Xing-Long Wu, Peng-Fei Jin, Hong-Ling Liu, Zhi-Teng Chen, Su Liu, Mao-Ye Li, De-Qiang Pu
{"title":"Chromosome-level genome assembly and annotation of the transverse lady beetle Coccinella transversoguttata.","authors":"Xing-Long Wu, Peng-Fei Jin, Hong-Ling Liu, Zhi-Teng Chen, Su Liu, Mao-Ye Li, De-Qiang Pu","doi":"10.1093/jhered/esag050","DOIUrl":"https://doi.org/10.1093/jhered/esag050","url":null,"abstract":"<p><p>The transverse lady beetle Coccinella transversoguttata Faldermann, 1835 is an ecologically important aphid predator and a declining native biocontrol agent in parts of its range. To provide a genomic resource for evolutionary, ecological, and applied research, we generated a chromosome-level genome assembly using PacBio HiFi long reads, Illumina whole-genome short reads, Hi-C chromatin conformation capture, and full-length transcriptome sequencing. The final assembly spans 376.3 Mb and comprises 58 scaffolds ≥1 kb, of which 363.4 Mb (96.6%) was anchored onto 10 chromosome-scale pseudomolecules. Assembly contiguity was high (contig N50 = 41.6 Mb; scaffold N50 = 41.6 Mb), and completeness was supported by 98.4% complete arthropod BUSCOs. Repetitive sequences constituted 58.2% of the genome, and 13,808 protein-coding genes were annotated with strong transcriptomic and homology-based support. Comparative analysis with a recently published conspecific genome revealed strong chromosome-scale collinearity but notable differences in total assembly size, repeat content, and local structural variation, suggesting either population-level genomic divergence or methodological differences in repeat resolution. Cross-species synteny with Coccinella septempunctata Linnaeus, 1758 further demonstrated substantial conservation of chromosome architecture across the genus. This resource provides a high-quality reference genome with broad utility for comparative genomics, predator ecology, biological control, and genome evolution studies in Coccinellidae.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148260584","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}
Mathieu Gautier, Pierre Nouhaud, Jacques Lagnel, Manuela Branco, Thomas Chertemps, Franck Dorkeld, Marie-Christine François, Bernhard Gschloessl, Frédérique Hilliou, Emmanuelle Jacquin-Joly, Fabrice Legeai, Gaëlle Le Goff, Céline Lopez-Roques, Martine Maibeche, William Marande, Hugues Parinello, Laure Sauné, Charles Perrier, Carole Kerdelhué
{"title":"A Chromosome-Level Assembly of the Pine Processionary Moth (Thaumetopoea pityocampa) genome.","authors":"Mathieu Gautier, Pierre Nouhaud, Jacques Lagnel, Manuela Branco, Thomas Chertemps, Franck Dorkeld, Marie-Christine François, Bernhard Gschloessl, Frédérique Hilliou, Emmanuelle Jacquin-Joly, Fabrice Legeai, Gaëlle Le Goff, Céline Lopez-Roques, Martine Maibeche, William Marande, Hugues Parinello, Laure Sauné, Charles Perrier, Carole Kerdelhué","doi":"10.1093/jhered/esag035","DOIUrl":"https://doi.org/10.1093/jhered/esag035","url":null,"abstract":"<p><p>We present a chromosome-level genome assembly and annotation of the pine processionary moth, Thaumetopoea pityocampa (Lepidoptera: Notodontidae), a key forest pest that is a public health concern. The nuclear genome spans 615.9 Mb, scaffolded into 50 pseudochromosomes and 115 smaller scaffolds, with high completeness (BUSCO score: 98.9%) that provides a decisive improvement over the previous assembly (537 Mb; 68,292 contigs; BUSCO 83.6%). Coverage differences in resequenced males and females allowed identification of the Z chromosome and several W-linked contigs. As expected from previous studies, we found that synteny was largely conserved with related Lepidoptera, although chromosomal fissions may explain the higher chromosome number of 49 autosomes compared to typical lepidopteran karyotypes. We also integrated into the assembly linkage map, allowing estimation of a genome-wide male recombination rate of 5.06 cM/Mb, varying from 11.6 cM/Mb to 1.98 cM/Mb from the smallest to the largest chromosomes. Repetitive elements represented 49.1% of this new assembly, dominated by LINEs (45.1% of classified repeats). Finally, gene prediction identified 12,898 gene models, among which 17 circadian rhythm genes were manually curated. Expert annotation further allowed to identify 51 genes of the odorant receptor (OR) family as well as a total of 236 detoxification genes, including 78 CYPs, 56 CCEs, 30 GSTs, 23 UGTs and 49 ABCs. Overall, this assembly represents the first chromosome-level genome for a member of the Thaumetopoeinae subfamily, significantly expanding the currently limited set of genomic resources available for Notodontidae. The fully annotated assembly is publicly accessible through the LepidoDB database (https://bipaa.genouest.org/is/lepidodb/) and will serve as a valuable resource for research on population genomics of this species.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148221068","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}
Jana Nickel, Sarah Fullmer, Ole K Tørresen, Giada Ferrari, Jan T Laine, Anders Romundset, Morten Skage, Ave Tooming-Klunderud, Andrew D Foote, Kjetill S Jakobsen
{"title":"Chromosome-level genome assembly of a Norwegian threespine stickleback (Gasterosteus aculeatus) improves mapping for ancient DNA and QTL associated with parallel loss of pelvic spines.","authors":"Jana Nickel, Sarah Fullmer, Ole K Tørresen, Giada Ferrari, Jan T Laine, Anders Romundset, Morten Skage, Ave Tooming-Klunderud, Andrew D Foote, Kjetill S Jakobsen","doi":"10.1093/jhered/esag047","DOIUrl":"https://doi.org/10.1093/jhered/esag047","url":null,"abstract":"<p><p>The threespine stickleback represents a model system for studying parallel evolution, due to the repeated phenotypic adaptation of ancestral marine/anadromous populations to freshwater. Consequently, the genomic architecture underpinning these phenotypic traits has been extensively studied, and an increasing number of genomic resources are available. These include high quality chromosomal reference genome assemblies for Pacific marine and freshwater sticklebacks. However, these reference genomes may bias mapping of short-read data from Atlantic stickleback, and do not fully resolve some repeat-rich regions. Here, we present a chromosome-level reference genome (fGasAcu404) generated from an Atlantic anadromous stickleback using PacBio HiFi and Hi-C data. The assembly improves representation of repeat-rich regions, including on chromosome VII, where the Pitx1 locus and upstream PelA enhancer (Quantitative Trait Loci underpinning repeated loss of the pelvic girdle and spines) are located. Syntenic comparisons and mapping of short reads from well-studied spined and spineless stickleback indicate these loci are incorporated into the new assembly. We evaluate the utility of this reference for paleogenomic analyses by mapping ancient (>10,000 years BP) Norwegian stickleback DNA and assessing inversion karyotypes. We find marginal mapping gains and the ability to robustly infer homozygous ancestral karyotypes at three inversions in two ancient genomes which have predominantly marine-adaptive ancestry. However, karyotype is more ambiguous in an ancient genome with predominantly freshwater ancestry, reflecting the need for further genomic resources for this system. This new reference represents an important step towards the construction of a pangenome that better encompasses genetic variation among ancient and contemporary threespine stickleback populations across their range.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148221105","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}
Caleb J Krueger, Robert D Cooper, Arun Sethuraman, H Bradley Shaffer
{"title":"An annotated, chromosome-level genome for the spotted turtle, Clemmys guttata.","authors":"Caleb J Krueger, Robert D Cooper, Arun Sethuraman, H Bradley Shaffer","doi":"10.1093/jhered/esag049","DOIUrl":"https://doi.org/10.1093/jhered/esag049","url":null,"abstract":"<p><p>The spotted turtle (Clemmys guttata) is the sole extant member of the genus Clemmys and can be found in shallow wetlands across eastern North America. In recent decades, habitat alterations and poaching have reduced spotted turtle populations by more than 50% range-wide, resulting in federal protection in Canada and state-level protection within the United States. Here, we provide an annotated, chromosome-level assembly of C. guttata derived from long- and ultra-long read data as an addition to the conservation genomics resources for the species. The assembly comprises 2,286,936,868 base pairs, 98.5% of which are assembled in 25 contigs, consistent with published karyotypic data (n = 25) and including 16 gapless, telomere-to-telomere chromosome sequences. BUSCO scores indicate a highly complete assembly (99.4%). Annotation of the genome yielded 21,335 protein-coding genes with a BUSCO completeness score of 98.4%. Comparisons with a separate assembly derived from long-read and Hi-C data show that substituting ultra-long for Hi-C sequencing can improve telomere assembly and reduce structural errors in this taxon at the cost of reduced haplotype phasing, though primary assemblies are highly syntenic overall. PSMC analyses of both assemblies independently revealed a long, essentially identical history of population declines in spotted turtles. Coupled with range-wide genomic sampling, these resources will provide critical data to understand genetic structure, patterns of local adaptation, and demographic history in this species and help stem further declines.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148221126","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":"Chromosome-level Genome Assembly of the Small Snakehead (Channa asiatica) Provides Insights into the Genetic Basis for its Pelvic Fin Loss.","authors":"Minmin Xie, Mingpeng Zheng, Yixuan Chen, Pinpin Zhang, Zhongyi Wang, Zhaobin Song, Yi Liu, Chuang Zhou","doi":"10.1093/jhered/esag046","DOIUrl":"https://doi.org/10.1093/jhered/esag046","url":null,"abstract":"<p><p>The paired appendages of vertebrates are a pivotal developmental innovation, of which the pelvic fins of teleosts are evolutionarily homologous to the hind limbs of tetrapods. The small snakehead (Channa asiatica), an important freshwater fish with significant commercial value, lacks the pelvic fins while some other fish species in the same genus have. To determine the genetic changes underlying the pelvic fin loss in the small snakehead, we assembled the chromosome-level genome of the species based on PacBio HiFi and Hi-C sequencing technology and performed comparative genomics analyses. The final genome assembly of the small snakehead has a total length of 714.57 Mb with 23 chromosomes (contig N50 of 27.93 Mb and scaffold N50 of 28.54 Mb), and 193.09 Mb (27.02%) interspersed repeats and 22,300 protein-coding genes were annotated. Phylogenetic and divergence analyses indicated that the small snakehead was the sister branch to the combination of the northern snakehead (C. argus) and the blotched snakehead (C. maculata) and diverged from the common ancestor approximately 24.7 Mya. Three small snakehead-specific missense mutations were identified in tbx4 gene whose loss could cause the pelvic fin loss. Significant chromosomal rearrangement and 214 small snakehead-specific structural variations (SSSVs) were detected between the small snakehead and other Channa species. Among these SSSVs, the deletion in pax7a was likely to play a role in the pelvic fin loss. Furthermore, the specific loss of conserved non-coding regulatory elements (CNEs) related to limb/fin development was detected in the small snakehead, which possibly led to the pelvic fin loss of the small snakehead. The present study generated the high-quality chromosome-scale reference genome of the small snakehead, which provided a valuable genomic resource for the follow-up studies, and our findings shed light on the important genetic clues regarding pelvic fin loss in the species.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148165709","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}
H K Baker, M Escalona, A P Kinziger, J Rodzen, S Parmenter, M P A Marimuthu, O Nguyen, N Chumchim, E Beraut, S Sacco, W Seligmann, C W Fairbairn, R D Cooper, C Miller, E Toffelmier, J C Garza, H B Shaffer, J B Shurin, D J Rennison
{"title":"A genome assembly of the speckled dace, Rhinichthys Osculus.","authors":"H K Baker, M Escalona, A P Kinziger, J Rodzen, S Parmenter, M P A Marimuthu, O Nguyen, N Chumchim, E Beraut, S Sacco, W Seligmann, C W Fairbairn, R D Cooper, C Miller, E Toffelmier, J C Garza, H B Shaffer, J B Shurin, D J Rennison","doi":"10.1093/jhered/esag041","DOIUrl":"https://doi.org/10.1093/jhered/esag041","url":null,"abstract":"<p><p>The speckled dace, Rhinichtyhs osculus, is a cyprinoid fish species complex (family: Leuciscidae) with one of the widest native ranges of any freshwater fish in western North America. It occupies a variety of freshwater habitats and exhibits considerable morphological and genetic variation across its range. Several endemic taxa within the species complex are imperiled, four of which are protected under the US Endangered Species Act, with two more proposed for listing. Here, we present an annotated, scaffold-level assembly of the speckled dace genome as part of the California Conservation Genomics Project (CCGP). Consistent with the CCGP genome assembly strategy, we used Pacific Biosciences HiFi long reads and Omni-C data for our de novo genome assembly and performed genome annotations on NCBI Eukaryotic Genome Annotation Pipeline using novel, species-specific RNA-Seq reads generated from five tissue types. The assembly consists of 490 scaffolds totaling approximately 1.15 Gb, with a contig N50 of 10.9 Mb and a scaffold N50 of 44.5 Mb. A BUSCO score of 97.7% reflects the assembly's strong completeness. The genome of Rhinichthys osculus is estimated to consist of 25 chromosomes. This is the first scaffold-level genome assembly within the genus Rhinichthys. We annotated a total of 39,919 genes with a BUSCO completeness score of 98.3%. This reference genome will be a valuable resource for understanding the phylogeography and evolution of speckled dace and informing its conservation.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148037830","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}
Douglas E Soltis, Shengchen Shan, Gregory W Stull, Pamela S Soltis
{"title":"Plant Species Extinction and Opportunities for De-extinction.","authors":"Douglas E Soltis, Shengchen Shan, Gregory W Stull, Pamela S Soltis","doi":"10.1093/jhered/esag036","DOIUrl":"https://doi.org/10.1093/jhered/esag036","url":null,"abstract":"<p><p>Extinction has received considerable attention in animals, particularly charismatic vertebrates. Plants, like animals, face alarming extinction risks with many of the same underlying causes including habitat loss, climate change, disease, invasive species, and over harvesting. However, habitat modifications by humans might make it much more challenging for plants to respond to rapid contemporary climate change by shifting distributions, either because suitable habitat no longer exists or because the human-altered landscapes pose too great a barrier to dispersal for some species. De-extinction (i.e., the revival of genes or phenotypes of extinct species) has similarly received considerable attention in animals with little discussion in plants. De-extinction is already possible in plants, particularly for those species with close relatives for which there are rich genomic resources as well as the capacity for CRISPR-mediated gene editing and regeneration. Herbarium collections offer one important source of DNA for plants that have gone extinct in that time frame. The opportunities for de-extinction in plants will only increase as genomic resources and the tools for regeneration and genome editing improve. We also consider some of the ethical issues to de-extinction in plants, focusing our discussion of the topic to those plants clearly driven to extinction by human activity in just the past few hundred years.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148007417","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}
Lorenz Dale Decena, Richard M Bevan, Jodie Brown, Vlatka Cubric-Curik, Aileen C Mill, Evelyn L Jensen
{"title":"Old goats, new insights: Origins and genetic diversity of feral Cheviot goats.","authors":"Lorenz Dale Decena, Richard M Bevan, Jodie Brown, Vlatka Cubric-Curik, Aileen C Mill, Evelyn L Jensen","doi":"10.1093/jhered/esag044","DOIUrl":"https://doi.org/10.1093/jhered/esag044","url":null,"abstract":"<p><p>Around the world, native breeds are increasingly recognised as important reservoirs of genetic variation that could prove vital for future livestock breeding and enhancing resilience to climate change. Accordingly, native goat (Capra hircus) breeds have been studied to understand their genetic diversity and adaptations to different environments. However, some breeds are confined to small, isolated, and feral populations. In the United Kingdom (UK), these effectively 'wild' populations are increasingly threatened with extinction due to ongoing culling practices and inadequate legal protection, which is further compounded by the limited understanding of their genetic status and origins, both of which are critical for informed conservation management. To address this knowledge gap, we examined the genetic structure and ancestry of 20 Cheviot goats residing within Northumberland National Park using SNP genotyping. This population is hypothesised to comprise of British primitive goats, the original landrace goat breed of the British Isles. We compared our findings against over 100 global breeds and found that the Cheviot goats exhibited low SNP heterozygosity (HO = 0.23), and very high levels of inbreeding (FROH = 0.45). Phylogenetic analyses positioned the Cheviot goats as a distinct lineage closely related to the Irish breeds, with no evidence of either recent or historical admixture. Our results identify the Cheviot goats as a genetically unique and historical breed. We suggest a re-evaluation of current population management strategies for the Cheviot and other wild goat populations across the UK with emphasis on the importance of conserving potentially rare and genetically unique populations.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148007470","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}
Rebecca Krohman, Simon Henriksson, Esben Moland Olsen, Halvor Knutsen, Rebekah A Oomen
{"title":"Atlantic cod (Gadus morhua) ecotypes, not inversion frequencies, underlie divergence in egg buoyancy.","authors":"Rebecca Krohman, Simon Henriksson, Esben Moland Olsen, Halvor Knutsen, Rebekah A Oomen","doi":"10.1093/jhered/esag042","DOIUrl":"https://doi.org/10.1093/jhered/esag042","url":null,"abstract":"<p><p>Life-history divergence between Atlantic cod (Gadus morhua) ecotypes in Skagerrak is maintained despite gene flow. Fjord and North Sea ecotypes differ in growth, body size, and reproductive ecology. One environmental heterogeneity in Skagerrak is salinity, as coastal habitats experience substantially lower and more variable salinities than offshore waters. Egg buoyancy is highly sensitive to salinity and represents a critical life-history trait shaping survival and recruitment. Inversions on chromosomes 2, 7, and 12 in cod are linked to salinity adaptation and might be important for egg buoyancy and survival. Here, we conducted a buoyancy test on Atlantic cod eggs, spawned from North Sea and Fjord ecotypes, using Coombs apparatus. Ecotypes and genotypes for the inversions on chromosomes 2, 7, and 12 were determined in all individuals (n = 242). We predicted that inversion genotypes and ecotypes would be associated with egg buoyancy. We found that buoyancy was variable and followed a bimodal distribution sorted by ecotype, with Fjord and North Sea individuals having mean buoyancies at neutral salinity (at 7 °C) of 27 and 31 ppt, respectively. Therefore, individuals with intermediate buoyancies might be selected against. This finding is consistent with our expectations, as Fjord ecotypes experience lower salinities compared to North Sea ecotypes. Interestingly, there was little evidence that the inversions on chromosomes 2, 7, and 12 impacted buoyancy. Overall, we provide experimental evidence of the relative contributions of ecotypic background and inversions on a key life history trait, which helps to explain the maintained divergence among ecotypes.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147989275","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":"Hybridization Drives High Genetic Diversity in the Japanese Fire-Bellied Newt, Cynops pyrrhogaster.","authors":"Hiroki Shiroma, Masatoshi Matsunami, Tomohiko Shimada, Masafumi Matsui, Kanto Nishikawa, Atsushi J Nagano, Atsushi Tominaga","doi":"10.1093/jhered/esag043","DOIUrl":"https://doi.org/10.1093/jhered/esag043","url":null,"abstract":"<p><p>Recent advances in evolutionary biology have highlighted the important roles of hybridization and gene flow in shaping genetic structure and diversification in many organisms. The Japanese fire-bellied newt, Cynops pyrrhogaster, comprises multiple diverged mitochondrial DNA (mtDNA) lineages. High genetic differentiation and strong reproductive isolation were observed among lineages, suggesting that some of these lineages may represent distinct species. To clarify the population structure and gene flow among lineages, we performed population genetic analyses based on genome-wide ddRAD-seq together with partial mitochondrial cytochrome-b sequences, using samples collected across the species' entire geographic range. Analyses of SNP data revealed three major groups (Northern, Central, and Western groups) with some hybrid populations in the contact zones. Estimation of the evolutionary history using an approximate Bayesian computation (ABC) approach suggested that the common ancestor of this species first diverged into the Northern and Western groups in middle Miocene, and that subsequent hybridization between these two groups gave rise to the Central group in the late Pliocene. An f4-test indicated gene flow from the Western group into the southwestern Central group, as well as that from the Northern group into the northeastern Central group. A mito-nuclear discordant population was also detected within the southwestern Central group, suggesting past hybridization. These results demonstrate that hybridization and subsequent gene flow play a crucial role in the formation of complex population structure and the maintenance of genetic diversity in the Japanese fire-bellied newt.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147984326","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}