Journal of Heredity最新文献

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Genomic erosion in the assessment of species' extinction risk and recovery potential. 基因组侵蚀在物种灭绝风险和恢复潜力评估中的应用。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-03 DOI: 10.1093/jhered/esag011
Cock van Oosterhout, Samuel A Speak, Thomas Birley, Lewis W G Hitchings, Chiara Bortoluzzi, Lawrence Percival-Alwyn, Lara Urban, Jim J Groombridge, Gernot Segelbacher, Hernán E Morales
{"title":"Genomic erosion in the assessment of species' extinction risk and recovery potential.","authors":"Cock van Oosterhout, Samuel A Speak, Thomas Birley, Lewis W G Hitchings, Chiara Bortoluzzi, Lawrence Percival-Alwyn, Lara Urban, Jim J Groombridge, Gernot Segelbacher, Hernán E Morales","doi":"10.1093/jhered/esag011","DOIUrl":"10.1093/jhered/esag011","url":null,"abstract":"<p><p>Many species are undergoing rapid population declines and environmental deterioration, leading to genomic erosion. Here we define genomic erosion as the loss of genetic diversity, accumulation of deleterious mutations, maladaptation, and introgression, all of which can undermine individual fitness and long-term population viability. Critically, this process continues even after demographic recovery due to a time-lagged impact of genetic drift, which is known as drift debt. Current conservation assessments, such as the International Union for Conservation of Nature Red List, focus on short-term extinction risk and do not capture the long-term consequences of genomic erosion. Likewise, the longer-term assessments of the International Union for Conservation of Nature Green Status may overestimate population recovery by failing to account for the enduring effects of genomic erosion. As genome sequencing becomes increasingly accessible, there is a growing opportunity to quantify genomic erosion and integrate it into conservation planning. Here, we use genomic simulations to illustrate how different genomic metrics are sensitive to the drift debt. We test how ancestral effective population size (Ne) and bottleneck history influence the tempo and severity of genomic erosion. Furthermore, we demonstrate how these dynamics shape genetic load and additive genetic variation, which are key indicators of long-term evolutionary potential. Finally, we present a proof-of-concept for a Genomic Green Status framework that aligns genomic metrics with conservation impact assessments, laying the foundation for genomics-informed strategies to support species recovery.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"1008-1021"},"PeriodicalIF":2.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13539449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146108434","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
Rapid derivation of cloning-competent cells from peripheral blood advances conservation biobanking. 外周血可克隆细胞的快速衍生——保护生物库的进展。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-03 DOI: 10.1093/jhered/esag048
Laura Knecht, Anthony Mastracci Iv, Riley Harbert, Fatima Charles, Laura L Kuperman-Yao, Tyler Miyawaki, Gregory L Gedman, Kathleen M Pirovich, Jason Herrick, Linda Lay, Alba Ledesma, Steve Metzler, Dennis Milutinovitch, James B Papizan, Parker Pennington, Lexie Russell, Kerry Ryan, Kanokwan Srirattana, Kaitlin Steiger, Darya A Tourzani, Kelcey Walker, Rafael V Sampaio, Sven Bocklandt, Ben Lamm, Matt James, Shawn Walker, Beth Shapiro, James Kehler
{"title":"Rapid derivation of cloning-competent cells from peripheral blood advances conservation biobanking.","authors":"Laura Knecht, Anthony Mastracci Iv, Riley Harbert, Fatima Charles, Laura L Kuperman-Yao, Tyler Miyawaki, Gregory L Gedman, Kathleen M Pirovich, Jason Herrick, Linda Lay, Alba Ledesma, Steve Metzler, Dennis Milutinovitch, James B Papizan, Parker Pennington, Lexie Russell, Kerry Ryan, Kanokwan Srirattana, Kaitlin Steiger, Darya A Tourzani, Kelcey Walker, Rafael V Sampaio, Sven Bocklandt, Ben Lamm, Matt James, Shawn Walker, Beth Shapiro, James Kehler","doi":"10.1093/jhered/esag048","DOIUrl":"10.1093/jhered/esag048","url":null,"abstract":"<p><p>Establishing viable cell lines from endangered species is essential for conservation, yet traditional fibroblast derivation from skin biopsies faces challenges including contamination risk and extended culture timelines. Here, we demonstrate that endothelial progenitor cells (EPCs) and pericytes isolated from peripheral blood represent robust alternatives to fibroblasts for biobanking. Compared to canid fibroblasts, canid blood-derived cells exhibit 2- to 3-fold faster doubling rates (15 to 20 h vs. ~35 h for fibroblasts) and reduced time to banked cell lines (1.5 to 2 wks vs. 3 to 4 wks for fibroblasts). Proteomic profiling of 32 canonical markers confirmed EPCs and pericytes represent distinct populations with lineage-specific molecular signatures. Optical genome mapping demonstrated equivalent genomic stability across cell types with no detectable structural variants or aneuploidies. Finally, interspecific somatic cell nuclear transfer (iSCNT) experiments confirmed both EPCs and pericytes generate viable canid embryos with efficiency meeting or exceeding fibroblasts. As a proof of concept for conservation cloning, iSCNT embryos made with gray wolf blood-derived cells had a 15% implantation rate following embryo transfer and resulted in six viable fetuses. These findings support integrating blood-derived cell banking into conservation programs, which enables opportunistic genetic preservation during standard management activities and expands options for genetic rescue through assisted reproductive technologies.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"1118-1129"},"PeriodicalIF":2.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13539446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148334502","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
Polygenic and monogenic adaptation drive evolutionary rescue at different magnitudes of environmental change. 多基因和单基因适应在不同程度的环境变化下驱动进化拯救。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-03 DOI: 10.1093/jhered/esag026
Tatiana Bellagio, Moises Exposito-Alonso
{"title":"Polygenic and monogenic adaptation drive evolutionary rescue at different magnitudes of environmental change.","authors":"Tatiana Bellagio, Moises Exposito-Alonso","doi":"10.1093/jhered/esag026","DOIUrl":"10.1093/jhered/esag026","url":null,"abstract":"<p><p>Understanding the genetic basis of rapid adaptation is key to predicting species' evolutionary responses to environmental change. However, it is still debatable whether many small-effect mutations or a few large-effect mutations underlie rapid adaptation, and how this knowledge can predict population survival or extinction. To address this question, we performed a series of ecologically grounded forward-in-time genetic simulations to study rapid adaptation and extinction with increasing magnitudes of environmental change. These simulations were seeded with genomic variation of the plant Arabidopsis thaliana to have a realistic genomic structure, with one (monogenic) to 1,000 (polygenic) variants with varying heritabilities contributing to an environmental adaptive trait. Our results revealed two distinct scenarios of rapid adaptation and population rescue. Under small-to-moderate environmental shifts, high polygenic traits increased evolutionary rescue probability. Under extreme environmental shifts, high polygenic traits lead predictably to extinction, yet monogenic traits sometimes produce one-off winning adaptive genotypes. We interpret our rapid evolutionary rescue findings in terms of the fundamental theorem of natural selection, where trait polygenicity shapes the distribution of genetic variance in fitness across replicates and, in turn, the probability of population survival, with polygenic architectures producing more stable and predictable fitness variance and monogenic architectures generating highly skewed and variable outcomes. These results highlight the insights genomics gives us into the (un)predictability of species' evolutionary responses to global change, with management implications for assisted adaptation and conservation.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"1073-1086"},"PeriodicalIF":2.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13539452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147640712","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
Ex situ reared black-footed ferrets exhibit altered sperm DNA methylation. 非原位饲养的黑足雪貂表现出精子DNA甲基化的改变。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-03 DOI: 10.1093/jhered/esaf056
Alexandra L DeCandia, Stavi R Tennenbaum, Rachel Santymire, Travis Livieri, Robyn Bortner, Della Garelle, Adrienne Crosier, Paul Marinari, Budhan S Pukazhenthi, Pierre Comizzoli, Jesús E Maldonado, Klaus-Peter Koepfli, Bridgett M vonHoldt
{"title":"Ex situ reared black-footed ferrets exhibit altered sperm DNA methylation.","authors":"Alexandra L DeCandia, Stavi R Tennenbaum, Rachel Santymire, Travis Livieri, Robyn Bortner, Della Garelle, Adrienne Crosier, Paul Marinari, Budhan S Pukazhenthi, Pierre Comizzoli, Jesús E Maldonado, Klaus-Peter Koepfli, Bridgett M vonHoldt","doi":"10.1093/jhered/esaf056","DOIUrl":"10.1093/jhered/esaf056","url":null,"abstract":"<p><p>Many endangered species rely on ex situ management for survival when external threats exist on the landscape. Yet, ex situ settings pose challenges through space limitation, altered environment, and diet. This can lead to environmentally determined inbreeding depression, where ex situ animals exhibit reduced reproductive fitness compared with their in situ counterparts, despite originating from the same genetic stock. We investigated epigenetic differences as a potential mechanism underlying environmentally determined inbreeding depression in black-footed ferrets (Mustela nigripes), a North American endemic species reliant on ex situ conservation. More specifically, we explored how environmental context may influence sperm DNA methylation in samples collected from 12 ex situ and 5 in situ males. Average sperm DNA methylation was significantly higher in ex situ individuals. We additionally identified more than 500 differentially methylated regions between ex situ and in situ sperm samples that were enriched for gene ontology terms pertaining to reproduction and development. Putative genes of interest included NPR2, WEE2, SLC15A1, PDE10A, PIP5K1B, CACNA1E, and CACNA1A, all of which have previously been linked to spermatogenesis, sperm motility, or fertilization in mammals. Results suggest that environmental conditions may alter sperm DNA methylation in black-footed ferrets, with possible links to decreased reproductive success in ex situ settings. These findings provide valuable insights into the molecular mechanisms underlying environmentally determined inbreeding depression in black-footed ferrets and other conservation-reliant species, and can serve as a foundation for future research on improving reproductive health in endangered wildlife.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"1093-1106"},"PeriodicalIF":2.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144979329","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
Inducing radiation resilience in frozen animal cells via mRNA coding for tardigrade damage-suppressor protein in support of space travel and Lunar storage. 通过编码缓步动物损伤抑制蛋白的mRNA诱导冰冻动物细胞的辐射恢复能力,以支持太空旅行和月球储存。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-03 DOI: 10.1093/jhered/esag030
Mary Hagedorn, Pierre Comizzoli, Lynne R Parenti, Robert A Craddock, Paula Mabee, Bonnie Meinke, John C Bischof, Rebecca D Sandlin, Shannon N Tessier, Mehmet Toner, Robert Ambrose, Baptiste Journaux, Garret Fitzpatrick
{"title":"Inducing radiation resilience in frozen animal cells via mRNA coding for tardigrade damage-suppressor protein in support of space travel and Lunar storage.","authors":"Mary Hagedorn, Pierre Comizzoli, Lynne R Parenti, Robert A Craddock, Paula Mabee, Bonnie Meinke, John C Bischof, Rebecca D Sandlin, Shannon N Tessier, Mehmet Toner, Robert Ambrose, Baptiste Journaux, Garret Fitzpatrick","doi":"10.1093/jhered/esag030","DOIUrl":"10.1093/jhered/esag030","url":null,"abstract":"<p><p>Earth's biodiversity is at risk. To help safeguard this biodiversity, a Lunar Biorepository at the Moon's south pole has been proposed to hold cryopreserved samples of fibroblast cells from animal species that support fundamental ecosystems on Earth. These samples could be used for revitalization of ecosystems on Earth, genetic rescue, space travel, or possibly terraformation. Initially, samples will be primarily animal cells, but the biorepository would be designed to ultimately include all species on Earth. This biorepository will take decades to build and will potentially span millennia. To make this project a reality, certain prior steps must be taken, such as defining species selection and collection and sample management on Earth before launching in the biorepository. Many of the steps leading to the creation of this biorepository are known, with long-term radiation exposure and risk to the cells being one of the greatest challenges to overcome. It is essential to understand the radiation sensitivity of cells and design strategies to avoid genetic modification to further protect cells from radiation during space travel and long-term storage. After considering various options, this review specifically focuses on exposing fibroblast cells to nanoparticles delivering modified mRNA tardigrade damage-suppressor protein. This protein minimizes DNA damage due to radiation without obvious harmful effects to the tissue and cells. This also could serve as a testbed to study countermeasures against the radiation effects during long-duration, crewed space flights.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"1087-1092"},"PeriodicalIF":2.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13539440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846369","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
Evolving conservation: The role of unconventional approaches to restore contemporary vertebrate populations and genomic biodiversity. 进化保护:非常规方法在恢复当代脊椎动物种群和基因组生物多样性中的作用。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-03 DOI: 10.1093/jhered/esag040
Bridgett M vonHoldt, Matt James, Stephen J Gaughran, Alexandra L DeCandia, Klaus-Peter Koepfli, Dan Flores, Nucharin Songsasen, Kristin E Brzeski, Evelyn L Jensen
{"title":"Evolving conservation: The role of unconventional approaches to restore contemporary vertebrate populations and genomic biodiversity.","authors":"Bridgett M vonHoldt, Matt James, Stephen J Gaughran, Alexandra L DeCandia, Klaus-Peter Koepfli, Dan Flores, Nucharin Songsasen, Kristin E Brzeski, Evelyn L Jensen","doi":"10.1093/jhered/esag040","DOIUrl":"10.1093/jhered/esag040","url":null,"abstract":"<p><p>Conservation biology and restoration ecology are two essential yet distinct disciplines that address the growing challenge of biodiversity loss. Traditionally, these fields have relied on ecological principles and management practices aimed at protecting or reestablishing natural systems. The crisis is no longer just ecological; it is evolutionary and genomic. The accelerating pace of environmental change has outstripped the capacity of conventional approaches, creating a pressing need for innovative solutions. Biotechnology offers potentially transformative tools that can enhance the effectiveness and precision of both conservation and restoration efforts, especially for species where conventional conservation approaches have proved insufficient. Techniques such as genetic rescue, synthetic biology, and gene editing are increasingly being explored to address critical challenges, such as invasive species control, genetic diversity loss, and habitat fragmentation, to both invigorate endangered species and restore historical biodiversity. Despite its promise, the integration of biotechnology into conservation and restoration has raised ethical, ecological, and regulatory concerns. These include ecological unpredictability and public resistance to genetic interventions in wild populations. This perspective examines the current landscape of biotechnological applications in conservation and restoration, highlighting successful case studies, ongoing controversies, and optimism for additional progress. We argue that thoughtful, transparent integration of biotechnology that is grounded in ecological knowledge and stakeholder engagement can reconcile the goals of conservation and restoration. As ecosystems face mounting pressures, biotech-enabled strategies may prove essential for fostering resilience and ensuring long-term ecological sustainability.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"993-1007"},"PeriodicalIF":2.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13539457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147984290","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
A chromosome-level genome for the spotted flying dragon (Draco maculatus). 斑点飞龙的染色体水平基因组。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-09-01 DOI: 10.1093/jhered/esag072
Haoteng Wei, Fan Zhang, Songhai Li, Amaël Borzée, Ran Tian, Inge Seim
{"title":"A chromosome-level genome for the spotted flying dragon (Draco maculatus).","authors":"Haoteng Wei, Fan Zhang, Songhai Li, Amaël Borzée, Ran Tian, Inge Seim","doi":"10.1093/jhered/esag072","DOIUrl":"https://doi.org/10.1093/jhered/esag072","url":null,"abstract":"<p><p>The Agamidae (agamids, also known as dragon lizards or dragons) is a species-rich squamate family adapted to all non-polar continents except the Americas. Flying dragons (Draco) belong to this family and are widespread across South and Southeast Asia. To date, no nuclear genome assemblies of flying dragons have been published, limiting our understanding of the genetic underpinnings of their unique adaptive gliding trait and population dynamics. We report a high-quality chromosome-level assembly of Draco maculatus (the spotted flying dragon) with a size of 1.73Gb, a scaffold N50 of 255.50 Mb, and 18,805 annotated protein-coding genes. The assembly (99.88% of assembled sequence) was anchored to 17 pseudochromosomes (6 macro-11 micro), consistent with the reported karyotype of Draco species in cytogenetic studies. We also provide transcriptomic data from the patagium, skin, and four internal tissues.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148876808","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
Little sharks in a genomic world: A high-resolution view of population structure in the California horn shark (Heterodontus francisci). 基因组世界中的小鲨鱼:加利福尼亚角鲨(Heterodontus francisci)种群结构的高分辨率视图。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-08-27 DOI: 10.1093/jhered/esag071
Sean J Canfield, Felipe Galván-Magaña, Brian W Bowen
{"title":"Little sharks in a genomic world: A high-resolution view of population structure in the California horn shark (Heterodontus francisci).","authors":"Sean J Canfield, Felipe Galván-Magaña, Brian W Bowen","doi":"10.1093/jhered/esag071","DOIUrl":"https://doi.org/10.1093/jhered/esag071","url":null,"abstract":"<p><p>The California horn shark (Heterodontus francisci) is a small demersal elasmobranch distributed along Pacific coastlines from California to Mexico, including several nearshore islands. Previous analyses of mitochondrial control region (mtCR) variation indicated that island populations are genetically distinct from mainland populations, while little to no structure was detected along contiguous coastlines over much larger distances, suggesting that deep-water channels may act as barriers to dispersal. However, this interpretation was inconsistent with the lack of detectable differentiation between the northern Channel Islands and Santa Catalina Island, separated by nearly 100 km of deep, cold water. To reexamine patterns of population connectivity, we used ddRADseq to genotype 3953 nuclear SNP loci from 175 specimens sampled across the range of H. francisci. Analyses identified at least five genetically distinct population units and recovered strong differentiation between the northern Channel Islands and Santa Catalina Island, supporting the hypothesis that deep-water channels are an important driver of population structure in H. francisci at spatial scales as small as 20 km (FST ≥ 0.020). Shallow but extensive population structure was associated with geographic distance along the mainland Pacific coast, spanning more than 1200 km of shoreline (FST ≤ 0.013). Overall, our results demonstrate substantial population subdivision across the range of H. francisci and reduced genetic diversity within island populations. These findings highlight the importance of considering population structure in the conservation and management of diminutive demersal sharks and support the development of stock-specific management strategies.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148842113","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
Population genetics simulations made easier: EASYPOP v3. 群体遗传学模拟变得更容易:EASYPOP v3。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-08-22 DOI: 10.1093/jhered/esag070
Ted Cosart, William Hemstrom, Jared Grummer, Gordon Luikart
{"title":"Population genetics simulations made easier: EASYPOP v3.","authors":"Ted Cosart, William Hemstrom, Jared Grummer, Gordon Luikart","doi":"10.1093/jhered/esag070","DOIUrl":"https://doi.org/10.1093/jhered/esag070","url":null,"abstract":"<p><p>We introduce an updated and enhanced version of EASYPOP, a widely used population-genetics simulation program. The previous version (2.0.1), released in 2006, runs natively only in Windows or the old Apple PPC architecture. The new version (3.1) preserves EASYPOP's ease of installation and use and runs natively in Windows, Linux, Apple Silicon, and Apple Intel environments. For quick re-runs, it can now write simulation parameters to and read them from a configuration file, removing the need to retype input parameters before each run. It also adds genotype output options that facilitate temporal studies by sampling any generations of interest. We also introduce an R package, easypopr, that further automates running EASYPOP 3.1 using R commands to easily setup and rerun simulations with changes in parameters. easypopr provides tools to visualize the effects of different parameter choices (Ne, mutation models, migration rates, demographic scenarios, etc.) on summary statistics, including subpopulation mean heterozygosity (Hs), total metapopulation heterozygosity (HT), FIS, FST, and N-e-estimates. Outputs from easypopr (and EASYPOP) are easily fed into snpR or other R packages for convenient, wide-ranging analysis to quantify the effects of demography on the power to detect genetic change, including integration with programs like NeEstimator and STRUCTURE. With these enhancements, available in executables for all common operating systems, EASYPOP 3.1 provides a streamlined approach for conducting forward-time genetic simulations across a wide range of scenarios.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148801816","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 contemporary Pacific gray whale (Eschrichtius robustus) gene pool includes ancestry from a potential ghost population: inferences from population genomics. 当代太平洋灰鲸(Eschrichtius robustus)基因库包括来自潜在幽灵种群的祖先:种群基因组学的推论。
IF 2.2 2区 生物学
Journal of Heredity Pub Date : 2026-08-20 DOI: 10.1093/jhered/esag059
Natalie M Allen, Anna Brüniche-Olsen, Jong Yoon Jeon, Andrew J Mularo, John W Bickham, Jorge Urbán Ramírez, J Andrew DeWoody
{"title":"The contemporary Pacific gray whale (Eschrichtius robustus) gene pool includes ancestry from a potential ghost population: inferences from population genomics.","authors":"Natalie M Allen, Anna Brüniche-Olsen, Jong Yoon Jeon, Andrew J Mularo, John W Bickham, Jorge Urbán Ramírez, J Andrew DeWoody","doi":"10.1093/jhered/esag059","DOIUrl":"https://doi.org/10.1093/jhered/esag059","url":null,"abstract":"<p><p>Local extirpations and extreme bottlenecks can deplete genetic variation and obscure population dynamics, especially in highly mobile species. The gray whale (Eschrichtius robustus) undertakes some of the longest known migrations among mammals, and two stocks (eastern and western gray whales) were historically recognized in the Pacific. Commercial whaling depleted both stocks, and while the Eastern North Pacific (ENP) stock has rebounded, the western stock was feared extirpated. In the post-whaling era, the origin of a small summer aggregation near Sakhalin Island, Russia (which we refer to as the Western North Pacific (WNP) stock) is unclear; this group may include descendants from the original western stock, founders from the eastern stock, or some combination of the two. To clarify the genetic affinities of WNP gray whales, we analyzed whole genome resequencing data for 71 individuals sampled from both geographic regions. Surprisingly, WNP whales are more genetically varied than ENP whales according to principal components and admixture analyses. We present evidence that this structure reflects mixed ancestry in the WNP, where some contemporary whales retain ancestry from the feared-extirpated western population, detectable as \"ghost\" introgression, while others are of eastern ancestry. Genomic signals based on both single nucleotide polymorphisms and on copy number variants indicate that despite mixed ancestry, the influx of recent eastern gene flow has largely homogenized genomic diversity across the Pacific. These findings highlight the ability of whole-genome data to help resolve questions of extirpation and to clarify complex gene flow dynamics in highly mobile species.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148801916","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
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