HeredityPub Date : 2025-04-30DOI: 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}
HeredityPub Date : 2025-04-25DOI: 10.1038/s41437-025-00764-y
Patrice S Albert, Hua Yang, Zhi Gao, Cassidy DeVore, James A Birchler
{"title":"Aneuploidy and ploidy variation conditioned by the B chromosome of maize.","authors":"Patrice S Albert, Hua Yang, Zhi Gao, Cassidy DeVore, James A Birchler","doi":"10.1038/s41437-025-00764-y","DOIUrl":"https://doi.org/10.1038/s41437-025-00764-y","url":null,"abstract":"<p><p>The supernumerary B chromosome of maize has a drive mechanism to maintain itself in a population despite being dispensible. This involves nondisjunction of the B centromere at the second pollen mitosis that produces the two sperm followed by preferential fertilization of the egg by the B containing sperm during double fertilization. During an introgression of the supernumerary B chromosome into the inbred line B73, an unusually high frequency of trisomies for A chromosomes was observed. Due to parallels to the High Loss phenomenon in which three or more B chromosomes in a specific genetic background cause chromosomal breakage at heterochromatic knob sites during the second pollen mitosis as well as ploidy changes, this phenomenon was revisited. Examination of pollen of the High Loss line revealed a high frequency of single sperm in the presence of the B chromosomes, which was previously not realized. Crosses to tetraploid females confirmed that the single sperm were diploid and functional but also revealed the presence of diploids with their A chromosomes derived solely from the tetraploid parent indicating a \"diploid induction\". Collectively, the results reveal two backgrounds in which the B drive mechanism is not confined to this chromosome causing detrimental effects by adherence of heterochromatic knobs and apparently A centromeres at the mitosis preceding sperm development. In most genetic backgrounds this process is restricted to the B chromosome but in B73 and the High Loss line, there is spillover to the normal chromosomes in distinct ways.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143995285","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}
HeredityPub Date : 2025-04-19DOI: 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}
HeredityPub Date : 2025-04-19DOI: 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}
HeredityPub Date : 2025-04-19DOI: 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}
HeredityPub Date : 2025-04-12DOI: 10.1038/s41437-025-00760-2
Ben J. Wiens, Lucas H. DeCicco, Jocelyn P. Colella
{"title":"triangulaR: an R package for identifying AIMs and building triangle plots using SNP data from hybrid zones","authors":"Ben J. Wiens, Lucas H. DeCicco, Jocelyn P. Colella","doi":"10.1038/s41437-025-00760-2","DOIUrl":"10.1038/s41437-025-00760-2","url":null,"abstract":"Hybridization provides a window into the speciation process and reshuffles parental alleles to produce novel recombinant genotypes. Presence or absence of specific hybrid classes across a hybrid zone can provide support for various modes of reproductive isolation. Early generation hybrid classes can be distinguished by their combination of hybrid index and interclass heterozygosity, which can be estimated with molecular data. Hybrid index and interclass heterozygosity are routinely calculated for studies of hybrid zones, but available resources for next-generation sequencing datasets are computationally demanding and tools for visualizing triangle plots are lacking. Here, we provide a resource for identifying ancestry-informative markers (AIMs) from single nucleotide polymorphism (SNP) datasets, calculating hybrid index and interclass heterozygosity, and visualizing the relationship as a triangle plot. Our methods are implemented in the R package triangulaR. We validate our methods on an empirical dataset and simulations of genetic data from a hybrid zone between two parental groups at low, medium, and high levels of divergence. triangulaR provides accurate and precise estimates of hybrid index and interclass heterozygosity with sample sizes as low as five individuals per parental group, and similar levels of error as another program for hybrid index and interclass heterozygosity estimation, bgchm. We explore various allele frequency difference thresholds for AIM identification, and how this threshold influences the accuracy and precision of hybrid index and interclass heterozygosity estimates. We contextualize interpretation of triangle plots by describing theoretical expectations under Hardy-Weinberg Equilibrium and provide recommendations for best practices for identifying AIMs and building triangle plots.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 5","pages":"251-262"},"PeriodicalIF":3.1,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00760-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143914781","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}
HeredityPub Date : 2025-03-27DOI: 10.1038/s41437-024-00739-5
Jinliang Wang
{"title":"EMIBD9: Estimating 9 condensed IBD coefficients, inbreeding and relatedness from marker genotypes","authors":"Jinliang Wang","doi":"10.1038/s41437-024-00739-5","DOIUrl":"10.1038/s41437-024-00739-5","url":null,"abstract":"EMIBD9 is a computer programme implementing two likelihood methods for estimating the 9 condensed IBD coefficients, Δ = {Δ1, Δ2, …, Δ9}, between a pair of individuals from their genotype data. Inbreeding coefficients of and relatedness (or kinship coefficient) between individuals are then calculated from the estimated Δ. One method is designed to apply to a small sample or a sample containing a high proportion of close relatives where allele frequencies and their powers or products are poorly estimated by assuming a large sample of non-inbred and unrelated individuals. It adopts an expectation maximisation (EM) algorithm to estimate both Δ and allele frequencies jointly and iteratively. The other method is designed to apply to a large sample of individuals containing few close relatives. It is fast because it, like all previous estimators, estimates Δ only and does not make iterative updates of allele frequencies by accounting for the inferred relatedness through the EM algorithm. EMIBD9 has both methods implemented for multiple computer platforms (Windows, Mac and Linux), and the Windows version has a GUI that facilitates data input and results visualisation. The GUI can also be used to simulate genotype data which are used to investigate factors affecting relatedness estimation accuracy, to optimise the experimental design of a relatedness study, and to compare the performance of different relatedness estimators.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 3-4","pages":"155-161"},"PeriodicalIF":3.1,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00739-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729897","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}
HeredityPub Date : 2025-03-24DOI: 10.1038/s41437-025-00757-x
Eduardo P. Cappa, Charles Chen, Jennifer G. Klutsch, Jaime Sebastian-Azcona, Blaise Ratcliffe, Xiaojing Wei, Letitia Da Ros, Yang Liu, Sudarshana Reddy Bhumireddy, Andy Benowicz, Shawn D. Mansfield, Nadir Erbilgin, Barb R. Thomas, Yousry A. El-Kassaby
{"title":"Correction: Revealing stable SNPs and genomic prediction insights across environments enhance breeding strategies of productivity, defense, and climate-adaptability traits in white spruce","authors":"Eduardo P. Cappa, Charles Chen, Jennifer G. Klutsch, Jaime Sebastian-Azcona, Blaise Ratcliffe, Xiaojing Wei, Letitia Da Ros, Yang Liu, Sudarshana Reddy Bhumireddy, Andy Benowicz, Shawn D. Mansfield, Nadir Erbilgin, Barb R. Thomas, Yousry A. El-Kassaby","doi":"10.1038/s41437-025-00757-x","DOIUrl":"10.1038/s41437-025-00757-x","url":null,"abstract":"","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 3-4","pages":"247-247"},"PeriodicalIF":3.1,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00757-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700361","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}
HeredityPub Date : 2025-03-22DOI: 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}
HeredityPub Date : 2025-03-18DOI: 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}