Yang, Z;
Rannala, B;
(2017)
Bayesian Species Identification under the Multispecies Coalescent Provides Significant Improvements to DNA Barcoding Analyses.
Molecular Ecology
, 26
(11)
pp. 3028-3036.
10.1111/mec.14093.
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Abstract
DNA barcoding methods use a single locus (usually the mitochondrial COI gene) to assign unidentified specimens to known species in a library based on a genetic distance threshold that distinguishes between-species divergence from within-species diversity. Recently developed species delimitation methods based on the multispecies coalescent (MSC) model offer an alternative approach to individual assignment using either single-locus or multi-loci sequence data. Here we use simulations to demonstrate three features of an MSC method implemented in the program bpp. First, we show that with one locus, MSC can accurately assign individuals to species without the need for arbitrarily determined distance thresholds (as required for barcoding methods). We provide an example in which no single threshold or barcoding gap exists that can be used to assign all specimens without incurring high error rates. Second, we show that bpp can identify cryptic species that may be mis-identified as a single species within the library, potentially improving the accuracy of barcoding libraries. Third, we show that taxon rarity does not present any particular problems for species assignments using bpp, and that accurate assignments can be achieved even when only one or a few loci are available. Thus, concerns that have been raised that MSC methods may have problems analyzing rare taxa (singletons) are unfounded. Currently barcoding methods enjoy a huge computational advantage over MSC methods and may be the only approach feasible for massively large datasets, but MSC methods may offer a more stringent test for species that are tentatively assigned by barcoding.
| Type: | Article |
|---|---|
| Title: | Bayesian Species Identification under the Multispecies Coalescent Provides Significant Improvements to DNA Barcoding Analyses |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1111/mec.14093 |
| Publisher version: | http://dx.doi.org/10.1111/mec.14093 |
| Language: | English |
| Additional information: | This is the peer reviewed version of the following article: Yang, Z; Rannala, B; (2017) Bayesian Species Identification under the Multispecies Coalescent Provides Significant Improvements to DNA Barcoding Analyses. Molecular Ecology (In press), which has been published in final form at 10.1111/mec.14093. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. |
| Keywords: | Coalescent, DNA barcoding, species delimitation, species identification, BPP |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1545188 |
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