Pub Date : 2024-06-04DOI: 10.1038/s41437-024-00689-y
Trent Newman, Teruhito Ishihara, Geoff Shaw, Marilyn B. Renfree
Parent-of-origin-specific expression of imprinted genes is critical for successful mammalian growth and development. Insulin, coded by the INS gene, is an important growth factor expressed from the paternal allele in the yolk sac placenta of therian mammals. The tyrosine hydroxylase gene TH encodes an enzyme involved in dopamine synthesis. TH and INS are closely associated in most vertebrates, but the mouse orthologues, Th and Ins2, are separated by repeated DNA. In mice, Th is expressed from the maternal allele, but the parental origin of expression is not known for any other mammal so it is unclear whether the maternal expression observed in the mouse represents an evolutionary divergence or an ancestral condition. We compared the length of the DNA segment between TH and INS across species and show that separation of these genes occurred in the rodent lineage with an accumulation of repeated DNA. We found that the region containing TH and INS in the tammar wallaby produces at least five distinct RNA transcripts: TH, TH-INS1, TH-INS2, lncINS and INS. Using allele-specific expression analysis, we show that the TH/INS locus is expressed from the paternal allele in pre- and postnatal tammar wallaby tissues. Determining the imprinting pattern of TH/INS in other mammals might clarify if paternal expression is the ancestral condition which has been flipped to maternal expression in rodents by the accumulation of repeat sequences.
印记基因的亲本特异性表达对哺乳动物的成功生长和发育至关重要。INS 基因编码的胰岛素是一种重要的生长因子，在有肝哺乳动物的卵黄囊胎盘中由父系等位基因表达。酪氨酸羟化酶基因 TH 编码一种参与多巴胺合成的酶。在大多数脊椎动物中，TH 和 INS 密切相关，但小鼠的同源基因 Th 和 Ins2 被重复的 DNA 分隔开来。在小鼠中，Th 是通过母系等位基因表达的，但其他哺乳动物的亲本表达起源尚不清楚，因此尚不清楚在小鼠中观察到的母系表达是代表进化分化还是祖先条件。我们比较了不同物种中 TH 和 INS 之间 DNA 区段的长度，结果表明这些基因的分离发生在啮齿动物的血统中，重复 DNA 不断积累。我们发现，在犭胥袋猴中，包含 TH 和 INS 的区域至少产生了五种不同的 RNA 转录本：TH、TH-INS1、TH-INS2、lncINS 和 INS。通过等位基因特异性表达分析，我们发现TH/INS基因座在达玛小袋鼠产前和产后组织中的表达来自父系等位基因。确定 TH/INS 在其他哺乳动物中的印记模式可能会澄清父系表达是否是啮齿类动物通过重复序列的积累而转变为母系表达的祖先条件。
{"title":"The structure of the TH/INS locus and the parental allele expressed are not conserved between mammals","authors":"Trent Newman, Teruhito Ishihara, Geoff Shaw, Marilyn B. Renfree","doi":"10.1038/s41437-024-00689-y","DOIUrl":"10.1038/s41437-024-00689-y","url":null,"abstract":"Parent-of-origin-specific expression of imprinted genes is critical for successful mammalian growth and development. Insulin, coded by the INS gene, is an important growth factor expressed from the paternal allele in the yolk sac placenta of therian mammals. The tyrosine hydroxylase gene TH encodes an enzyme involved in dopamine synthesis. TH and INS are closely associated in most vertebrates, but the mouse orthologues, Th and Ins2, are separated by repeated DNA. In mice, Th is expressed from the maternal allele, but the parental origin of expression is not known for any other mammal so it is unclear whether the maternal expression observed in the mouse represents an evolutionary divergence or an ancestral condition. We compared the length of the DNA segment between TH and INS across species and show that separation of these genes occurred in the rodent lineage with an accumulation of repeated DNA. We found that the region containing TH and INS in the tammar wallaby produces at least five distinct RNA transcripts: TH, TH-INS1, TH-INS2, lncINS and INS. Using allele-specific expression analysis, we show that the TH/INS locus is expressed from the paternal allele in pre- and postnatal tammar wallaby tissues. Determining the imprinting pattern of TH/INS in other mammals might clarify if paternal expression is the ancestral condition which has been flipped to maternal expression in rodents by the accumulation of repeat sequences.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00689-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141247245","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}
Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a GWAS dataset of Arabidopsis thaliana. We demonstrate the efficiency of dual-phenotype analysis to uncover hidden genetic loci masked by population structure via a series of simulations. In real data analysis, a common allele, strongly confounded with population structure, is discovered to be associated with late flowering and slow maturation of the plant. The discovered genetic effect on flowering time is further replicated in independent datasets. Using Mendelian randomization analysis based on summary statistics from our GWAS and expression QTL scans, we predicted and replicated a candidate gene AT1G11560 that potentially causes this association. Further analysis indicates that this locus is co-selected with flowering-time-related genes. The discovered pleiotropic genotype-phenotype map provides new insights into understanding the genetic correlation of complex traits.
{"title":"Dual-trait genomic analysis in highly stratified Arabidopsis thaliana populations using genome-wide association summary statistics","authors":"Xiao Feng, Yanjun Zan, Ting Li, Yue Yao, Zheng Ning, Jiabei Li, Hadi Charati, Weilin Xu, Qianhui Wan, Dongyu Zeng, Ziyi Zeng, Yang Liu, Xia Shen","doi":"10.1038/s41437-024-00688-z","DOIUrl":"10.1038/s41437-024-00688-z","url":null,"abstract":"Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a GWAS dataset of Arabidopsis thaliana. We demonstrate the efficiency of dual-phenotype analysis to uncover hidden genetic loci masked by population structure via a series of simulations. In real data analysis, a common allele, strongly confounded with population structure, is discovered to be associated with late flowering and slow maturation of the plant. The discovered genetic effect on flowering time is further replicated in independent datasets. Using Mendelian randomization analysis based on summary statistics from our GWAS and expression QTL scans, we predicted and replicated a candidate gene AT1G11560 that potentially causes this association. Further analysis indicates that this locus is co-selected with flowering-time-related genes. The discovered pleiotropic genotype-phenotype map provides new insights into understanding the genetic correlation of complex traits.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183290","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 : 2024-05-31DOI: 10.1038/s41437-024-00690-5
Thinh Tuan Chu, Peter Skov Kristensen, Just Jensen
Stochastic simulation software is commonly used to aid breeders designing cost-effective breeding programs and to validate statistical models used in genetic evaluation. An essential feature of the software is the ability to simulate populations with desired genetic and non-genetic parameters. However, this feature often fails when non-additive effects due to dominance or epistasis are modeled, as the desired properties of simulated populations are estimated from classical quantitative genetic statistical models formulated at the population level. The software simulates underlying functional effects for genotypic values at the individual level, which are not necessarily the same as effects from statistical models in which dominance and epistasis are included. This paper provides the theoretical basis and mathematical formulas for the transformation between functional and statistical effects in such simulations. The transformation is demonstrated with two statistical models analyzing individual phenotypes in a single population (common in animal breeding) and plot phenotypes of three-way hybrids involving two inbred populations (observed in some crop breeding programs). We also describe different methods for the simulation of functional effects for additive genetics, dominance, and epistasis to achieve the desired levels of variance components in classical statistical models used in quantitative genetics.
{"title":"Simulation of functional additive and non-additive genetic effects using statistical estimates from quantitative genetic models","authors":"Thinh Tuan Chu, Peter Skov Kristensen, Just Jensen","doi":"10.1038/s41437-024-00690-5","DOIUrl":"10.1038/s41437-024-00690-5","url":null,"abstract":"Stochastic simulation software is commonly used to aid breeders designing cost-effective breeding programs and to validate statistical models used in genetic evaluation. An essential feature of the software is the ability to simulate populations with desired genetic and non-genetic parameters. However, this feature often fails when non-additive effects due to dominance or epistasis are modeled, as the desired properties of simulated populations are estimated from classical quantitative genetic statistical models formulated at the population level. The software simulates underlying functional effects for genotypic values at the individual level, which are not necessarily the same as effects from statistical models in which dominance and epistasis are included. This paper provides the theoretical basis and mathematical formulas for the transformation between functional and statistical effects in such simulations. The transformation is demonstrated with two statistical models analyzing individual phenotypes in a single population (common in animal breeding) and plot phenotypes of three-way hybrids involving two inbred populations (observed in some crop breeding programs). We also describe different methods for the simulation of functional effects for additive genetics, dominance, and epistasis to achieve the desired levels of variance components in classical statistical models used in quantitative genetics.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00690-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183465","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 : 2024-05-31DOI: 10.1038/s41437-024-00692-3
Javad Sadeghi, Farwa Zaib, Daniel D. Heath
Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.
通过选择产生的种群分化可以推动自然种群的局部适应，这对有效恢复衰退和灭绝的种群具有重要意义。然而，当宿主及其相关微生物组必须通过共同进化变化做出反应时，对当地环境条件的适应就变得复杂了。然而，要想通过选择实现适应，宿主和微生物组性状的变异应包括遗传效应的叠加。在此，我们将重点放在宿主免疫功能上，并量化影响早期生命阶段大鳞大麻哈鱼（Oncorhynchus tshawytscha）肠道免疫基因转录和肠道细菌群落组成变异的因素。具体来说，我们利用重复因子育种设计来确定肠道免疫基因转录和微生物群组成的遗传结构（父系、母系和父系与母系之间的相互作用）。此外，我们还探讨了宿主肠道基因转录与微生物群组成之间的相关性。基因转录采用纳米流体 qPCR 阵列（22 个目标基因）进行量化，微生物群组成采用 16 S rRNA 基因（V5-V6）扩增片段测序。我们发现了肠道微生物群组成和转录特征中有限但重要的遗传结构。我们还确定了肠道基因转录与微生物群组成之间的重要相关性，突出了两者之间功能性相互作用的潜在机制。总之，这项研究为大鳞大麻哈鱼这种被公认为适应当地环境的物种的宿主免疫功能及其肠道微生物群的共同进化提供了支持。因此，将免疫基因转录谱和肠道微生物组组成作为因素纳入保护和商业饲养实践的发展中，可能会为人工饲养提供更有效的新方法。
{"title":"Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha)","authors":"Javad Sadeghi, Farwa Zaib, Daniel D. Heath","doi":"10.1038/s41437-024-00692-3","DOIUrl":"10.1038/s41437-024-00692-3","url":null,"abstract":"Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183365","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 : 2024-05-27DOI: 10.1038/s41437-024-00685-2
Brooklyn S. Cars, Camille Kessler, Eric A. Hoffman, Steeve D. Côté, Daniel Koelsch, Aaron B. A. Shafer
When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force and results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number (~50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.
{"title":"Island demographics and trait associations in white-tailed deer","authors":"Brooklyn S. Cars, Camille Kessler, Eric A. Hoffman, Steeve D. Côté, Daniel Koelsch, Aaron B. A. Shafer","doi":"10.1038/s41437-024-00685-2","DOIUrl":"10.1038/s41437-024-00685-2","url":null,"abstract":"When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force and results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number (~50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158236","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 : 2024-05-27DOI: 10.1038/s41437-024-00691-4
Agata Plesnar-Bielak, Jonathan M. Parrett, Sebastian Chmielewski, Katarzyna Dudek, Aleksandra Łukasiewicz, Marzena Marszałek, Wiesław Babik, Mateusz Konczal
The information about the magnitude of differences in thermal plasticity both between and within populations, as well as identification of the underlying molecular mechanisms are key to understanding the evolution of thermal plasticity. In particular, genes underlying variation in the physiological response to temperature can provide raw material for selection acting on plastic traits. Using RNAseq, we investigate the transcriptional response to temperature in males and females from bulb mite populations selected for the increased frequency of one of two discrete male morphs (fighter- and scrambler-selected populations) that differ in relative fitness depending on temperature. We show that different mechanisms underlie the divergence in thermal response between fighter- and scrambler-selected populations at decreased vs. increased temperature. Temperature decrease to 18 °C was associated with higher transcriptomic plasticity of males with more elaborate armaments, as indicated by a significant selection-by-temperature interaction effect on the expression of 40 genes, 38 of which were upregulated in fighter-selected populations in response to temperature decrease. In response to 28 °C, no selection-by-temperature interaction in gene expression was detected. Hence, differences in phenotypic response to temperature increase likely depended on genes associated with their distinct morph-specific thermal tolerance. Selection of males also drove gene expression patterns in females. These patterns could be associated with temperature-dependent fitness differences between females from fighter- vs. scrambler-selected populations reported in previous studies. Our study shows that selection for divergent male sexually selected morphologies and behaviors has a potential to drive divergence in metabolic pathways underlying plastic response to temperature in both sexes.
{"title":"Transcriptomics of differences in thermal plasticity associated with selection for an exaggerated male sexual trait","authors":"Agata Plesnar-Bielak, Jonathan M. Parrett, Sebastian Chmielewski, Katarzyna Dudek, Aleksandra Łukasiewicz, Marzena Marszałek, Wiesław Babik, Mateusz Konczal","doi":"10.1038/s41437-024-00691-4","DOIUrl":"10.1038/s41437-024-00691-4","url":null,"abstract":"The information about the magnitude of differences in thermal plasticity both between and within populations, as well as identification of the underlying molecular mechanisms are key to understanding the evolution of thermal plasticity. In particular, genes underlying variation in the physiological response to temperature can provide raw material for selection acting on plastic traits. Using RNAseq, we investigate the transcriptional response to temperature in males and females from bulb mite populations selected for the increased frequency of one of two discrete male morphs (fighter- and scrambler-selected populations) that differ in relative fitness depending on temperature. We show that different mechanisms underlie the divergence in thermal response between fighter- and scrambler-selected populations at decreased vs. increased temperature. Temperature decrease to 18 °C was associated with higher transcriptomic plasticity of males with more elaborate armaments, as indicated by a significant selection-by-temperature interaction effect on the expression of 40 genes, 38 of which were upregulated in fighter-selected populations in response to temperature decrease. In response to 28 °C, no selection-by-temperature interaction in gene expression was detected. Hence, differences in phenotypic response to temperature increase likely depended on genes associated with their distinct morph-specific thermal tolerance. Selection of males also drove gene expression patterns in females. These patterns could be associated with temperature-dependent fitness differences between females from fighter- vs. scrambler-selected populations reported in previous studies. Our study shows that selection for divergent male sexually selected morphologies and behaviors has a potential to drive divergence in metabolic pathways underlying plastic response to temperature in both sexes.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158243","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 : 2024-05-14DOI: 10.1038/s41437-024-00687-0
Elena Gimmi, Jesper Wallisch, Christoph Vorburger
Different host plants represent ecologically dissimilar environments for phytophagous insects. The resulting divergent selection can promote the evolution of specialized host races, provided that gene flow is reduced between populations feeding on different plants. In black bean aphids belonging to the Aphis fabae complex, several morphologically cryptic taxa have been described based on their distinct host plant preferences. However, host choice and mate choice are largely decoupled in these insects: they are host-alternating and migrate between specific summer host plants and shared winter hosts, with mating occurring on the shared hosts. This provides a yearly opportunity for gene flow among aphids using different summer hosts, and raises the question if and to what extent the ecologically defined taxa are reproductively isolated. Here, we analyzed a geographically and temporally structured dataset of microsatellite genotypes from A. fabae that were mostly collected from their main winter host Euonymus europaeus, and additionally from another winter host and fourteen summer hosts. The data reveals multiple, strongly differentiated genetic clusters, which differ in their association with different summer and winter hosts. The clusters also differ in the frequency of infection with two heritable, facultative endosymbionts, separately hinting at reproductive isolation and divergent ecological selection. Furthermore, we found evidence for occasional hybridization among genetic clusters, with putative hybrids collected more frequently in spring than in autumn. This suggests that similar to host races in other phytophagous insects, both prezygotic and postzygotic barriers including selection against hybrids maintain genetic differentiation among A. fabae taxa, despite a common mating habitat.
{"title":"Ecological divergence despite common mating sites: Genotypes and symbiotypes shed light on cryptic diversity in the black bean aphid species complex","authors":"Elena Gimmi, Jesper Wallisch, Christoph Vorburger","doi":"10.1038/s41437-024-00687-0","DOIUrl":"10.1038/s41437-024-00687-0","url":null,"abstract":"Different host plants represent ecologically dissimilar environments for phytophagous insects. The resulting divergent selection can promote the evolution of specialized host races, provided that gene flow is reduced between populations feeding on different plants. In black bean aphids belonging to the Aphis fabae complex, several morphologically cryptic taxa have been described based on their distinct host plant preferences. However, host choice and mate choice are largely decoupled in these insects: they are host-alternating and migrate between specific summer host plants and shared winter hosts, with mating occurring on the shared hosts. This provides a yearly opportunity for gene flow among aphids using different summer hosts, and raises the question if and to what extent the ecologically defined taxa are reproductively isolated. Here, we analyzed a geographically and temporally structured dataset of microsatellite genotypes from A. fabae that were mostly collected from their main winter host Euonymus europaeus, and additionally from another winter host and fourteen summer hosts. The data reveals multiple, strongly differentiated genetic clusters, which differ in their association with different summer and winter hosts. The clusters also differ in the frequency of infection with two heritable, facultative endosymbionts, separately hinting at reproductive isolation and divergent ecological selection. Furthermore, we found evidence for occasional hybridization among genetic clusters, with putative hybrids collected more frequently in spring than in autumn. This suggests that similar to host races in other phytophagous insects, both prezygotic and postzygotic barriers including selection against hybrids maintain genetic differentiation among A. fabae taxa, despite a common mating habitat.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00687-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140922135","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 : 2024-05-08DOI: 10.1038/s41437-024-00686-1
Cortland K. Griswold, Saira Asif
{"title":"Correction: Meiosis at three loci in autotetraploids: Probabilities of gamete modes and genotypes without and with preferential cross-over formation","authors":"Cortland K. Griswold, Saira Asif","doi":"10.1038/s41437-024-00686-1","DOIUrl":"10.1038/s41437-024-00686-1","url":null,"abstract":"","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00686-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140892019","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}
Callicarpa subpubescens, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Post-mating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.
Callicarpa subpubescens是小笠原群岛特有的植物，被认为在八幡岛（特别是小笠原群岛中部）有多种生态型。本研究调查了八幡岛和卫星壬小岛上各遗传群与空间分布、栖息地、叶片形态、大小结构和开花时间之间的关系。利用 EST-SSR 标记确定了遗传组，并根据形态特征命名了四个生态型：生态型 D 适应干燥环境，特点是树体小，叶片浓密厚实，有大量绒毛，分布在干燥的灌丛中。生态型 G 适应于中度森林的林下，缺乏叶毛。生态类型 T 适应中生林的树冠，叶片有毛，树高较高。生态类型 M 适应中生灌丛或中生森林边缘的树冠，叶片有毛，但树高比生态类型 T 短。除 G 和 M 外，所有生态型对的花期都不相同，但所有生态型的花期或多或少都有重叠，这表明生态型之间的交配前隔离并不完美。交配后的隔离被认为是不存在的，因为生态型间和生态型内杂交的结果、发芽率和一年生幼苗的存活率均无差异。这种生态型的存在为了解适应海洋岛屿环境的持续物种演化过程提供了宝贵的信息。
{"title":"Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: genetic, phenotypic, and environmental insights","authors":"Suzuki Setsuko, Kyoko Sugai, Ichiro Tamaki, Kayo Hayama, Hidetoshi Kato","doi":"10.1038/s41437-024-00684-3","DOIUrl":"10.1038/s41437-024-00684-3","url":null,"abstract":"Callicarpa subpubescens, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Post-mating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876345","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 : 2024-04-18DOI: 10.1038/s41437-024-00683-4
Fernando Faria Franco, Danilo Trabuco Amaral, Isabel A. S. Bonatelli, Jared B. Meek, Evandro Marsola Moraes, Daniela Cristina Zappi, Nigel Paul Taylor, Deren A. R. Eaton
Here we use population genomic data (ddRAD-Seq) and ecological niche modeling to test biogeographic hypotheses for the divergence of the island-endemic cactus species Cereus insularis Hemsl. (Cereeae; Cactaceae) from its sister species C. fernambucensis Lem. The Cereus insularis grows in the Fernando de Noronha Islands (FNI), a Neotropical archipelago located 350 km off the Brazilian Atlantic Forest (BAF) coast. Phylogeographic reconstructions support a northward expansion by the common ancestor of C. insularis and C. fernambucensis along the mainland BAF coast, with C. insularis diverging from the widespread mainland taxon C. fernambucensis after colonizing FNI in the late Pleistocene. The morphologically distinct C. insularis is monophyletic and nested within C. fernambucensis, as expected from a progenitor-derivative speciation model. We tested alternative biogeographic and demographic hypotheses for the colonization of the FNI using Approximate Bayesian Computation. We found the greatest support for a stepping-stone path that emerged during periods of decreased sea level (the “bridge” hypothesis), in congruence with historical ecological niche modeling that shows highly suitable habitats on stepping-stone islands during glacial periods. The outlier analyses reveal signatures of selection in C. insularis, suggesting a putative role of adaptation driving rapid anagenic differentiation of this species in FNI.
在这里，我们利用种群基因组数据（ddRAD-Seq）和生态位建模来检验岛屿特有仙人掌物种 Cereus insularis Hemsl.（仙人掌科）与其姊妹物种 C. fernambucensis Lem 的生物地理学分化假说。海岛仙人掌（Cereus insularis）生长在费尔南多-德诺罗尼亚群岛（Fernando de Noronha Islands，FNI），这是一个距离巴西大西洋森林（BAF）海岸 350 公里的新热带群岛。系统地理学重建支持 C. insularis 和 C. fernambucensis 的共同祖先沿着巴西大西洋森林大陆海岸向北扩张，C. insularis 在更新世晚期殖民到 FNI 后与广泛分布的大陆类群 C. fernambucensis 发生分化。形态上独特的 C. insularis 是单系的，嵌套在 C. fernambucensis 中，这是祖先-衍生物模式所期望的。我们使用近似贝叶斯计算法测试了蕨类植物在蕨类地区殖民的其他生物地理学和人口学假说。我们发现，海平面下降时期出现的阶石路径（"桥梁 "假说）得到了最大的支持，这与历史生态位建模显示冰川时期阶石岛上非常适合栖息的情况一致。离群点分析揭示了海岛杉的选择特征，表明在 FNI 中该物种的快速衰老分化可能是由适应性驱动的。
{"title":"A historical stepping-stone path for an island-colonizing cactus across a submerged “bridge” archipelago","authors":"Fernando Faria Franco, Danilo Trabuco Amaral, Isabel A. S. Bonatelli, Jared B. Meek, Evandro Marsola Moraes, Daniela Cristina Zappi, Nigel Paul Taylor, Deren A. R. Eaton","doi":"10.1038/s41437-024-00683-4","DOIUrl":"10.1038/s41437-024-00683-4","url":null,"abstract":"Here we use population genomic data (ddRAD-Seq) and ecological niche modeling to test biogeographic hypotheses for the divergence of the island-endemic cactus species Cereus insularis Hemsl. (Cereeae; Cactaceae) from its sister species C. fernambucensis Lem. The Cereus insularis grows in the Fernando de Noronha Islands (FNI), a Neotropical archipelago located 350 km off the Brazilian Atlantic Forest (BAF) coast. Phylogeographic reconstructions support a northward expansion by the common ancestor of C. insularis and C. fernambucensis along the mainland BAF coast, with C. insularis diverging from the widespread mainland taxon C. fernambucensis after colonizing FNI in the late Pleistocene. The morphologically distinct C. insularis is monophyletic and nested within C. fernambucensis, as expected from a progenitor-derivative speciation model. We tested alternative biogeographic and demographic hypotheses for the colonization of the FNI using Approximate Bayesian Computation. We found the greatest support for a stepping-stone path that emerged during periods of decreased sea level (the “bridge” hypothesis), in congruence with historical ecological niche modeling that shows highly suitable habitats on stepping-stone islands during glacial periods. The outlier analyses reveal signatures of selection in C. insularis, suggesting a putative role of adaptation driving rapid anagenic differentiation of this species in FNI.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140611196","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：