Pub Date : 2026-03-16DOI: 10.1038/s41437-026-00830-z
Augustin Chen, Francisco J Ruiz-Ruano, Orlando Contreras-López, Simone Fouché, Alexander Suh, Yifan Pei
The germline-restricted chromosome (GRC) of passerines is a remarkable tissue-specific chromosome that accumulated paralogs of genes from the regular "A chromosomes" over millions of years, often amplified into dozens of gene copies. In addition to its repetitive content, typically uniparental inheritance, and lack of recombination, the GRC resembles non-recombining sex chromosomes and some B chromosomes, for all of which assembly and single-nucleotide polymorphisms (SNPs) calling are difficult. Here, we first show that much of the Australian zebra finch macro-GRC can be assembled using accurate long reads. We then describe a paralog-aware Snakemake pipeline, ParaVar, to map short reads from the GRC to retrieve GRC regions suitable for haplotype-based analysis. ParaVar reliably calls hundreds of SNPs across the GRC, thereby providing an estimate of nucleotide diversity on the highly repetitive zebra finch macro-GRC. Our results show significantly lower nucleotide diversity (20- to 50-fold lower) on the GRC compared to the mitogenome and autosomes, and a strong phylogenetic discordance between the GRC and the mitochondrial genome. Beyond the contribution of background selection, our results suggest that a single GRC haplotype recently spread through the populations while jumping across matrilines via occasional paternal inheritance. We anticipate that our paralog-aware pipeline will be useful for SNP calling and population genetics analyses of repetitive GRCs, sex chromosomes, and B chromosomes.
{"title":"Paralog-aware assembly and filtering strategies reveal minimal nucleotide variation on the macro germline-restricted chromosome of the zebra finch.","authors":"Augustin Chen, Francisco J Ruiz-Ruano, Orlando Contreras-López, Simone Fouché, Alexander Suh, Yifan Pei","doi":"10.1038/s41437-026-00830-z","DOIUrl":"https://doi.org/10.1038/s41437-026-00830-z","url":null,"abstract":"<p><p>The germline-restricted chromosome (GRC) of passerines is a remarkable tissue-specific chromosome that accumulated paralogs of genes from the regular \"A chromosomes\" over millions of years, often amplified into dozens of gene copies. In addition to its repetitive content, typically uniparental inheritance, and lack of recombination, the GRC resembles non-recombining sex chromosomes and some B chromosomes, for all of which assembly and single-nucleotide polymorphisms (SNPs) calling are difficult. Here, we first show that much of the Australian zebra finch macro-GRC can be assembled using accurate long reads. We then describe a paralog-aware Snakemake pipeline, ParaVar, to map short reads from the GRC to retrieve GRC regions suitable for haplotype-based analysis. ParaVar reliably calls hundreds of SNPs across the GRC, thereby providing an estimate of nucleotide diversity on the highly repetitive zebra finch macro-GRC. Our results show significantly lower nucleotide diversity (20- to 50-fold lower) on the GRC compared to the mitogenome and autosomes, and a strong phylogenetic discordance between the GRC and the mitochondrial genome. Beyond the contribution of background selection, our results suggest that a single GRC haplotype recently spread through the populations while jumping across matrilines via occasional paternal inheritance. We anticipate that our paralog-aware pipeline will be useful for SNP calling and population genetics analyses of repetitive GRCs, sex chromosomes, and B chromosomes.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147467813","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 : 2026-03-12DOI: 10.1038/s41437-026-00831-y
Gerardo J. Soria-Ortiz, Ella Vázquez-Domínguez
Human-modified environments constitute evolutionary scenarios where novel environmental conditions impose multiple selective pressures on wild species. Rapid adaptation to such environments is critical for species survival. Hence, deciphering the environmental factors associated with species tolerance to modified habitats is fundamental for understanding local adaptation processes across populations. We studied the Giant Toad Rhinella horribilis from two landscapes characterized by land-use changes resulting from combined traditional and intensive agriculture and livestock practices. We identified potential outlier loci, assessed genotype-environment associations, annotated candidate genes, and tested for signals of repeated genomic selection in the two landscapes. We used an integrative analytical approach and assessed patterns of genetic repeatability at the genome scale, which improve confidence in identifying true selection signals and provide insights into genetic responses contributing to adaptive evolution. We found positive genotype-environment associations (GEA) related to suboptimal climatic and water physiochemical conditions. Candidate genes were negatively and positively linked with different environmental variables (temperature, solar radiation, oxygen availability, potassium levels in water bodies). Our findings provide evidence of repeated genomic evolution at the functional level, with successful annotation of 34 shared (statistically overlapped) genes between landscapes. Seven genes were enriched for biological processes and metabolic pathways, associated mainly with embryonic development, sexual maturation, and immune responses. These repeated genomic GEA patterns likely reflect rapid local adaptive responses to stressful conditions imposed by these human-modified environments.
{"title":"Signatures of repeated genomic selection associated with human-modified landscapes in genetically independent populations of Rhinella horribilis","authors":"Gerardo J. Soria-Ortiz, Ella Vázquez-Domínguez","doi":"10.1038/s41437-026-00831-y","DOIUrl":"10.1038/s41437-026-00831-y","url":null,"abstract":"Human-modified environments constitute evolutionary scenarios where novel environmental conditions impose multiple selective pressures on wild species. Rapid adaptation to such environments is critical for species survival. Hence, deciphering the environmental factors associated with species tolerance to modified habitats is fundamental for understanding local adaptation processes across populations. We studied the Giant Toad Rhinella horribilis from two landscapes characterized by land-use changes resulting from combined traditional and intensive agriculture and livestock practices. We identified potential outlier loci, assessed genotype-environment associations, annotated candidate genes, and tested for signals of repeated genomic selection in the two landscapes. We used an integrative analytical approach and assessed patterns of genetic repeatability at the genome scale, which improve confidence in identifying true selection signals and provide insights into genetic responses contributing to adaptive evolution. We found positive genotype-environment associations (GEA) related to suboptimal climatic and water physiochemical conditions. Candidate genes were negatively and positively linked with different environmental variables (temperature, solar radiation, oxygen availability, potassium levels in water bodies). Our findings provide evidence of repeated genomic evolution at the functional level, with successful annotation of 34 shared (statistically overlapped) genes between landscapes. Seven genes were enriched for biological processes and metabolic pathways, associated mainly with embryonic development, sexual maturation, and immune responses. These repeated genomic GEA patterns likely reflect rapid local adaptive responses to stressful conditions imposed by these human-modified environments.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 4","pages":"289-298"},"PeriodicalIF":3.9,"publicationDate":"2026-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41437-026-00831-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147443483","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 : 2026-03-12DOI: 10.1038/s41437-026-00834-9
Pavla Klusáčková, Agata Woźniewska, Petra Dufková, Beth L Dumont, Jan M Wójcik, Jaroslav Piálek
Hybrid sterility is a critical postzygotic barrier that limits gene flow during speciation, yet the genetic architecture underlying evolution of such barriers in the early stages of speciation remains poorly characterized. In house mice, F1 male sterility observed in crosses between Mus musculus musculus and M. m. domesticus has been attributed to incompatibilities between heterozygous autosomal Prdm9, which controls primarily the position of recombination hotspots, and copy number variation in X-linked Mir465 miRNA genes. This molecular mechanism, identified in laboratory crosses, provided the first genetic evidence of a Dobzhansky-Muller incompatibility causing F1 hybrid sterility in vertebrates and has been considered a general model across strains and laboratories. Here, we use mice from natural populations and find that F1 hybrid sterility is polymorphic and asymmetric, with fertility phenotypes modulated by the direction of the cross. Although sterile males carried incompatible Prdm9 alleles, quantitative trait loci (QTL) mapping in backcross progeny revealed no significant associations with chromosome 17, where Prdm9 resides. Instead, sterility consistently mapped to X-linked loci, and the genomic position of sterility-associated QTL shifted between reciprocal backcrosses. These findings uncover a previously unrecognized mode of hybrid sterility in which X-linked incompatibilities act independently of Prdm9, a mechanism we term Prdm9-independent X-linked sterility (PIXLS). Our results extend the established Prdm9/Mir465 model by demonstrating that hybrid sterility in house mice can arise through alternative genetic routes, highlighting the evolutionary diversity of reproductive barriers in their natural hybrid zone.
{"title":"Beyond the Prdm9 model: independent evolution of hybrid male sterility in house mice.","authors":"Pavla Klusáčková, Agata Woźniewska, Petra Dufková, Beth L Dumont, Jan M Wójcik, Jaroslav Piálek","doi":"10.1038/s41437-026-00834-9","DOIUrl":"https://doi.org/10.1038/s41437-026-00834-9","url":null,"abstract":"<p><p>Hybrid sterility is a critical postzygotic barrier that limits gene flow during speciation, yet the genetic architecture underlying evolution of such barriers in the early stages of speciation remains poorly characterized. In house mice, F1 male sterility observed in crosses between Mus musculus musculus and M. m. domesticus has been attributed to incompatibilities between heterozygous autosomal Prdm9, which controls primarily the position of recombination hotspots, and copy number variation in X-linked Mir465 miRNA genes. This molecular mechanism, identified in laboratory crosses, provided the first genetic evidence of a Dobzhansky-Muller incompatibility causing F1 hybrid sterility in vertebrates and has been considered a general model across strains and laboratories. Here, we use mice from natural populations and find that F1 hybrid sterility is polymorphic and asymmetric, with fertility phenotypes modulated by the direction of the cross. Although sterile males carried incompatible Prdm9 alleles, quantitative trait loci (QTL) mapping in backcross progeny revealed no significant associations with chromosome 17, where Prdm9 resides. Instead, sterility consistently mapped to X-linked loci, and the genomic position of sterility-associated QTL shifted between reciprocal backcrosses. These findings uncover a previously unrecognized mode of hybrid sterility in which X-linked incompatibilities act independently of Prdm9, a mechanism we term Prdm9-independent X-linked sterility (PIXLS). Our results extend the established Prdm9/Mir465 model by demonstrating that hybrid sterility in house mice can arise through alternative genetic routes, highlighting the evolutionary diversity of reproductive barriers in their natural hybrid zone.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147443546","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 : 2026-03-09DOI: 10.1038/s41437-026-00829-6
Marieke J. W. Jeuken
Gene-gene incompatibilities—caused by deleterious allele combinations at different loci — can impair gametophyte or zygote viability, reducing fertility or overall viability in hybrids or hybrid-derived populations. These incompatibilities can be detected through transmission ratio distortion (TRD), which reflects deviations from Mendelian inheritance due to selection against incompatible allele combinations. However, identifying epistatic TRD locus pairs remains challenging, as standard multiple-testing approaches are underpowered. To address this limitation, a stepwise workflow is introduced that achieves higher sensitivity than standard approaches by using targeted subsampling of the population. This strategy effectively concentrates TRD signals shared between two interacting loci into a single locus, thereby strengthening the signal, simplifying the analysis, and eliminating the need for multiple-testing correction. In addition, incompatibility models were developed to predict TRD patterns under various selection mechanisms (gametophytic or zygotic) and inheritance modes (symmetric or asymmetric) across common mapping populations (F2, BC1, RIL). Applied to 17 F2 and 2 RIL intraspecific Arabidopsis thaliana populations, the stepwise workflow identified seven novel and two known TRD locus pairs. In most cases, the observed TRD patterns offered insights into potential selection mechanisms. The demonstrated sensitivity and robustness of the proposed method highlight its potential to uncover numerous additional incompatibility locus pairs across diverse species. Systematic application of the method could elevate the discovery of hybrid incompatibilities beyond current incidental discoveries and open new avenues for understanding the genetic architecture of speciation.
{"title":"How population subsampling to concentrate selection effects can help to find epistatic interactions of transmission ratio distortion","authors":"Marieke J. W. Jeuken","doi":"10.1038/s41437-026-00829-6","DOIUrl":"10.1038/s41437-026-00829-6","url":null,"abstract":"Gene-gene incompatibilities—caused by deleterious allele combinations at different loci — can impair gametophyte or zygote viability, reducing fertility or overall viability in hybrids or hybrid-derived populations. These incompatibilities can be detected through transmission ratio distortion (TRD), which reflects deviations from Mendelian inheritance due to selection against incompatible allele combinations. However, identifying epistatic TRD locus pairs remains challenging, as standard multiple-testing approaches are underpowered. To address this limitation, a stepwise workflow is introduced that achieves higher sensitivity than standard approaches by using targeted subsampling of the population. This strategy effectively concentrates TRD signals shared between two interacting loci into a single locus, thereby strengthening the signal, simplifying the analysis, and eliminating the need for multiple-testing correction. In addition, incompatibility models were developed to predict TRD patterns under various selection mechanisms (gametophytic or zygotic) and inheritance modes (symmetric or asymmetric) across common mapping populations (F2, BC1, RIL). Applied to 17 F2 and 2 RIL intraspecific Arabidopsis thaliana populations, the stepwise workflow identified seven novel and two known TRD locus pairs. In most cases, the observed TRD patterns offered insights into potential selection mechanisms. The demonstrated sensitivity and robustness of the proposed method highlight its potential to uncover numerous additional incompatibility locus pairs across diverse species. Systematic application of the method could elevate the discovery of hybrid incompatibilities beyond current incidental discoveries and open new avenues for understanding the genetic architecture of speciation.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 4","pages":"278-288"},"PeriodicalIF":3.9,"publicationDate":"2026-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147389860","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 : 2026-03-07DOI: 10.1038/s41437-026-00833-w
Kylee R Noel, Carly Kallembach, Mahica Iyer, Carla E Cáceres, Chris M Stone
Anthropogenic changes can drive rapid evolution in wild populations, but the role of phenotypic plasticity in such scenarios remains unclear. This uncertainty can affect applications like the design of resistance management approaches. In the case of insecticide resistance in mosquitoes, however, little is known regarding how environmental conditions, genetic variation, and their interactions jointly shape resistance phenotypes. To address this, we employed a full-sibling design to investigate the effects of larval food availability on adult broad-sense heritability and phenotypic plasticity in resistance to permethrin. Two experiments measured resistance levels in West Nile virus vectors (laboratory colony of Culex pipiens and two field populations of Culex restuans) using CDC bottle bioassays, and the time until death was tracked. Wing lengths were measured to assess if there is a relationship between body size and permethrin resistance. Based on likelihood ratio tests, the broad-sense heritability values for resistance were significant. There was substantial variance and phenotypic plasticity in both Cx. restuans field populations, while the laboratory colony of Cx. pipiens exhibited less variation. Larval food availability significantly affected resistance, but the sign of the effect varied across populations from different geographic regions, highlighting the importance of genotype by environmental interactions in this system. Our results offer valuable insights into the potential for insecticide resistance to evolve in mosquito populations and have important implications for how resistance in vectors can be assessed. We suggest changes to improve the current methodology for insecticide resistance testing and recommend that population-specific data should inform vector control schemes.
{"title":"Genotype by environmental interactions shape insecticide resistance phenotypes in Culex pipiens and Culex restuans.","authors":"Kylee R Noel, Carly Kallembach, Mahica Iyer, Carla E Cáceres, Chris M Stone","doi":"10.1038/s41437-026-00833-w","DOIUrl":"https://doi.org/10.1038/s41437-026-00833-w","url":null,"abstract":"<p><p>Anthropogenic changes can drive rapid evolution in wild populations, but the role of phenotypic plasticity in such scenarios remains unclear. This uncertainty can affect applications like the design of resistance management approaches. In the case of insecticide resistance in mosquitoes, however, little is known regarding how environmental conditions, genetic variation, and their interactions jointly shape resistance phenotypes. To address this, we employed a full-sibling design to investigate the effects of larval food availability on adult broad-sense heritability and phenotypic plasticity in resistance to permethrin. Two experiments measured resistance levels in West Nile virus vectors (laboratory colony of Culex pipiens and two field populations of Culex restuans) using CDC bottle bioassays, and the time until death was tracked. Wing lengths were measured to assess if there is a relationship between body size and permethrin resistance. Based on likelihood ratio tests, the broad-sense heritability values for resistance were significant. There was substantial variance and phenotypic plasticity in both Cx. restuans field populations, while the laboratory colony of Cx. pipiens exhibited less variation. Larval food availability significantly affected resistance, but the sign of the effect varied across populations from different geographic regions, highlighting the importance of genotype by environmental interactions in this system. Our results offer valuable insights into the potential for insecticide resistance to evolve in mosquito populations and have important implications for how resistance in vectors can be assessed. We suggest changes to improve the current methodology for insecticide resistance testing and recommend that population-specific data should inform vector control schemes.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147372528","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 : 2026-03-07DOI: 10.1038/s41437-026-00832-x
Charikleia Karageorgiou, Ellen M. Leffler, Megan Y. Dennis, Omer Gokcumen
Genomic structural variants (SVs) are central to modern genetics. However, they do not fit easily into the simple classifications and analytical frameworks that work well for single‑nucleotide polymorphisms (SNPs). The papers in this special issue underscore that SVs cannot be treated as a homogeneous class, nor can their evolutionary consequences be inferred directly from their structural category alone. Instead, they compel us to engage explicitly with mutational mechanism, genomic context, and selection regime, and to recognize that the structural category only weakly predicts their functional and evolutionary impact.
{"title":"Structural variation in context: mechanisms, functions and selection regimes across the tree of life","authors":"Charikleia Karageorgiou, Ellen M. Leffler, Megan Y. Dennis, Omer Gokcumen","doi":"10.1038/s41437-026-00832-x","DOIUrl":"10.1038/s41437-026-00832-x","url":null,"abstract":"Genomic structural variants (SVs) are central to modern genetics. However, they do not fit easily into the simple classifications and analytical frameworks that work well for single‑nucleotide polymorphisms (SNPs). The papers in this special issue underscore that SVs cannot be treated as a homogeneous class, nor can their evolutionary consequences be inferred directly from their structural category alone. Instead, they compel us to engage explicitly with mutational mechanism, genomic context, and selection regime, and to recognize that the structural category only weakly predicts their functional and evolutionary impact.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 3","pages":"121-125"},"PeriodicalIF":3.9,"publicationDate":"2026-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41437-026-00832-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147372535","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 : 2026-02-24DOI: 10.1038/s41437-026-00827-8
Temitope Opeyemi Oriowo, Sophie Helen Smith, Jana Thorman, Nils Sternberg, Astrid Böhne, Madlen Stange
Sex determination systems in teleost fishes are highly diverse, and even closely related species often evolve different mechanisms. Although hybridisation among Eurasian minnows (Phoxinus: Cypriniformes, Leuciscidae) is well documented, their sex determination systems remain unexplored. Here, we investigated the genetic basis of sex determination in Phoxinus phoxinus and Phoxinus csikii using whole-genome sequencing, with a combination of coverage, SNP-, and k-mer-based approaches to identify sex-associated genomic regions. Whole-genome coverage analyses revealed no chromosomes with significantly sex-biased coverage, consistent with homomorphic sex chromosomes in both species. In P. phoxinus, male-specific heterozygosity at sex-linked SNPs showed genotypic differences within two regions, namely on chromosomes 3 and 12. Analysis of SNPs in these regions revealed drainage-specific, sex-associated patterns, indicating the presence of population-specific sex-associated genomic loci and a male heterogametic (XX/XY) system in this species. In contrast, P. csikii females displayed unique genotypic differences in a different part of chromosome 3, pointing to a female heterogametic (ZZ/ZW) system. We further observed overrepresentation of male-specific DNA sequences in P. phoxinus and female-specific sequences in P. csikii, providing additional evidence for the presence of sex-specific genomic regions and differing sex determination mechanisms in both species. These results provide evidence that two closely related Phoxinus species possess distinct sex determination systems, which may contribute to reproductive isolation.
{"title":"Different sex determination systems in two closely related Eurasian minnow (Phoxinus) species","authors":"Temitope Opeyemi Oriowo, Sophie Helen Smith, Jana Thorman, Nils Sternberg, Astrid Böhne, Madlen Stange","doi":"10.1038/s41437-026-00827-8","DOIUrl":"10.1038/s41437-026-00827-8","url":null,"abstract":"Sex determination systems in teleost fishes are highly diverse, and even closely related species often evolve different mechanisms. Although hybridisation among Eurasian minnows (Phoxinus: Cypriniformes, Leuciscidae) is well documented, their sex determination systems remain unexplored. Here, we investigated the genetic basis of sex determination in Phoxinus phoxinus and Phoxinus csikii using whole-genome sequencing, with a combination of coverage, SNP-, and k-mer-based approaches to identify sex-associated genomic regions. Whole-genome coverage analyses revealed no chromosomes with significantly sex-biased coverage, consistent with homomorphic sex chromosomes in both species. In P. phoxinus, male-specific heterozygosity at sex-linked SNPs showed genotypic differences within two regions, namely on chromosomes 3 and 12. Analysis of SNPs in these regions revealed drainage-specific, sex-associated patterns, indicating the presence of population-specific sex-associated genomic loci and a male heterogametic (XX/XY) system in this species. In contrast, P. csikii females displayed unique genotypic differences in a different part of chromosome 3, pointing to a female heterogametic (ZZ/ZW) system. We further observed overrepresentation of male-specific DNA sequences in P. phoxinus and female-specific sequences in P. csikii, providing additional evidence for the presence of sex-specific genomic regions and differing sex determination mechanisms in both species. These results provide evidence that two closely related Phoxinus species possess distinct sex determination systems, which may contribute to reproductive isolation.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 4","pages":"259-270"},"PeriodicalIF":3.9,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41437-026-00827-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147283331","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 : 2026-02-20DOI: 10.1038/s41437-026-00828-7
Gwanwoou Yun, Ronchen Liu, Nathaniel P. Sharp
Traumatic brain injury is a major cause of chronic neurological impairment worldwide, and there is evidence that both genetic and environmental variation contribute to the likelihood of recovery. Using an insect model of traumatic brain injury, we examined variation in the risk of mortality using quantitative genetic approaches applied previously for life history traits in Drosophila melanogaster. We quantified additive genetic variance for mortality risk using a controlled breeding design and found levels of variation consistent with existing data on major fitness components. We did not detect inbreeding depression for mortality risk, suggesting that this trait is not strongly affected by recessive deleterious alleles. To explain the high level of standing genetic variation, we considered whether mortality risk depends on the metabolic resources available to an individual, also known as “condition”. We manipulated condition by inducing random mutations and by restricting calories during larval development. We found that reduced condition due to both random mutations and resource limitation significantly increased the risk of mortality following trauma. Among inbred lines, greater mortality risk was associated with lower viability, fecundity and longevity, consistent with an effect of genome-wide genetic quality. Our results suggest that further consideration of individual condition would be valuable for understanding and predicting variation in the outcomes of traumatic brain injury.
{"title":"Quantitative genetics of trauma induced mortality in Drosophila melanogaster","authors":"Gwanwoou Yun, Ronchen Liu, Nathaniel P. Sharp","doi":"10.1038/s41437-026-00828-7","DOIUrl":"10.1038/s41437-026-00828-7","url":null,"abstract":"Traumatic brain injury is a major cause of chronic neurological impairment worldwide, and there is evidence that both genetic and environmental variation contribute to the likelihood of recovery. Using an insect model of traumatic brain injury, we examined variation in the risk of mortality using quantitative genetic approaches applied previously for life history traits in Drosophila melanogaster. We quantified additive genetic variance for mortality risk using a controlled breeding design and found levels of variation consistent with existing data on major fitness components. We did not detect inbreeding depression for mortality risk, suggesting that this trait is not strongly affected by recessive deleterious alleles. To explain the high level of standing genetic variation, we considered whether mortality risk depends on the metabolic resources available to an individual, also known as “condition”. We manipulated condition by inducing random mutations and by restricting calories during larval development. We found that reduced condition due to both random mutations and resource limitation significantly increased the risk of mortality following trauma. Among inbred lines, greater mortality risk was associated with lower viability, fecundity and longevity, consistent with an effect of genome-wide genetic quality. Our results suggest that further consideration of individual condition would be valuable for understanding and predicting variation in the outcomes of traumatic brain injury.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 4","pages":"271-277"},"PeriodicalIF":3.9,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41437-026-00828-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146258137","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 : 2026-02-17DOI: 10.1038/s41437-026-00826-9
Portia Y.-H. Wong, Ying Chen, Tracey-Leigh Prigge, Huarong Zhang, Liz Rose-Jeffreys, Gary Ades, Mariano Roy M. Duya, Ian Kendrich C. Fontanilla, Anmol Kanwal, Najeebah Ibnat Fayeeja, Lily Kam Ping Ng, Samuel Yeung, Tommy T. Y. Lam, Paolo Momigliano, Timothy C. Bonebrake
It is important to have clearly delineated taxonomic units informed by eco-evolutionary processes to ensure effective implementation of conservation efforts. For a group as threatened as Asian pangolins, a timely understanding and recognition of cryptic species is especially critical to inform policy and management decisions. Recent genomic investigations into the group have revealed genomic distinctions between currently recognised species and the putative Manis cf. mysteria, but only incorporate limited representation of the new lineage and its sister taxa, M. javanica and M. culionensis, which may obscure evolutionary inferences within the group and overlook important genetic variation at species boundaries. In this study, we broadly sample seizure materials to incorporate as holistic a representation of each lineage as possible so as to further verify genomic distinctions between the lineages, including new samples of M. cf. mysteria and M. culionensis, the latter of which was only genomically represented by one museum sample previously. We find that while M. cf. mysteria, M. javanica and M. culionensis do form distinct clades with deep divergences, new samples of M. cf. mysteria demonstrate mitonuclear discordance and admixture with M. javanica, illuminating more evolutionary complexity between the three lineages than previously reported. We also find much higher variation in individual heterozygosity within M. cf. mysteria than its sister taxa. Our findings highlight gaps in our understanding of the contemporary evolutionary dynamics of Southeast Asian pangolins, but also demonstrate the barriers these gaps create for practical and timely implementations of conservation effort trafficked taxa at large.
{"title":"Seizure samples reveal complex evolutionary dynamics among Southeast Asian pangolins","authors":"Portia Y.-H. Wong, Ying Chen, Tracey-Leigh Prigge, Huarong Zhang, Liz Rose-Jeffreys, Gary Ades, Mariano Roy M. Duya, Ian Kendrich C. Fontanilla, Anmol Kanwal, Najeebah Ibnat Fayeeja, Lily Kam Ping Ng, Samuel Yeung, Tommy T. Y. Lam, Paolo Momigliano, Timothy C. Bonebrake","doi":"10.1038/s41437-026-00826-9","DOIUrl":"10.1038/s41437-026-00826-9","url":null,"abstract":"It is important to have clearly delineated taxonomic units informed by eco-evolutionary processes to ensure effective implementation of conservation efforts. For a group as threatened as Asian pangolins, a timely understanding and recognition of cryptic species is especially critical to inform policy and management decisions. Recent genomic investigations into the group have revealed genomic distinctions between currently recognised species and the putative Manis cf. mysteria, but only incorporate limited representation of the new lineage and its sister taxa, M. javanica and M. culionensis, which may obscure evolutionary inferences within the group and overlook important genetic variation at species boundaries. In this study, we broadly sample seizure materials to incorporate as holistic a representation of each lineage as possible so as to further verify genomic distinctions between the lineages, including new samples of M. cf. mysteria and M. culionensis, the latter of which was only genomically represented by one museum sample previously. We find that while M. cf. mysteria, M. javanica and M. culionensis do form distinct clades with deep divergences, new samples of M. cf. mysteria demonstrate mitonuclear discordance and admixture with M. javanica, illuminating more evolutionary complexity between the three lineages than previously reported. We also find much higher variation in individual heterozygosity within M. cf. mysteria than its sister taxa. Our findings highlight gaps in our understanding of the contemporary evolutionary dynamics of Southeast Asian pangolins, but also demonstrate the barriers these gaps create for practical and timely implementations of conservation effort trafficked taxa at large.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 4","pages":"249-258"},"PeriodicalIF":3.9,"publicationDate":"2026-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146212998","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 : 2026-02-07DOI: 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}
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