The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics
Abstract
We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data that the method outperforms Blast searches as a measure of confidence and can help eliminate 80% of all false assignment based on best Blast hit. However, the most important advance of the method is that it provides statistically meaningful measures of confidence. We apply the method to a re-analysis of previously published ancient DNA data and show that, with high statistical confidence, most of the published sequences are in fact of Neanderthal origin. However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA.
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Cites
MRBAYES: Bayesian inference of phylogenetic trees.
Huelsenbeck, J. P., & Ronquist, F. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.8.754 · Cited by 21,937
Self-citationEnvironmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960
DNA barcoding: error rates based on comprehensive sampling
Meyer, C. P., & Paulay, G. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030422 · Cited by 1,957
In All Likelihood: Statistical Modelling and Inference Using Likelihood
Pawitan, Y. (2001) · doi:10.1093/oso/9780198507659.001.0001 · Cited by 874
Cited by
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
Deiner, K., Bik, H. M., Mächler, E., Seymour, M., Lacoursière‐Roussel, A., Altermatt, F., Creer, S., Bista, I., Lodge, D. M., de Vere, N., et al. (2017) · Molecular Ecology · doi:10.1111/mec.14350 · Cited by 1,918
Leray, M., Yang, J. Y., Meyer, C. P., Mills, S. C., Agudelo, N., Ranwez, V., Boehm, J. T., & Machida, R. J. (2013) · Frontiers in Zoology · doi:10.1186/1742-9994-10-34 · Cited by 1,636
Matsen, F. A., Kodner, R. B., & Armbrust, E. V. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-538 · Cited by 1,050
Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
Yu, D. W., Ji, Y., Emerson, B. C., Wang, X., Ye, C., Yang, C., & Ding, Z. (2012) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2012.00198.x · Cited by 744
Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding
Ji, Y., Ashton, L., Pedley, S. M., Edwards, D. P., Tang, Y., Nakamura, A., Kitching, R., Dolman, P. M., Woodcock, P., Edwards, F. A., et al. (2013) · Ecology Letters · doi:10.1111/ele.12162 · Cited by 662
Metadata
- Authors
- Munch, K., Boomsma, W., Huelsenbeck, J. P., Willerslev, E., & Nielsen, R.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-10-01
- Volume
- 57
- Issue
- 5
- Pages
- 750-757
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2135691213
- Cited by
- 195
- References
- 5
- FWCI
- 3.23
- Type
- journal article
- Language
- en
- Open access
- closed
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- Munch, K., Boomsma, W., Huelsenbeck, J. P., Willerslev, E., & Nielsen, R. (2008). Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics. Systematic Biology. https://doi.org/10.1080/10635150802422316
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
