Pub Date : 2026-02-07DOI: 10.1038/s41437-026-00823-y
Cinnamon S. Mittan-Moreau, Daryl Trumbo, Kelly R. Zamudio
Introduced species that successfully establish in new areas are a powerful system for investigating the genetic, ecological, and adaptive processes underlying range expansion. Rhinella marina is the focus of many studies of invasion dynamics, rapid evolution, and range limits. However, comparatively little is known about the nearly simultaneous establishment of closely related R. horribilis in Florida, USA. We sequenced 280 individuals using double-digest restriction-associated DNAseq (ddRAD) to investigate the role of introduction history, standing genetic diversity, and adaptation in R. horribilis’ establishment in Florida. We test the hypothesis of a single introduction event versus the alternative of several cryptic introductions. Second, we characterize population structure and genetic diversity to elucidate the roles of genetic bottlenecks and subsequent gene flow. Third, we use redundancy analyses to identify climate-associated genetic variants that may play a role in adaptation in Florida, which is colder than the cane toad’s native range. Lastly, we analyze a morphological trait, limb length, to investigate potential evolution of dispersal at the range edge. We find evidence for a single introduction of R. horribilis and complex range expansion characterized by range-wide gene flow, a lack of isolation by distance or environment, and no range edge dispersal phenotype. We also find evidence of selection related to range-wide gradients of precipitation, temperature, and urbanization. Together, our results indicate that range-wide gene flow maintains genetic diversity and adaptive capacity, likely supporting the neotropical species’ success in adapting to and establishing in this temperate environment.
{"title":"Complex range expansion and selective regime in the introduced Florida cane toad","authors":"Cinnamon S. Mittan-Moreau, Daryl Trumbo, Kelly R. Zamudio","doi":"10.1038/s41437-026-00823-y","DOIUrl":"10.1038/s41437-026-00823-y","url":null,"abstract":"Introduced species that successfully establish in new areas are a powerful system for investigating the genetic, ecological, and adaptive processes underlying range expansion. Rhinella marina is the focus of many studies of invasion dynamics, rapid evolution, and range limits. However, comparatively little is known about the nearly simultaneous establishment of closely related R. horribilis in Florida, USA. We sequenced 280 individuals using double-digest restriction-associated DNAseq (ddRAD) to investigate the role of introduction history, standing genetic diversity, and adaptation in R. horribilis’ establishment in Florida. We test the hypothesis of a single introduction event versus the alternative of several cryptic introductions. Second, we characterize population structure and genetic diversity to elucidate the roles of genetic bottlenecks and subsequent gene flow. Third, we use redundancy analyses to identify climate-associated genetic variants that may play a role in adaptation in Florida, which is colder than the cane toad’s native range. Lastly, we analyze a morphological trait, limb length, to investigate potential evolution of dispersal at the range edge. We find evidence for a single introduction of R. horribilis and complex range expansion characterized by range-wide gene flow, a lack of isolation by distance or environment, and no range edge dispersal phenotype. We also find evidence of selection related to range-wide gradients of precipitation, temperature, and urbanization. Together, our results indicate that range-wide gene flow maintains genetic diversity and adaptive capacity, likely supporting the neotropical species’ success in adapting to and establishing in this temperate environment.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 4","pages":"211-223"},"PeriodicalIF":3.9,"publicationDate":"2026-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146131069","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}
Pub Date : 2026-02-06DOI: 10.1038/s41437-026-00824-x
Reid S. Brennan, Lynsey A. Wilcox Talbot, Anthony Martinez, Lance P. Garrison, Dan Engelhaupt, Nicole L. Vollmer, Patricia E. Rosel
Marine mammals have high potential for dispersal, yet behavioral or environmental constraints can limit gene flow. This is true for the endangered sperm whale, Physeter macrocephalus, which has a global distribution and long-distance migrations. While previous studies revealed mitochondrial population structure with weak nuclear structure globally, genomic approaches examining this pattern have been limited. Understanding connectivity is critical for the management of this species due to population declines relative to pre-whaling numbers and increased recent anthropogenic stressors. We investigated connectivity between two regions, the U.S. Gulf of Mexico and the western North Atlantic Ocean, using reduced representation genomic and mitochondrial control region sequencing of 73 sperm whales. Relatedness decreased with geographic distance, likely due to the presence of social groups and familial structure. Nuclear markers showed no population structure (FST = 0.001–0.008), while mitochondrial structure was high (FST = 0.36–0.65), consistent with male-biased dispersal and female philopatry. Female-only analyses showed higher differentiation for mitochondrial but not nuclear markers; male-only analyses revealed no structure. Across all samples, genetic diversity (nuclear: 0.0014; mitochondrial: 0.0017) and effective population size (Ne = 460) were low. Given this low diversity and evidence for partitioning of genetic variation, we recommend managers treat these two regions as distinct to preserve existing variation and promote resilience of this species. These results illustrate that despite the increased power of a genomic approach, it is essential to consider the biology of the species at hand and leverage both mitochondrial and nuclear markers to understand the genetic structure of threatened species.
{"title":"Mitochondrial structure despite nuclear panmixia: sex-specific dispersal dictates population structure in sperm whales","authors":"Reid S. Brennan, Lynsey A. Wilcox Talbot, Anthony Martinez, Lance P. Garrison, Dan Engelhaupt, Nicole L. Vollmer, Patricia E. Rosel","doi":"10.1038/s41437-026-00824-x","DOIUrl":"10.1038/s41437-026-00824-x","url":null,"abstract":"Marine mammals have high potential for dispersal, yet behavioral or environmental constraints can limit gene flow. This is true for the endangered sperm whale, Physeter macrocephalus, which has a global distribution and long-distance migrations. While previous studies revealed mitochondrial population structure with weak nuclear structure globally, genomic approaches examining this pattern have been limited. Understanding connectivity is critical for the management of this species due to population declines relative to pre-whaling numbers and increased recent anthropogenic stressors. We investigated connectivity between two regions, the U.S. Gulf of Mexico and the western North Atlantic Ocean, using reduced representation genomic and mitochondrial control region sequencing of 73 sperm whales. Relatedness decreased with geographic distance, likely due to the presence of social groups and familial structure. Nuclear markers showed no population structure (FST = 0.001–0.008), while mitochondrial structure was high (FST = 0.36–0.65), consistent with male-biased dispersal and female philopatry. Female-only analyses showed higher differentiation for mitochondrial but not nuclear markers; male-only analyses revealed no structure. Across all samples, genetic diversity (nuclear: 0.0014; mitochondrial: 0.0017) and effective population size (Ne = 460) were low. Given this low diversity and evidence for partitioning of genetic variation, we recommend managers treat these two regions as distinct to preserve existing variation and promote resilience of this species. These results illustrate that despite the increased power of a genomic approach, it is essential to consider the biology of the species at hand and leverage both mitochondrial and nuclear markers to understand the genetic structure of threatened species.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 4","pages":"224-232"},"PeriodicalIF":3.9,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146131360","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}
Pub Date : 2026-01-29DOI: 10.1038/s41437-026-00821-0
Maria Shlyakonova, Katy M. Monteith, Laura Ross, Robert B. Baird
Sex determination mechanisms in insects are extraordinarily diverse, although most species have zygotic genotypic sex determination where sex is established by sex chromosomes upon fertilisation. Dark-winged fungus gnats (Diptera: Sciaridae) are a large and speciose family of flies where sex determination is a result of an unusual interplay of zygotic, maternal, and environmental factors. This causes some species to produce broods that deviate considerably from the standard 1:1 sex ratio. An early study suggested that these primary sex ratios may be heritable from mother to daughter, but this observation has not been corroborated and the genetic basis for this trait remains unknown. Other studies have found that in some species, there is an additional temperature effect on the primary sex ratio, but again the mechanism is unknown. Here, we perform sibling crosses and temperature-shift experiments in the common mushroom pest Lycoriella ingenua and find evidence for highly variable and heritable primary sex ratios, but no significant environmental effect. We discuss the consequences of our findings for understanding the mechanisms that produce these unusual sex ratios, and the evolution of sex determination more broadly in this clade.
{"title":"Maternal inheritance of primary sex ratios in the dark-winged fungus gnat Lycoriella ingenua","authors":"Maria Shlyakonova, Katy M. Monteith, Laura Ross, Robert B. Baird","doi":"10.1038/s41437-026-00821-0","DOIUrl":"10.1038/s41437-026-00821-0","url":null,"abstract":"Sex determination mechanisms in insects are extraordinarily diverse, although most species have zygotic genotypic sex determination where sex is established by sex chromosomes upon fertilisation. Dark-winged fungus gnats (Diptera: Sciaridae) are a large and speciose family of flies where sex determination is a result of an unusual interplay of zygotic, maternal, and environmental factors. This causes some species to produce broods that deviate considerably from the standard 1:1 sex ratio. An early study suggested that these primary sex ratios may be heritable from mother to daughter, but this observation has not been corroborated and the genetic basis for this trait remains unknown. Other studies have found that in some species, there is an additional temperature effect on the primary sex ratio, but again the mechanism is unknown. Here, we perform sibling crosses and temperature-shift experiments in the common mushroom pest Lycoriella ingenua and find evidence for highly variable and heritable primary sex ratios, but no significant environmental effect. We discuss the consequences of our findings for understanding the mechanisms that produce these unusual sex ratios, and the evolution of sex determination more broadly in this clade.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 2","pages":"113-119"},"PeriodicalIF":3.9,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41437-026-00821-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146148334","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}
Pub Date : 2026-01-29DOI: 10.1038/s41437-026-00820-1
Vitor Sudbrack, Charles Mullon
Tandem repeat (TR) sequences occur when short DNA motifs are repeated head-to-tail along chromosomes and are a major source of genetic variation. Population genetic models of TR evolution have focused on large, randomly mating, haploid populations. Yet many organisms reproduce partially through self-fertilisation (‘selfing’), which increases homozygosity and thus may alter the evolutionary processes shaping TR sequences. Here we use mathematical modelling and simulations to study the evolution of homologous TR sequences in partially selfing, diploid populations under four different selective regimes that may be relevant to TRs: (i) additive purifying selection, (ii) truncation-like purifying selection, (iii) selection against heterozygotes due to misalignment costs, and (iv) stabilising selection favouring an intermediate TR sequence length. We show that selfing influences TR evolution primarily by increasing homozygosity, with two main consequences: (1) it enhances the variation produced by unequal recombination within individuals, and (2) it increases variation between individuals. Consequently, selection on TRs becomes more effective under partial selfing across all modes of selection considered, resulting in lower genetic load, despite higher genetic drift. Overall, our results suggest that mating systems and inbreeding are important factors shaping variation in TR sequences.
{"title":"The evolution of tandem repeat sequences under partial selfing and different modes of selection","authors":"Vitor Sudbrack, Charles Mullon","doi":"10.1038/s41437-026-00820-1","DOIUrl":"10.1038/s41437-026-00820-1","url":null,"abstract":"Tandem repeat (TR) sequences occur when short DNA motifs are repeated head-to-tail along chromosomes and are a major source of genetic variation. Population genetic models of TR evolution have focused on large, randomly mating, haploid populations. Yet many organisms reproduce partially through self-fertilisation (‘selfing’), which increases homozygosity and thus may alter the evolutionary processes shaping TR sequences. Here we use mathematical modelling and simulations to study the evolution of homologous TR sequences in partially selfing, diploid populations under four different selective regimes that may be relevant to TRs: (i) additive purifying selection, (ii) truncation-like purifying selection, (iii) selection against heterozygotes due to misalignment costs, and (iv) stabilising selection favouring an intermediate TR sequence length. We show that selfing influences TR evolution primarily by increasing homozygosity, with two main consequences: (1) it enhances the variation produced by unequal recombination within individuals, and (2) it increases variation between individuals. Consequently, selection on TRs becomes more effective under partial selfing across all modes of selection considered, resulting in lower genetic load, despite higher genetic drift. Overall, our results suggest that mating systems and inbreeding are important factors shaping variation in TR sequences.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 2","pages":"99-112"},"PeriodicalIF":3.9,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146085655","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}
Pub Date : 2026-01-24DOI: 10.1038/s41437-026-00822-z
Laura Tensen, Anubhab Khan, Carlos Sarabia, Jacqueline Bishop, Gerrie Camacho, Klaus Fischer, Kathryn S. Williams
The adaptive value of intraspecific phenotypic variability, as well as the extent to which this is balanced by selection and genetic drift, is still relatively poorly explored. An intriguing population of leopard (Panthera pardus) occurs in the Cape Floristic Region, South Africa, where body mass is almost half that of leopards occurring in the savanna biome. In this study, we used whole-genome resequencing data of 43 leopards, including 10 from the Western Cape province (WCP). We explored spatial population structure and measured genome-wide diversity, including runs of homozygosity and genetic load. We compared their population demographic history to ‘savanna leopards’ in northern South Africa, and tested for signatures of selection that drive genomic and phenotypic differences. We found that WCP is distinct from other leopards in Africa, and that it diverged 20-24 thousand years ago from northern South Africa, which is in contrast to a lack of genome-wide differentiation found in previous studies. Because we found no obvious signs of genetic drift in WCP, the divergence is likely to have been caused by their population demographic history. We also found enriched genes that may relate to the local phenotype, possibly as an evolutionary response to food-scarce conditions. Leopards in the Cape Floristic Region utilize a unique landscape, which varies biologically in prey availability and vegetation structure, and anthropogenically with the province’s rapidly growing human population. Considering the local adaptation and divergence found in both mitochondrial and nuclear genomes, leopards in the Cape can be considered an evolutionary significant unit (ESU).
{"title":"Genomic divergence of leopards in the Cape Floristic Region of South Africa: potential drivers for local adaptation","authors":"Laura Tensen, Anubhab Khan, Carlos Sarabia, Jacqueline Bishop, Gerrie Camacho, Klaus Fischer, Kathryn S. Williams","doi":"10.1038/s41437-026-00822-z","DOIUrl":"10.1038/s41437-026-00822-z","url":null,"abstract":"The adaptive value of intraspecific phenotypic variability, as well as the extent to which this is balanced by selection and genetic drift, is still relatively poorly explored. An intriguing population of leopard (Panthera pardus) occurs in the Cape Floristic Region, South Africa, where body mass is almost half that of leopards occurring in the savanna biome. In this study, we used whole-genome resequencing data of 43 leopards, including 10 from the Western Cape province (WCP). We explored spatial population structure and measured genome-wide diversity, including runs of homozygosity and genetic load. We compared their population demographic history to ‘savanna leopards’ in northern South Africa, and tested for signatures of selection that drive genomic and phenotypic differences. We found that WCP is distinct from other leopards in Africa, and that it diverged 20-24 thousand years ago from northern South Africa, which is in contrast to a lack of genome-wide differentiation found in previous studies. Because we found no obvious signs of genetic drift in WCP, the divergence is likely to have been caused by their population demographic history. We also found enriched genes that may relate to the local phenotype, possibly as an evolutionary response to food-scarce conditions. Leopards in the Cape Floristic Region utilize a unique landscape, which varies biologically in prey availability and vegetation structure, and anthropogenically with the province’s rapidly growing human population. Considering the local adaptation and divergence found in both mitochondrial and nuclear genomes, leopards in the Cape can be considered an evolutionary significant unit (ESU).","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 2","pages":"86-98"},"PeriodicalIF":3.9,"publicationDate":"2026-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41437-026-00822-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043990","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}
Pub Date : 2026-01-13DOI: 10.1038/s41437-025-00816-3
Yu Cheng, Filip Kolář, Roswitha Schmickl, Josselin Clo
It is broadly assumed that polyploidy success results from increased fitness associated with whole genome duplication due to higher tolerance to stressful conditions. In agreement, several theoretical models found that, among other factors, a better tolerance to new environmental conditions can promote polyploidy establishment. Here, we investigated the effect of the genetic and environmental factors affecting the architecture of unreduced gamete production, to see how it affects the origin and persistence of autopolyploids in both stable and disturbed environments. We developed a theoretical model in which we modeled the joint evolution of a quantitative trait under selection and the production of unreduced gametes; both traits were pleiotropically linked. We followed the adaptation of initially diploid populations to a new environment to which tetraploid individuals were directly adapted. The generation of these autotetraploid individuals was enabled by the genetic production of unreduced gametes and by the environmental change modifying the average production of these gametes. We found that for realistic values of unreduced gamete production adaptation to new environmental conditions was mainly achieved through adaptation of diploids to the new optimum rather than the persistence of newly adapted tetraploid individuals. In broader parameter sets, we found that the adaptation process led to mixed-ploidy populations, except when the populations were swamped with unreduced gametes, and that pleiotropy and environmental effects favored the co-existence of both cytotypes.
{"title":"How environment and genetic architecture of unreduced gametes shape the establishment of autopolyploids","authors":"Yu Cheng, Filip Kolář, Roswitha Schmickl, Josselin Clo","doi":"10.1038/s41437-025-00816-3","DOIUrl":"10.1038/s41437-025-00816-3","url":null,"abstract":"It is broadly assumed that polyploidy success results from increased fitness associated with whole genome duplication due to higher tolerance to stressful conditions. In agreement, several theoretical models found that, among other factors, a better tolerance to new environmental conditions can promote polyploidy establishment. Here, we investigated the effect of the genetic and environmental factors affecting the architecture of unreduced gamete production, to see how it affects the origin and persistence of autopolyploids in both stable and disturbed environments. We developed a theoretical model in which we modeled the joint evolution of a quantitative trait under selection and the production of unreduced gametes; both traits were pleiotropically linked. We followed the adaptation of initially diploid populations to a new environment to which tetraploid individuals were directly adapted. The generation of these autotetraploid individuals was enabled by the genetic production of unreduced gametes and by the environmental change modifying the average production of these gametes. We found that for realistic values of unreduced gamete production adaptation to new environmental conditions was mainly achieved through adaptation of diploids to the new optimum rather than the persistence of newly adapted tetraploid individuals. In broader parameter sets, we found that the adaptation process led to mixed-ploidy populations, except when the populations were swamped with unreduced gametes, and that pleiotropy and environmental effects favored the co-existence of both cytotypes.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 2","pages":"55-66"},"PeriodicalIF":3.9,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41437-025-00816-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145965743","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}
Pub Date : 2026-01-07DOI: 10.1038/s41437-025-00818-1
Wanting Ge, Ying Liu, Junhui Wang, Jie Li, Fuyu Wang, Shen Zhang, Minggang Zhang, Lei Wang, Junhong Zhang, Wenjun Ma
Catalpa huangxin, a distinctive taxon within the genus Catalpa in China, is valued for its ornamental beauty and durable yellow heartwood. However, its wild populations are declining due to climate change and human activities, posing urgent conservation challenges. The unclear genetic diversity and population structure further complicate its protection and breeding efforts. To address these issues, this study employed RAD-seq to analyze 198 samples, including 169 C. huangxin, 24 Catalpa duclouxii, and 5 Catalpa ovata (outgroup), focusing on phylogeny, genetic diversity, gene flow, and dispersal routes. The results show that C. huangxin and C. duclouxii are distinct but closely related taxa. C. huangxin was divided into five subgroups with moderate genetic diversity (He = 0.2935, Ho = 0.4401). Subgroup 5 exhibited the highest diversity, but significant genetic differentiation (FST = 0.1983) was observed between subgroups, limiting gene flow and adaptation. Human activities, reproductive traits, and habitat fragmentation contribute to this differentiation. The study recommends in-situ conservation of genetically diverse subgroups, particularly Subgroup 5, artificial population restoration, germplasm banks, and expansion of its current distribution range. These strategies are essential for C. huangxin’s protection and genetic improvement, offering valuable insights for the conservation of other species with similarly restricted distributions.
黄新梓（Catalpa huangxin）是中国梓属中一个独特的分类群，因其观赏美和耐用的黄色心材而受到重视。然而，由于气候变化和人类活动的影响，其野生种群数量正在减少，面临着紧迫的保护挑战。不明确的遗传多样性和种群结构进一步使其保护和育种工作复杂化。为了解决这些问题，本研究采用RAD-seq分析了198份样品，其中包括169份C。黄鑫，24个duclouxii梓，5个Catalpa ovata（外群），重点研究系统发育、遗传多样性、基因流动和传播途径。结果表明，黄心木与杜氏木是两个不同但亲缘关系密切的分类群。黄新分5个亚群，遗传多样性中等（He = 0.2935, Ho = 0.4401）。亚群5多样性最高，但亚群间存在显著的遗传分化（FST = 0.1983），限制了基因流动和适应。人类活动、生殖特征和生境破碎化是造成这种分化的原因。该研究建议就地保护遗传多样性亚群，特别是第5亚群，人工种群恢复，种质资源库和扩大其现有分布范围。这些策略对黄青的保护和遗传改良具有重要意义，也为其他分布受限的物种的保护提供了有价值的启示。
{"title":"Genetic structure and conservation relevance in the narrowly distributed tree Catalpa huangxin revealed by RAD-Seq","authors":"Wanting Ge, Ying Liu, Junhui Wang, Jie Li, Fuyu Wang, Shen Zhang, Minggang Zhang, Lei Wang, Junhong Zhang, Wenjun Ma","doi":"10.1038/s41437-025-00818-1","DOIUrl":"10.1038/s41437-025-00818-1","url":null,"abstract":"Catalpa huangxin, a distinctive taxon within the genus Catalpa in China, is valued for its ornamental beauty and durable yellow heartwood. However, its wild populations are declining due to climate change and human activities, posing urgent conservation challenges. The unclear genetic diversity and population structure further complicate its protection and breeding efforts. To address these issues, this study employed RAD-seq to analyze 198 samples, including 169 C. huangxin, 24 Catalpa duclouxii, and 5 Catalpa ovata (outgroup), focusing on phylogeny, genetic diversity, gene flow, and dispersal routes. The results show that C. huangxin and C. duclouxii are distinct but closely related taxa. C. huangxin was divided into five subgroups with moderate genetic diversity (He = 0.2935, Ho = 0.4401). Subgroup 5 exhibited the highest diversity, but significant genetic differentiation (FST = 0.1983) was observed between subgroups, limiting gene flow and adaptation. Human activities, reproductive traits, and habitat fragmentation contribute to this differentiation. The study recommends in-situ conservation of genetically diverse subgroups, particularly Subgroup 5, artificial population restoration, germplasm banks, and expansion of its current distribution range. These strategies are essential for C. huangxin’s protection and genetic improvement, offering valuable insights for the conservation of other species with similarly restricted distributions.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 2","pages":"67-78"},"PeriodicalIF":3.9,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145917526","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}
Pub Date : 2025-12-27DOI: 10.1038/s41437-025-00819-0
Eugenio López-Cortegano, Jobran Chebib, Anika Jonas, Sven Künzel, Peter D. Keightley, Diethard Tautz
New mutations are the source of all genetic variation, including variation affecting quantitative phenotypes. Here, in order to evaluate the impact of mutations on the integrated function of entire tissues, we estimated the mutational variation (Vm) introduced by new mutations each generation for gene expression. Using deep transcriptome sequencing, we estimated Vm for brain and liver gene expression in individuals from a mutation accumulation experiment (MA) with the C3H inbred mouse strain. Expression was measured in 200 mice from 40 MA lines maintained for 15–19 generations and in 100 mice from 20 control lines. The control lines allow us to account for environmental variation in gene expression. Based on the difference in the between-line variance component for expression between the MA lines and controls, the median Vm in the brain was 2.22 × 10−3, while in the liver it was markedly lower (Vm = 0.35 × 10−3). A greater proportion of genes also showed Vm values statistically higher than zero in the brain (29%) than in the liver (7%). These differences could be due to a higher rate of mutation-driven transcriptome evolution in the brain compared to the liver, which we discuss in the context of differences in the mutational target, distribution of mutation effects, cellular complexity, and estimation biases. A differential expression analysis revealed minimal contributions to Vm from the subset of genes that have significant variation in expression. This indicates that most new mutations exert small effects on gene expression and go undetected in differential expression analyses.
{"title":"Tissue-specific differences of gene expression variance in mutation accumulation lines of mice","authors":"Eugenio López-Cortegano, Jobran Chebib, Anika Jonas, Sven Künzel, Peter D. Keightley, Diethard Tautz","doi":"10.1038/s41437-025-00819-0","DOIUrl":"10.1038/s41437-025-00819-0","url":null,"abstract":"New mutations are the source of all genetic variation, including variation affecting quantitative phenotypes. Here, in order to evaluate the impact of mutations on the integrated function of entire tissues, we estimated the mutational variation (Vm) introduced by new mutations each generation for gene expression. Using deep transcriptome sequencing, we estimated Vm for brain and liver gene expression in individuals from a mutation accumulation experiment (MA) with the C3H inbred mouse strain. Expression was measured in 200 mice from 40 MA lines maintained for 15–19 generations and in 100 mice from 20 control lines. The control lines allow us to account for environmental variation in gene expression. Based on the difference in the between-line variance component for expression between the MA lines and controls, the median Vm in the brain was 2.22 × 10−3, while in the liver it was markedly lower (Vm = 0.35 × 10−3). A greater proportion of genes also showed Vm values statistically higher than zero in the brain (29%) than in the liver (7%). These differences could be due to a higher rate of mutation-driven transcriptome evolution in the brain compared to the liver, which we discuss in the context of differences in the mutational target, distribution of mutation effects, cellular complexity, and estimation biases. A differential expression analysis revealed minimal contributions to Vm from the subset of genes that have significant variation in expression. This indicates that most new mutations exert small effects on gene expression and go undetected in differential expression analyses.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 2","pages":"79-85"},"PeriodicalIF":3.9,"publicationDate":"2025-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145846570","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}
Pub Date : 2025-12-24DOI: 10.1038/s41437-025-00817-2
Handung Nuryadi, V. K. Anoop, Ryo Kakioka, Jun Gojobori, Rajeev Raghavan, Kazunori Yamahira
Duplications and concerted evolution of control regions (CRs) in animal mitogenomes have been reported across diverse taxa, yet the tempo and mechanism of gene conversion remain poorly understood. Here, we assembled the complete mitochondrial genome of the western Indian ricefish Oryzias setnai and found that the CR is duplicated. Comparative analysis of CR1 and CR2 sequences across individuals sampled throughout the species’ range revealed that they are identical in most individuals, and differ by only one or two mutations in the rest—indicating recent and ongoing concerted evolution. We estimated that gene conversion events occur at a rapid pace, on the order of once every 1000 years or less. Using both short- and long-read amplicon sequencing, we directly detected a substantial number of recombinant mitogenome molecules resulting from homologous recombination between CR paralogues. This provides the first clear evidence that homologous recombination is the mechanism driving mitochondrial gene conversion. Our findings challenge the prevailing view that recombination in animal mitochondria is exceedingly rare, and demonstrate that mitogenome recombination can occur routinely in natural populations.
{"title":"Routine mitochondrial recombination drives rapid concerted evolution of duplicated control regions in a wild fish","authors":"Handung Nuryadi, V. K. Anoop, Ryo Kakioka, Jun Gojobori, Rajeev Raghavan, Kazunori Yamahira","doi":"10.1038/s41437-025-00817-2","DOIUrl":"10.1038/s41437-025-00817-2","url":null,"abstract":"Duplications and concerted evolution of control regions (CRs) in animal mitogenomes have been reported across diverse taxa, yet the tempo and mechanism of gene conversion remain poorly understood. Here, we assembled the complete mitochondrial genome of the western Indian ricefish Oryzias setnai and found that the CR is duplicated. Comparative analysis of CR1 and CR2 sequences across individuals sampled throughout the species’ range revealed that they are identical in most individuals, and differ by only one or two mutations in the rest—indicating recent and ongoing concerted evolution. We estimated that gene conversion events occur at a rapid pace, on the order of once every 1000 years or less. Using both short- and long-read amplicon sequencing, we directly detected a substantial number of recombinant mitogenome molecules resulting from homologous recombination between CR paralogues. This provides the first clear evidence that homologous recombination is the mechanism driving mitochondrial gene conversion. Our findings challenge the prevailing view that recombination in animal mitochondria is exceedingly rare, and demonstrate that mitogenome recombination can occur routinely in natural populations.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 1","pages":"46-54"},"PeriodicalIF":3.9,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145819070","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}
Pub Date : 2025-12-19DOI: 10.1038/s41437-025-00815-4
Derek Kong Lam, Simon Yung Wa Sin
Gene duplication and loss play an important role in the evolution of the major histocompatibility complex (MHC). Variations in copy number and sequence diversity of MHC genes can have significant fitness consequences. Here, we characterized both MHC class I and class II genes in a group of parrots—lovebirds (Agapornis spp.) using cloning and sequencing, quantitative PCR, and depth-of-coverage (DoC) analysis with whole-genome re-sequencing data. We identified copy number variation in MHC class II genes, with A. roseicollis having a single MHCIIB gene copy, whereas A. canus possesses at least three gene copies. Conversely, the copy number of class I genes is invariable, with only one copy identified in each Agapornis species. Phylogenetic reconstructions revealed both concerted evolution and trans-species polymorphism of MHC genes. In both MHC class I and II genes, sequences from the recently diverged eye-ringed species (e.g., A. fischeri, A. personatus, and A. nigrigenis) and their sister species A. roseicollis showed an intercalating pattern with no species-specific clustering, consistent with trans-species polymorphism. In contrast, sequences from the early-diverged species (e.g., A. canus and A. pullarius) clustered by species, which is typical for avian MHC genes undergoing concerted evolution. The pattern of MHC copy number variation and modes of evolution observed are associated with the timescale of species divergence. We suggest that future studies should include both MHC class I and II genes and multiple species spanning a range of divergence time to enhance our understanding of the evolution of avian MHC diversity.
{"title":"Copy number variation and evolution of MHC class I and II genes in lovebirds (Agapornis, Psittaculidae, Psittaciformes)","authors":"Derek Kong Lam, Simon Yung Wa Sin","doi":"10.1038/s41437-025-00815-4","DOIUrl":"10.1038/s41437-025-00815-4","url":null,"abstract":"Gene duplication and loss play an important role in the evolution of the major histocompatibility complex (MHC). Variations in copy number and sequence diversity of MHC genes can have significant fitness consequences. Here, we characterized both MHC class I and class II genes in a group of parrots—lovebirds (Agapornis spp.) using cloning and sequencing, quantitative PCR, and depth-of-coverage (DoC) analysis with whole-genome re-sequencing data. We identified copy number variation in MHC class II genes, with A. roseicollis having a single MHCIIB gene copy, whereas A. canus possesses at least three gene copies. Conversely, the copy number of class I genes is invariable, with only one copy identified in each Agapornis species. Phylogenetic reconstructions revealed both concerted evolution and trans-species polymorphism of MHC genes. In both MHC class I and II genes, sequences from the recently diverged eye-ringed species (e.g., A. fischeri, A. personatus, and A. nigrigenis) and their sister species A. roseicollis showed an intercalating pattern with no species-specific clustering, consistent with trans-species polymorphism. In contrast, sequences from the early-diverged species (e.g., A. canus and A. pullarius) clustered by species, which is typical for avian MHC genes undergoing concerted evolution. The pattern of MHC copy number variation and modes of evolution observed are associated with the timescale of species divergence. We suggest that future studies should include both MHC class I and II genes and multiple species spanning a range of divergence time to enhance our understanding of the evolution of avian MHC diversity.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 1","pages":"34-45"},"PeriodicalIF":3.9,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145793529","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：