Khuram Zaman, Audrey McCombs, Diane M Debinski, Sean D Schoville
{"title":"Combining multiscale replication in network and landscape genetic analyses to assess functional connectivity and population resilience in Parnassius clodius butterflies.","authors":"Khuram Zaman, Audrey McCombs, Diane M Debinski, Sean D Schoville","doi":"10.1093/jhered/esaf033","DOIUrl":"https://doi.org/10.1093/jhered/esaf033","url":null,"abstract":"<p><p>Characterizing functional connectivity is an important challenge in the face of ongoing environmental change. Approaches combining landscape genetic and network methodologies have shown promise in allowing for simultaneous identification of strong and vulnerable populations, and the landscape factors that may inhibit or facilitate population connectivity. Here we leverage these tools to assess the genetic structure and functional connectivity of Parnassius clodius butterflies in three protected regions in the United States, North Cascades National Park (WA), Grand Teton National Park (WY), and Yosemite National Park (CA), and determine whether these metrics vary with differences in sampling scale among regions. We also test the resilience of population connectivity to extirpation using graph-theoretic analyses (e.g. network analyses) and test the relative importance of isolation by distance (IBD), isolation by resistance (IBR), and isolation by environment (IBE) in limiting population connectivity, using butterfly habitat suitability, host plant data, terrain roughness, percent forest cover, and climate variables. Both traditional genetic clustering analyses and network analyses revealed fine-scale genetic structure across all three regions. Our network analyses revealed similarity in topology across regions despite significant landscape variation, and network sensitivity analyses revealed that P. clodius subpopulations within the Grand Teton and Yosemite NP regions are more vulnerable to perturbations. Our landscape genetic analyses suggest that environmental variation has an important impact on genetic differentiation in addition to geographical distance, but the contribution of specific variables varies across replicate landscapes.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182909","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}
Josephine R Paris, Megan A Criss, Jessica L Walsh, Joan Ferrer Obiol, Christopher S Murray, Jason Q Boone, Ann M Petersen
{"title":"Two genomes of the white perch (Morone americana), an ecologically important teleost.","authors":"Josephine R Paris, Megan A Criss, Jessica L Walsh, Joan Ferrer Obiol, Christopher S Murray, Jason Q Boone, Ann M Petersen","doi":"10.1093/jhered/esaf034","DOIUrl":"https://doi.org/10.1093/jhered/esaf034","url":null,"abstract":"<p><p>The white perch, Morone americana, is a widely distributed and ecologically important teleost, native to the east coast of North America. Due to its ease of capture and high abundance across a range of ecological conditions, the white perch has been used, and continues to be developed, as a bioindicator of contaminant exposure. Outside of its native range, the white perch is invasive, negatively impacting local ecology and hybridizing with congeneric species. Using PacBio HiFi data, we present two (female and male) highly contiguous genome assemblies. The female assembly spans 694 Mb (264 contigs, N50: 24.9 Mb), with 85% of the total assembly size captured in the largest 24 contigs (the karyotype for the species is 2n = 48). The male assembly spans 688 Mb (265 contigs, N50: 26.4 Mb), with 89% of the total assembly size captured in the largest 24 contigs. Both assemblies have high BUSCO completeness scores of 98.7% (female) and 98.8% (male), and a high k-mer completeness (>98% for both genomes). Combining evidence derived from transcriptomic data and a large protein database, we constructed a high-quality annotation (99% BUSCO completeness, 87% OMArk completeness) including 20,699 predicted protein-coding genes, of which 20,406 have a functional annotation, and 16,187 have an associated gene name. These reference genomes will support the development of the white perch as a bioindicator and serve as an important resource for studying the species' invasiveness and monitoring intraspecific hybridization using genomic tools.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182667","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}
Cassandre B Pyne, Jillian N Campbell, S Eryn McFarlane, Elizabeth G Mandeville
{"title":"A novel sex-associated genomic region in Catostomus fish species.","authors":"Cassandre B Pyne, Jillian N Campbell, S Eryn McFarlane, Elizabeth G Mandeville","doi":"10.1093/jhered/esaf007","DOIUrl":"https://doi.org/10.1093/jhered/esaf007","url":null,"abstract":"<p><p>Genomic regions that influence sex are hypothesized to play a key role in evolutionary di- versification, as sex determination mechanisms may promote or impede reproductive isolation between closely related species. Remarkably, these mechanisms are almost completely un- known in many taxa, especially in clades like fish with extremely variable sex determination. In Catostomus fishes, contemporary hybridization is extensive but variable, and factors influ- encing hybridization dynamics are not fully understood. We used genotyping-by-sequencing data from three Catostomus species (bluehead, white, and flannelmouth suckers) to identify regions of the genome associated with sex using a genome-wide association study. We identi- fied a genomic region in bluehead suckers from Colorado on chromosome 4 that significantly associates with sex and is suggestive of a sex-determining region. This region is not signifi- cant in the other species studied here, or in a divergent lineage of bluehead suckers, implying that either the sex-determining region of the genome differs in these species and populations, or that technical limitations precluded identification of sex determination. These results pro- vide the first description of sex-determination systems in Catostomus species, and suggest that further investigation of sex determination in the Catostomidae are needed to better characterize evolutionary turnover of sex determination in this species-rich group.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175863","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}
Erin S Kelleher, Shahrzad Hajiarbabi, Llewellyn Green
{"title":"Extraordinary variation in radiation tolerance: mechanisms and evolution.","authors":"Erin S Kelleher, Shahrzad Hajiarbabi, Llewellyn Green","doi":"10.1093/jhered/esaf015","DOIUrl":"https://doi.org/10.1093/jhered/esaf015","url":null,"abstract":"<p><p>Ionizing radiation is a potent environmental mutagen, producing damaged bases and single and double-stranded DNA breaks. Acute high-dose radiation exposure is therefore toxic, causing cellular and organismal mortality, while lower doses can give rise to high mutation rates and cancer. Radiation sensitivity furthermore varies dramatically between organisms and cell types, with certain organisms exhibiting extreme tolerance to ionizing radiation. It is puzzling however, how such radiotolerance evolved in nature, as toxic radiation doses are not observed outside of medical and nuclear settings. In this review, we explore the mechanisms and evolution of extraordinary radiotolerance in metazoans. We contrast two extensively studied genetic models, mammals and Caenorhabditis elegans, as well as two lineages known to tolerate extreme radiation when compared to closely related species: naked mole rats and tardigrades. We describe similar strategies employed by these disparate lineages to protect DNA, repair DNA, and attenuate cellular responses following radiation exposure. We further discuss how these mechanisms may have evolved in response to other extreme conditions tolerated by each species in their natural environment, giving rise to radiotolerance as a correlated response.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175865","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}
Yu Wang, Yitian Bai, Gang Ni, Shikai Liu, Lingfeng Kong, Qi Li
{"title":"Chromosomal Fusions Reshape Gene Expression and Environmental Responses in Corbicula Clams.","authors":"Yu Wang, Yitian Bai, Gang Ni, Shikai Liu, Lingfeng Kong, Qi Li","doi":"10.1093/jhered/esaf030","DOIUrl":"https://doi.org/10.1093/jhered/esaf030","url":null,"abstract":"<p><p>Genome-structural evolution on a large scale is prevalent in various organisms. The role of genome-structural rearrangements, including chromosome fusions, has been revealed in genome evolution and species divergence. However, the empirical evidence in adaptation remains debated at the current time. We investigated the phylogenetic relationship, genomic divergence and environmental associations of closely related Asian clams: the freshwater species Corbicula fluminea and brackish-freshwater species Corbicula mortoni. The chromosome-level genome assembly of brackish-freshwater C. mortoni using single-molecule and Hi-C sequencing revealed a chromosome-scale rearrangement relative to freshwater C. fluminea. Strikingly, genomic characterization studies including outgroup species Archivesica marissinica indicated two independent fusion events in these closely related species. Transcriptome analysis under salinity stress identified differentially expressed genes (DEGs) and revealed a significant enrichment of significantly down-regulated genes (SDGs) on the fused chromosome of C. mortoni, suggesting possible regulatory shifts associated with fusion. In summary, our genomic and transcriptomic analyses document important chromosome-scale evolutionary events during Corbicula speciation and provides insights into the relationship between genomic reorganization and gene regulation in response to environmental variation.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082163","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}
Nicolas Alexandre, Jennifer Balacco, Tatiana Tilley, Linelle Abueg, Nadolina Brajuka, Lucas R Moreira, Conor Whelan, Erika Schwarz Taylor, Erich D Jarvis, Olivier Fedrigo, Beth Shapiro, Anna L Keyte
{"title":"A Chromosome-level genome of the Nicobar pigeon, Caloenas nicobarica.","authors":"Nicolas Alexandre, Jennifer Balacco, Tatiana Tilley, Linelle Abueg, Nadolina Brajuka, Lucas R Moreira, Conor Whelan, Erika Schwarz Taylor, Erich D Jarvis, Olivier Fedrigo, Beth Shapiro, Anna L Keyte","doi":"10.1093/jhered/esaf031","DOIUrl":"https://doi.org/10.1093/jhered/esaf031","url":null,"abstract":"<p><p>The Nicobar pigeon (Caloenas nicobarica), the closest living relative of the extinct Dodo (Raphus cucullatus), is endemic to Southeast Asia with a fragmented distribution across numerous small islands. It suffers from habitat loss, hunting, and predation from invasive species, resulting in its classification as Near-Threatened by the International Union for the Conservation of Nature (IUCN). We have generated a haplotype-resolved and chromosome-level genome assembly of the Nicobar pigeon using a combination of PacBio HiFi long-read sequencing and Arima Hi-C chromatin interaction mapping. This assembly includes two haplotypes, each spanning approximately 1.2 Gb. Haplotype 1 has a contig N50 of 25.2 Mb and a scaffold N50 of 79.7 Mb, while haplotype 2 has a contig N50 of 24.7 Mb and a scaffold N50 of 107.9 Mb. As the first high-quality genome assembly of any bird in the Columbidae Indo-Pacific clade, this resource provides valuable insights for phylogenetic studies. Furthermore, the phylogenetic proximity of the Nicobar pigeon to the Dodo (Raphus cucullatus) and the Rodrigues Solitaire (Pezophaps solitaria) offers a unique opportunity to study these extinct species, making this assembly a critical resource for evolutionary studies. It also offers a unique model for studying genetic diversity, adaptation, and speciation in island environments. This genomic resource will not only enhance our understanding of the evolutionary history of the Nicobar pigeon but also serves as a valuable tool for future conservation efforts aimed at preserving this unique species and its fragile island ecosystem.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082160","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}
Victor L N Araújo, José H Grau, Luis Alberto Rueda-Solano, José D Barros-Castañeda, Sandra V Flechas, Andrew J Crawford
{"title":"Genome assembly of the endangered Santa Marta Harlequin Toad, Atelopus laetissimus, endemic to the Sierra Nevada de Santa Marta of Colombia.","authors":"Victor L N Araújo, José H Grau, Luis Alberto Rueda-Solano, José D Barros-Castañeda, Sandra V Flechas, Andrew J Crawford","doi":"10.1093/jhered/esaf029","DOIUrl":"https://doi.org/10.1093/jhered/esaf029","url":null,"abstract":"<p><p>Despite the critical conservation status of many harlequin toads (Anura: Bufonidae: Atelopus) and their significance in elucidating the impacts of emerging diseases on amphibians, genomic data for this genus are scarce. Here, we present a de novo genome assembly of the Santa Marta Harlequin Toad, Atelopus laetissimus, using PacBio HiFi sequencing data, representing the first published Atelopus genome assembly and only the second amphibian genome assembly from Colombia. The assembly consists of 1,487 contigs at 35X coverage with an N50 of 31 Mb and a total length of 3.5 Gb. A Tetrapoda BUSCO score of 92% suggests our assembly is very nearly complete. Analysis revealed a high repeat content, with 70% of the genome consisting of interspersed repeats. This high-contiguity draft assembly will drive the search for a possible genetic basis of pathogen resistance in these endangered toads of the Sierra Nevada de Santa Marta, as well as facilitate ongoing evolutionary studies.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082166","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":"A chromosome-level genome assembly of the Chinese herring (Ilisha elongata) uncovered its population dynamics and genes related to lipid metabolism.","authors":"Tianqin Wu, Jiantao Hu, Vanthu Giap, Qian Wang, Liang Lu, Chenhong Li","doi":"10.1093/jhered/esaf028","DOIUrl":"https://doi.org/10.1093/jhered/esaf028","url":null,"abstract":"<p><p>The Chinese herring (Ilisha elongata) is an economically important clupeiform fish, mostly found along the coast of China and Japan in the western Pacific Ocean. Overfishing and climate change have caused a substantial decline in its annual catch, which may have impacted its population size and structure. Here, we present a chromosome-level genome assembly of the Chinese herring, generated using a combination of Nanopore sequencing, Illumina sequencing, and high-throughput chromatin conformation capture (Hi-C) technologies. The total length of this assembly is802.47 Mbp, anchored to 24 chromosomes, with contig N50 and scaffold N50 values of 13.22 Mbpand 33.10 Mbp, respectively. BUSCO analysis indicated high completeness of this assembly, with 94.9% of universal single-copy orthologs. Analysis of resequencing samples from various coastal regions of China and Japan revealed four distinct genetic populations of Chinese herring along the East Asian coast. The Dandong population (Yellow Sea) diverged earliest, exhibiting unique genetic structures and selective sweep signals, whereas the other three populations expanded from a tropical South China Sea ancestral population to the East China Sea and to Japanese waters. Among 23,366 protein-coding genes, several families related to metabolism of very-long-chain unsaturated fatty acids are particularly contracted compared to the American shad. Additionally, several genes associated with fatty acid synthesis formation have undergone accelerated positive selection. These findings may explain the differential fatty acid ratios in marine versus riverine migratory clupeiforms. This high-quality genome assembly of the Chinese herring may provide valuable resources for comparative study of coastal fishes and benefit the development of a sustainable management strategy for fisheries of the Chinese herring.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058365","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}
Susan Fawcett, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Eric Beraut, William Seligmann, Colin W Fairbairn, Erin Toffelmier, Courtney Miller, H Bradley Shaffer, Lucas C Majure
{"title":"A Chromosome-level Genome Assembly of the Beavertail Cactus, Opuntia basilaris.","authors":"Susan Fawcett, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Eric Beraut, William Seligmann, Colin W Fairbairn, Erin Toffelmier, Courtney Miller, H Bradley Shaffer, Lucas C Majure","doi":"10.1093/jhered/esaf027","DOIUrl":"https://doi.org/10.1093/jhered/esaf027","url":null,"abstract":"<p><p>Few genomic resources currently exist for the American endemic family Cactaceae, a group of around 1850 species, which are world renowned for their amazing growth forms and succulent habits. These icons of arid landscapes across the Americas are threatened in many parts of their range, including in parts of California, and developing more comprehensive genomic data will aid efforts to better understand and preserve these plants. We sequenced and assembled the genome of the beavertail cactus, Opuntia basilaris, which is represented by three varieties in California, one of which is threatened, and another endangered. The genome assembly has a BUSCO complete score of 98.1%, and a total scaffold length of 980 Mb, with a scaffold N50 length of 83 Mb. The genome size of diploid O. basilaris is markedly smaller than other diploid members of Cactaceae that have been assembled to date. This is the first nuclear genome sequenced in subfamily Opuntioideae and the most complete nuclear genome for Cactaceae to date and will lay the foundation for future genomic work across the biologically and taxonomically complicated prickly pear cacti.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144065078","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}
Rishi De-Kayne, Stacy Li, Merly Escalona, Runyang Nicolas Lou, Gregory L Owens, Sree Rohit Raj Kolora, Conner Jainese, Katelin Seeto, Merit McCrea, Oanh Nguyen, Noravit Chumchim, Ruta M Sahasrabudhe, Colin W Fairbairn, Richard E Green, William E Seligmann, Milton Love, Peter H Sudmant
{"title":"A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis.","authors":"Rishi De-Kayne, Stacy Li, Merly Escalona, Runyang Nicolas Lou, Gregory L Owens, Sree Rohit Raj Kolora, Conner Jainese, Katelin Seeto, Merit McCrea, Oanh Nguyen, Noravit Chumchim, Ruta M Sahasrabudhe, Colin W Fairbairn, Richard E Green, William E Seligmann, Milton Love, Peter H Sudmant","doi":"10.1093/jhered/esaf026","DOIUrl":"https://doi.org/10.1093/jhered/esaf026","url":null,"abstract":"<p><p>Rockfishes (genus Sebastes) are one of the most diverse clades amongst teleosts (ray-finned fishes). The genus includes more than 110 species which are distributed broadly across the North Pacific Ocean, North and South Atlantic Ocean, and Southeastern Pacific Ocean. Rockfishes exhibit particularly high diversity along the western coast of the United States, where their abundance plays a critical role in local marine ecosystems and fisheries. Sebastes paucispinis (\"bocaccio\") is a rockfish species most commonly found off the coast of California. In 2005, Bocaccio were federally declared overfished following massive depletion by commercial and recreational fisheries from the 1980s to early 2000s. Implementation of significant restrictions have bolstered recovery of critical rockfish populations along the California and Oregon coasts, but the impact of anthropogenic stressors on bocaccio, and other Sebastes species, has yet to be fully evaluated. Here, we present the first de novo reference-quality genome assembly of Sebastes paucispinis, as part of the California Conservation Genomics Project (CCGP).</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144057898","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}