Journal of Heredity最新文献_第5页

A Reference Genome Assembly for the Pink Volcano Barnacle, Tetraclita Rubescens, Nilsson-Cantell, 1931. 粉红色火山藤壶的参考基因组组装，Rubescens, Nilsson-Cantell, 1931。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-24 DOI: 10.1093/jhered/esaf052

Bailey J Carlson, Melissa B DeBiasse, Carmen Del R Pedraza-Marrón, Merly Escalona, Noravit Chumchim, Mohan P A Marimuthu, Courtney Miller, Oanh Nguyen, William E Seligmann, Michael N Dawson

{"title":"A Reference Genome Assembly for the Pink Volcano Barnacle, Tetraclita Rubescens, Nilsson-Cantell, 1931.","authors":"Bailey J Carlson, Melissa B DeBiasse, Carmen Del R Pedraza-Marrón, Merly Escalona, Noravit Chumchim, Mohan P A Marimuthu, Courtney Miller, Oanh Nguyen, William E Seligmann, Michael N Dawson","doi":"10.1093/jhered/esaf052","DOIUrl":"https://doi.org/10.1093/jhered/esaf052","url":null,"abstract":"The pink volcano barnacle, Tetraclita rubescens, has experienced a poleward range expansion along the eastern Pacific coastline amidst recent climate changes, likely facilitated by high gene flow and high genetic diversity in a large population. A high-quality reference genome provides the next step to investigate these patterns in more detail. We present a highly contiguous, chromosome-level genome assembly for T. rubescens using long-read sequencing and short-read proximity ligation data. The genome assembly is 2.44 Gb, contains 92.5% complete ortholog genes based on the known Arthropoda gene list, the largest N50 compared to other high-quality barnacle genomes (~107 Mb), and a low L50 score (10 scaffolds). With this chromosome-level assembly, we will be better able to contrast the roles of drift, migration, and selection in population and spatial expansion dynamics, the roles of dispersal and adaptation within the range, and to investigate the genomic diversity of the species, including the roles of transposable elements in the genome. T. rubescens is an iconic barnacle on central and southern Californian rocky intertidal shores, and understanding its dynamics can help inform and support the conservation of intertidal communities along the northeastern Pacific coastline.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144700350","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 data from the extinct California brown bear suggests a source population for reintroduction to California. 来自已灭绝的加州棕熊的基因组数据表明了一个重新引入加州的来源种群。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-21 DOI: 10.1093/jhered/esaf018

T Brock Wooldridge, Ming-Shan Wang, Nedda F Saremi, Joshua D Kapp, Katherine L Moon, Peter D Heintzman, John P Dumbacher, Peter S Alagona, Barney Long, Beth Shapiro

{"title":"Genomic data from the extinct California brown bear suggests a source population for reintroduction to California.","authors":"T Brock Wooldridge, Ming-Shan Wang, Nedda F Saremi, Joshua D Kapp, Katherine L Moon, Peter D Heintzman, John P Dumbacher, Peter S Alagona, Barney Long, Beth Shapiro","doi":"10.1093/jhered/esaf018","DOIUrl":"10.1093/jhered/esaf018","url":null,"abstract":"California brown bears, also known as California grizzlies or golden bears, are an extinct group that once thrived in North America's western coastal habitats. Despite being common in the region as recently as the early 19th century, intense poisoning, trapping, and hunting led to their extinction by 1924. Today, California is emerging as a candidate for brown bear reintroduction as a component of larger ecosystem restoration efforts. Questions remain, however, about whether living brown bears are suitable proxies for the bears that once inhabited California. While recent work suggests that brown bears from California were similar in size and overall diet to brown bears living today in continental North America, the 1) extent to which California bears were genetically differentiated from other populations, and 2) what this means for proposed reintroductions, remain outstanding questions. We generated genomes from two of the last living California brown bears and compared them to genomes from living brown bears. Genomic estimates of divergence time combined with radiocarbon dating points towards brown bears arriving recently in California, having diverged within the last 10,000 years from a common ancestor with brown bears found today in Yellowstone National Park, Wyoming. This timeline, the overall genetic similarity between the California and Yellowstone populations, and the strong pattern of isolation-by-distance we observe all suggest that no closer living relatives are likely to be found. If genetic background is to be a consideration for reintroduction efforts in California, brown bears from Yellowstone might serve as a source population.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"422-434"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12277570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144045298","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

Evidence for the existence of the distinct Alia camel breed contributes to the conservation of dromedary camels in Europe. 存在独特的阿利亚骆驼品种的证据有助于欧洲单峰骆驼的保护。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-21 DOI: 10.1093/jhered/esaf009

Marcel Smits

引用次数: 0

Carotenoids, instead of pteridines, determine color of xanthophores and erythrophores in tilapia. 类胡萝卜素代替蝶啶决定罗非鱼黄细胞和红细胞的颜色。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-21 DOI: 10.1093/jhered/esaf017

Guangyuan Liang, Jiawen Yao, Jinzhi Wu, Xiayue Liu, Zilong Wen, Hao Liu, Baoyue Lu, Chenxu Wang, Xingyong Liu, Deshou Wang

{"title":"Carotenoids, instead of pteridines, determine color of xanthophores and erythrophores in tilapia.","authors":"Guangyuan Liang, Jiawen Yao, Jinzhi Wu, Xiayue Liu, Zilong Wen, Hao Liu, Baoyue Lu, Chenxu Wang, Xingyong Liu, Deshou Wang","doi":"10.1093/jhered/esaf017","DOIUrl":"10.1093/jhered/esaf017","url":null,"abstract":"There has been controversy over whether the chromogenic substances of xanthophores and erythrophores are pteridines or carotenoids in fish. In this study, we first extracted and quantified carotenoids and pteridines from erythrophores and xanthophores in tilapia, respectively. The results showed that the carotenoids and pteridines in erythrophores were significantly higher than those of xanthophores, and the carotenoids were significantly higher than the pteridines in both types of cells. Then, we established homozygous mutant lines of the key genes for pteridine synthesis (xdh) and carotenoid metabolism (plin6) in Nile tilapia. Compared with the wild type (WT), there were no significant changes in the body color of xdh-/-, while the pigmentation, fluorescence intensity, and size of both xanthophores and erythrophores were significantly reduced in plin6-/-. The pteridines were significantly decreased in xdh-/-, but not in plin6-/-, while the carotenoids were significantly decreased in plin6-/-, but not in xdh-/-. To confirm these results, we further established homozygous mutant lines for another two key genes involved in pteridine synthesis (gch2) and carotenoid absorption (scarb1). Consistently, no significant body color changes were observed in gch2-/-, while no pigmented xanthophores and erythrophores were observed in scarb1-/-. The pteridines were significantly reduced in gch2-/-, but not in scarb1-/-, while almost no carotenoids were detected in scarb1-/-, but carotenoids remained unchanged in gch2-/- compared with WT. Taken together, these results, combined with existing findings in cyprinid fish, demonstrate that the color of xanthophores and erythrophores is determined by carotenoids rather than pteridines in fish.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"466-478"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702349","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 mountain lion, Puma concolor. 山狮（Puma concolor）染色体级基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-21 DOI: 10.1093/jhered/esae063

Megan A Supple, Merly Escalona, Nicolas Alexandre, Michael R Buchalski, Seth P D Riley, Justin A Dellinger, T Winston Vickers, Ruta Sahasrabudhe, Oanh Nguyen, Colin W Fairbairn, William E Seligmann, Christopher C Wilmers, Beth Shapiro

{"title":"A chromosome-level genome assembly of the mountain lion, Puma concolor.","authors":"Megan A Supple, Merly Escalona, Nicolas Alexandre, Michael R Buchalski, Seth P D Riley, Justin A Dellinger, T Winston Vickers, Ruta Sahasrabudhe, Oanh Nguyen, Colin W Fairbairn, William E Seligmann, Christopher C Wilmers, Beth Shapiro","doi":"10.1093/jhered/esae063","DOIUrl":"10.1093/jhered/esae063","url":null,"abstract":"Mountain lions, Puma concolor, are widespread and adaptable carnivores. However, due to their large home ranges and long distance dispersals, they are strongly impacted by habitat fragmentation, which results in small and isolated populations. Genomic analyses play an important role in understanding and predicting the impacts of increased isolation of populations, such as decreased genetic diversity and increased levels of inbreeding. Here we report a high-quality, chromosome-level reference genome of P. concolor that was generated as part of the California Conservation Genomics Project. The primary assembly has a total length of 2.5 Gb contained in 258 scaffolds, a contig N50 of 42.3 Mb, a scaffold N50 of 149.8 Mb, and a BUSCO completeness score of 95%. This P. concolor genome assembly will provide an important resource for genomic analyses that aid decision-makers in managing the species in fragmented landscapes.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"479-487"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12277564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142592309","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

Forensic assessment of kinship, genomic ancestry, and natural history of an iconic tiger of Harlem, New York City. 哈莱姆-纽约标志性老虎的亲属关系、基因组祖先和自然史的法医评估。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-07-21 DOI: 10.1093/jhered/esaf003

Zhen-Bo Wu, Zheng-Yan Sui, Lan-Hui Peng, Mirna Ghemrawi, George Duncan, Henry Jones, Stephen J O'Brien, Shu-Jin Luo

{"title":"Forensic assessment of kinship, genomic ancestry, and natural history of an iconic tiger of Harlem, New York City.","authors":"Zhen-Bo Wu, Zheng-Yan Sui, Lan-Hui Peng, Mirna Ghemrawi, George Duncan, Henry Jones, Stephen J O'Brien, Shu-Jin Luo","doi":"10.1093/jhered/esaf003","DOIUrl":"10.1093/jhered/esaf003","url":null,"abstract":"In the fall of 2003, a 2-yr-old tiger named Ming, weighing around 300 pounds, was discovered living in an apartment in Harlem, New York. Ming's rescue by NYPD was witnessed, recalled, and venerated by scores of neighbors. The tiger's history and ancestry stimulated considerable media interest, investigative sleuthing, and forensic genomic analyses. The Harlem tiger's subspecies makeup, his relationship to his putative sibling named Cheeky living in Homestead, Florida, and his genetic distinctiveness from wild tigers was assessed by whole-genome sequence (WGS) analyses of trace materials from plucked whiskers. Verified subspecies ancestry of Ming and Cheeky was determined by comparing their WGS to single-nucleotide polymorphism (SNP) annotation from WGS of 35 voucher (pure subspecies) tiger specimens from six living subspecies. Genome-wide structure analyses based on the full set of 3,422,109 SNPs and a subset of 6,724 and 110 ancestry-informative markers showed that Ming has an admixed genetic background from five subspecies: Indochinese tiger (Panthera tigris corbetti 35 ~ 40%), Bengal tiger (P. t. tigris 17 ~ 23%), Sumatran tiger (P. t. sumatrae 12 ~ 14%), Amur tiger (P. t. altaica ~ 10%), and Malayan tiger (P. t. jacksoni 1 ~ 10%). Cheeky is confirmed to be a full sibling to Ming and displayed an admixed genetic background with similar subspecies proportions as Ming's. The forensic assessment of the tigers' subspecies composition, kinship, and recent history of animal transaction provides an analytical pipeline and holds promise for supporting global tiger conservation efforts through standardized genomic analysis of tigers or tiger products with unknown origins.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"397-407"},"PeriodicalIF":2.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048770","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 Alia Camel of Jordan: a genetically distinct dromedary breed. 约旦的阿利亚骆驼：一种遗传上独特的单峰骆驼品种。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-07-21 DOI: 10.1093/jhered/esae076

Nizar J Haddad, Mohamad A Al-Araishi, Sami Awabdeh, Rajesh Patidar, Ryan Bell, Khaleel Jawasreh, Heba Alhurani, Leqaa J Alharbed, Rawad Sweidan, Eman N Al-Anaswah, Mohammad Brake, Monther T Sadder, Omar A Blanco, Loai Sbeih, Mohamed Uduman, Saquib A Lakhani, Mustafa K Khokha, Ahmed Weir

{"title":"The Alia Camel of Jordan: a genetically distinct dromedary breed.","authors":"Nizar J Haddad, Mohamad A Al-Araishi, Sami Awabdeh, Rajesh Patidar, Ryan Bell, Khaleel Jawasreh, Heba Alhurani, Leqaa J Alharbed, Rawad Sweidan, Eman N Al-Anaswah, Mohammad Brake, Monther T Sadder, Omar A Blanco, Loai Sbeih, Mohamed Uduman, Saquib A Lakhani, Mustafa K Khokha, Ahmed Weir","doi":"10.1093/jhered/esae076","DOIUrl":"10.1093/jhered/esae076","url":null,"abstract":"The Dromedary camel has a remarkable history amongst cultures across Asia and northern Africa, serving multiple purposes ranging from providing milk, textiles, racing, and acting as pack animals. Recent genetic studies have revealed that many dromedaries are genetically homogenous, indicating that they do not represent different breeds, advocating for camel \"type\" over camel \"breed.\" In this study, we leveraged whole genome sequencing (WGS) to sequence 15 Jordanian Alia camels for the first time, alongside 9 Jordanian mixed camels from diverse locations within the country. Additionally, we analyzed 48 publicly available whole genomes of dromedary camels from the Arabian Peninsula for comparison. We demonstrate that the Alia camel is a distinct breed of camel, carefully bred in Jordan for racing and milk production. Compared with other dromedary camels, the Alia is genetically distinct and a unique breed that should be conserved. Our data further suggest that WGS of different camel populations may identify additional breeds and inform approaches to optimize traits and preserve genetic diversity.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":"116 4","pages":"435-440"},"PeriodicalIF":2.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144676625","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-quality genome assembly for a desert-adapted rodent, Merriam's kangaroo rat (Dipodomys merriami). 一个高质量的基因组组装的沙漠适应啮齿动物，梅里亚姆袋鼠鼠（Dipodomys梅里亚米）。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-21 DOI: 10.1093/jhered/esaf023

Erin R Voss, Merly Escalona, Oanh Nguyen, Mohan P A Marimuthu, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Eric Beraut, Christopher J Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman

{"title":"A high-quality genome assembly for a desert-adapted rodent, Merriam's kangaroo rat (Dipodomys merriami).","authors":"Erin R Voss, Merly Escalona, Oanh Nguyen, Mohan P A Marimuthu, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Eric Beraut, Christopher J Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman","doi":"10.1093/jhered/esaf023","DOIUrl":"10.1093/jhered/esaf023","url":null,"abstract":"Merriam's kangaroo rat (Dipodomys merriami) is a member of a unique family of primarily desert-adapted North American rodents (Heteromyidae). Of the 20 species in the genus, D. merriami is one of the most wide-ranging and ecologically flexible, inhabiting desert scrub, grassland, sagebrush steppe, and juniper-piñon woodland in the southwestern deserts of the United States and Mexico. We present a de novo reference genome for D. merriami generated from PacBio HiFi long-read and Omni-C chromatin proximity sequencing as a part of the California Conservation Genomics Project. The primary pseudo-haplotype assembly comprises 3,110 scaffolds, with a contig N50 of 8.6 Mb, scaffold N50 of 49.1 Mb, and a total length of 3.57 Gb. Further, a BUSCO completeness score of 97.8% suggests that the assembly is highly complete. This reference genome will serve as a resource for future studies of Dipodomys conservation genomics, desert adaptation, and phylogeography.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"524-531"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12277566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052392","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 assembly for the desert scorpion Mesobuthus przewalskii from Asian drylands. 亚洲旱地沙漠蝎 Mesobuthus przewalskii 染色体级基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-21 DOI: 10.1093/jhered/esae059

Yan-Kai Su, Ming-Hua Xiu, Hao-Yan Yang, Cheng-Min Shi

引用次数: 0

Evidence of extensive home range sharing among mother-daughter bobcat pairs in the wildland-urban interface of the Tucson Mountains. 图森山脉野地-城市交界地区山猫母女广泛共享活动范围的证据。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-07-21 DOI: 10.1093/jhered/esae072

Natalie Payne, Desiree Andersen, Robert Davis, Cheryl Mollohan, Kerry Baldwin, Albert L LeCount, Melanie Culver

{"title":"Evidence of extensive home range sharing among mother-daughter bobcat pairs in the wildland-urban interface of the Tucson Mountains.","authors":"Natalie Payne, Desiree Andersen, Robert Davis, Cheryl Mollohan, Kerry Baldwin, Albert L LeCount, Melanie Culver","doi":"10.1093/jhered/esae072","DOIUrl":"10.1093/jhered/esae072","url":null,"abstract":"Urbanization impacts the structure and viability of wildlife populations. Some habitat generalists, such as bobcats (Lynx rufus), maintain populations at the intersection of wild and urban habitats (wildland-urban interface), but the impacts of urbanization on bobcat social structure are not well understood. Although commonly thought to establish exclusive home ranges among females, instances of mother-daughter home range sharing have been documented. We combined Global Positioning System (GPS) localities with genomic relatedness inferences from double-digest restriction site associated DNA sequencing to investigate mother-daughter home range sharing in bobcats (n = 38) at the wildland-urban interface in the Tucson Mountains, Arizona, USA. We found the highest relatedness among females, which showed stronger isolation by distance than males and the population as a whole. Using mother-daughter relationships inferred from pedigree reconstruction, we found extensive mother-daughter home range sharing, compared with other females. Every mother identified as having at least one daughter, shared home ranges with one daughter, while other confirmed daughters established adjacent home ranges. Our results provide substantial support for the mother-daughter home range sharing hypothesis, as well as evidence of spatiotemporal overlap between mothers and daughters, adding to the body of research complicating the solitary felid paradigm. These results additionally challenge the notion of home range partitioning by prior-rights land tenure, suggesting a role of matrilineal land tenure in the home range establishment of daughters. Habitat fragmentation due to human population growth and urbanization thus has the potential to alter landscape genetic structure and social dynamics in bobcats.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"408-421"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830841","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