Statistical assignment of DNA sequences using Bayesian phylogenetics - PubMed (original) (raw)
Statistical assignment of DNA sequences using Bayesian phylogenetics
Kasper Munch et al. Syst Biol. 2008 Oct.
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.
Similar articles
- Bayesian inference of phylogeny and its impact on evolutionary biology.
Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. Huelsenbeck JP, et al. Science. 2001 Dec 14;294(5550):2310-4. doi: 10.1126/science.1065889. Science. 2001. PMID: 11743192 - Bayesian coestimation of phylogeny and sequence alignment.
Lunter G, Miklós I, Drummond A, Jensen JL, Hein J. Lunter G, et al. BMC Bioinformatics. 2005 Apr 1;6:83. doi: 10.1186/1471-2105-6-83. BMC Bioinformatics. 2005. PMID: 15804354 Free PMC article. - Elevated substitution rates estimated from ancient DNA sequences.
Ho SY, Kolokotronis SO, Allaby RG. Ho SY, et al. Biol Lett. 2007 Dec 22;3(6):702-5. doi: 10.1098/rsbl.2007.0377. Biol Lett. 2007. PMID: 17785261 Free PMC article. - Are you my mother? Bayesian phylogenetic inference of recombination among putative parental strains.
Sinsheimer JS, Suchard MA, Dorman KS, Fang F, Weiss RE. Sinsheimer JS, et al. Appl Bioinformatics. 2003;2(3):131-44. Appl Bioinformatics. 2003. PMID: 15130798 Review. - Bayesian phylogenetics and its influence on insect systematics.
Ronquist F, Deans AR. Ronquist F, et al. Annu Rev Entomol. 2010;55:189-206. doi: 10.1146/annurev.ento.54.110807.090529. Annu Rev Entomol. 2010. PMID: 19961329 Review.
Cited by
- Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods.
Delrieu-Trottin E, Durand JD, Limmon G, Sukmono T, Kadarusman, Sugeha HY, Chen WJ, Busson F, Borsa P, Dahruddin H, Sauri S, Fitriana Y, Zein MSA, Hocdé R, Pouyaud L, Keith P, Wowor D, Steinke D, Hanner R, Hubert N. Delrieu-Trottin E, et al. Evol Appl. 2020 Feb 11;13(6):1451-1467. doi: 10.1111/eva.12926. eCollection 2020 Jul. Evol Appl. 2020. PMID: 32684969 Free PMC article. - Seasonal and spatial variability of zooplankton diversity in the Poyang Lake Basin using DNA metabarcoding.
Qiu X, Liu X, Lu Q, Chen J, Liang T, Wang W, Ouyang S, Zhou C, Wu X. Qiu X, et al. Ecol Evol. 2022 Jun 5;12(6):e8972. doi: 10.1002/ece3.8972. eCollection 2022 Jul. Ecol Evol. 2022. PMID: 35784091 Free PMC article. - Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants.
Tanabe AS, Toju H. Tanabe AS, et al. PLoS One. 2013 Oct 18;8(10):e76910. doi: 10.1371/journal.pone.0076910. eCollection 2013. PLoS One. 2013. PMID: 24204702 Free PMC article. - Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data.
Lusk RW. Lusk RW. PLoS One. 2014 Oct 29;9(10):e110808. doi: 10.1371/journal.pone.0110808. eCollection 2014. PLoS One. 2014. PMID: 25354084 Free PMC article. - phyloBARCODER: A Web Tool for Phylogenetic Classification of Eukaryote Metabarcodes Using Custom Reference Databases.
Inoue J, Shinzato C, Hirai J, Itoh S, Minegishi Y, Ito SI, Hyodo S. Inoue J, et al. Mol Biol Evol. 2024 Aug 2;41(8):msae111. doi: 10.1093/molbev/msae111. Mol Biol Evol. 2024. PMID: 38850168 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials