{"title":"南非小型哺乳动物条形码序列文库的评估:对未来食肉动物DNA饮食分析的启示","authors":"Vimbai I. Siziba, Sandi Willows-Munro","doi":"10.1111/aje.13233","DOIUrl":null,"url":null,"abstract":"<p>DNA metabarcoding requires reference libraries that link DNA sequences to species. Mitochondrial gene regions cytochrome c oxidase I (COI), 12S ribosomal RNA (12S rRNA), 16S ribosomal RNA (16S rRNA), cytochrome <i>b</i> (cyt <i>b</i>) and the hypervariable control region (D-loop) are routinely used in studies that measure genetic diversity in animal species. This study aimed to review the state of DNA reference libraries for small South African mammals as small mammals constitute a large portion of small and medium carnivore diet. Analyses of DNA records revealed that of 193 small mammal species in South Africa, only 141 have DNA sequences available for one or more of the mitochondrial genes examined. Cyt <i>b</i> had the highest species coverage, with 59.1% of South African species represented in the reference libraries. COI only has 33.7%, 12S rRNA has 23.8%, D-loop has 17.6%, and 16S rRNA has the lowest species coverage of 15%. This study supports the use of multiple gene regions when performing scat metabarcoding, particularly when wanting to determine the small mammal component of the diet. Additionally, it emphasises the need to build comprehensive DNA reference libraries linking sequences to taxonomically identified species.</p>","PeriodicalId":7844,"journal":{"name":"African Journal of Ecology","volume":null,"pages":null},"PeriodicalIF":1.1000,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/aje.13233","citationCount":"0","resultStr":"{\"title\":\"An assessment of South African small mammal barcode sequence libraries: Implications for future carnivore diet analyses by DNA\",\"authors\":\"Vimbai I. Siziba, Sandi Willows-Munro\",\"doi\":\"10.1111/aje.13233\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>DNA metabarcoding requires reference libraries that link DNA sequences to species. Mitochondrial gene regions cytochrome c oxidase I (COI), 12S ribosomal RNA (12S rRNA), 16S ribosomal RNA (16S rRNA), cytochrome <i>b</i> (cyt <i>b</i>) and the hypervariable control region (D-loop) are routinely used in studies that measure genetic diversity in animal species. This study aimed to review the state of DNA reference libraries for small South African mammals as small mammals constitute a large portion of small and medium carnivore diet. Analyses of DNA records revealed that of 193 small mammal species in South Africa, only 141 have DNA sequences available for one or more of the mitochondrial genes examined. Cyt <i>b</i> had the highest species coverage, with 59.1% of South African species represented in the reference libraries. COI only has 33.7%, 12S rRNA has 23.8%, D-loop has 17.6%, and 16S rRNA has the lowest species coverage of 15%. This study supports the use of multiple gene regions when performing scat metabarcoding, particularly when wanting to determine the small mammal component of the diet. Additionally, it emphasises the need to build comprehensive DNA reference libraries linking sequences to taxonomically identified species.</p>\",\"PeriodicalId\":7844,\"journal\":{\"name\":\"African Journal of Ecology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.1000,\"publicationDate\":\"2023-11-27\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1111/aje.13233\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"African Journal of Ecology\",\"FirstCategoryId\":\"93\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1111/aje.13233\",\"RegionNum\":4,\"RegionCategory\":\"环境科学与生态学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"ECOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"African Journal of Ecology","FirstCategoryId":"93","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/aje.13233","RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"ECOLOGY","Score":null,"Total":0}
An assessment of South African small mammal barcode sequence libraries: Implications for future carnivore diet analyses by DNA
DNA metabarcoding requires reference libraries that link DNA sequences to species. Mitochondrial gene regions cytochrome c oxidase I (COI), 12S ribosomal RNA (12S rRNA), 16S ribosomal RNA (16S rRNA), cytochrome b (cyt b) and the hypervariable control region (D-loop) are routinely used in studies that measure genetic diversity in animal species. This study aimed to review the state of DNA reference libraries for small South African mammals as small mammals constitute a large portion of small and medium carnivore diet. Analyses of DNA records revealed that of 193 small mammal species in South Africa, only 141 have DNA sequences available for one or more of the mitochondrial genes examined. Cyt b had the highest species coverage, with 59.1% of South African species represented in the reference libraries. COI only has 33.7%, 12S rRNA has 23.8%, D-loop has 17.6%, and 16S rRNA has the lowest species coverage of 15%. This study supports the use of multiple gene regions when performing scat metabarcoding, particularly when wanting to determine the small mammal component of the diet. Additionally, it emphasises the need to build comprehensive DNA reference libraries linking sequences to taxonomically identified species.
期刊介绍:
African Journal of Ecology (formerly East African Wildlife Journal) publishes original scientific research into the ecology and conservation of the animals and plants of Africa. It has a wide circulation both within and outside Africa and is the foremost research journal on the ecology of the continent. In addition to original articles, the Journal publishes comprehensive reviews on topical subjects and brief communications of preliminary results.