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":"https://doi.org/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":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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":"https://doi.org/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":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Local adaptation has a role in reducing vulnerability to climate change in a widespread Amazonian forest lizard. 在广泛分布的亚马逊森林蜥蜴中，当地适应在减少对气候变化的脆弱性方面发挥了作用。

IF 3.1 2区生物学

Heredity Pub Date : 2025-05-05 DOI: 10.1038/s41437-025-00765-x

André Yves, Josué A R Azevedo, Renata M Pirani, Fernanda P Werneck

{"title":"Local adaptation has a role in reducing vulnerability to climate change in a widespread Amazonian forest lizard.","authors":"André Yves, Josué A R Azevedo, Renata M Pirani, Fernanda P Werneck","doi":"10.1038/s41437-025-00765-x","DOIUrl":"https://doi.org/10.1038/s41437-025-00765-x","url":null,"abstract":"The extant genetic variation within and among taxa reflects a long history of diversification and adaptive mechanisms in response to climate change and landscape alterations. However, the velocity of current anthropogenic changes poses an imminent threat to global biodiversity. Understanding how species and populations might respond to global climate change provides valuable information for conservation in the face of these impacts. Here, we use genomic data to observe candidate loci under climate selection and test for genetic vulnerability to climate change in a widespread Amazonian ombrophilous lizard population. We found nine populations across Amazonia with a considerable amount of admixture among them. Distinct approaches of genome-environment association analyses revealed 56 candidate single-nucleotide polymorphisms (SNPs) under climatic selection, showing an east-west gradient in the adaptive landscape and a signal of local climate adaptation across the species range. According to our results, signals of local adaptation indicate that the species may not respond equally throughout its range, with some populations facing higher extinction risks. Genomic offset analysis predicts the southern and central portions of Amazonia to have a higher vulnerability to future climate change. Our findings highlight the importance of considering spatially explicit contexts with a large sampling coverage to evaluate how local adaptation and climatic vulnerability affect Amazonian forest ectothermic fauna.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143965163","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

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":"https://doi.org/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":" ","pages":""},"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

Aneuploidy and ploidy variation conditioned by the B chromosome of maize. 玉米的非整倍性和倍性变异由B染色体决定。

IF 3.1 2区生物学

Heredity Pub Date : 2025-04-25 DOI: 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":"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.","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}

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":"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.","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":"https://doi.org/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":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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

triangulaR: an R package for identifying AIMs and building triangle plots using SNP data from hybrid zones 三角形：一个R包，用于识别AIMs和建立三角图使用SNP数据从杂交区

IF 3.1 2区生物学

Heredity Pub Date : 2025-04-12 DOI: 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}

引用次数: 0

EMIBD9: Estimating 9 condensed IBD coefficients, inbreeding and relatedness from marker genotypes EMIBD9：估计9个浓缩IBD系数，近交和标记基因型的相关性。

IF 3.1 2区生物学

Heredity Pub Date : 2025-03-27 DOI: 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}

引用次数: 0

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