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Tudor domain containing protein 5-like (Tdrd5l) identifies a novel germline body and regulates maternal RNAs during oogenesis in Drosophila.
IF 3.3 3区 生物学
Genetics Pub Date : 2025-02-21 DOI: 10.1093/genetics/iyaf024
Caitlin Pozmanter, Leif Benner, Sydney E Kelly, Harrison Curnutte, Laura Emilfork, Mark Van Doren
{"title":"Tudor domain containing protein 5-like (Tdrd5l) identifies a novel germline body and regulates maternal RNAs during oogenesis in Drosophila.","authors":"Caitlin Pozmanter, Leif Benner, Sydney E Kelly, Harrison Curnutte, Laura Emilfork, Mark Van Doren","doi":"10.1093/genetics/iyaf024","DOIUrl":"https://doi.org/10.1093/genetics/iyaf024","url":null,"abstract":"<p><p>Tudor domain-containing proteins are conserved across the animal kingdom for their function in germline development and fertility. Previously, we demonstrated that Tudor domain-containing protein 5-like (Tdrd5l) plays an important role in the germline where it promotes male identity. However, Tdrd5l is also expressed in both the ovary and testis during later stages of germline development, suggesting that it plays a role in germline differentiation in both sexes. We found that Tdrd5l localizes to a potentially novel germline body and plays a role in post-transcriptional gene regulation. Additionally, embryos laid by Tdrd5l-mutant females exhibited reduced viability and displayed dorsal appendage defects suggesting a failure of proper dorsal-ventral (D/V) patterning. As D/V patterning is dependent on gurken (grk), we examined Grk expression during oogenesis. We observed premature accumulation of Grk protein in nurse cells indicating that translation is no longer properly repressed during mRNA transport to the oocyte. We also observed increased nurse cell accumulation of the cytoplasmic polyadenylation element binding protein Oo18 RNA-Binding Protein (Orb or CPEB), a translational activator of grk. Decreasing orb function was able to partially rescue the Tdrd5l-mutant phenotype, and so defects in Orb are likely a primary cause of the defects in Tdrd5l mutants. Our data indicate that Tdrd5l is important for translational repression of maternal mRNAs such as orb, and possibly others, following their synthesis in the nurse cells and during their transport to the oocyte.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dynamic changes in neuronal and glial GAL4 driver expression during Drosophila aging.
IF 3.3 3区 生物学
Genetics Pub Date : 2025-02-14 DOI: 10.1093/genetics/iyaf014
Caroline Delandre, John P D McMullen, Owen J Marshall
{"title":"Dynamic changes in neuronal and glial GAL4 driver expression during Drosophila aging.","authors":"Caroline Delandre, John P D McMullen, Owen J Marshall","doi":"10.1093/genetics/iyaf014","DOIUrl":"https://doi.org/10.1093/genetics/iyaf014","url":null,"abstract":"<p><p>Understanding how diverse cell types come together to form a functioning brain relies on the ability to specifically target these cells. This is often done using genetic tools such as the GAL4/UAS system in Drosophila melanogaster. Surprisingly, despite its extensive usage during studies of the aging brain, detailed spatiotemporal characterization of GAL4 driver lines in adult flies has been lacking. Here, we show that 3 commonly used neuronal drivers (elav[C155]-GAL4, nSyb[R57C10]-GAL4, and ChAT-GAL4) and the commonly used glial driver repo-GAL4 all show rapid and pronounced decreases in activity over the first 1.5 weeks of adult life, with activity becoming undetectable in some regions after 30 days (at 18°C). In addition to an overall decrease in GAL4 activity over time, we found notable differences in spatial patterns, mostly occurring soon after eclosion. Although all lines showed these changes, the nSyb-GAL4 line exhibited the most consistent and stable expression patterns over aging. Our findings suggest that gene transcription of key loci decreases in the aged brain, a finding broadly similar to previous work in mammalian brains. Our results also raise questions over past work on long-term expression of disease models in the brain and stress the need to find better genetic tools for ageing studies.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparing the predictors of mutability among healthy human tissues inferred from mutations in single-cell genome data.
IF 3.3 3区 生物学
Genetics Pub Date : 2025-02-14 DOI: 10.1093/genetics/iyae215
Madeleine Oman, Rob W Ness
{"title":"Comparing the predictors of mutability among healthy human tissues inferred from mutations in single-cell genome data.","authors":"Madeleine Oman, Rob W Ness","doi":"10.1093/genetics/iyae215","DOIUrl":"https://doi.org/10.1093/genetics/iyae215","url":null,"abstract":"<p><p>Studying mutation in healthy somatic tissues is the key for understanding the genesis of cancer and other genetic diseases. Mutation rate varies from site to site in the human genome by up to 100-fold and is influenced by numerous epigenetic and genetic factors including GC content, trinucleotide sequence context, and DNAse accessibility. These factors influence mutation at both local and regional scales and are often interrelated with one another, meaning that predicting mutability or uncovering its drivers requires modelling multiple factors and scales simultaneously. Historically, most investigations have focused either on analyzing the local sequence scale through triplet signatures or on examining the impact of epigenetic processes at larger scales, but not both concurrently. Additionally, sequencing technology limitations have restricted analyses of healthy mutations to coding regions (RNA-seq) or to those that have been influenced by selection (e.g. bulk samples from cancer tissue). Here, we leverage single-cell mutations and present a comprehensive analysis of epigenetic and genetic factors at multiple scales in the germline and 3 healthy somatic tissues. We create models that predict mutability with on average 2% error and find up to 63-fold variation among sites within the same tissue. We observe varying degrees of similarity between tissues: the mutability of genomic positions was 93.4% similar between liver and germline tissues, but sites in germline and skin were only 85.9% similar. We observe both universal and tissue-specific mutagenic processes in healthy tissues, with implications for understanding the maintenance of germline vs soma and the mechanisms underlying early tumorigenesis.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Experimental evolution in maize with replicated divergent selection identifies two plant-height-associated regions.
IF 3.3 3区 生物学
Genetics Pub Date : 2025-02-14 DOI: 10.1093/genetics/iyaf012
Mila Tost, Cathy Westhues, Ginnie Morrison, Dietrich Kaufmann, Timothy Beissinger
{"title":"Experimental evolution in maize with replicated divergent selection identifies two plant-height-associated regions.","authors":"Mila Tost, Cathy Westhues, Ginnie Morrison, Dietrich Kaufmann, Timothy Beissinger","doi":"10.1093/genetics/iyaf012","DOIUrl":"https://doi.org/10.1093/genetics/iyaf012","url":null,"abstract":"<p><p>Experimental evolution studies are common in agricultural research, where they are often deemed \"long-term selection.\" These are often used to perform selection mapping, which involves identifying markers that were putatively under selection based on finding signals of selection left in the genome. A challenge of previous selection mapping studies, especially in agricultural research, has been the specification of robust significance thresholds. This is in large part because long-term selection studies in crops have rarely included replication. Usually, significance thresholds in long-term selection experiments are based on outliers from an empirical distribution. This approach is prone to missing true positives or including false positives. Under laboratory conditions with model species, replicated selection has been shown to be a powerful tool, especially for the specification of significance thresholds. Another challenge is that commonly used single-marker-based statistics may identify neutral linked loci which have hitchhiked along with regions that are actually under selection. In this study, we conducted divergent, replicated selection for short and tall plant height in a random-mating maize population under real field conditions. Selection of the 5% tallest and shortest plants was conducted for 3 generations. Significance thresholds were specified using the false discovery rate for selection (FDRfS) based on a window-based statistic applied to a statistic leveraging replicated selection (FSTSum). Overall, we found 2 significant regions putatively under selection. One region was located on chromosome 3 close to the plant-height genes Dwarf1 and iAA8. We applied a haplotype block analysis to further dissect the pattern of selection in significant regions of the genome. We observed patterns of strong selection in the subpopulations selected for short plant height on chromosome 3.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Detecting deviations from Kingman coalescence using two-site frequency spectra.
IF 3.3 3区 生物学
Genetics Pub Date : 2025-02-07 DOI: 10.1093/genetics/iyaf023
Eliot F Fenton, Daniel P Rice, John Novembre, Michael M Desai
{"title":"Detecting deviations from Kingman coalescence using two-site frequency spectra.","authors":"Eliot F Fenton, Daniel P Rice, John Novembre, Michael M Desai","doi":"10.1093/genetics/iyaf023","DOIUrl":"https://doi.org/10.1093/genetics/iyaf023","url":null,"abstract":"<p><p>Demographic inference methods in population genetics typically assume that the ancestry of a sample can be modeled by the Kingman coalescent. A defining feature of this stochastic process is that it generates genealogies that are binary trees: no more than two ancestral lineages may coalesce at the same time. However, this assumption breaks down under several scenarios. For example, pervasive natural selection and extreme variation in offspring number can both generate genealogies with \"multiple-merger\" events in which more than two lineages coalesce instantaneously. Therefore, detecting violations of the Kingman assumptions (e.g. due to multiple mergers) is important both for understanding which forces have shaped the diversity of a population and for avoiding fitting misspecified models to data. Current methods to detect deviations from Kingman coalescence in genomic data rely primarily on the site frequency spectrum (SFS). However, the signatures of some non-Kingman processes (e.g. multiple mergers) in the SFS are also consistent with a Kingman coalescent with a time-varying population size. Here, we present a new statistical test for determining whether the Kingman coalescent with any population size history is consistent with population data. Our approach is based on information contained in the two-site joint frequency spectrum (2-SFS) for pairs of linked sites, which has a different dependence on the topologies of genealogies than the SFS. Our statistical test is global in the sense that it can detect when the genome-wide genetic diversity is inconsistent with the Kingman model, rather than detecting outlier regions, as in selection scan methods. We validate this test using simulations, and then apply it to demonstrate that genomic diversity data from Drosophila melanogaster is inconsistent with the Kingman coalescent.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143371253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Differentiating mechanism from outcome for ancestry-assortative mating in admixed human populations.
IF 3.3 3区 生物学
Genetics Pub Date : 2025-02-07 DOI: 10.1093/genetics/iyaf022
Dashiell J Massey, Zachary A Szpiech, Amy Goldberg
{"title":"Differentiating mechanism from outcome for ancestry-assortative mating in admixed human populations.","authors":"Dashiell J Massey, Zachary A Szpiech, Amy Goldberg","doi":"10.1093/genetics/iyaf022","DOIUrl":"10.1093/genetics/iyaf022","url":null,"abstract":"<p><p>Population genetic theory, and the empirical methods built upon it, often assume that individuals pair randomly for reproduction. However, natural populations frequently violate this assumption, which may potentially confound genome-wide association studies, selection scans, and demographic inference. Within several recently admixed human populations, empirical genetic studies have reported a correlation in global ancestry proportion between spouses, referred to as ancestry-assortative mating. Here, we use forward genomic simulations to link correlations in global ancestry proportion between mates to the underlying mechanistic mate-choice process. We consider the impacts of two types of mate-choice model, using either ancestry-based preferences or social groups as the basis for mate pairing. We find that multiple mate-choice models can produce the same correlations in global ancestry proportion between spouses; however, we also highlight alternative analytic approaches and circumstances in which these models may be distinguished. With this work, we seek to highlight potential pitfalls when interpreting correlations in empirical data as evidence for a particular model of human mating practices, as well as to offer suggestions toward development of new best practices for analysis of human ancestry-assortative mating.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143371264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Maintenance of long-term transposable element activity through regulation by nonautonomous elements. 通过非自主元件的调节维持长期转座元件的活性。
IF 3.3 3区 生物学
Genetics Pub Date : 2025-02-05 DOI: 10.1093/genetics/iyae209
Adekanmi Daniel Omole, Peter Czuppon
{"title":"Maintenance of long-term transposable element activity through regulation by nonautonomous elements.","authors":"Adekanmi Daniel Omole, Peter Czuppon","doi":"10.1093/genetics/iyae209","DOIUrl":"10.1093/genetics/iyae209","url":null,"abstract":"<p><p>Transposable elements are DNA sequences that can move and replicate within genomes. Broadly, there are 2 types: autonomous elements, which encode the necessary enzymes for transposition, and nonautonomous elements, which rely on the enzymes produced by autonomous elements for their transposition. Nonautonomous elements have been proposed to regulate the numbers of transposable elements, which is a possible explanation for the persistence of transposition activity over long evolutionary times. However, previous modeling studies indicate that interactions between autonomous and nonautonomous elements usually result in the extinction of one type. Here, we study a stochastic model that allows for the stable coexistence of autonomous and nonautonomous retrotransposons. We determine the conditions for this coexistence and derive an analytical expression for the stationary distribution of their copy numbers, showing that nonautonomous elements regulate stochastic fluctuations and the number of autonomous elements in stationarity. We find that the stationary variances of each element can be expressed as a function of the average copy numbers and their covariance, enabling data comparison and model validation. These results suggest that continued transposition activity of transposable elements, regulated by nonautonomous elements, is a possible evolutionary outcome that could for example explain the long coevolutionary history of autonomous LINE1 and nonautonomous Alu element transposition in the human ancestry.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Different complex regulatory phenotypes underlie hybrid male sterility in divergent rodent crosses. 不同啮齿动物杂交雄性不育的复杂调控表型各不相同。
IF 3.3 3区 生物学
Genetics Pub Date : 2025-02-05 DOI: 10.1093/genetics/iyae198
Kelsie E Hunnicutt, Colin M Callahan, Sara Keeble, Emily C Moore, Jeffrey M Good, Erica L Larson
{"title":"Different complex regulatory phenotypes underlie hybrid male sterility in divergent rodent crosses.","authors":"Kelsie E Hunnicutt, Colin M Callahan, Sara Keeble, Emily C Moore, Jeffrey M Good, Erica L Larson","doi":"10.1093/genetics/iyae198","DOIUrl":"10.1093/genetics/iyae198","url":null,"abstract":"<p><p>Hybrid incompatibilities are a critical component of species barriers and may arise due to negative interactions between divergent regulatory elements in parental species. We used a comparative approach to identify common themes in the regulatory phenotypes associated with hybrid male sterility in two divergent rodent crosses, dwarf hamsters and house mice. We investigated three potential characteristic gene expression phenotypes in hybrids including the propensity of transgressive differentially expressed genes toward over or underexpression, the influence of developmental stage on patterns of misexpression, and the role of the sex chromosomes on misexpression phenotypes. In contrast to near pervasive overexpression in hybrid house mice, we found that misexpression in hybrid dwarf hamsters was dependent on developmental stage. In both house mouse and dwarf hamster hybrids, however, misexpression increased with the progression of spermatogenesis, although to varying extents and with potentially different consequences. In both systems, we detected sex chromosome-specific overexpression in stages of spermatogenesis where inactivated X chromosome expression was expected, but the hybrid overexpression phenotypes were fundamentally different. Importantly, misexpression phenotypes support the presence of multiple developmental blocks to spermatogenesis in dwarf hamster hybrids, including a potential role of meiotic stalling or breakdown early in spermatogenesis. Collectively, we demonstrate that while there are some similarities in hybrid expression phenotypes of house mice and dwarf hamsters, there are also clear differences that point toward unique mechanisms underlying hybrid male sterility. Our results highlight the potential of comparative approaches in helping to understand the causes and consequences of disrupted gene expression in speciation.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142733801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A mutation in DNA polymerase γ harbors a shortened lifespan and high sensitivity to mutagens in the filamentous fungus Neurospora crassa. 丝状真菌粗神经孢子菌的DNA聚合酶γ突变具有缩短的寿命和对诱变剂的高度敏感性。
IF 3.3 3区 生物学
Genetics Pub Date : 2025-02-05 DOI: 10.1093/genetics/iyae201
Ryouhei Yoshihara, Yuzuki Shimakura, Satoshi Kitamura, Katsuya Satoh, Manami Sato, Taketo Aono, Yu Akiyama, Shin Hatakeyama, Shuuitsu Tanaka
{"title":"A mutation in DNA polymerase γ harbors a shortened lifespan and high sensitivity to mutagens in the filamentous fungus Neurospora crassa.","authors":"Ryouhei Yoshihara, Yuzuki Shimakura, Satoshi Kitamura, Katsuya Satoh, Manami Sato, Taketo Aono, Yu Akiyama, Shin Hatakeyama, Shuuitsu Tanaka","doi":"10.1093/genetics/iyae201","DOIUrl":"10.1093/genetics/iyae201","url":null,"abstract":"<p><p>Hyphal elongation is the vegetative growth of filamentous fungi, and many species continuously elongate their hyphal tips over long periods. The details of the mechanisms for maintaining continuous growth are not yet clear. A novel short lifespan mutant of N. crassa that ceases hyphal elongation early was screened and analyzed to better understand the mechanisms for maintaining hyphal elongation in filamentous fungi. The mutant strain also exhibited high sensitivity to mutagens such as hydroxyurea and ultraviolet radiation. Based on these observations, we named the novel mutant \"mutagen sensitive and short lifespan 1 (ms1).\" The mutation responsible for the short lifespan and mutagen sensitivity in the ms1 strain was identified in DNA polymerase γ (mip-1:NCU00276). This mutation changed the amino acid at position 814 in the polymerase domain from leucine to arginine (MIP-1 L814R). A dosage analysis by next-generation sequencing reads suggested that mitochondrial DNA (mtDNA) sequences are decreased nonuniformly throughout the genome of the ms1 strain. This observation was confirmed by quantitative PCR for 3 representative loci and restriction fragment length polymorphisms in purified mtDNA. Direct repeat-mediated deletions, which had been reported previously, were not detected in the mitochondrial genome by our whole-genome sequencing analysis. These results imply the presence of novel mechanisms to induce the nonuniform decrease in the mitochondrial genome by DNA polymerase γ mutation. Some potential reasons for the nonuniform distribution of the mitochondrial genome are discussed in relation to the molecular functions of DNA polymerase γ.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142752192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Spatially explicit estimation of recent migration rates in plants using genotypic data.
IF 3.3 3区 生物学
Genetics Pub Date : 2025-02-05 DOI: 10.1093/genetics/iyae218
Igor J Chybicki, Juan J Robledo-Arnuncio
{"title":"Spatially explicit estimation of recent migration rates in plants using genotypic data.","authors":"Igor J Chybicki, Juan J Robledo-Arnuncio","doi":"10.1093/genetics/iyae218","DOIUrl":"10.1093/genetics/iyae218","url":null,"abstract":"<p><p>We present a new hierarchical Bayesian method using multilocus genotypes to estimate recent seed and pollen migration rates in a spatially explicit framework that incorporates distance effects separately for each type of dispersal. The method additionally estimates population allelic frequencies, population divergence values, individual inbreeding coefficients, individual maternal and paternal ancestries, and allelic dropout rates. We conduct a numerical simulation analysis that indicates that the method can provide reliable estimates of seed and pollen migration rates and allow accurate inference of spatial effects on migration, at affordable sample sizes (25-50 individuals/population) when population genetic divergence is not low (FST≥0.05), or by increasing sampling (to at least 100 individuals/population) under weaker levels of divergence (FST=0.025). Simulations also show that the accuracy provided by assays with about one thousand unlinked polymorphic SNP loci may approach, for a given sample size, the theoretical maximum achievable under categorical origin discrimination. We apply our method to Taxus baccata data, revealing low but significant seed and pollen migration among nearby population remnants during the last generation, with a negative effect of interpopulation distance on migration that was detectable for pollen but not for seeds.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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