Quantifying uncertainty of taxonomic placement in DNA barcoding and 2 metabarcoding
文献类型：期刊论文
| 作者 | Wirta H7; Somervuo P*1; Hultman J2; Ovaskainen O1,6; Ji YQ5; Yu D*3,5; Xu C4,5 |
| 刊名 | Methods in Ecology and Evolution
 |
| 出版日期 | 2017 |
| 卷号 | **期号:**页码:in press |
| 关键词 | Dna Barcoding Dna Metabarcoding Molecular Species Identification Multinomial Regression |
| 英文摘要 | A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because there is natural variation among sequences within a species, and because reference data bases are incomplete and can have false annotations. However, most existing bioinformatics methods for taxonomic placement either exclude uncertainty, or quantify it using metrics other than probability. In this paper we evaluate the performance of the recently proposed probabilistic taxonomic placement method PROTAX by applying it to both annotated reference sequence data as well as to unknown environmental data. Our four case studies include contrasting taxonomic groups (fungi, bacteria, mammals and insects), variation in the length and quality of the barcoding sequences (from individually Sanger-sequenced sequences to short Illumina reads), variation in the structures and sizes of the taxonomies (800-130 000 species) and variation in the completeness of the reference data bases (representing 15-100% of known species). Our results demonstrate that PROTAX yields essentially unbiased probabilities of taxonomic placement, which means its quantification of species identification uncertainty is reliable. As expected, the accuracy of taxonomic placement increases with increasing coverage of taxonomic and reference sequence data bases, and with increasing ratio of genetic variation among taxonomic levels over within taxonomic levels. We conclude that reliable species-level identification from environmental samples is still challenging and that neglecting identification uncertainty can lead to spurious inference. A key aim for future research is the completion of taxonomic and reference sequence data bases and making these two types of data compatible. |
| 语种 | 英语 |
| 资助机构 | We thank Mikko Tiusanen and Tomas Roslin for providing the empirical sequence data for the 578 insect case study, and Paul Kirk and Kessy Abarenkov for providing the taxonomy and reference 579 databases for the fungal case study, and Otto Miettinen for providing the list of Finnish fungal 580 species. OO and PS were supported by funding from the Academy of Finland (Grants no. 1273253 581 and 250444 to OO) and the Research Council of Norway (CoE grant no. 223257). DWY and YQJ 582 were supported by WWF-Vietnam (9S084701), the National Natural Science Foundation of China 583 (31400470, 41661144002), the Ministry of Science and Technology of China (2012FY110800), the 584 University of East Anglia and its GRACE computing cluster, and the State Key Laboratory of Genetic 585 Resources and Evolution at the Kunming Institute of Zoology (GREKF13-13, GREKF14-13, and 586 GREKF16-09). CX was supported by the MEME Erasmus Mundus Programme in Evolutionary 587 Biology, and the Marco Polo Exchange Fund of the University of Groningen. ; We thank Mikko Tiusanen and Tomas Roslin for providing the empirical sequence data for the 578 insect case study, and Paul Kirk and Kessy Abarenkov for providing the taxonomy and reference 579 databases for the fungal case study, and Otto Miettinen for providing the list of Finnish fungal 580 species. OO and PS were supported by funding from the Academy of Finland (Grants no. 1273253 581 and 250444 to OO) and the Research Council of Norway (CoE grant no. 223257). DWY and YQJ 582 were supported by WWF-Vietnam (9S084701), the National Natural Science Foundation of China 583 (31400470, 41661144002), the Ministry of Science and Technology of China (2012FY110800), the 584 University of East Anglia and its GRACE computing cluster, and the State Key Laboratory of Genetic 585 Resources and Evolution at the Kunming Institute of Zoology (GREKF13-13, GREKF14-13, and 586 GREKF16-09). CX was supported by the MEME Erasmus Mundus Programme in Evolutionary 587 Biology, and the Marco Polo Exchange Fund of the University of Groningen. |
| 源URL | [http://159.226.149.26:8080/handle/152453/12073]  |
| 专题 | 昆明动物研究所_遗传资源与进化国家重点实验室 昆明动物研究所_动物生态学研究中心 |
| 作者单位 | 1.Department of Biosciences, P.O. Box 65, FI-00014, University of Helsinki, Finland 2.Department of Food and Environmental Sciences, P.O. Box 56, FI-00014, University of Helsinki, Finland 3.School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ 11 UK 4.Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC 13 Groningen, The Netherlands 5.State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy 9 of Sciences, 32 Jiaochang East Road, Kunming, Yunnan 650223, China 6.Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and 17 Technology, N-7491 Trondheim, Norway 7.Department of Agricultural Sciences, P.O. Box 27, FI-00014, University of Helsinki, Finland |
| 推荐引用方式 GB/T 7714 | Wirta H,Somervuo P*,Hultman J,et al. Quantifying uncertainty of taxonomic placement in DNA barcoding and 2 metabarcoding[J]. Methods in Ecology and Evolution,2017,**(**):in press. |
| APA | Wirta H.,Somervuo P*.,Hultman J.,Ovaskainen O.,Ji YQ.,...&Xu C.(2017).Quantifying uncertainty of taxonomic placement in DNA barcoding and 2 metabarcoding.Methods in Ecology and Evolution,**(**),in press. |
| MLA | Wirta H,et al."Quantifying uncertainty of taxonomic placement in DNA barcoding and 2 metabarcoding".Methods in Ecology and Evolution **.**(2017):in press. |
入库方式： OAI收割
来源：昆明动物研究所
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