Journal of Heredity最新文献_第2页

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

A Highly Contiguous Genome Assembly for the Wrentit (Chamaea Fasciata), the Sole Representative of the Babbler Radiation in the Americas. 美洲语鸟辐射的唯一代表鹪鹩（Chamaea Fasciata）的高度连续基因组组装。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-05 DOI: 10.1093/jhered/esaf063

Phred M Benham, Carla Cicero, Kevin Burns, Merly Escalona, Eric Beraut, Colin W Fairbairn, William E Seligmann, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Erin Toffelmier, Michael W Nachman, Rauri C K Bowie

{"title":"A Highly Contiguous Genome Assembly for the Wrentit (Chamaea Fasciata), the Sole Representative of the Babbler Radiation in the Americas.","authors":"Phred M Benham, Carla Cicero, Kevin Burns, Merly Escalona, Eric Beraut, Colin W Fairbairn, William E Seligmann, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Erin Toffelmier, Michael W Nachman, Rauri C K Bowie","doi":"10.1093/jhered/esaf063","DOIUrl":"https://doi.org/10.1093/jhered/esaf063","url":null,"abstract":"The wrentit (Chamaea fasciata) is a chaparral and scrub specialist bird found from coastal Oregon to northern Baja California. We generated a draft reference assembly for the species using PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 1342 scaffolds totaling 1.19 Gb in length. A contig N50 of 4.5 Mb, scaffold N50 of 73.3 Mb, and BUSCO completeness score of 96.8% indicate that the wrentit genome is a highly contiguous assembly in line with other high quality avian assemblies. An annotation of the assembly identified 16 821 protein-coding genes. We detected a translocation between chromosome 4A of the zebra finch to the Z chromosome of the wrentit. This translocation has previously been identified as a neo-sex chromosome shared across the superfamily Sylvioidea. Finally, we found a negative correlation between transposable element richness and gene density across the genome, but a positive relationship between GC content and gene density. This reference will serve as an essential resource for studies on the biogeography, local adaptation, and conservation genetics of this iconic species of California's chaparral.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145001896","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

Bovine SNP array-based genetic assessment of American plains bison at American Prairie. 基于牛SNP阵列的美国草原美洲平原野牛遗传评估。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-03 DOI: 10.1093/jhered/esaf051

Shawna J Zimmerman, Rebecca M Gooley, Sara J Oyler-McCance, Scott Heidebrink, Emily Herman, Paul Stothard, Hila Shamon, Cody W Edwards, Miranda Terwilliger, Budhan S Pukazhenthi, Klaus-Peter Koepfli

{"title":"Bovine SNP array-based genetic assessment of American plains bison at American Prairie.","authors":"Shawna J Zimmerman, Rebecca M Gooley, Sara J Oyler-McCance, Scott Heidebrink, Emily Herman, Paul Stothard, Hila Shamon, Cody W Edwards, Miranda Terwilliger, Budhan S Pukazhenthi, Klaus-Peter Koepfli","doi":"10.1093/jhered/esaf051","DOIUrl":"10.1093/jhered/esaf051","url":null,"abstract":"American plains bison (Bison bison bison, bison hereafter) experienced an extreme demographic bottleneck in the late 1800s. The species has since rebounded but is primarily managed as small and isolated herds due to habitat and sociopolitical limitations. Thus, reintroducing bison and allowing herds to achieve as much of their natural dynamics as possible is a major conservation goal. Concerns about genetic diversity loss in small, isolated herds and the persistence of cattle-origin variants from historical crossbreeding efforts have made genetic analysis an important part of bison conservation. The limitations of the current conservation genetic tools which are based on traditional markers such as microsatellites and mitochondrial DNA sequences, may be overcome with genome-wide genotyping panels commonly developed for agricultural species. Bison reintroduction in the grasslands at The Nature Conservancy's American Prairie began in 2005. Genetic analysis on these herds has yet to be conducted. We used the Illumina 777 K Bovine genotyping panel to obtain data from 197 bison and 179 domestic cows to understand the current population genetic state of bison at American Prairie and gain insight on cattle (Bos taurus) introgression. Overall, bison at American Prairie currently have relatively high genetic diversity, low inbreeding, and no obvious signs of cattle introgression. A more comprehensive evaluation of introgression, likely including whole-genome sequence data, would clarify this finding. These results can serve as a baseline for future comparison as part of a genetic monitoring framework.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144979305","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

Correction to: Life history and chromosome organization determine chemoreceptor gene expression in rattlesnakes. 更正：生命史和染色体组织决定了响尾蛇的化学受体基因表达。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-08-31 DOI: 10.1093/jhered/esaf061

引用次数: 0