Journal of Heredity最新文献_第2页

Mixed evidence for intralocus sexual conflict from male-limited selection in Drosophila melanogaster. 黑腹果蝇雄性有限选择引起的室内性冲突的混合证据。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-29 DOI: 10.1093/jhered/esaf072

Harshavardhan Thyagarajan, Imran Sayyed, Mindy G Baroody, Joshua A Kowal, Troy Day, Adam K Chippindale

{"title":"Mixed evidence for intralocus sexual conflict from male-limited selection in Drosophila melanogaster.","authors":"Harshavardhan Thyagarajan, Imran Sayyed, Mindy G Baroody, Joshua A Kowal, Troy Day, Adam K Chippindale","doi":"10.1093/jhered/esaf072","DOIUrl":"https://doi.org/10.1093/jhered/esaf072","url":null,"abstract":"Sexual conflict over shared traits-intralocus sexual conflict (IaSC)-may be common and consequential, but experimental tests of its relative magnitude are challenging and limited in number. We use a sex-limited selection experiment, designed to subject haplotypes of Drosophila melanogaster to selection for male fitness without opposing selection acting on female fitness. Importantly, we use three novel base populations to compare results with those from the LHM population, the sole population investigated using this technique. In contrast with previous studies, we find that male fitness of haplotypes subject to male-limited selection (ML populations) are not consistently better than their matched (MC) controls when tested in the 'wildtype' state. Males from ML lines did not outperform controls in competitive fitness assays, mate choice trials, fecundity induction or sperm offense tests. As predicted, genetic variation for male fitness was reduced, with low fitness haplotypes apparently removed by selection, but this was only surveyed in one replicate population pair and included a potential artefact in the protocol. Female fitness was markedly reduced by carriage of ML haplotypes, as predicted by sexual antagonism. Hence, our results are only partially consistent with the IaSC hypothesis, raising questions about the relative contribution of sexual conflict to the standing genetic variation in these populations and the potential role of artefacts in the protocol that may have obscured our ability to detect IaSC.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145187234","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

Development, history, and impact of "Recent Advances in Conservation Genetics", the ConGen Global training course. ConGen全球培训课程“保护遗传学最新进展”的发展、历史和影响。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-25 DOI: 10.1093/jhered/esaf060

Taras K Oleksyk, Klaus-Peter Koepfli, Stephen J O'Brien

{"title":"Development, history, and impact of \"Recent Advances in Conservation Genetics\", the ConGen Global training course.","authors":"Taras K Oleksyk, Klaus-Peter Koepfli, Stephen J O'Brien","doi":"10.1093/jhered/esaf060","DOIUrl":"https://doi.org/10.1093/jhered/esaf060","url":null,"abstract":"The ConGen Global course \"Recent Advances in Conservation Genetics\" was established to educate and empower new generations of researchers and practitioners in genetic and genomic approaches to biodiversity conservation. Since its first offering in 1996, the course has evolved from a focus on sample collection, population diversity assessment, and molecular phylogeography using (polymerase chain reaction (PCR) and Sanger sequencing to a curriculum centered on next-generation sequencing, whole-genome assembly, demographic inference, and bioinformatic analyses. Originally hosted at venues near Washington, D.C., the course expanded internationally in 2011 and has since been held near biodiversity hotspots across the globe, incorporating local researchers, and drawing an increasingly diverse global audience from every part of the world. Each edition integrates region-specific conservation challenges with hands-on tutorials, case studies, and personal narratives from leading conservation geneticists. This combination of rigorous science, practical applications, and international participation has created a uniquely impactful and inclusive program. Here, we review the last decade of ConGen Global (2015 to 2025), highlighting its contributions to conservation genetics education, its role in standardizing and disseminating new genomic methods, and its influence on policy-relevant research agendas. Beyond training, the course has shaped the broader field of conservation genetics by accelerating the adoption of genomic tools, strengthening global research networks, and translating genetic insights into conservation practice. Drawing on nearly three decades of experience, ConGen Global continues to serve as a model for advancing conservation genetics education and for inspiring future training programs worldwide.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139537","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 forked fungus beetle Bolitotherus cornutus, a model system for studying social evolution in the wild. 分叉真菌甲虫Bolitotherus cornutus的染色体水平基因组组装，这是研究野生社会进化的模式系统。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-24 DOI: 10.1093/jhered/esaf071

Kyle M Benowitz, Zachery M Esterline, Allina A Win, Vincent A Formica, Edmund D Brodie

引用次数: 0

De-extinction technology and its application to conservation. 灭绝物种恢复技术及其在保护中的应用。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-24 DOI: 10.1093/jhered/esaf069

Stephen D Turner, Anna Keyte, Andrew Pask, Beth Shapiro

引用次数: 0

The annotated, chromosome-scale Salicornia depressa (American pickleweed) genome. 注释的，染色体尺度的Salicornia depressa（美国pickleweed）基因组。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-23 DOI: 10.1093/jhered/esaf062

Cooper Kimball-Rhines, Alice E Kaisla, Scarlet Taveras Guzman, Emily Mello, Karol Vanessa Rojas Ramirez, Alex Harkess, Brook Moyers

{"title":"The annotated, chromosome-scale Salicornia depressa (American pickleweed) genome.","authors":"Cooper Kimball-Rhines, Alice E Kaisla, Scarlet Taveras Guzman, Emily Mello, Karol Vanessa Rojas Ramirez, Alex Harkess, Brook Moyers","doi":"10.1093/jhered/esaf062","DOIUrl":"https://doi.org/10.1093/jhered/esaf062","url":null,"abstract":"Salicornia depressa (American pickleweed) is the most widespread member of its salt-loving genus in North America. Pickleweeds typically colonize high marsh areas that tides make highly saline. Most other salt marsh plants cannot withstand the same salt pressure, so these bare patches are free from competitive pressures. Understanding the genetic origin of American Pickleweed's high salinity adaptations has potential application to salt-tolerant agriculture and salt marsh conservation but requires genome resources to study. S. depressa is a tetraploid species, which presents unique challenges to traditional genome assembly pipelines. We present a high-quality, chromosome-scale reference genome of S. depressa and the pipeline we used to assemble it. Our reference is phased to each of the tetraploid's ancestral subgenomes with a scaffold N50 of 69.3 Mb, BUSCO completeness of 96.4%, and k-mer completeness of 98.4%. The subassemblies are evenly split, with subassembly A containing 56.7% and subassembly B containing 59.1% of genomic k-mers. Our gene annotation identifies 80 883 genes and our methylome annotation contains 2.5 million methylated cytosines. We find that gene and methylation density are negatively correlated across the genome. We also assembled and annotated a chloroplast assembly which includes all expected photosystem, tRNA, and rRNA genes. We provide a guide to our successful assembly pipeline involving > 30 programs. Our reference and annotation join resources for three other Salicornia species, allowing global scale ecological-evolutionary studies.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126635","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

From Environmental DNA into Actionable Biodiversity Data: Towards the Implementation of the Kunming-Montreal Global Biodiversity Framework. 从环境DNA到可操作的生物多样性数据：面向昆明-蒙特利尔全球生物多样性框架的实施。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-23 DOI: 10.1093/jhered/esaf068

Mark Louie D Lopez, Neha Acharya-Patel, Michael J Allison, Amy Migneault, Sarah Trilesky, Caren C Helbing

{"title":"From Environmental DNA into Actionable Biodiversity Data: Towards the Implementation of the Kunming-Montreal Global Biodiversity Framework.","authors":"Mark Louie D Lopez, Neha Acharya-Patel, Michael J Allison, Amy Migneault, Sarah Trilesky, Caren C Helbing","doi":"10.1093/jhered/esaf068","DOIUrl":"https://doi.org/10.1093/jhered/esaf068","url":null,"abstract":"Biodiversity is declining at an alarming rate due to ongoing habitat destruction, climate change, pollution, the spread of invasive species, and unsustainable use of natural resources. In response, the Kunming-Montreal Global Biodiversity Framework (KMGBF), adopted in 2022, outlines a transformative goal to reverse biodiversity loss by 2030. The framework focuses on three main pillars: mitigating biodiversity threats, advancing implementation, and ensuring fair and sustainable use of biological resources. Meeting these objectives requires the adoption of innovative, adaptable, and inclusive monitoring strategies. Among these, environmental DNA (eDNA) has gained recognition as a non-invasive biodiversity assessment method that detects trace genetic material in environmental samples like sediment, soil, water, and air. Compared to conventional survey techniques, eDNA offers improved accuracy, sampling flexibility, and a non-destructive approach to monitoring ecosystems. Herein, we examine eDNA's role in achieving KMGBF goals to enable fulfilment of the Convention on Biological Diversity's vision of living in harmony with nature by 2050. We discuss its use in meeting several KMGBF targets including early detection of invasive species, enhancing biosecurity, monitoring species recovery, assessing pollution impacts, and supporting climate resilience. The standardization of eDNA protocols and alignment with FAIR (Findable, Accessible, Interoperable, Reusable) data principles ensure that results are transparent and interoperable across regions and platforms. Integrating eDNA into existing biodiversity monitoring networks enhances conservation planning, restoration efforts, and the management of protected areas. Additionally, eDNA facilitates inclusive conservation by supporting Indigenous-led and community-based monitoring, promoting stewardship, and enabling equitable access to biodiversity data worldwide.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126650","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

Levels and partitioning of genetic variation of northeastern populations of diamondback terrapin (Malaclemys terrapin). 东北菱形龟种群遗传变异的水平和分配。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-19 DOI: 10.1093/jhered/esaf066

Amanda L Lyons, Rebecca Y Kartzinel, Bianca R P Brown, Scott W Buchanan, Lisa M Ferguson, Brian A Williamson, Tyler R Kartzinel

{"title":"Levels and partitioning of genetic variation of northeastern populations of diamondback terrapin (Malaclemys terrapin).","authors":"Amanda L Lyons, Rebecca Y Kartzinel, Bianca R P Brown, Scott W Buchanan, Lisa M Ferguson, Brian A Williamson, Tyler R Kartzinel","doi":"10.1093/jhered/esaf066","DOIUrl":"https://doi.org/10.1093/jhered/esaf066","url":null,"abstract":"The diamondback terrapin (Malaclemys terrapin) is a mid-sized turtle that serves as a keystone predator in salt marsh ecosystems of eastern North America. The terrapin has historically faced population declines due to habitat loss and overharvesting, which has resulted in its listing under multiple jurisdictions across the northern part of its range. To characterize levels and partitioning of terrapin genetic variation throughout the northeast region, we used restriction site-associated DNA sequencing (RADseq). We analyzed genetic variation among 116 individuals sampled across 18 sites. Within-population genetic diversity was relatively low (He = 0.080-0.122), and we observed a strong negative correlation between diversity and latitude. Furthermore, levels of genetic differentiation were moderate (pairwise FST = 0.00-0.19), with the mean pairwise FST of each population exhibiting a strong positive correlation with latitude. Together, these results are consistent with a model of serial colonization from a Pleistocene refugium in the mid-Atlantic. Spatial genetic variation was best explained by a landscape model that considered migration to be limited to coastal habitats, where northern range-edge populations maintained comparatively low genetic diversity and were more genetically distinct than populations to the south-consistent with their greater geographic isolation. Admixture analyses revealed weak genetic clustering, with the distribution of genetic clusters reflecting the combined historical effects of isolation-by-distance and human-mediated translocations. Regional efforts to restore terrapin habitat or reintroduce captive individuals should consider patterns of historic gene flow, cognizant of the relatively distinct and isolated populations at the northeastern range edge.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145092919","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 highly contiguous genome assembly for the California vole, Microtus californicus, provides insight into phylogenetic relationships and patterns of synteny among voles. 加利福尼亚田鼠（Microtus californicus）的高度连续基因组组装，为田鼠之间的系统发育关系和合群模式提供了见解。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-17 DOI: 10.1093/jhered/esaf067

Krzysztof M Kozak, Merly Escalona, Isaac J Linn, Noravit Chumchim, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, William Seligmann, Chris J Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman

{"title":"A highly contiguous genome assembly for the California vole, Microtus californicus, provides insight into phylogenetic relationships and patterns of synteny among voles.","authors":"Krzysztof M Kozak, Merly Escalona, Isaac J Linn, Noravit Chumchim, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, William Seligmann, Chris J Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman","doi":"10.1093/jhered/esaf067","DOIUrl":"https://doi.org/10.1093/jhered/esaf067","url":null,"abstract":"The California vole (Microtus californicus) is a small cricetid rodent and one of 20 species of Microtus in North America and 60 worldwide. Several subspecies are listed as being of conservation concern in California, and one is federally protected. Here we present the first de novo genome assembly for the California vole, generated as a part of the California Conservation Genomics Project. The M. californicus genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. Our high-quality genome is one of the most complete vole assemblies available, with a contig N50 of 49.8 Mb, scaffold N50 of 83.7 Mb, and BUSCO completeness score of 96.4%. Analysis of this genome together with genomes of closely related species revealed phylogenetic relationships and high levels of synteny among voles. The California vole genome provides an important new resource for comparative work across cricetid and muroid genomes. It will also serve as a reference for the analysis of within-species genetic diversity across widespread subspecies as well as more restricted populations of conservation concern.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145092955","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 high-contiguous genome assembly of Apis andreniformis (Hymenoptera: Apidae). 蜜蜂和蜂科的高度连续基因组组装（膜翅目：蜂科）。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-13 DOI: 10.1093/jhered/esaf065

Ye Xiao, Lifei Qiu, Min Tang, Shanlin Liu, Xin Zhou

引用次数: 0

NUMTsearcher: advancing detection and evolutionary insights of nuclear mitochondrial DNA segments across human, rabbit, and fish genomes. NUMTsearcher：推进人类、兔子和鱼类基因组核线粒体DNA片段的检测和进化见解。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-09 DOI: 10.1093/jhered/esaf064

Kai Liu, Nan Xie

{"title":"NUMTsearcher: advancing detection and evolutionary insights of nuclear mitochondrial DNA segments across human, rabbit, and fish genomes.","authors":"Kai Liu, Nan Xie","doi":"10.1093/jhered/esaf064","DOIUrl":"https://doi.org/10.1093/jhered/esaf064","url":null,"abstract":"Nuclear mitochondrial DNA segments (NUMTs), which are mitochondrial DNA fragments integrated into the nuclear genome, serve as markers of evolutionary history. This study aims to enhance the detection and analysis of NUMTs by developing a script named NUMTsearcher. Utilizing the latest chromosome-level genome assemblies from various species, including human, rabbit, and six fish species, the study compares NUMTsearcher's performance against traditional methods such as LAST (Local Alignment Search Tool), BLAST (Basic Local Alignment Search Tool), BLAT (BLAST-Like Alignment Tool), and the pan-mitogenome approach, which integrates mitogenomes from diverse sources to identify fixed NUMTs in the nuclear genome. Simulation analyses indicate that false NUMTs affect the detection capabilities of both NUMTsearcher and LAST, with NUMTsearcher mitigating false positives by increasing the hspthresh value (also known as the K value), which sets the score threshold for high-scoring segment pairs (HSPs). In a comparative analysis with LAST on the rabbit genome, following optimization of the hspthresh value, NUMTsearcher reported only ten NUMTs as chromosomal inserts. A comparative analysis with the pan-mitogenome method identified 41 common NUMTs on chromosome 1 of the human genome and 22 previously unreported NUMTs. Our findings confirm the presence of NUMTs in Danio rerio, Takifugu rubripes, Tetraodon nigroviridis, Megalobrama amblycephala, Culter alburnus, and Chanodichthys erythropterus. The study further reveals that NUMT insertion timing varies across the six fish species, suggesting a significant degree of randomness. These results underscore the potential of NUMTs to influence evolutionary interpretations and deepen our understanding of their prevalence across diverse taxa.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145024773","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