Pub Date : 2025-11-07DOI: 10.1038/s41437-025-00809-2
Shalvi Chirmade, Zhuozhi Wang, Scott Mastromatteo, Eric Sanders, Bhooma Thiruvahindrapuram, Thomas Nalpathamkalam, Giovanna Pellecchia, Fan Lin, Katherine Keenan, Rohan V. Patel, Wilson WL Sung, Delnaz Roshandel, Joe Whitney, Sana Allana, Julie Avolio, Paul DW Eckford, Felix Ratjen, Lisa J. Strug
Genome-wide association studies (GWAS) have been successful in identifying single nucleotide polymorphisms (SNPs) associated with phenotypic traits. However, SNPs form an incomplete set of variation across the genome and since a large percentage of GWAS-significant SNPs lie in non-coding regions, their impact on a given trait is difficult to decipher. Recognizing whether these SNPs are tagging other polymorphisms, like structural variations (SV), is an important step towards understanding the putative causal variation at GWAS loci. Here, we develop GWAS SVatalog ( https://svatalog.research.sickkids.ca/ ), a novel open-source web tool that computes and visualizes linkage disequilibrium (LD) between SVs and GWAS-associated SNPs throughout the human genome. The tool combines GWAS Catalog’s SNP-trait association data across 14,479 phenotypes with LD statistics calculated between 35,732 SVs and 116,870 SNPs identified in 101 whole-genome long-read sequences. We show that different SV types are more likely to overlap regulatory features, and that SVs less directly tagged by GWAS-associated SNPs more frequently overlap CpG islands and promoters. We use GWAS SVatalog to identify SVs that may explain GWAS loci for iron levels, refractive error, and Alzheimer’s disease, where previously SNPs were unable to provide a causal explanation. GWAS SVatalog advances the fine-mapping of GWAS loci with structural variations, enabling researchers to associate 35,732 common SVs with 14,479 phenotypes, accelerating the understanding of disease etiology.
{"title":"GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations","authors":"Shalvi Chirmade, Zhuozhi Wang, Scott Mastromatteo, Eric Sanders, Bhooma Thiruvahindrapuram, Thomas Nalpathamkalam, Giovanna Pellecchia, Fan Lin, Katherine Keenan, Rohan V. Patel, Wilson WL Sung, Delnaz Roshandel, Joe Whitney, Sana Allana, Julie Avolio, Paul DW Eckford, Felix Ratjen, Lisa J. Strug","doi":"10.1038/s41437-025-00809-2","DOIUrl":"10.1038/s41437-025-00809-2","url":null,"abstract":"Genome-wide association studies (GWAS) have been successful in identifying single nucleotide polymorphisms (SNPs) associated with phenotypic traits. However, SNPs form an incomplete set of variation across the genome and since a large percentage of GWAS-significant SNPs lie in non-coding regions, their impact on a given trait is difficult to decipher. Recognizing whether these SNPs are tagging other polymorphisms, like structural variations (SV), is an important step towards understanding the putative causal variation at GWAS loci. Here, we develop GWAS SVatalog ( https://svatalog.research.sickkids.ca/ ), a novel open-source web tool that computes and visualizes linkage disequilibrium (LD) between SVs and GWAS-associated SNPs throughout the human genome. The tool combines GWAS Catalog’s SNP-trait association data across 14,479 phenotypes with LD statistics calculated between 35,732 SVs and 116,870 SNPs identified in 101 whole-genome long-read sequences. We show that different SV types are more likely to overlap regulatory features, and that SVs less directly tagged by GWAS-associated SNPs more frequently overlap CpG islands and promoters. We use GWAS SVatalog to identify SVs that may explain GWAS loci for iron levels, refractive error, and Alzheimer’s disease, where previously SNPs were unable to provide a causal explanation. GWAS SVatalog advances the fine-mapping of GWAS loci with structural variations, enabling researchers to associate 35,732 common SVs with 14,479 phenotypes, accelerating the understanding of disease etiology.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 3","pages":"199-210"},"PeriodicalIF":3.9,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41437-025-00809-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145470968","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 : 2025-11-05DOI: 10.1038/s41437-025-00808-3
Léa A. Nicolas, Emma L. Berdan, Maren Wellenreuther, Hervé Colinet, Andréa Clouard, Pierre De Wit, Sylvain Glémin, Claire Mérot
Chromosomal inversion supergenes, which form blocks of linked genes, are increasingly recognized for their role in maintaining intra-specific diversity. They are predicted to be relevant genetic architectures for local adaptation in the face of gene flow. However, pinpointing the underlying traits and functional mechanisms under selection remains challenging. The seaweed fly Coelopa frigida harbors several large polymorphic inversions, of which the Cf-Inv(4.1) inversion displays a latitudinal cline of frequencies along the North American Atlantic Coast, suggesting a putative role in adaptation along the eco-climatic gradient. To investigate this hypothesis, we designed a molecular marker for karyotyping and studied natural and experimental populations from North America and Europe. We confirmed that this inversion is also polymorphic in Europe, and displays parallel latitudinal clines across continents, providing strong indirect support that Cf-Inv(4.1) is under natural selection along similar environmental gradients. We found that Cf-Inv(4.1) had a significant impact on egg-to-adult survival and fecundity under different thermal conditions. However, no effect on cold tolerance could be determined using supercooling point and chill coma recovery time. We speculate that fitness associated with Cf-Inv(4.1) is shaped by subtle life-history differences whose relative advantage depends on climate. While our experimental approaches provided insights into genotype-phenotype associations, it is worth noting that selection acts on the overall fitness, involving complex sets of traits. This is especially relevant for inversions linking hundreds of genes. This multi-gene property also explains why inversions are frequently involved in repeated parallel adaptation to environmental gradients, as demonstrated here in the seaweed fly.
{"title":"Parallel clines of chromosomal inversion frequencies in seaweed flies are associated with thermal variation","authors":"Léa A. Nicolas, Emma L. Berdan, Maren Wellenreuther, Hervé Colinet, Andréa Clouard, Pierre De Wit, Sylvain Glémin, Claire Mérot","doi":"10.1038/s41437-025-00808-3","DOIUrl":"10.1038/s41437-025-00808-3","url":null,"abstract":"Chromosomal inversion supergenes, which form blocks of linked genes, are increasingly recognized for their role in maintaining intra-specific diversity. They are predicted to be relevant genetic architectures for local adaptation in the face of gene flow. However, pinpointing the underlying traits and functional mechanisms under selection remains challenging. The seaweed fly Coelopa frigida harbors several large polymorphic inversions, of which the Cf-Inv(4.1) inversion displays a latitudinal cline of frequencies along the North American Atlantic Coast, suggesting a putative role in adaptation along the eco-climatic gradient. To investigate this hypothesis, we designed a molecular marker for karyotyping and studied natural and experimental populations from North America and Europe. We confirmed that this inversion is also polymorphic in Europe, and displays parallel latitudinal clines across continents, providing strong indirect support that Cf-Inv(4.1) is under natural selection along similar environmental gradients. We found that Cf-Inv(4.1) had a significant impact on egg-to-adult survival and fecundity under different thermal conditions. However, no effect on cold tolerance could be determined using supercooling point and chill coma recovery time. We speculate that fitness associated with Cf-Inv(4.1) is shaped by subtle life-history differences whose relative advantage depends on climate. While our experimental approaches provided insights into genotype-phenotype associations, it is worth noting that selection acts on the overall fitness, involving complex sets of traits. This is especially relevant for inversions linking hundreds of genes. This multi-gene property also explains why inversions are frequently involved in repeated parallel adaptation to environmental gradients, as demonstrated here in the seaweed fly.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 3","pages":"162-173"},"PeriodicalIF":3.9,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41437-025-00808-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145451699","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 : 2025-10-31DOI: 10.1038/s41437-025-00807-4
Gabrielle E. Sanfilippo, Kentaro Inoue, David T. Zanatta
Pressodonta viridis (Bivalvia: Unionida) is a species of freshwater mussel considered rare and imperiled in 14 U.S. states and Ontario, Canada. Limited population-level genetic information is available for P. viridis despite the species’ imperilment status. We used 13,661 single nucleotide polymorphisms (SNPs) derived from double digest restriction site-associated sequencing (ddRAD-seq) to examine patterns in population genetic diversity, structure, and differentiation among P. viridis populations in the Upper Mississippi River, Ohio and Wabash rivers, and Great Lakes watersheds. Structure analyses revealed significant differentiation related to major drainage among groups of P. viridis populations. Evidence of founder effects in Great Lakes populations by colonization routes from Upper Mississippi River and Ohio/Wabash River systems was found in admixture analyses. Limited evidence of isolation-by-distance effects was found, suggesting that multiple colonization routes and glacial refugia are responsible for current P. viridis genetic structure. A combination of ancient river hydrological patterns and more recent headwater stream capture events following the last glacial retreat likely correspond to considerable admixture found among populations of P. viridis in the Upper Mississippi, Wabash, and Ohio Rivers. Population genetic variation, structure, and differentiation described in this study should be used to inform conservation efforts of P. viridis in the future, particularly if recovery actions include population augmentation from translocations or hatchery propagation.
{"title":"Patterns of genetic diversity and structure in Pressodonta viridis, Slippershell Mussel, in streams of the U.S. Midwest","authors":"Gabrielle E. Sanfilippo, Kentaro Inoue, David T. Zanatta","doi":"10.1038/s41437-025-00807-4","DOIUrl":"10.1038/s41437-025-00807-4","url":null,"abstract":"Pressodonta viridis (Bivalvia: Unionida) is a species of freshwater mussel considered rare and imperiled in 14 U.S. states and Ontario, Canada. Limited population-level genetic information is available for P. viridis despite the species’ imperilment status. We used 13,661 single nucleotide polymorphisms (SNPs) derived from double digest restriction site-associated sequencing (ddRAD-seq) to examine patterns in population genetic diversity, structure, and differentiation among P. viridis populations in the Upper Mississippi River, Ohio and Wabash rivers, and Great Lakes watersheds. Structure analyses revealed significant differentiation related to major drainage among groups of P. viridis populations. Evidence of founder effects in Great Lakes populations by colonization routes from Upper Mississippi River and Ohio/Wabash River systems was found in admixture analyses. Limited evidence of isolation-by-distance effects was found, suggesting that multiple colonization routes and glacial refugia are responsible for current P. viridis genetic structure. A combination of ancient river hydrological patterns and more recent headwater stream capture events following the last glacial retreat likely correspond to considerable admixture found among populations of P. viridis in the Upper Mississippi, Wabash, and Ohio Rivers. Population genetic variation, structure, and differentiation described in this study should be used to inform conservation efforts of P. viridis in the future, particularly if recovery actions include population augmentation from translocations or hatchery propagation.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 12","pages":"680-694"},"PeriodicalIF":3.9,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145421548","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 : 2025-10-30DOI: 10.1038/s41437-025-00803-8
Owen W. Moosman, Joanna L. Kelley, Samuel N. Bogan
Phased genomes and pangenomes are enhancing our understanding of genetic variation. Accurate phasing and assembly in repetitive regions of the genome remain challenging, however. Addressing this obstacle is crucial for studying structural genomic variation, such as copy number variations (CNVs) common to repetitive regions. Polar fishes, for example, evolved repetitive tandem arrays of antifreeze protein (AFP) genes that facilitate adaptation to freezing and expanded in copy number in colder environments. AFP CNVs remain poorly characterized in polar fishes and may be illuminated by haplotype-aware approaches. We performed long-read sequencing for two polar fishes in the suborder Zoarcoidei and leveraged additional published long-read data to assemble phased genomes. We developed a workflow to measure haplotype diversity in CNV while controlling for misassembly and switch errors—a change from one parental haplotype to another in a contiguous assembly. We present gfa_parser, which computes and extracts all possible contiguous sequences for phased or primary assemblies from graphical fragment assembly (GFA) files, and switch_error_screen, which flags potential switch errors. gfa_parser revealed that assembly uncertainty was ubiquitous across AFP array haplotypes and that standard processing of graphical fragment assemblies can bias measurement of haplotype CNVs. We detected no switch errors in AFP arrays. After controlling for misassembly and switch error, we detected haplotype diversity of AFP CNVs in all studied polar Zoarcoidei species and in 60% of AFP arrays. Intraindividual haplotype diversity spanned differences of 3–16 copies. Our workflow revealed intraspecific genomic diversity in zoarcoids that likely fueled the evolution of AFP copy number across temperature.
{"title":"Mitigating assembly and switch errors in phased genomes of polar fishes reveals haplotype diversity in copy number of antifreeze protein genes","authors":"Owen W. Moosman, Joanna L. Kelley, Samuel N. Bogan","doi":"10.1038/s41437-025-00803-8","DOIUrl":"10.1038/s41437-025-00803-8","url":null,"abstract":"Phased genomes and pangenomes are enhancing our understanding of genetic variation. Accurate phasing and assembly in repetitive regions of the genome remain challenging, however. Addressing this obstacle is crucial for studying structural genomic variation, such as copy number variations (CNVs) common to repetitive regions. Polar fishes, for example, evolved repetitive tandem arrays of antifreeze protein (AFP) genes that facilitate adaptation to freezing and expanded in copy number in colder environments. AFP CNVs remain poorly characterized in polar fishes and may be illuminated by haplotype-aware approaches. We performed long-read sequencing for two polar fishes in the suborder Zoarcoidei and leveraged additional published long-read data to assemble phased genomes. We developed a workflow to measure haplotype diversity in CNV while controlling for misassembly and switch errors—a change from one parental haplotype to another in a contiguous assembly. We present gfa_parser, which computes and extracts all possible contiguous sequences for phased or primary assemblies from graphical fragment assembly (GFA) files, and switch_error_screen, which flags potential switch errors. gfa_parser revealed that assembly uncertainty was ubiquitous across AFP array haplotypes and that standard processing of graphical fragment assemblies can bias measurement of haplotype CNVs. We detected no switch errors in AFP arrays. After controlling for misassembly and switch error, we detected haplotype diversity of AFP CNVs in all studied polar Zoarcoidei species and in 60% of AFP arrays. Intraindividual haplotype diversity spanned differences of 3–16 copies. Our workflow revealed intraspecific genomic diversity in zoarcoids that likely fueled the evolution of AFP copy number across temperature.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 3","pages":"174-186"},"PeriodicalIF":3.9,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41437-025-00803-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145408817","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 : 2025-10-28DOI: 10.1038/s41437-025-00806-5
Andrew D. Foote, M. Thomas P. Gilbert, Shyam Gopalakrishnan, Marie Louis, Michael D. Martin, Phillip A. Morin, Milaja Nykänen, Camilla Hjorth Scharff-Olsen, Laurent Excoffier
Genomes of high latitude killer whales (Orcinus orca) harbour signatures of post-glacial founding and expansion. Here, we investigate whether reduced efficacy of selection increased the predicted mutation burden in founder populations with low Ne, or whether recessive deleterious mutations exposed to selection in homozygous genotypes were purged. Comparing the accumulation of synonymous and non-synonymous mutations across pairs of globally sampled genomes reveals that high latitude North Atlantic genomes have accumulated proportionally fewer non-synonymous mutations than other populations. The genome of a 7.5-Kyr-old North Atlantic killer whale, inferred to be closely related to the direct ancestors of the present-day Icelandic and Norwegian populations, was used to calibrate the timing of the action of selection on non-synonymous mutations predominantly to the Holocene. Non-synonymous mutations purged in modern Norwegian killer whale genomes are found as globally shared standing variation in heterozygote genotypes more often than expected, suggesting associative- or pseudo-overdominance. Taken together, our findings are consistent with purging of recessive non-synonymous mutations exposed to selection in founder-associated homozygous genotypes.
{"title":"Evidence of long-term purging of mutation burden in killer whale Orcinus orca genomes","authors":"Andrew D. Foote, M. Thomas P. Gilbert, Shyam Gopalakrishnan, Marie Louis, Michael D. Martin, Phillip A. Morin, Milaja Nykänen, Camilla Hjorth Scharff-Olsen, Laurent Excoffier","doi":"10.1038/s41437-025-00806-5","DOIUrl":"10.1038/s41437-025-00806-5","url":null,"abstract":"Genomes of high latitude killer whales (Orcinus orca) harbour signatures of post-glacial founding and expansion. Here, we investigate whether reduced efficacy of selection increased the predicted mutation burden in founder populations with low Ne, or whether recessive deleterious mutations exposed to selection in homozygous genotypes were purged. Comparing the accumulation of synonymous and non-synonymous mutations across pairs of globally sampled genomes reveals that high latitude North Atlantic genomes have accumulated proportionally fewer non-synonymous mutations than other populations. The genome of a 7.5-Kyr-old North Atlantic killer whale, inferred to be closely related to the direct ancestors of the present-day Icelandic and Norwegian populations, was used to calibrate the timing of the action of selection on non-synonymous mutations predominantly to the Holocene. Non-synonymous mutations purged in modern Norwegian killer whale genomes are found as globally shared standing variation in heterozygote genotypes more often than expected, suggesting associative- or pseudo-overdominance. Taken together, our findings are consistent with purging of recessive non-synonymous mutations exposed to selection in founder-associated homozygous genotypes.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 12","pages":"671-679"},"PeriodicalIF":3.9,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145389027","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 : 2025-10-23DOI: 10.1038/s41437-025-00805-6
Wenjun Zhou, Daniele Kunz, Chris D. Jiggins
Structural variants such as chromosomal rearrangements and gene duplications can play an important role in the adaptation and diversification of organisms. Here, we used comparative genomics to study the functional implications of structural variants across two families of flies. We compared the reference genomes of eight Asilidae species and six Stratiomyidae species, including the black soldier fly (Hermetia illucens), a species with an ability to convert organic waste into biomass and a recently expanded global range. Our results show that the genomes of Stratiomyidae are generally larger than Asilidae and contain a higher proportion of transposable elements, many of which are recently expanded. Gene families showing more gene duplications are enriched for life history related functions such as metabolism in Stratiomyidae which are known to be active decomposers, and longevity in Asilidae which are predators and have generally longer lifespan than Stratiomyidae. Gene families showing more gene duplications that are specific to H. illucens are mostly related to olfactory and immune responses, while across the Stratiomyidae there is enrichment of digestive and metabolic functions such as proteolysis, providing an explanation for the higher decomposing efficiency and adaptive ability of H. illucens compared to other Stratiomyidae species in decomposing environments. Together, our results shed light on the contribution of structural variants to functional adaptation and gene family expansions that have likely played a role in the ecological success of the black soldier fly.
{"title":"Comparative analysis of gene family evolution demonstrates expansion of digestive, immunity and olfactory functions in the black soldier fly (Hermetia illucens) lineage","authors":"Wenjun Zhou, Daniele Kunz, Chris D. Jiggins","doi":"10.1038/s41437-025-00805-6","DOIUrl":"10.1038/s41437-025-00805-6","url":null,"abstract":"Structural variants such as chromosomal rearrangements and gene duplications can play an important role in the adaptation and diversification of organisms. Here, we used comparative genomics to study the functional implications of structural variants across two families of flies. We compared the reference genomes of eight Asilidae species and six Stratiomyidae species, including the black soldier fly (Hermetia illucens), a species with an ability to convert organic waste into biomass and a recently expanded global range. Our results show that the genomes of Stratiomyidae are generally larger than Asilidae and contain a higher proportion of transposable elements, many of which are recently expanded. Gene families showing more gene duplications are enriched for life history related functions such as metabolism in Stratiomyidae which are known to be active decomposers, and longevity in Asilidae which are predators and have generally longer lifespan than Stratiomyidae. Gene families showing more gene duplications that are specific to H. illucens are mostly related to olfactory and immune responses, while across the Stratiomyidae there is enrichment of digestive and metabolic functions such as proteolysis, providing an explanation for the higher decomposing efficiency and adaptive ability of H. illucens compared to other Stratiomyidae species in decomposing environments. Together, our results shed light on the contribution of structural variants to functional adaptation and gene family expansions that have likely played a role in the ecological success of the black soldier fly.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"135 3","pages":"187-198"},"PeriodicalIF":3.9,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41437-025-00805-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145354670","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 : 2025-10-14DOI: 10.1038/s41437-025-00798-2
James R. P. Worth, James R. Marthick, Yoshihisa Suyama, Gregory J. Jordan
The impact of past anthropogenic disturbance on the amount and distribution of genetic diversity is a key factor in determining the resilience of tree species to environmental change. This is particularly the case for narrowly distributed species where disturbance has impacted most of the species’ range. Here we examine the legacy of post-colonial logging and fire on patterns of genetic diversity in the Tasmanian palaeoendemic conifer Lagarostrobos franklinii (Podocarpaceae), a fire-sensitive and slow growing rainforest tree valued for its durable timber. Thirty-three populations (12 of which represent primary stands) from across the species range were genotyped using eight nuclear SSRs (871 samples) and MIG-seq-based single nucleotide polymorphisms (254 samples). Genetic differentiation was relatively high for conifers (Fst of 0.113 and 0.143 for nuclear SSR and MIG-seq, respectively) with cryptic divergence between populations geographically close but in differing river catchments likely reflecting postglacial dispersal from distinct Last Glacial refugia and low levels of gene flow. Population level genetic diversity was greatest in the core of the range with no significant correlation with the history of post-colonial human disturbance (i.e. primary vs. non primary stands). Unexpectedly, given the greater impact of logging at lower elevations, a significant decline in allelic richness with increasing elevation was observed. Overall, this study shows that L. franklinii has been resilient to past timber exploitation and uncovers previously undetected genetic patterns. This demonstrates that genetic tools can be invaluable in characterising species specific impacts of disturbance and in helping guide the ongoing conservation of important species.
{"title":"Last Glacial and Holocene dynamics override post-colonial disturbance in shaping genetic diversity of a heavily exploited palaeoendemic conifer, Lagarostrobos franklinii","authors":"James R. P. Worth, James R. Marthick, Yoshihisa Suyama, Gregory J. Jordan","doi":"10.1038/s41437-025-00798-2","DOIUrl":"10.1038/s41437-025-00798-2","url":null,"abstract":"The impact of past anthropogenic disturbance on the amount and distribution of genetic diversity is a key factor in determining the resilience of tree species to environmental change. This is particularly the case for narrowly distributed species where disturbance has impacted most of the species’ range. Here we examine the legacy of post-colonial logging and fire on patterns of genetic diversity in the Tasmanian palaeoendemic conifer Lagarostrobos franklinii (Podocarpaceae), a fire-sensitive and slow growing rainforest tree valued for its durable timber. Thirty-three populations (12 of which represent primary stands) from across the species range were genotyped using eight nuclear SSRs (871 samples) and MIG-seq-based single nucleotide polymorphisms (254 samples). Genetic differentiation was relatively high for conifers (Fst of 0.113 and 0.143 for nuclear SSR and MIG-seq, respectively) with cryptic divergence between populations geographically close but in differing river catchments likely reflecting postglacial dispersal from distinct Last Glacial refugia and low levels of gene flow. Population level genetic diversity was greatest in the core of the range with no significant correlation with the history of post-colonial human disturbance (i.e. primary vs. non primary stands). Unexpectedly, given the greater impact of logging at lower elevations, a significant decline in allelic richness with increasing elevation was observed. Overall, this study shows that L. franklinii has been resilient to past timber exploitation and uncovers previously undetected genetic patterns. This demonstrates that genetic tools can be invaluable in characterising species specific impacts of disturbance and in helping guide the ongoing conservation of important species.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 10-11","pages":"624-636"},"PeriodicalIF":3.9,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145292011","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 : 2025-10-13DOI: 10.1038/s41437-025-00800-x
Marion Herbette, Laura Ross
The mealybug Pseudococcus viburni is a plant-feeding insect with a non-Mendelian genetic system known as paternal genome elimination (PGE). In PGE, males eliminate their paternally inherited chromosomes during meiosis, transmitting only the maternal genome to the next generation. This involves genome-wide imprinting, where paternal chromosomes are heterochromatinised in embryogenesis and throughout adulthood. In this species, a non-essential B chromosome can escape paternal genome elimination, thereby enhancing its transmission rate to the next generation. Previous studies show that the B chromosome escapes elimination by changing its chromatin compaction during meiosis to resemble that of maternal chromosomes. Although the exact mechanism underlying this change is poorly understood. Here we investigated histone methylation and acetylation modifications, as well as the Heterochromatin Protein 1 (HP1), to characterise differences between maternal, paternal and B chromosomes during male meiosis of P. viburni. Maternal and paternal chromosomes show distinct histone modification patterns, with marks associated with euchromatin present on maternal chromosomes and marks associated with heterochromatin present on paternal chromosomes. We then identified key histone modification changes that coincide with chromatin remodelling of the B chromosome, which allows it to segregate with maternal chromosomes. In addition, we showed that these chromatin modifications occur regardless of the parental origin of the B chromosome. Overall, our findings support the role of histone modifications for proper chromosome segregation during meiosis in mealybugs and provide insight into the mechanisms by which the B chromosome exploits PGE for its preferential transmission.
{"title":"Chromatin state dynamics of autosomes and the B chromosome during spermatogenesis in Pseudococcus viburni.","authors":"Marion Herbette, Laura Ross","doi":"10.1038/s41437-025-00800-x","DOIUrl":"https://doi.org/10.1038/s41437-025-00800-x","url":null,"abstract":"<p><p>The mealybug Pseudococcus viburni is a plant-feeding insect with a non-Mendelian genetic system known as paternal genome elimination (PGE). In PGE, males eliminate their paternally inherited chromosomes during meiosis, transmitting only the maternal genome to the next generation. This involves genome-wide imprinting, where paternal chromosomes are heterochromatinised in embryogenesis and throughout adulthood. In this species, a non-essential B chromosome can escape paternal genome elimination, thereby enhancing its transmission rate to the next generation. Previous studies show that the B chromosome escapes elimination by changing its chromatin compaction during meiosis to resemble that of maternal chromosomes. Although the exact mechanism underlying this change is poorly understood. Here we investigated histone methylation and acetylation modifications, as well as the Heterochromatin Protein 1 (HP1), to characterise differences between maternal, paternal and B chromosomes during male meiosis of P. viburni. Maternal and paternal chromosomes show distinct histone modification patterns, with marks associated with euchromatin present on maternal chromosomes and marks associated with heterochromatin present on paternal chromosomes. We then identified key histone modification changes that coincide with chromatin remodelling of the B chromosome, which allows it to segregate with maternal chromosomes. In addition, we showed that these chromatin modifications occur regardless of the parental origin of the B chromosome. Overall, our findings support the role of histone modifications for proper chromosome segregation during meiosis in mealybugs and provide insight into the mechanisms by which the B chromosome exploits PGE for its preferential transmission.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145285950","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 : 2025-10-10DOI: 10.1038/s41437-025-00791-9
Bruno Marchetti de Souza, João Ricardo Bachega Feijó Rosa, Evandro Vagner Tambarussi, Marcos Silveira Wrege, Elenice Fritzsons, Lucileide Vilela Resende, Eliseu Binneck, Leandro Eugenio Cardamone Diniz, Alexandre Magno Sebbenn, Dario Grattapaglia, Valderês Aparecida de Sousa, Miguel Luiz Menezes Freitas, Ananda Virgínia de Aguiar
Araucaria angustifolia (araucaria) is a conifer tree of high ecological and social values in the Brazilian subtropical region. However, the species is threatened with extinction. We examined the genetic variability and gene flow between populations of araucaria through a coalescent approach. DNA samples were collected from 185 trees in a provenance and progeny established with seeds collected in 15 natural populations. The genotyping was performed using a 3 K Axiom SNPs array to verify the intensity and direction of the migratory flow between neighboring populations. All models were run with MIGRATE-N software. The migration rate, the effective number of migrants per generation ( $$x{N}_{i}{m}_{{ij}}$$ ), and the effective population size (Ne) were estimated. The mean Ne observed for the southernmost populations (729 ± 293) was found higher than that of the northernmost ones (390 ± 176). We identified neighboring populations that stand out as the main sources of migrant individuals and the ones that receive a high migration flow. By correlating the migration parameters with climatic variables, we observed that the minimum average temperature in the coldest month, and the amount of rain in the driest month show a high and significant correlation with $$x{N}_{i}{m}_{{ij}}$$ values. In general, the observed gene flow suggests a connection between the remnant populations of araucaria, which constitute the greatest sources of genetic diversity of the species found in the southernmost region of Brazil.
巴西针叶树（Araucaria angustifolia）是巴西亚热带地区一种具有很高生态和社会价值的针叶树。然而，该物种正面临灭绝的威胁。我们研究了遗传变异和基因流动之间的群体通过一个凝聚的方法。从一个种源的185棵树和15个自然种群中收集的种子建立的后代中收集了DNA样本。利用3 K Axiom snp阵列进行基因分型，以验证邻近种群之间迁移流动的强度和方向。所有模型都使用MIGRATE-N软件运行。估计了迁移率、每代有效迁移数（x N im ij）和有效种群规模（Ne）。最南端种群平均Ne值（729±293）高于最北部种群（390±176）。我们确定了作为移民个人的主要来源和接收高移民流量的邻近人口。通过将迁移参数与气候变量进行关联，我们发现最冷月份的最低平均气温和最干燥月份的降雨量与x N im ij值呈高度显著相关。总的来说，观察到的基因流动表明，在巴西最南端地区发现的araucaria的残余种群之间存在联系，这些种群构成了该物种遗传多样性的最大来源。
{"title":"Genetic structure and historical gene flow in Araucaria angustifolia populations across two Brazilian regions","authors":"Bruno Marchetti de Souza, João Ricardo Bachega Feijó Rosa, Evandro Vagner Tambarussi, Marcos Silveira Wrege, Elenice Fritzsons, Lucileide Vilela Resende, Eliseu Binneck, Leandro Eugenio Cardamone Diniz, Alexandre Magno Sebbenn, Dario Grattapaglia, Valderês Aparecida de Sousa, Miguel Luiz Menezes Freitas, Ananda Virgínia de Aguiar","doi":"10.1038/s41437-025-00791-9","DOIUrl":"10.1038/s41437-025-00791-9","url":null,"abstract":"Araucaria angustifolia (araucaria) is a conifer tree of high ecological and social values in the Brazilian subtropical region. However, the species is threatened with extinction. We examined the genetic variability and gene flow between populations of araucaria through a coalescent approach. DNA samples were collected from 185 trees in a provenance and progeny established with seeds collected in 15 natural populations. The genotyping was performed using a 3 K Axiom SNPs array to verify the intensity and direction of the migratory flow between neighboring populations. All models were run with MIGRATE-N software. The migration rate, the effective number of migrants per generation ( $$x{N}_{i}{m}_{{ij}}$$ ), and the effective population size (Ne) were estimated. The mean Ne observed for the southernmost populations (729 ± 293) was found higher than that of the northernmost ones (390 ± 176). We identified neighboring populations that stand out as the main sources of migrant individuals and the ones that receive a high migration flow. By correlating the migration parameters with climatic variables, we observed that the minimum average temperature in the coldest month, and the amount of rain in the driest month show a high and significant correlation with $$x{N}_{i}{m}_{{ij}}$$ values. In general, the observed gene flow suggests a connection between the remnant populations of araucaria, which constitute the greatest sources of genetic diversity of the species found in the southernmost region of Brazil.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 10-11","pages":"584-595"},"PeriodicalIF":3.9,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274345","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 : 2025-10-08DOI: 10.1038/s41437-025-00804-7
Vivak Soni, Cyril J. Versoza, Susanne P. Pfeifer, Jeffrey D. Jensen
The common marmoset (Callithrix jacchus) is of considerable biomedical importance, yet there remains a need to characterize the evolutionary forces shaping empirically observed patterns of genomic variation in the species. However, two uncommon biological traits potentially prevent the use of standard population genetic approaches in this primate: a high frequency of twin births and the prevalence of hematopoietic chimerism. Here we characterize the impact of these biological features on the inference of natural selection, and directly model twinning and chimerism when performing inference of the distribution of fitness effects to characterize general selective dynamics as well as when scanning the genome for loci shaped by the action of episodic positive and balancing selection. Results suggest a generally increased degree of purifying selection relative to human populations, consistent with the larger estimated effective population size of common marmosets. Furthermore, genomic scans based on an appropriate evolutionary baseline model reveal a small number of genes related to immunity, sensory perception, and reproduction to be strong sweep candidates. Notably, two genes in the major histocompatibility complex were found to have strong evidence of being maintained by balancing selection, in agreement with observations in other primate species. Taken together, this work, presenting the first whole-genome characterization of selective dynamics in the common marmoset, thus provides important insights into the landscape of both persistent and episodic selective forces in this species.
{"title":"Investigating the effects of chimerism on the inference of selection: quantifying genomic targets of purifying, positive, and balancing selection in common marmosets (Callithrix jacchus)","authors":"Vivak Soni, Cyril J. Versoza, Susanne P. Pfeifer, Jeffrey D. Jensen","doi":"10.1038/s41437-025-00804-7","DOIUrl":"10.1038/s41437-025-00804-7","url":null,"abstract":"The common marmoset (Callithrix jacchus) is of considerable biomedical importance, yet there remains a need to characterize the evolutionary forces shaping empirically observed patterns of genomic variation in the species. However, two uncommon biological traits potentially prevent the use of standard population genetic approaches in this primate: a high frequency of twin births and the prevalence of hematopoietic chimerism. Here we characterize the impact of these biological features on the inference of natural selection, and directly model twinning and chimerism when performing inference of the distribution of fitness effects to characterize general selective dynamics as well as when scanning the genome for loci shaped by the action of episodic positive and balancing selection. Results suggest a generally increased degree of purifying selection relative to human populations, consistent with the larger estimated effective population size of common marmosets. Furthermore, genomic scans based on an appropriate evolutionary baseline model reveal a small number of genes related to immunity, sensory perception, and reproduction to be strong sweep candidates. Notably, two genes in the major histocompatibility complex were found to have strong evidence of being maintained by balancing selection, in agreement with observations in other primate species. Taken together, this work, presenting the first whole-genome characterization of selective dynamics in the common marmoset, thus provides important insights into the landscape of both persistent and episodic selective forces in this species.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 10-11","pages":"645-657"},"PeriodicalIF":3.9,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12577292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145250856","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}
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