Journal of Heredity最新文献

A chromosome-level reference genome of the largest cervid species - the European moose (Alces alces; Linnaeus, 1758). 最大的鹿科物种——欧洲驼鹿（Alces Alces; Linnaeus, 1758）的染色体水平参考基因组。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-10-27 DOI: 10.1093/jhered/esag088

Ole K Tørresen, Atle Mysterud, Morten Skage, Bram Danneels, Marius A Strand, Giada Ferrari, Ave Tooming-Klunderud, Kjetill S Jakobsen

引用次数: 0

An exact formula for the contribution of sampling error to r2, a common measure of linkage disequilibrium. 抽样误差对r2的贡献的精确公式，r2是连杆不平衡的常用度量。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-10-24 DOI: 10.1093/jhered/esag087

Robin S Waples

{"title":"An exact formula for the contribution of sampling error to r2, a common measure of linkage disequilibrium.","authors":"Robin S Waples","doi":"10.1093/jhered/esag087","DOIUrl":"https://doi.org/10.1093/jhered/esag087","url":null,"abstract":"Interest in quantifying linkage disequilibrium (LD, non-random associations of alleles at different loci) has skyrocketed in recent years as researchers have focused on use of LD in genome-wide association studies (GWAS), for studying historical demography, and for estimating effective population size (Ne). The most widely used LD metric is r2 = the squared correlation of alleles at a pair of loci. Despite a half century of efforts, developing an unbiased expectation of r2 as a function of the many factors that can affect it (physical linkage, genetic drift, selection, migration, mutation, mating systems) remains elusive. Furthermore, even when all of these other factors are absent, empirical estimates of r2 are upwardly biased by sampling a finite number (S) of individuals, and that must be accounted for if one wants to focus on the desired signal of LD. Previous approaches to estimate ${r}_{sample}^2$ have been shown to be biased to greater or lesser degrees. The purpose of this short paper is to demonstrate that a simple and exact expression for $Eleft({r}_{sample}^2right)$ does exist for the special case where sampling error is the only factor contributing to r2, in which case $Eleft({r}_{sample}^2right)=1/left(S-1right)$. When other factors contribute heavily to LD, $Eleft({r}_{sample}^2right)$ shrinks toward 0 as empirical r2 ➔ 1. However, for estimating contemporary Ne with unlinked markers, empirical r2 will generally be small and $1/left(S-1right)$ will provide a robust estimate of $Eleft({r}_{sample}^2right)$.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149277396","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

Element F expansion tracks parthenogenetic ability in Drosophila mercatorum. F元件的扩展跟踪墨卡托果蝇的孤雌生殖能力。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-10-13 DOI: 10.1093/jhered/esag084

Alexis L Sperling, Anthony A Gutierrez, D K Fabian, D M Glover

{"title":"Element F expansion tracks parthenogenetic ability in Drosophila mercatorum.","authors":"Alexis L Sperling, Anthony A Gutierrez, D K Fabian, D M Glover","doi":"10.1093/jhered/esag084","DOIUrl":"https://doi.org/10.1093/jhered/esag084","url":null,"abstract":"The dramatic transition to parthenogenetic reproduction is often accompanied by similarly dramatic changes in genome organisation. Genomic changes may precede or succeed the onset of parthenogenesis and may directly or indirectly contribute to the success of this reproductive transition and fitness of parthenogenetic animals. To gain greater understanding of these changes, we combined cytogenetic and comparative analyses to document variation in heterochromatin and large-scale rearrangements among 18 strains of Drosophila mercatorum capable of varying degrees of parthenogenetic reproduction. This revealed that element F is 4.4-fold larger (95% confidence interval 4.0-4.8) in strains capable of parthenogenesis but that multiple large chromosomal inversions (2.8-9 megabases) on element B likely arose earlier. We combined phylogenetic analysis with comparisons of these genomic changes and parthenogenetic ability in D. mercatorum strains collected in South America, North America, Hawaii, and Africa. This indicated that the heterochromatin expansion has arisen once and appears to gradually increase with the rate of parthenogenetic ability. However, since this increase was also present in obligate sexually reproducing strains, heterochromatin expansion was not a consequence of parthenogenesis. It is therefore possible that heterochromatin expansion and parthenogenetic ability are unrelated but are carried together; that a shared underlying mechanism promotes both; or that heterochromatin expansion itself drives the capacity for parthenogenetic reproduction.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149186102","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

Genome size estimation and genome assembly completeness assessment. 基因组大小估计和基因组组装完整性评估。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-10-13 DOI: 10.1093/jhered/esag086

Ion Udroiu

{"title":"Genome size estimation and genome assembly completeness assessment.","authors":"Ion Udroiu","doi":"10.1093/jhered/esag086","DOIUrl":"https://doi.org/10.1093/jhered/esag086","url":null,"abstract":"Evaluation of genome size has been extensively used in different fields. In many studies, it has been employed to test correlation with other parameters such as metabolic rates, longevity and ecological/geographical distribution. Moreover, genome size assessed with cytometrical methods can be useful to evaluate the completeness of genome assemblies. In this latter case, knowledge of the accuracy of cytometry-based genome size measurement is fundamental, and a pivotal factor is the internal standard used during measurement. In the present article, I tested the correlation between cytometry-measured genome sizes and assembly sizes, finding a probable systemic error. Indeed, the two most widely used internal standard, i.e., human and chicken, are traditionally set equal to 3.5 and 1.25 pg, respectively. With the advent of telomere-to-telomere genome assembly, we can now know the real genome size for several species, being actually 3.19 pg for human and 1.12 pg for chicken. Recalculating the genome size for 912 vertebrate species, I assessed the level of genome assembly completeness, explored the influence of factors such as sequencing platform and gave some suggestions for future studies.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149186085","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

Retraction of: Genetic Diversity of Amaranthus Species from the Indo-Gangetic Plains Revealed by RAPD Analysis Leading to the Development of Ecotype-Specific SCAR Marker. 印度恒河平原苋属植物遗传多样性的RAPD分析与SCAR标记的建立

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-10-09 DOI: 10.1093/jhered/esag083

引用次数: 0

Population genetics, trait mapping and fungal pathogen surveillance using untargeted sequencing in timber rattlesnakes (Crotalus horridus). 木响尾蛇（Crotalus horridus）群体遗传学、性状定位和真菌病原体非靶向测序监测。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-10-06 DOI: 10.1093/jhered/esag080

Christopher Husted, Jacob Alonso, Ross Swofford, Anne G Stengle, Lucas R Moreira, Daniel E Neafsey, Rachel A Johnston, Eric Baitchman, Diane P Genereux, Rachel Daniels, Elinor K Karlsson

{"title":"Population genetics, trait mapping and fungal pathogen surveillance using untargeted sequencing in timber rattlesnakes (Crotalus horridus).","authors":"Christopher Husted, Jacob Alonso, Ross Swofford, Anne G Stengle, Lucas R Moreira, Daniel E Neafsey, Rachel A Johnston, Eric Baitchman, Diane P Genereux, Rachel Daniels, Elinor K Karlsson","doi":"10.1093/jhered/esag080","DOIUrl":"https://doi.org/10.1093/jhered/esag080","url":null,"abstract":"Genomic tools are increasingly important for conservation and wildlife health surveillance, yet their use is often constrained by limited resources, sample quality, and the need for minimally invasive approaches. Here we show that untargeted low-coverage sequencing applied to scale-clip DNA can jointly address population structure, genotype-phenotype associations, and pathogen surveillance in timber rattlesnakes (Crotalus horridus), a species threatened by habitat fragmentation, human encroachment, and the emerging fungal pathogen Ophidiomyces ophidiicola. We sequenced 107 snakes sampled from eight populations in the Appalachian Mountains of the northeastern United States to a mean depth of 0.94x per individual. Population differentiation is pronounced and only weakly correlated with geographic distance, and inbreeding coefficients in some populations are high enough to suggest fitness consequences. Genome-wide association analysis identifies a locus for black-to-yellow color morph containing ALDH4A1, a member of a gene family implicated in vertebrate pigmentation but distinct from melanin pathway pigmentation genes. Our untargeted sequencing method also captures host-associated microbes: O. ophidiicola loads are higher in snakes with clinical signs of snake fungal disease, though some asymptomatic individuals carry substantial loads, and skin-associated microbial communities are disrupted in snakes with higher fungal burdens. That all of these inferences derive from the same minimally invasive sampling and sequencing workflow highlights the scalability of this approach for biodiversity conservation.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149118828","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

A chromosome-level genome assembly of the Eurasian great grey owl, Strix nebulosa lapponica (Thunberg 1798). 欧亚大灰猫头鹰，Strix nebulosa lapponica的染色体水平基因组组装（Thunberg 1798）。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-10-06 DOI: 10.1093/jhered/esag085

Marius A Strand, Inga A Frøland Steindal, Erlend Ragnhildstveit, Roar Solheim, Ole K Tørresen, Morten Skage, Giada Ferrari, Ave Tooming-Klunderud, Kjetill S Jakobsen

{"title":"A chromosome-level genome assembly of the Eurasian great grey owl, Strix nebulosa lapponica (Thunberg 1798).","authors":"Marius A Strand, Inga A Frøland Steindal, Erlend Ragnhildstveit, Roar Solheim, Ole K Tørresen, Morten Skage, Giada Ferrari, Ave Tooming-Klunderud, Kjetill S Jakobsen","doi":"10.1093/jhered/esag085","DOIUrl":"https://doi.org/10.1093/jhered/esag085","url":null,"abstract":"We present a chromosome-level genome assembly of a female great grey owl (Strix nebulosa lapponica). The assembly comprises two pseudo-haplotypes of 1554 Mb and 1242 Mb, with 83.2% and 91.4% scaffolded into 40 autosomal chromosomes, in addition to the Z and W sex chromosomes both placed in hap1. Assembly completeness is high (BUSCO 99.2% and 94.8%), with 18,493 and 17,279 annotated protein-coding genes for hap1 and hap2, respectively. This genome establishes a reference for investigating genetic variation and chromosome evolution in great grey owls. Compared with the previous S. nebulosa assembly, this assembly includes both sex chromosomes, separates regions that were previously misassembled, and supports a diploid chromosome number of 2n = 82. While larger chromosomes show broadly conserved synteny across owl assemblies, the recovery of additional conserved dot microchromosome-associated marker proteins suggests that ONT reads improved resolution of the smallest chromosomes relative to HiFi-based assemblies.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149118858","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

Phenotypic divergence persists despite substantial gene flow in a Mimulus guttatus metapopulation. 表型差异持续存在，尽管大量的基因流动，在一个拟态guttatus元群体。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-09-26 DOI: 10.1093/jhered/esag082

Andrea Turcu, Nicholas J Kooyers

{"title":"Phenotypic divergence persists despite substantial gene flow in a Mimulus guttatus metapopulation.","authors":"Andrea Turcu, Nicholas J Kooyers","doi":"10.1093/jhered/esag082","DOIUrl":"https://doi.org/10.1093/jhered/esag082","url":null,"abstract":"Local adaptation at fine spatial scales depends on whether selection can maintain trait divergence despite ongoing gene flow, yet the spatial scale at which this occurs remains poorly resolved in natural populations. Heterogeneous landscapes containing geographically proximate populations provide natural experiments to test how gene flow and selection jointly shape adaptive divergence. We studied 12 annual populations of Mimulus guttatus distributed across two nearby ridges in the Cascade Mountains of Oregon, USA, and combined field fitness estimates, common garden phenotyping, and genome-wide SNP data to assess genetic variation, quantify phenotypic divergence, and test whether contemporary selection explains observed population differences. Populations had high levels of genetic diversity yet exhibited clear population structure between mountain ridges. Phenotypic divergence among populations exceeded expectations from genetic structure for several traits including flowering time, stem height, and trichome number. Earlier flowering time and larger flower sizes were associated with hotter and drier populations, matching patterns of temporally-fluctuating selection in a nearby population. Phenotypic selection analyses indicated that contemporary selection gradients were generally weak or non-significant, indicating that past selection likely produced variation between populations. Together, our results demonstrate that strong phenotypic differentiation can arise at microgeographic scales despite substantial gene flow and temporal heterogeneity in environments.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149066036","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

Limited recent introgression and ancient shared ancestry in Ethiopian wolves (Canis simensis). 埃塞俄比亚狼（Canis simensis）有限的近期遗传渗入和古老的共同祖先。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-09-24 DOI: 10.1093/jhered/esag081

Laura Tensen

{"title":"Limited recent introgression and ancient shared ancestry in Ethiopian wolves (Canis simensis).","authors":"Laura Tensen","doi":"10.1093/jhered/esag081","DOIUrl":"https://doi.org/10.1093/jhered/esag081","url":null,"abstract":"Hybridization between domestic and wild species is an increasing conservation concern, as continued introgression could lead to genomic extinction. The Endangered Ethiopian wolf (Canis simensis) is thought to be threatened by hybridization with free-roaming domestic dogs (C. familiaris) and African golden wolves (C. lupaster), particularly in human-dominated landscapes. Phenotype-based assessments during two field seasons in 1989 and 1991 have suggested that 8-17% of individuals in the Bale Mountains show signs of admixture, but the extent and timing of gene flow remain unresolved. This study analyzed 27 whole genomes, including nine Ethiopian wolves that showed no obvious signs of admixture, collected in 2003, to quantify patterns of introgression among African canids. Population structure analyses identified limited signals of hybridization, with most Ethiopian wolves forming a distinct genetic cluster. Although two related Ethiopian wolves exhibited subtle but significant excess allele sharing with African golden wolves, the overall genomic data provide little support for strong recent or directional introgression. Linkage disequilibrium decay analyses suggest an admixture event occurring approximately 800 generations ago; however, estimates of timing and admixture proportion were not robust, indicating substantial uncertainty in the precise parameters. Forward-in-time simulations indicate that, despite currently limited introgression, continued small population sizes could facilitate gradual genomic replacement over evolutionary timescales. Therefore, hybridization may become increasingly important under sustained demographic decline.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149042024","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

Genomic Diversity and Population Structure of Semi-Domesticated Reindeer populations in Southern Norway and wild reindeer from Iceland. 挪威南部半驯化驯鹿种群和冰岛野生驯鹿种群的基因组多样性和种群结构。

IF 2.2 2区生物学

Journal of Heredity Pub Date : 2026-09-22 DOI: 10.1093/jhered/esag078

Mariel Wictoria Holmen, Arturo Vera Ponce de León, Dag Inge Våge, Peer Berg, Morten Tryland, Ingebjørg Helena Nymo, Ester Malmström, Michael Andreas Tranulis, Matthew Peter Kent

{"title":"Genomic Diversity and Population Structure of Semi-Domesticated Reindeer populations in Southern Norway and wild reindeer from Iceland.","authors":"Mariel Wictoria Holmen, Arturo Vera Ponce de León, Dag Inge Våge, Peer Berg, Morten Tryland, Ingebjørg Helena Nymo, Ester Malmström, Michael Andreas Tranulis, Matthew Peter Kent","doi":"10.1093/jhered/esag078","DOIUrl":"https://doi.org/10.1093/jhered/esag078","url":null,"abstract":"Reindeer and caribou (Rangifer tarandus) play key ecological, cultural, and economical roles across Arctic and Subarctic regions. However, genome-wide patterns of genetic diversity and population structure in semi-domesticated reindeer from Norway remain insufficiently characterized. Here we generated a high-quality chromosome-level genome assembly (GCA_965153185.1) for Norwegian semi-domesticated Eurasian tundra reindeer (Rangifer tarandus tarandus). The genome spans 2.54 Gb, with a scaffold N50 of 75.6 Mb, 96.1% complete BUSCOs, and 39,855 predicted protein-coding genes. Using this reference, we performed whole-genome resequencing of 175 individuals from five reindeer populations from Norway and 28 individuals from Iceland, identifying ~19.9 million genetic variants. Genetic differentiation was low among Norwegian populations (FST = 0.005-0.011), but substantially higher between Norway and Iceland (FST = 0.140-0.161). Populations from Norway exhibited similar levels of nucleotide diversity (π = 1.39-1.62 × 10-3), whereas the Icelandic population showed reduced diversity (π = 0.99 × 10-3) and approximately half as many segregating variants. Analyses of runs of homozygosity (ROH) and genome-wide heterozygosity indicated low levels of recent inbreeding across all populations, with long ROHs (>8 Mb) being rare. Despite reduced genetic diversity, the Icelandic population showed limited evidence of recent inbreeding. These patterns are consistent with contrasting demographic histories, with gene flow maintaining diversity among populations from Norway, while founder effects combined with long-term isolation have shaped the Icelandic population.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018768","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