Journal of Heredity最新文献

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Highly Contiguous Is Not Chromosomally Accurate: Integrated Cytogenetic and Genomic Mapping in Two Turtle Genome. 高度连续不是染色体准确:整合细胞遗传学和基因组图谱在两个海龟基因组。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-17 DOI: 10.1093/jhered/esag079
Anastasia A Proskuryakova, Katerina V Tishakova, Maria M Kulak, Arina V Ilina, Sergey A Marchenko, Lada S Lisachova, Guzel I Davletshina, Elena I Shagimardanova, Alessio Iannucci, Vladimir A Trifonov, Svetlana A Romanenko
{"title":"Highly Contiguous Is Not Chromosomally Accurate: Integrated Cytogenetic and Genomic Mapping in Two Turtle Genome.","authors":"Anastasia A Proskuryakova, Katerina V Tishakova, Maria M Kulak, Arina V Ilina, Sergey A Marchenko, Lada S Lisachova, Guzel I Davletshina, Elena I Shagimardanova, Alessio Iannucci, Vladimir A Trifonov, Svetlana A Romanenko","doi":"10.1093/jhered/esag079","DOIUrl":"https://doi.org/10.1093/jhered/esag079","url":null,"abstract":"<p><p>High-quality genome assemblies are essential for robust research across biological and medical fields. Assembly errors can have far-reaching consequences for downstream analyses, including gene annotation and the inference of synteny. In contrast to the rapid growth of genomic data volume, there is a notable lag in the integration of chromosome-level assemblies with cytogenetic data. We conducted the first direct genome-to-genome comparison, integrating comparative chromosome painting, the alignment of chromosome-specific probes to available genome assemblies, and synteny-based comparison of independent chromosome-level assemblies of the loggerhead sea turtle (Caretta caretta, 2n = 56) and the red-eared slider (Trachemys scripta elegans, 2n = 50). Using two independent sets of flow-sorted chromosome-specific probes in cross-species hybridizations, together with the sequencing and mapping of chromosome-derived DNA libraries, we assigned assembled scaffolds to all physical chromosomes of both species. In C. caretta, chromosomal assignments and genome-wide synteny were fully consistent with the published assembly, except for the reduced sizes of two microchromosome scaffolds, which we attribute to under-representation of repetitive DNA. In contrast, in T. s. elegans, cytogenetic validation of the assemblies revealed a false rearrangement compared to a missed one. Our results show that even highly contiguous vertebrate genome assemblies can misrepresent chromosome structure. When cytogenetic analyses reveal such inaccuracies, updated reference genomes should be generated for widely studied species to enable accurate inference of karyotype evolution and downstream comparative genomic analyses.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992579","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}
引用次数: 0
The evolutionary origins of the parthenogenetic lizard Aspidoscelis tesselatus. 孤雌蜥蜴的进化起源。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-16 DOI: 10.1093/jhered/esag077
Sonal Singhal, Maggie R Grundler, Danielle Rivera, Sam Fisher, Alexander S Hall, Kathleen Currie, Adrián Nieto Montes de Oca, Corey Roelke, Adam D Leaché, Matthew K Fujita
{"title":"The evolutionary origins of the parthenogenetic lizard Aspidoscelis tesselatus.","authors":"Sonal Singhal, Maggie R Grundler, Danielle Rivera, Sam Fisher, Alexander S Hall, Kathleen Currie, Adrián Nieto Montes de Oca, Corey Roelke, Adam D Leaché, Matthew K Fujita","doi":"10.1093/jhered/esag077","DOIUrl":"https://doi.org/10.1093/jhered/esag077","url":null,"abstract":"<p><p>Most vertebrate species reproduce sexually. The whiptail lizards (Aspidoscelis) are a notable exception; at least 11 of the 45 recognized species are parthenogenetic. Here, we focus on one such species (Aspidoscelis tesselatus) as a case study to understand how parthenogenetic species originate and evolve. Using genome-wide sequence data and ecological niche modelling, we find that A. tesselatus likely arose from a single hybrid speciation event between A. scalaris and A. marmoratus less than 500,000 years ago. The geographic ranges of A. tesselatus and its parental species overlap currently, and niche modelling shows this zone of sympatry was even broader during the period when A. tesselatus likely formed. We additionally show evidence that A. tesselatus has a dynamic genome post-formation, with de novo mutations, introgression, and double-strand break associated events all contributing to variation within the species. These results show that asexual lineages can continue to be shaped by ongoing genomic and ecological dynamics, illuminating the processes that influence transitions in reproductive mode.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148978411","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}
引用次数: 0
Reference genomes of Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica). 日本貉(Nyctereutes viverrinus)和日本赤狐(Vulpes Vulpes japonica)的参考基因组。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-15 DOI: 10.1093/jhered/esag075
Kei Nabeshima, Haruto Sugeno, Ryota Koba, Manabu Onuma
{"title":"Reference genomes of Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica).","authors":"Kei Nabeshima, Haruto Sugeno, Ryota Koba, Manabu Onuma","doi":"10.1093/jhered/esag075","DOIUrl":"https://doi.org/10.1093/jhered/esag075","url":null,"abstract":"<p><p>We established primary fibroblast cultures from a Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica) and generated highly contiguous reference genome assemblies using Oxford Nanopore Technologies PromethION long-read sequencing. The Japanese raccoon dog assembly spanned 2.69 Gb in 813 scaffolds, with a scaffold N50 of 52 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 98.2%. The Japanese red fox assembly spanned 2.47 Gb in 903 scaffolds, with a scaffold N50 of 139 Mb and a BUSCO completeness score of 97.5%. Phylogenomic analysis placed the Japanese raccoon dog in a lineage distinct from the continental raccoon dog, supporting its evolutionary differentiation within Nyctereutes. The Japanese red fox formed a distinct lineage within the red fox clade, consistent with its recognized regional differentiation. These genome assemblies and associated fibroblast cultures provide resources for studies of canid systematics, population history, local adaptation, comparative genome evolution, and conservation genetics.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148971976","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}
引用次数: 0
Reference genome of the Californian trapdoor spider Aptostichus stephencolberti Bond 2008 (Araneae: Mygalomorphae: Euctenizidae). 加州活门蜘蛛Aptostichus stephencolberti Bond的参考基因组2008(蜘蛛目:mygalomorae: Euctenizidae)。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-08 DOI: 10.1093/jhered/esag069
Stephen Richards, Emma Jochim, Lacie Newton, James Starrett, Ruta Sahasrabudhe, Oanh Nguyen, Eric Beraut, Colin Fairbairn, Samuel Sacco, William Seligmann, Merly Escalona, Robert D Cooper, H Bradley Shaffer, Erin Toffelmier, Jason E Bond
{"title":"Reference genome of the Californian trapdoor spider Aptostichus stephencolberti Bond 2008 (Araneae: Mygalomorphae: Euctenizidae).","authors":"Stephen Richards, Emma Jochim, Lacie Newton, James Starrett, Ruta Sahasrabudhe, Oanh Nguyen, Eric Beraut, Colin Fairbairn, Samuel Sacco, William Seligmann, Merly Escalona, Robert D Cooper, H Bradley Shaffer, Erin Toffelmier, Jason E Bond","doi":"10.1093/jhered/esag069","DOIUrl":"https://doi.org/10.1093/jhered/esag069","url":null,"abstract":"<p><p>We present a reference genome assembly for the trapdoor spider Aptostichus stephencolberti. This species, described in 2008, is endemic to the highly fragmented coastal dune habitats of Northern California from Monterey to the San Francisco Bay Area. Trapdoor spiders are ideal taxa for landscape scale genomic studies owing to their extreme site fidelity and limited dispersal capabilities; these same characteristics make them prone to extinction. Genomic studies of species like A. stephencolberti can reveal novel areas of endemism and high conservation value that may not be evident in species with wider ranges and greater dispersal capabilities. As part of the California Conservation Genomics Project, we constructed the A. stephencolberti reference genome from high quality long-read sequences, scaffolded with proximity ligation Omni-C data. The primary assembly comprises 551 scaffolds spanning 3.63 Gbp, a scaffold N50 of 62.2 Mbp and BUSCO completeness of 95.6%. We estimate 52 chromosomes yet find no (TTAGG)n telomer repeats. Expanding the telomeric repeat search finds an ancestral loss of the repeat from all spiders. Automated annotation using the NCBI refseq pipeline and RNAseq data from whole adults finds 14,067 genes with a BUSCO annotation completeness of 95.56%. Repeat annotation identified 77% of the genome to be interspersed repeats. This resource, the first for family Euctenizidae will facilitate future study and resulting conservation actions of A. stephencolberti and other Aptostichus sp. populations associated with the rapidly changing California coastal dune ecosystem.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148908251","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}
引用次数: 0
Improved Genomic Resources for the swordtail cricket, Laupala kohalensis Otte 1994. 剑尾蟋蟀基因组资源的改良,Laupala kohalensis Otte 1994。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-06 DOI: 10.1093/jhered/esag073
Nicholai M Hensley, Benjamin A Sandkam, Kerry L Shaw
{"title":"Improved Genomic Resources for the swordtail cricket, Laupala kohalensis Otte 1994.","authors":"Nicholai M Hensley, Benjamin A Sandkam, Kerry L Shaw","doi":"10.1093/jhered/esag073","DOIUrl":"https://doi.org/10.1093/jhered/esag073","url":null,"abstract":"<p><p>Advances in genetic tools such as next and third generation sequencing, paired with a focus on representative clades, provide insight into how processes including adaptation, admixture, and genome structure shape the evolution and maintenance of species. However, our understanding of the genomics of speciation is dominated by systems where ecological adaptations are thought to cause initial barriers to gene exchange. In contrast to other model systems, the 38 species of the genus Laupala constitute a very rapid radiation, where evolution of reproductive barriers and speciation is thought to be driven by sexual selection. Here, with novel PacBio HiFi reads and RNA- and Iso-Seq data, we provide a highly contiguous, chromosome-level genome and markedly improved annotation of the endemic Hawaiian cricket, Laupala kohalensis Otte, 1994. Our new resources advance previous efforts, placing 99% of 47 scaffolds on 7 autosomes and 1 sex chromosome in the 1.67 Gb assembly, with a 98.8% BUSCO score (insecta_db10), N50 of ~268 Mb, and L50 of 3. Using a custom repeat library, we estimate the genome to have 46.09% repeat content, and the new annotation includes an increased estimate of 17,670 genes, which coincides with that known from other Orthopterans. Notably, we find a large nuclear DNA segment of mitochondrial origin on chromosome 7. This new resource provides a powerful tool to identify and compare genomic causes of phenotypic diversification in a system characterized by strong signatures of sexual differentiation, representing an underappreciated but potentially widespread cause of speciation.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148901659","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}
引用次数: 0
Comparative analysis of olfactory receptor repertoires reveals evolutionary dynamics and high-altitude adaptation in Schizopygopsis younghusbandi based on the chromosome-level genomes. 基于染色体水平基因组的嗅觉受体谱比较分析揭示了扬氏裂腹虫(Schizopygopsis younghusbandi)的进化动力学和高原适应性。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-05 DOI: 10.1093/jhered/esag074
Huayan Zhao, Weidong Wu, Changkun Fu, Yawen Wu, Qichao Liu, Yi Liu, Chuang Zhou
{"title":"Comparative analysis of olfactory receptor repertoires reveals evolutionary dynamics and high-altitude adaptation in Schizopygopsis younghusbandi based on the chromosome-level genomes.","authors":"Huayan Zhao, Weidong Wu, Changkun Fu, Yawen Wu, Qichao Liu, Yi Liu, Chuang Zhou","doi":"10.1093/jhered/esag074","DOIUrl":"https://doi.org/10.1093/jhered/esag074","url":null,"abstract":"<p><p>The olfactory receptor (OR) gene represent a significant multigene family in vertebrates, forming the core molecular basis of olfactory perception and playing a crucial role in the environmental adaptation of species. High-altitude ecosystems represent extreme habitats characterized by specific abiotic stresses, including low oxygen levels, low temperatures, and intense ultraviolet radiation. These environments also exhibit low aquatic biodiversity and a limited variety of odor molecules, factors that have influenced the adaptive evolution of the sensory systems in endemic species. However, the genetic mechanisms underlying olfactory adaptation in high-altitude freshwater fish remained inadequately understood. In this study, we performed comparative genomics analyses to reveal the evolutionary processes underlying the adaptive and functional evolution of OR genes in S. younghusbandi, a cyprinid fish endemic to the Qinghai-Xizang Plateau. The results indicated that, compared to their low-altitude relatives, S. younghusbandi possessed a significantly smaller number of OR genes, with only 98 genes, which revealed the contraction of the gene family. Phylogenetic analysis revealed that the OR genes of cyprinid fish could be categorized into two major lineages: type I and type II. The η and δ families, which perceive water-soluble odors, in S. younghusbandi underwent significant and specific expansion, while the ε family was completely absent. This pattern reflected adaptive changes in olfactory recognition to accommodate the simplified odor spectrum of high-altitude water bodies. Chromosomal localization analysis demonstrated that OR genes were clustered, and collinearity analysis confirmed the presence of conserved genomic fragments among species. Selection pressure analysis revealed that the Ka/Ks values of all homologous gene pairs were less than 1, indicating that the OR genes of S. younghusbandi underwent strong purifying selection as a group to preserve core olfactory function. A few genes exhibited relaxed selection characteristics, which may have facilitated the fine-tuning of adaptability to high-altitude environments. In conclusion, this study elucidated the evolutionary dynamics and adaptive characteristics of the OR gene in S. younghusbandi, offering a new perspective on the molecular mechanisms underlying olfactory adaptation at high altitudes and enriching the research on sensory evolution in vertebrates.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148898518","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}
引用次数: 0
Bycatch in a bottle: what taxa are recoverable from metabarcoding DNA in historical invertebrate collection preservative fluid? 瓶中副渔获物:从历史无脊椎动物收集保存液中的元条形码DNA中可恢复哪些分类群?
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-03 DOI: 10.1093/jhered/esag001
Ajith Seresinghe, David Herbst, Jen Quick-Cleveland, Severyn Korneyev, Benjamin K Maples, Eva Sofia Horna Lowell, Malia Mosser, Robert N Fisher, Eric P Palkovacs, Daniel Gluesenkamp, Rachel S Meyer
{"title":"Bycatch in a bottle: what taxa are recoverable from metabarcoding DNA in historical invertebrate collection preservative fluid?","authors":"Ajith Seresinghe, David Herbst, Jen Quick-Cleveland, Severyn Korneyev, Benjamin K Maples, Eva Sofia Horna Lowell, Malia Mosser, Robert N Fisher, Eric P Palkovacs, Daniel Gluesenkamp, Rachel S Meyer","doi":"10.1093/jhered/esag001","DOIUrl":"10.1093/jhered/esag001","url":null,"abstract":"<p><p>Natural history museum collections are invaluable repositories of biodiversity, offering insights into life on Earth. Genomic approaches provide powerful tools to characterize biodiversity in these collections. However using these collections for genomics without damaging specimens is a challenge. Here, we develop and test non-destructive DNA metabarcoding methods to capture biodiversity from the preservative fluids of archived insect collections ('Bycatch'). We optimized workflows for extracting and amplifying the partial CO1 locus (CO1) and fungal ITS1 locus from ethanol-based preservative fluids, validating ethanol preparation methods, comparing DNA extraction kits, and refining PCR protocols. Our results demonstrate that from museum collections with low DNA yields, CO1 and fungal ITS1 loci can often be recovered from preservative fluids, and we present detailed methodology and workflows. We test metabarcoding success to recover taxa in several museum collections ranging in age and storage condition. This is to support the State of California's effort to catalog and sequence all insects and fungi, building baselines of California biodiversity with help from museum collections. Lastly, we investigate the complementarity of metabarcoding water versus ethanol and morphological identifications aimed to capture benthic macroinvertebrate biodiversity in streams. Our findings highlight that DNA metabarcoding of the preservative fluid is a non-destructive tool for capturing biodiversity in historical specimens, but there are limitations on the overlaps between DNA results and physical contents, where morphological identification still reigns in taxon counts, but metabarcoding sometimes provides more taxonomic resolution, and can be used to track DNA from other organisms such as fungi beyond the directly surveyed specimens.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"1036-1048"},"PeriodicalIF":2.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13539438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145953943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A chromosome-level genome of the Nicobar pigeon, Caloenas nicobarica. Nicobar鸽子的染色体水平基因组。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-03 DOI: 10.1093/jhered/esaf031
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":"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. 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, whereas 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 (R. 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 serve 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":"1144-1149"},"PeriodicalIF":2.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13539444/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The paradoxical extinction: Exploring signatures of assortative mating as a possible mechanism that maintains canonical Red Wolf genetic ancestry in the American Gulf Coast canids. 矛盾的灭绝:探索分类交配的特征作为一种可能的机制,在美国墨西哥湾沿岸的犬科动物中维持典型的红狼遗传祖先。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-03 DOI: 10.1093/jhered/esag010
Bridgett M vonHoldt, India Macaire, Kristin E Brzeski
{"title":"The paradoxical extinction: Exploring signatures of assortative mating as a possible mechanism that maintains canonical Red Wolf genetic ancestry in the American Gulf Coast canids.","authors":"Bridgett M vonHoldt, India Macaire, Kristin E Brzeski","doi":"10.1093/jhered/esag010","DOIUrl":"10.1093/jhered/esag010","url":null,"abstract":"<p><p>Admixed genomes, particularly those with an evolutionary history of genetic exchange with an endangered or extinct species, are valued for innovative and unconventional conservation actions. Here, we show the substantial conservation value that the admixed canids of the Gulf Coast have as they retain high amounts of contemporary Red Wolf ancestry and unique genetic variation of past Red Wolf lineages (e.g. ghost ancestry). We analyzed 54,439 loci genotyped across the genome of 413 North American canids and investigated the role that assortative mating with respect to ancestry proportions played in the retention of endangered genetic variation. We report high correlations of inter-chromosomal ancestry proportions that varied with geographic location along Texas and Louisiana Gulf Coast populations, with the stronger signatures reported in the latter. We found that models of assortative mating promoted greater ancestry variance compared with random mating leading to increased efficiency of selection for Red Wolf and ghost alleles. Despite the Red Wolf being extinct in the wild, original, and ghost genomic variation persists in Gulf Coast admixed canids. We suggest two conservation strategies that value and preserve this unique and endangered genomic variation through designed breeding programs. Ultimately the incorporation of this ghost genetic variation would be valuable to boost the genetic viability of the ex situ Red Wolf breeding program, create in situ redundancy, and avoid extinction for this endemic American wolf species.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"1059-1072"},"PeriodicalIF":2.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13539447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146088187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The value of structural variants to conservation genomics in the pangenome era. 泛基因组时代结构变异对保护基因组学的价值。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-03 DOI: 10.1093/jhered/esaf098
Teresa M Pegan, Ashwin H Sivakumar, Christian A Burns, Kelsie A Lopez, Bohao Fang, Nicole M Melendez, Lauren Bartel, Scott V Edwards
{"title":"The value of structural variants to conservation genomics in the pangenome era.","authors":"Teresa M Pegan, Ashwin H Sivakumar, Christian A Burns, Kelsie A Lopez, Bohao Fang, Nicole M Melendez, Lauren Bartel, Scott V Edwards","doi":"10.1093/jhered/esaf098","DOIUrl":"10.1093/jhered/esaf098","url":null,"abstract":"<p><p>Structural variants (SVs) comprise an axis of genetic diversity with strong consequences for phenotype and fitness, making them a potentially important target for conservation genomics. Here, we review how and why SVs can play a role in conservation genomics; the different types of SVs and how they can affect phenotype; and how pangenomes and long-read sequencing are illuminating their evolution in populations, including small populations and those of conservation concern. SVs comprise multinucleotide mutations including insertions, deletions, transpositions, inversions, and other multinucleotide mutations, often overlapping genes and other functional genome regions. As a result, SVs often play important roles in phenotypic evolution and local adaptation and can contribute substantially to genetic load in inbred populations. However, our understanding of the factors influencing SV diversity in populations is still in its infancy and is complicated by the vast range of sizes, effects, and mechanisms of formation of these mutations. We argue that SVs are an important axis of genetic diversity which should be characterized alongside more traditional metrics of genetic diversity in conservation contexts. There are a number of analytical challenges to detecting and studying SVs, but analyses aimed at understanding the role of SVs in inbreeding load and population health are rapidly becoming realizable goals, accelerated by new technologies and analytical approaches. New tools, including population-scale long-read sequencing and pangenome approaches, are beginning to make SVs accessible in ways which can be readily applied in conservation settings.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"975-992"},"PeriodicalIF":2.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589614","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}
引用次数: 0
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