ABGD, Automatic Barcode Gap Discovery for primary species delimitation

Abstract

Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. 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, called Automatic Barcode Gap Discovery (ABGD), 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. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD 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, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.

Geographic distribution of Theileria sp. (buffalo) and Theileria sp. (bougasvlei) in Cape buffalo (Syncerus caffer) in southern Africa: implications for speciation

“…The alignment was submitted to the Automatic Barcode Gap Discovery (ABGD) Server (http:// wwwabi.snv.jussieu.fr/public/abgd/) that calculates a barcode gap from the inference of a model-based one-sided confidence limit for intraspecific divergence (Puillandre et al 2012). Minimum prior intraspecific divergence (0·001) and maximum prior intraspecific divergence (0·1) were scanned over 10 steps with a minimum gap width (1·5) and distance distribution Nn bins (20).…”

Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy

“…These groups were considered to be equivalent to species (Puillandre et al, 2012). ABGD was used through its online tool (http://wwwabi.snv.jussieu.fr/ public/abgd/abgdweb.html) with default settings.…”

Lack of correlation between micro fungi species and chemical control method of Atta treated with toxic baits

“…Alignment was done using the default settings and optimized manually when necessary. Initial identification was carried out using BLAST n searches in the NCBI and BOLD databases and then by using the "Automatic Barcode Gap Discovery Software" (PUILLANDRE et al, 2012) for identifying DNA barcodes. Interspecific pairwise distances between all species were calculated using Kimura's two-parameter (K2P) model (KIMURA,1980).…”

“…Identification using Automatic Barcode Gap Discovery (PUILLANDRE et al 2012) showed nine different groups that corresponded to species identified using BLAST n searches in the NCBI database, indicating the efficiency of DNA barcoding for species identification. NeighborJoining phylogenetic analysis, generated from K2P distances, showed that species are grouped according to the groups identified using Automatic Barcode Gap Discovery analysis (Figure 1).…”