Conservation Genetics Resources最新文献

Development of a 96 SNP panel for fecal genotyping and individual identification of bobcats (Lynx rufus) in California 为加州山猫（Lynx rufus）的粪便基因分型和个体鉴定开发 96 SNP 面板

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-09-11 DOI: 10.1007/s12686-024-01368-0

Kristen D. Ahrens, Benjamin N. Sacks, Sophie Preckler-Quisquater, Michael R. Buchalski

{"title":"Development of a 96 SNP panel for fecal genotyping and individual identification of bobcats (Lynx rufus) in California","authors":"Kristen D. Ahrens, Benjamin N. Sacks, Sophie Preckler-Quisquater, Michael R. Buchalski","doi":"10.1007/s12686-024-01368-0","DOIUrl":"https://doi.org/10.1007/s12686-024-01368-0","url":null,"abstract":"Spatial mark-recapture abundance estimates obtained from fecal genotyping are becoming an essential component of conservation of carnivores. The bobcat (Lynx rufus) is a widespread carnivore in California, USA, that until recently lacked robust demographic data. To facilitate a statewide abundance study, we created a single nucleotide polymorphism (SNP) genotyping panel for individual identification. For SNP discovery, we performed restriction site-associated DNA sequencing (RADseq) on 78 samples collected throughout California and subsequently designed a panel of 96 SNPs for sequencing on a microfluidic platform. This panel includes loci to identify sex and differentiate bobcats from other common carnivores. The panel reliably differentiates individuals when using DNA extracted from feces, with 89% of samples amplifying at > 90% of SNPs. Importantly, we found autosomal SNPs were monomorphic in the closely related Canada lynx (L. canadensis) suggesting the panel would still be effective for bobcat study in areas of sympatry. Fecal genotyping provides a cost-effective, noninvasive method for population monitoring and detecting individual movement. Our panel generates standardized genotypes that can be analyzed across laboratories and used for continued bobcat monitoring in California and other western states.","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"26 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Isolation and characterization of forty-two polymorphic simple sequence repeat markers from Mastacembelus armatus (Symbranchiformes: Mastacembelidae) 四十二个多态简单序列重复标记的分离和特征描述

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-09-11 DOI: 10.1007/s12686-024-01365-3

Laifu Luo, Liqin Ji, Congcong Wu, Wei Li, Xiaoli Liu, Xiaoyou Hong, Xinping Zhu, Yijun Ni, Jiansong Li, Chen Chen, Jiping Zhang

引用次数: 0

Development of a microfluidic SNP assay for lineage discrimination in the endangered hazel dormouse 开发用于濒危榛睡鼠血统鉴别的微流控 SNP 检测方法

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-09-06 DOI: 10.1007/s12686-024-01367-1

Tobias Beez, Johanna Leyhausen, Sarah Mueller, Alina von Thaden, Sandro Bertolino, Sven Büchner, Joanna Fietz, Johannes Lang, Johan Michaux, Goedele Verbeylen, Carsten Nowak, Berardino Cocchiararo

{"title":"Development of a microfluidic SNP assay for lineage discrimination in the endangered hazel dormouse","authors":"Tobias Beez, Johanna Leyhausen, Sarah Mueller, Alina von Thaden, Sandro Bertolino, Sven Büchner, Joanna Fietz, Johannes Lang, Johan Michaux, Goedele Verbeylen, Carsten Nowak, Berardino Cocchiararo","doi":"10.1007/s12686-024-01367-1","DOIUrl":"https://doi.org/10.1007/s12686-024-01367-1","url":null,"abstract":"The application of Genotyping-by-Sequencing (GBS) approaches is often restricted in wildlife monitoring and conservation genetics, as those fields often rely on noninvasively collected samples with low DNA content. Here we selected a subset of informative single-nucleotide polymorphisms (SNPs) from genome-wide data for lineage discrimination of a locally endangered Eurasian rodent, the hazel dormouse (Muscardinus avellanarius), and designed a microfluidic 96 SNP genotyping assay suitable for noninvasively collected samples. Analyses of 43 samples from different European countries confirmed successful discrimination of the Eastern and Western lineage and local substructure within those lineages, proving the suitability of the developed panel for identifying evolutionary significant units and conservation units. Application with 94 hair and scat samples collected in a recent monitoring study on the hazel dormouse in Southern Germany resulted in > 99.5% amplification success showing the applicability of the new tool in genetic wildlife monitoring and conservation studies.","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"19 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development and characterization of 40 SNP markers of endangered species Cuora flavomarginata by whole-genome resequencing 通过全基因组重测序技术开发濒危物种 Cuora flavomarginata 的 40 个 SNP 标记并确定其特征

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-08-28 DOI: 10.1007/s12686-024-01366-2

Huan Wang, Guoqing Duan, Huaxing Zhou, Yuting Hu, Amei Liu

引用次数: 0

Mitochondrial ND4-based duplex PCR for identifying tiger species 基于线粒体 ND4 的双链 PCR 鉴定老虎物种

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-07-29 DOI: 10.1007/s12686-024-01364-4

Yang Gao, Shiyao Wu, Xuanye Wu, Wulin Liu, Dong Zheng, Xuedong Liu, Kun Jin

引用次数: 0

Environmental effects on faecal genotyping success in mesocarnivores 环境对中食肉动物粪便基因分型成功率的影响

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-07-01 DOI: 10.1007/s12686-024-01363-5

Lukas G. Scholz, Henriette Tripke, Cornelia Ebert, Thomas Alef, Jim-Lino Kämmerle, Ilse Storch, Manisha Bhardwaj

{"title":"Environmental effects on faecal genotyping success in mesocarnivores","authors":"Lukas G. Scholz, Henriette Tripke, Cornelia Ebert, Thomas Alef, Jim-Lino Kämmerle, Ilse Storch, Manisha Bhardwaj","doi":"10.1007/s12686-024-01363-5","DOIUrl":"https://doi.org/10.1007/s12686-024-01363-5","url":null,"abstract":"Non-invasive genetic sampling can be used in research, monitoring, and conservation of wild animals to, for example, provide insights into diets, identify individuals and estimate population sizes. Non-invasive genetic sampling may be especially useful to monitor elusive species because DNA can be derived from materials such as hairs and faeces without handling individuals. However, the reliability of the results derived from this technique is dependent on the quality of DNA obtained from samples, which can deteriorate from exposure to environmental conditions and sample age. While freshness of the sample is an important factor, the combined effect of different field conditions on the genotyping success is not fully understood. To address this gap, we systematically investigated the effects of sample age and environmental conditions on genotyping success of faeces, in an experimental setting of four treatments that combined rain and temperature conditions typical of central European climates. We compared the performance of a microsatellite marker set and a SNP panel for red fox (Vulpes vulpes), as well as a microsatellite marker set for pine marten (Martes martes) from faeces resampled over 21 days. We found that genotyping success decreased significantly with sample age, however environmental treatments did not impact the success. Furthermore, the SNPs we used amplified more successfully over time than the respective microsatellites. Therefore, the use of SNPs instead of conventional microsatellites, when using faecal samples for analysis relying on correct amplifications, could be advantageous. We recommend to prioritise the collection of fresh faeces regardless of environmental conditions.","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"31 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141529529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Association of TCF7L2 Gene Variant (rs12255372) with Polycystic Ovary Syndrome and its Effect Modification of the Disease Phenotype. TCF7L2基因变异（rs12255372）与多囊卵巢综合征的关系及其对疾病表型的改变作用

IF 1.5 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-07-01 Epub Date: 2023-01-30 DOI: 10.1007/s12291-023-01115-6

Rabiya Rashid, Idrees A Shah, Mudassir Jan Makhdoomi, Aafia Rashid, Meena Godha, Bashir A Ganai, Mohd Ashraf Ganie

{"title":"Association of TCF7L2 Gene Variant (rs12255372) with Polycystic Ovary Syndrome and its Effect Modification of the Disease Phenotype.","authors":"Rabiya Rashid, Idrees A Shah, Mudassir Jan Makhdoomi, Aafia Rashid, Meena Godha, Bashir A Ganai, Mohd Ashraf Ganie","doi":"10.1007/s12291-023-01115-6","DOIUrl":"10.1007/s12291-023-01115-6","url":null,"abstract":"Polycystic ovary syndrome (PCOS) and type-2 diabetes mellitus (T2DM) share common genetic features. Transcription factor 7-like-2 (TCF7L2) is consistently studied T2DM susceptibility locus. However, limited studies on TCF7L2 have failed to demonstrate any link with the PCOS risk. Therefore, we investigated the association of TCF7L2 polymorphic variant (rs12255372) with the PCOS risk. We recruited 120 PCOS cases, diagnosed as per Rotterdam 2003 criteria, and an equal number of age-matched controls. Besides a detailed clinical assessment, subjects underwent biochemical and hormonal profiling. Genotyping for rs12255372 was done by PCR-RFLP. Conditional logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (95%CIs) of genotype-phenotype correlations. The PCOS cases reported fewer menstrual cycles per year and exhibited signs of hyperandrogenism. The heterozygous genotype of rs12255372 was strongly associated with the PCOS risk (OR = 2.00; 95%CI: 1.07-3.76). Unlike controls, only 3 cases harbored TT genotype, and the PCOS risk persisted in the dominant model (GT + TT) as well. Moreover, we found a synergistic effect modification by the variant genotype in the subjects who had family histories of T2DM, hirsutism, or menstrual irregularities. We report a significant association of the TCF7L2 polymorphic variant rs12255372 with the PCOS risk.","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"7 1","pages":"373-379"},"PeriodicalIF":1.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11239628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74404586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of an 8K SNP chip to assess adaptive diversity and hybridization in polar bears 开发用于评估北极熊适应多样性和杂交的 8K SNP 芯片

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-06-13 DOI: 10.1007/s12686-024-01359-1

Joshua M. Miller, René M. Malenfant, L. Ruth Rivkin, Todd C. Atwood, Steven Baryluk, Erik W. Born, Rune Dietz, Kristin L. Laidre, Jodie Pongracz, Evan S. Richardson, Øystein Wiig, Corey S. Davis

{"title":"Development of an 8K SNP chip to assess adaptive diversity and hybridization in polar bears","authors":"Joshua M. Miller, René M. Malenfant, L. Ruth Rivkin, Todd C. Atwood, Steven Baryluk, Erik W. Born, Rune Dietz, Kristin L. Laidre, Jodie Pongracz, Evan S. Richardson, Øystein Wiig, Corey S. Davis","doi":"10.1007/s12686-024-01359-1","DOIUrl":"https://doi.org/10.1007/s12686-024-01359-1","url":null,"abstract":"The polar bear (Ursus maritimus) is a species particularly vulnerable to the effects of climate change. As the climate warms, polar bears will be forced to move to more suitable habitats which are likely to shrink, adapt to the new conditions, or decline in population size. However, the genomic diversity within and among all 19 subpopulations of polar bears, and therefore their adaptive potential, is currently unknown. In addition, warmer climates are likely to result in more frequent contact between polar bears and grizzly bears (U. arctos), with which they can hybridize. Here we describe the development, quality control, and application of the Ursus maritimus V2 SNP chip. This 8 K SNP chip contains loci explicitly selected to assess both RAD-derived and transcriptome-derived loci, as well as SNPs to detect hybridization between species. A total of 7,239 loci (90.3% of those printed) were successfully genotyped, with over 99% genotype concordance for individuals typed in duplicate on this chip, and between individuals typed here and on the Ursus maritimus V1 SNP chip. Using simulations, we demonstrate that the markers have high accuracy and efficiency to detect hybridization and backcrosses between polar bears and grizzly bears. However, empirical analysis of 371 polar bears, 440 grizzly bears, and 8 known hybrids found no novel instances of recent hybridization. The Ursus maritimus V2 SNP chip provides a powerful tool for monitoring the adaptive potential of this species along with assessing population structure, quantitative genomics, and hybridization in polar bears.","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"120 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141507013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Detection of environmental DNA of finless porpoise (Neophocaena asiaeorientalis) in Osaka Bay, Japan 日本大阪湾江豚（Neophocaena asiaeorientalis）环境 DNA 的检测

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-05-25 DOI: 10.1007/s12686-024-01361-7

Nagisa Hashimoto, Takashi Iwata, Natsumi Kihara, Kiyomi Nakamura, Masayuki K. Sakata, Toshifumi Minamoto

{"title":"Detection of environmental DNA of finless porpoise (Neophocaena asiaeorientalis) in Osaka Bay, Japan","authors":"Nagisa Hashimoto, Takashi Iwata, Natsumi Kihara, Kiyomi Nakamura, Masayuki K. Sakata, Toshifumi Minamoto","doi":"10.1007/s12686-024-01361-7","DOIUrl":"https://doi.org/10.1007/s12686-024-01361-7","url":null,"abstract":"Finless porpoises (Neophocaena asiaeorientalis) currently face population decline caused by significant human activities and are categorized as endangered on the International Union for Conservation of Nature (IUCN) Red List; however, information on their habitats is currently insufficient. Although conducting visual surveys to determine the distribution of cetaceans is common, visual observation of finless porpoises is challenging owing to their specific morphological and ecological characteristics. In this study, we developed an environmental DNA (eDNA) assay for species-specific detection of finless porpoises. To test the utility of the assay, we conducted a visual survey in parallel with an eDNA survey by collecting water samples from 50 sites throughout Osaka Bay. We visually found a finless porpoise at one location and detected eDNA at nine sites, including sites near the visual observation site and those with rare sightings of finless porpoises. Therefore, in this study, we suggest that the use of eDNA analysis for distribution surveys of finless porpoises will enable more efficient surveys. The proposed eDNA technique can not only be applied to the distribution surveys finless porpoises but also to those of other cetacean species.","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"21 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2024-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141148000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of novel microsatellite markers for aquaculture important species, milkfish (Chanos chanos Forsskål, 1775) with implications of conservation and management 为重要水产养殖物种虱目鱼（Chanos chanos Forsskål，1775 年）开发新型微卫星标记及其对保护和管理的影响

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-04-30 DOI: 10.1007/s12686-024-01354-6

Divya Merin Jose, Divya Prema Radhakrishnan, Kuldeep Kumar Lal

引用次数: 0