Heredity最新文献_第2页

Multiple source locations and long-distance dispersal explain the rapid spread of a recent amphibian invasion 多种来源和远距离传播解释了最近两栖动物入侵的快速传播。

IF 3.1 2区生物学

Heredity Pub Date : 2025-05-16 DOI: 10.1038/s41437-025-00766-w

Teun Everts, Io Deflem, Charlotte Van Driessche, Sabrina Neyrinck, Tom Ruttink, Hans Jacquemyn, Rein Brys

{"title":"Multiple source locations and long-distance dispersal explain the rapid spread of a recent amphibian invasion","authors":"Teun Everts, Io Deflem, Charlotte Van Driessche, Sabrina Neyrinck, Tom Ruttink, Hans Jacquemyn, Rein Brys","doi":"10.1038/s41437-025-00766-w","DOIUrl":"10.1038/s41437-025-00766-w","url":null,"abstract":"Rapid range expansions are characteristic for non-native invasive species when introduced outside their native range. Understanding the dynamics and mechanisms of expanding non-native invasive species is key for regional management. While population genetics and long-term occurrence records are often used in this context, each provides only partial insights, highlighting the need for a combined approach. We demonstrate this synergy using the American bullfrog (Lithobates catesbeianus) invasion in the Grote Nete river valley (Belgium) as a case study. It is commonly believed that this invasion constitutes a single metapopulation established by one primary introduction followed by downstream dispersal. However, recent evidence suggests a more complex scenario, involving introduction at multiple locations and bidirectional dispersal. To differentiate between both scenarios, we analysed nearly three decades of occurrence records and 8592 single nucleotide polymorphisms across 372 individuals from 31 localities, and determined the number of source locations, the range expansion rate, the population genetic structure, and the magnitude and direction of gene flow. We found that invasive spread originated from up to six source locations followed by bidirectional dispersal and downstream long-distance dispersal (LDD) events. Our results suggest that at least two source locations were founded by primary introductions, two from LDD events, while the remaining resulted from secondary introductions. A canal crossing the river was identified as a dispersal barrier, leading to different invasion dynamics on both sides. Our study shows how asynchronous introductions at multiple locations, dispersal barriers, and environmental heterogeneity can lead to distinct spread dynamics within a seemingly continuous and interconnected metapopulation.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 6","pages":"362-373"},"PeriodicalIF":3.1,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00766-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086176","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}

引用次数: 0

Female-mediated selective sperm activation may remodel major histocompatibility complex-based mate choice decisions in humans 女性介导的选择性精子激活可能重塑人类主要的基于组织相容性复合物的配偶选择决策。

IF 3.1 2区生物学

Heredity Pub Date : 2025-05-09 DOI: 10.1038/s41437-025-00759-9

Annalaura Jokiniemi, Tanja Turunen, Mikko Kohonen, Martina Magris, Jarmo Ritari, Liisa Kuusipalo, Jukka Partanen, Jukka Kekäläinen

{"title":"Female-mediated selective sperm activation may remodel major histocompatibility complex-based mate choice decisions in humans","authors":"Annalaura Jokiniemi, Tanja Turunen, Mikko Kohonen, Martina Magris, Jarmo Ritari, Liisa Kuusipalo, Jukka Partanen, Jukka Kekäläinen","doi":"10.1038/s41437-025-00759-9","DOIUrl":"10.1038/s41437-025-00759-9","url":null,"abstract":"Major histocompatibility complex (MHC) genes are known to mediate mate choice both at the individual and gamete level. However, it has remained unclear how different episodes of MHC-associated mate choice interact and contribute to the total selection on MHC genes. Here, we clarified this interaction in humans by performing a full-factorial experiment where 10 females first ranked the attractiveness and intensity of the body odours of 11 males. Then we studied whether female odour preferences in these same 110 male-female combinations predicted sperm performance in the presence of follicular fluid (sperm-stimulating female reproductive fluid). When analyzing the total MHC similarity (including classical and non-classical MHC genes) of the male-female combinations, we found that females preferred the body odours of MHC-similar males, but that sperm motility was positively affected by the MHC dissimilarity of the male-female combinations. No associations were found for classical MHC genes only. Furthermore, odour preferences were negatively associated with sperm motility at the end of the follicular fluid treatment. Together, our results indicate that individual and gamete-level mate choice processes may act in opposing directions and that the most attractive males are not necessarily the most optimal partners at the post-copulatory level. Finally, our findings suggest that gamete-mediated mate choice may have a definitive role in disfavouring genetically incompatible partners from fertilizing oocytes.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 6","pages":"321-330"},"PeriodicalIF":3.1,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00759-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144003476","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}

引用次数: 0

The genetic basis of a colorful signal: the polymorphic dewlap of the slender anole (Anolis apletophallus) 一种彩色信号的遗传基础：细长的变色蛇（Anolis apletophallus）的多态脱壳。

IF 3.1 2区生物学

Heredity Pub Date : 2025-04-30 DOI: 10.1038/s41437-025-00763-z

Renata M. Pirani, Carlos F. Arias, John David Curlis, Daniel J. Nicholson, Jessica Stapley, W. Owen McMillan, Christian L. Cox, Michael L. Logan

{"title":"The genetic basis of a colorful signal: the polymorphic dewlap of the slender anole (Anolis apletophallus)","authors":"Renata M. Pirani, Carlos F. Arias, John David Curlis, Daniel J. Nicholson, Jessica Stapley, W. Owen McMillan, Christian L. Cox, Michael L. Logan","doi":"10.1038/s41437-025-00763-z","DOIUrl":"10.1038/s41437-025-00763-z","url":null,"abstract":"Organisms often use colorful morphological traits to communicate with members of their own or other species. While “colorful signaling” systems exemplify well-known examples of the evolution of phenotypic diversity, the genetic basis of most of these traits remains unknown. Male lizards of the genus Anolis possess a colorful throat fan, or “dewlap”, that is flashed during social displays. These displays have been extensively studied in the context of their role in the adaptive radiation of the genus. In contrast, the genetic basis of the Anolis dewlap has received relatively little attention. Here, we studied the dewlap of the slender anole (Anolis apletophallus) which exhibits a dewlap polymorphism: males have either an entirely orange dewlap (“solid” morph) or a white dewlap with a basal orange spot (“bicolor” morph). To understand the inheritance of this polymorphism, we conducted 99 crosses between individuals from populations that were fixed for one morph (single/fixed/monomorphic) or contained both morphs (mixed/polymorphic). Next, we investigated the genetic architecture of this trait using a pooled population sequencing (Pool-seq) experiment. Our findings indicate that the slender anole dewlap polymorphism is best explained as an autosomal, single-locus, Mendelian trait with the solid morph allele dominant to the bicolor morph allele. Our outlier analysis of the Pool-seq data identified a region strongly associated with this trait and within this region we identified a promising candidate locus—the transcription factor single-minded 1 (SIM1)—that may underly the dewlap polymorphism.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 6","pages":"343-351"},"PeriodicalIF":3.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143968147","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}

引用次数: 0

Does chromoanagenesis play a role in the origin of B chromosomes? 染色体再生在B染色体的起源中起作用吗？

IF 3.1 2区生物学

Heredity Pub Date : 2025-04-19 DOI: 10.1038/s41437-025-00758-w

Andreas Houben, Jörg Fuchs, Ali Mohammad Banaei-Moghaddam, Jianyong Chen, Gihwan Kim, Taoran Liu

{"title":"Does chromoanagenesis play a role in the origin of B chromosomes?","authors":"Andreas Houben, Jörg Fuchs, Ali Mohammad Banaei-Moghaddam, Jianyong Chen, Gihwan Kim, Taoran Liu","doi":"10.1038/s41437-025-00758-w","DOIUrl":"https://doi.org/10.1038/s41437-025-00758-w","url":null,"abstract":"<p><p>B chromosomes (Bs) exist in addition to the standard (A) chromosomes in a wide range of species. The process underlying their origin is still unclear. We propose pathways of intra- and interspecific origin of B chromosomes based on known mechanisms of chromosome evolution and available knowledge of their sequence composition in different species. We speculate that a mitotic or meiotic segregation error of one or more A chromosomes initiates, via chromoanagenesis, the formation of a proto-B chromosome. In the second step, proto-B chromosomes accumulate A chromosome- and organelle-derived sequences over time, most likely via DNA double-strand break (DSB) mis-repair. Consequently, the original structure of the early stage proto-B chromosomes becomes masked by continuous sequence incorporation. The similarity between A chromosome sequences integrated into B chromosomes and the original sequences on the donor chromosomes decreases over time if there is no selection pressure on these sequences on B chromosomes. However, besides chromoanagenesis, also other mechanisms leading to the formation of B chromosomes might exist.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005541","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}

引用次数: 0

Phylogeography of introgression: Spatial and temporal analyses identify two introgression events between brown and American black bears 进化演化的系统地理学：空间和时间分析确定了棕熊和美洲黑熊之间的两个进化演化事件。

IF 3.1 2区生物学

Heredity Pub Date : 2025-04-19 DOI: 10.1038/s41437-025-00762-0

Emily E. Puckett

{"title":"Phylogeography of introgression: Spatial and temporal analyses identify two introgression events between brown and American black bears","authors":"Emily E. Puckett","doi":"10.1038/s41437-025-00762-0","DOIUrl":"10.1038/s41437-025-00762-0","url":null,"abstract":"Brown bears (Ursus arctos) colonized North America from Eurasia in two distinct and temporally separated waves. Once in North America they encountered endemic American black bears (U. americanus) during range expansions from eastern Beringia southwards into the interior of the continent. The establishment of sympatry between these species provided the opportunity for hybridization and introgression, which was previously identified at the species level using D-statistics. Both species have broad spatial ranges that should limit the extent of introgression, such that it is found primarily between sympatric populations. Here, we used range-wide sampling and whole genome sequencing of both bear species to test for spatial variability in introgression. We identified two pulses of introgression between brown and American black bears, and demonstrate the introgressed segments occur across spatially structured lineages in both species. The first pulse occurred 270–120 kya, near the initiation of intraspecific divergence, approximately 99–93 kya, within each species. This pulse occurred as sympatry was established in western North America. The second pulse occurred between western American black bears and North American brown bears and lasted to 9 kya. Introgression was bidirectional and sympatric lineages had more introgressed tracts and a larger proportion of the genome introgressed from the other species. This study advances our phylogeographic understanding of both iconic bear species through investigating the timing of divergence and gene flow as bears expanded and contracted their ranges across North America.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 6","pages":"331-342"},"PeriodicalIF":3.1,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00762-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143990411","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}

引用次数: 0

Recent habitat modification of a tropical dry forest hotspot drives population genetic divergence in the Mexican leaf frog: a landscape genetics approach 最近热带干旱森林热点的栖息地改变驱动墨西哥叶蛙种群遗传分化：景观遗传学方法

IF 3.1 2区生物学

Heredity Pub Date : 2025-04-19 DOI: 10.1038/s41437-025-00761-1

Sara Covarrubias, Carla Gutiérrez-Rodríguez, Clementina González

{"title":"Recent habitat modification of a tropical dry forest hotspot drives population genetic divergence in the Mexican leaf frog: a landscape genetics approach","authors":"Sara Covarrubias, Carla Gutiérrez-Rodríguez, Clementina González","doi":"10.1038/s41437-025-00761-1","DOIUrl":"10.1038/s41437-025-00761-1","url":null,"abstract":"Tropical dry forests (TDF) are among the ecosystems with the highest deforestation and transformation rates. Because of habitat loss and fragmentation, modified landscapes can impose resistance to the movement of individuals, with important genetic consequences. One of the most affected taxa due to habitat alteration are amphibians, which currently face extreme population declines globally. Here, we used single nucleotide polymorphisms (SNPs) to evaluate genetic diversity, genetic structure, and the effect of landscape elements on genetic connectivity of the Mexican tree frog (Agalychnis dacnicolor) in a TDF biodiversity hotspot in Mexico. We collected samples of 96 individuals from 16 sites located within fragmented areas of TDF and within continuous forest in the Chamela-Cuixmala region. Sampling sites from the fragmented forest showed slightly lower genetic diversity and effective population size compared to those in the continuous forest. We detected three admixed genetic groups, in which most of the sites within the fragmented forest were differentiated from the sites within continuous forest. Although these analyses suggest historical gene flow, we did not detect significant recent migration among the three genetic groups. While original vegetation (TDF + tropical evergreen forest), and in some areas, agriculture facilitated genetic connectivity, open-areas (grasslands + human settlements + exposed soil), and agriculture in other areas limited genetic connectivity in A. dacnicolor. This study helps to understand the factors shaping contemporary population divergence in highly modified complex landscapes, and highlights the importance to maintain connectivity in a rapidly changing ecosystem.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 5","pages":"306-320"},"PeriodicalIF":3.1,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143914774","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}

引用次数: 0

Environmentally induced variation in sperm sRNAs is linked to gene expression and transposable elements in zebrafish offspring 环境诱导的精子sRNAs变异与斑马鱼后代的基因表达和转座因子有关。

IF 3.1 2区生物学

Heredity Pub Date : 2025-03-22 DOI: 10.1038/s41437-025-00752-2

Alice M. Godden, Willian T. A. F. Silva, Berrit Kiehl, Cécile Jolly, Leighton Folkes, Ghazal Alavioon, Simone Immler

{"title":"Environmentally induced variation in sperm sRNAs is linked to gene expression and transposable elements in zebrafish offspring","authors":"Alice M. Godden, Willian T. A. F. Silva, Berrit Kiehl, Cécile Jolly, Leighton Folkes, Ghazal Alavioon, Simone Immler","doi":"10.1038/s41437-025-00752-2","DOIUrl":"10.1038/s41437-025-00752-2","url":null,"abstract":"Environmental factors affect not only paternal condition but may translate into the following generations where sperm-mediated small RNAs (sRNAs) can contribute to the transmission of paternal effects. sRNAs play a key role in the male germ line in genome maintenance and repair, and particularly in response to environmental stress and the resulting increase in transposable element (TE) activity. Here, we investigated how the social environment (high competition, low competition) of male zebrafish Danio rerio affects sRNAs in sperm and how these are linked to gene expression and TE activity in their offspring. In a first experiment, we collected sperm samples after exposing males to each social environment for 2 weeks to test for differentially expressed sperm micro- (miRNA) and piwi-interacting RNAs (piRNA). In a separate experiment, we performed in vitro fertilisations after one 2-week period using a split-clutch design to control for maternal effects and collected embryos at 24 h to test for differentially expressed genes and TEs. We developed new computational prediction tools to link sperm sRNAs with differentially expressed TEs and genes in the embryos. Our results support the idea that the molecular stress response in the male germ line has significant down-stream effects on the molecular pathways, and we provide a direct link between sRNAs, TEs and gene expression.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 3-4","pages":"234-246"},"PeriodicalIF":3.1,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00752-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691844","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}

引用次数: 0

Sperm DNA methylation landscape and its links to male fertility in a non-model teleost using EM-seq 精子DNA甲基化景观及其与非模型硬骨鱼男性生育能力的联系。

IF 3.1 2区生物学

Heredity Pub Date : 2025-03-18 DOI: 10.1038/s41437-025-00756-y

Fotis Pappas, Martin Johnsson, Göran Andersson, Paul V. Debes, Christos Palaiokostas

{"title":"Sperm DNA methylation landscape and its links to male fertility in a non-model teleost using EM-seq","authors":"Fotis Pappas, Martin Johnsson, Göran Andersson, Paul V. Debes, Christos Palaiokostas","doi":"10.1038/s41437-025-00756-y","DOIUrl":"10.1038/s41437-025-00756-y","url":null,"abstract":"Differential DNA methylation due to epigenetic phenomena is crucial in regulating gene expression. Understanding the consequences of such differential expression on sperm quality parameters may provide insights into the underlying mechanisms of male reproductive success. Nonetheless, male fertility in fish remains understudied despite its critical importance to overall reproductive success in nature and captivity. This study investigated the DNA methylation landscape in spermatozoa of domesticated Arctic charr (Salvelinus alpinus) and its associations with sperm quality parameters. Computer assisted-semen analysis (CASA) was performed in 47 sperm samples of farmed Arctic charr, followed by enzymatic methylation sequencing (EM-seq). Our results showed that the DNA of Arctic charr sperm is highly methylated (mean value of ~86%), though variations were observed in genomic features involved in gene regulation. Methylation at variable CpG sites exhibited regional correlation decaying by physical distance, while methylation similarities among individuals were strongly coupled with genetic variation and mirrored pedigree structure. Comethylation network analyses for promoters, CpG islands and first introns revealed genomic modules significantly correlated with sperm quality traits (p < 0.05; Bonferroni adjusted), with distinct patterns suggesting a resource trade-off between sperm concentration and kinematics. Furthermore, annotation and gene-set enrichment analysis highlighted biological mechanisms related to spermatogenesis, cytoskeletal regulation, and mitochondrial function, all vital to sperm physiology. These findings suggest that DNA methylation is a critical and fundamental factor influencing male fertility in Arctic charr, providing insights into the underlying mechanisms of male reproductive success.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 5","pages":"293-305"},"PeriodicalIF":3.1,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00756-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143648424","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}

引用次数: 0

Forest tree breeding using genomic Markov causal models: a new approach to genomic tree breeding improvement 利用基因组马尔可夫因果模型进行林木育种：基因组林木育种改进的新途径。

IF 3.1 2区生物学

Heredity Pub Date : 2025-03-17 DOI: 10.1038/s41437-025-00755-z

Esteban J. Jurcic, Joaquín Dutour, Pamela V. Villalba, Carmelo Centurión, Rodolfo J. C. Cantet, Sebastián Munilla, Eduardo P. Cappa

{"title":"Forest tree breeding using genomic Markov causal models: a new approach to genomic tree breeding improvement","authors":"Esteban J. Jurcic, Joaquín Dutour, Pamela V. Villalba, Carmelo Centurión, Rodolfo J. C. Cantet, Sebastián Munilla, Eduardo P. Cappa","doi":"10.1038/s41437-025-00755-z","DOIUrl":"10.1038/s41437-025-00755-z","url":null,"abstract":"Traditionally, a pedigree-based individual-tree mixed model (ABLUP) has been used in forest genetic evaluations to identify individuals with the highest breeding values (BVs). ABLUP is a Markovian causal model, as any individual BV can be expressed as a linear regression on its parental BVs. The regression coefficients are based on the genealogical parent-offspring relationship and are equal to one-half. This study aimed to develop and apply two new causal models that replace these fixed coefficients with ones calculated using genomic information, specifically derived from the genomic-based relationship matrix. We compared the performance of these genomic-based causal models with ABLUP and non-causal GBLUP models. To do so, we evaluated a four-generation population of Eucalyptus grandis, consisting of 3082 genotyped trees with 14,033 single nucleotide polymorphism markers. Six traits were assessed in 1219 trees across the first three breeding cycles. The heritability and genetic means estimates were higher in the causal pedigree- and genomic-based models compared to GBLUP. Realized genetic gains were similar across all models, but the causal models more closely matched the predicted gains than GBLUP. In turn, GBLUP demonstrated better predictive performance, albeit with lower precision. The causal models developed in this study enable discerning intra-familial variations in the predictions of BVs at a lower computational burden and offer a potential alternative to the GBLUP model.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 5","pages":"280-292"},"PeriodicalIF":3.1,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143648421","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}

引用次数: 0

Quantifying the effects of computational filter criteria on the accurate identification of de novo mutations at varying levels of sequencing coverage 量化计算筛选标准对在不同测序覆盖率水平上准确识别新突变的影响。

IF 3.1 2区生物学

Heredity Pub Date : 2025-03-13 DOI: 10.1038/s41437-025-00754-0

Mark Milhaven, Aman Garg, Cyril J. Versoza, Susanne P. Pfeifer

{"title":"Quantifying the effects of computational filter criteria on the accurate identification of de novo mutations at varying levels of sequencing coverage","authors":"Mark Milhaven, Aman Garg, Cyril J. Versoza, Susanne P. Pfeifer","doi":"10.1038/s41437-025-00754-0","DOIUrl":"10.1038/s41437-025-00754-0","url":null,"abstract":"The rate of spontaneous (de novo) germline mutation is a key parameter in evolutionary biology, impacting genetic diversity and contributing to the evolution of populations and species. Mutation rates themselves evolve over time but the mechanisms underlying the mutation rate variation observed across the Tree of Life remain largely to be elucidated. In recent years, whole genome sequencing has enabled the estimation of mutation rates for several organisms. However, due to a lack of community standards, many previous studies differ both empirically – most notably, in the depth of sequencing used to reliably identify de novo mutations – and computationally – utilizing different computational pipelines to detect germline mutations as well as different analysis strategies to mitigate technical artifacts – rendering comparisons between studies challenging. Using a pedigree of Western chimpanzees as an illustrative example, we here quantify the effects of commonly utilized quality metrics to reliably identify de novo mutations at different levels of sequencing coverage. We demonstrate that datasets with a mean depth of ≤ 30X are ill-suited for the detection of de novo mutations due to high false positive rates that can only be partially mitigated by computational filter criteria. In contrast, higher coverage datasets enable a comprehensive identification of de novo mutations at low false positive rates, with minimal benefits beyond a sequencing coverage of 60X, suggesting that future work should favor breadth (by sequencing additional individuals) over depth. Importantly, the simulation and analysis framework described here provides conceptual guidelines that will allow researchers to take study design and species-specific resources into account when determining computational filtering strategies for their organism of interest.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 5","pages":"273-279"},"PeriodicalIF":3.1,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00754-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624439","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}

引用次数: 0