For little explored groups, DNA barcoding can be directly used to assign organisms into hypothetical species. One feature of barcode datasets that can be used to delimit species is the so-called ``barcode gap'' in the distribution of pairwise differences. Such a gap can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. The method is extremely efficient in computation time. Using five published datasets of metazoans, we show that species predictions were good for standard prior maximum intraspecific divergences (a few percent of divergence for the five datasets). We further explore ABGD theoretical limitations through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, we propose a fast, simple method to split a sequences alignment dataset into candidate species that should be complemented with other evidence in an integrative taxonomic approach.
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C sources are publicaly available and can be downloaded from Abgd .
*WARNING* Any version of the source downloaded in recent months (2017- 2018) must be erased. The source code had an error that the latest version fixes. We apologize to those who have had an error in execution or inconsistent results. Already compiled abgd command-line binaries will be available from here in a very near future.
Please ask for them in the mean time by email.
If you are using the software, please cite:
N Puillandre, A Lambert, S Brouillet and G Achaz ABGD, Automatic Barcode Gap Discovery for primary species delimitation, Mol Ecol. 2011.
If you have any comment, suggestion or bug report, or if you want to be kept informed about possible updates, please contact G. Achaz.
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