservation needs in golden eagle populations across California and its North American range more broadly.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"945-956"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326411/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147517058","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":"Chromosome-scale genome assembly of the rice stink bug (Hemiptera: Oebalus pugnax) illuminates genome structure and gene family evolution in Pentatomidae.","authors":"Rokeya Akter, Mahamad Sayab Miya, Allen Szalanski, Duane D McKenna, Richard Adams","doi":"10.1093/jhered/esag053","DOIUrl":"https://doi.org/10.1093/jhered/esag053","url":null,"abstract":"<p><p>The rice stink bug (Oebalus pugnax; RSB) is a major agricultural pest that poses significant threats to rice production throughout the United States. Yet, despite its economic significance, almost nothing is known about genome structure, function, and evolution in this species. Here, we sequenced, assembled, and annotated the first high-quality reference genome for RSB and conducted comparative analyses with related hemipteran genomes to understand its historical evolutionary context. The assembly spans 826.62 Mb across 211 contigs, with an N50 of 17.25 Mb, the largest contig of 67.15 Mb, and a BUSCO representation of 99.30% completeness. Hi-C-based scaffolding supported six putative chromosome-scale scaffolds. Genome-wide repeats comprised 47.55% of the genome, consisting largely of interspersed elements, including DNA transposons, LINEs, and LTRs, with evidence of recent expansions. Our annotation identified 13,175 putative genes, with predicted functions for 97.87% of them. We further uncovered candidate genes and enzyme families involved in detoxification and insecticide resistance, including cytochrome P450s, UDP-glycosyltransferases, and glycoside hydrolases. Comparative analyses revealed rapid expansion and contraction of gene families associated with feeding, host specialization, and insecticide resistance. Together, these resources provide a new framework for future investigations into genome structure, function, and evolution in this ecologically and economically important insect clade.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148370950","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}

{"title":"Genomic vulnerability to climate change of a poorly dispersing and threatened fish, the southern pygmy perch (Nannoperca australis).","authors":"Emily J Booth, Chris J Brauer, Jonathan Sandoval-Castillo, Scotte D Wedderburn, Nick S Whiterod, Peter J Unmack, Michael P Hammer, Luciano B Beheregaray","doi":"10.1093/jhered/esag052","DOIUrl":"https://doi.org/10.1093/jhered/esag052","url":null,"abstract":"<p><p>Small and isolated populations often have low levels of standing genetic variation, which limits their capacity to evolutionarily adapt to climate change. In freshwater ecosystems, habitat fragmentation caused by instream barriers and water regulation is a prominent global issue impacting on connectivity among populations. We investigated genomic vulnerability to climate change in a small-bodied and poorly dispersing species, the southern pygmy perch, in Australia's Murray-Darling Basin (MDB). We used a genome-wide dataset for 467 individuals from 30 sites covering the range of the species in the MDB. This included temporal sampling of a population in the Lower Lakes region, prior to its extirpation during the Millennium Drought and after its re-establishment through a captive breeding and reintroduction program. Southern pygmy perch exhibited high levels of population structure, with 11 distinct genetic clusters mainly delineated by river catchments. Genetic diversity was low, especially in small and isolated headwater populations. Genomic vulnerability, assessed via a genomic offset approach, correlated positively with elevation, being generally higher in upland and lower in lowland populations. We suggest that elevation could potentially serve as a proxy for climate change vulnerability in dendritic freshwater systems, particularly for species with limited dispersal capacity. The signal of low genomic vulnerability for the Lower Lakes population was consistent both before and after ex situ captive breeding and reintroduction. This highlights the importance of downstream populations as sinks of diversity. It also shows that integrating genetic management into captive breeding programs can help maintain climatic adaptive potential in threatened populations.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148310394","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}

{"title":"The complete genomes of two hybridizing field crickets, Gryllus pennsylvanicus and Gryllus firmus.","authors":"Michael S Grapin, Alberto Aleman, Leonardo T Gonçalves, Alyson H Emery, Thomas J Firneno, Kristi L Montooth, Colin D Meiklejohn, Emily C Moore, Erica L Larson","doi":"10.1093/jhered/esag051","DOIUrl":"https://doi.org/10.1093/jhered/esag051","url":null,"abstract":"<p><p>The field crickets, Gryllus pennsylvanicus and Gryllus firmus, share a well-studied hybrid zone in the eastern US and are a key study system in speciation research. We report the genome assembly for each species using PacBio HiFi long-read sequencing data. We assembled the sequenced reads for G. pennsylvanicus into 2,924 scaffolds totaling 2.1 Gb and for G. firmus into 3,010 scaffolds totaling 2.0 Gb. Using a reference-based protocol, we achieved chromosome-level assemblies comprising 15 chromosomes for each species (totaling 1.86 and 1.84 Gb, respectively). The assemblies were nearly complete, with scaffold N50s of 115.64 and 119.52 Mb, respectively, and BUSCO scores of 97%. We characterized structural variants (SVs) between the two species using both genome assemblies and HiFi sequencing data. The longest SV found was a potential inversion spanning 10.12 Mb along the X chromosome; this inversion may represent a key component of divergence between the two species. Both reference genomes will be essential resources for ongoing studies of the evolution of reproductive isolation and comparative studies across field crickets.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148280013","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}