Molecular taxonomic identification in the absence of a ‘barcoding gap’: a test with the endemic flora of the Canarian oceanic hotspot

Abstract

We use a comprehensive subset of Canarian angiosperms corresponding to 23 families, 35 genera and 60 Canarian endemic taxa to test whether this flora is suitable to taxonomic identification with the two proposed plant DNA barcode sequences and whether these sequences may reveal the existence of cryptic species overlooked by morphology. The rate of discrimination success between the insular congeneric samples using the rbcL+matK combination and a 'character-based' approach (where we use only the combination of nucleotide positions in an alignment that allows unambiguous species identification) is higher (82.29%) than that obtained with the 'distance-based' approach (80.20%) used by the CBOL Plant Working Group in 2009 and also when compared with tests conducted in other floras. This suggests that the molecular identification of the Canarian endemic flora can be achieved as successfully as in other floras where the incidence of radiation is not as relevant. The facts that (i) a distance-based criterion was unable to discriminate between congeneric and conspecific comparisons and (ii) only the character-based discrimination criterion resolved cases that the distance-based criterion did not, further support the use of a character discrimination approach for a more efficient DNA barcoding of floras from oceanic islands like the Canaries. Thus, a barcoding gap seems not to be necessary for the correct molecular characterization of the Canarian flora. DNA barcodes also suggest the possible existence of cryptic taxa to be further investigated by morphology and that the current taxonomic status of some of the taxa analysed may need revision.

Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks (Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes

“…Ambiguous sites and poly (A and T) structures were removed, while indels were retained for potential informative characters (Jaen-Molina et al, 2015). To choose potential barcoding markers for species discrimination, all alignments were visually scanned, and markers displaying species-specific characters (including gaps) in individual oak species were retained as candidate barcodes.…”

18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species

“…S1), a custom script (Aguirre ) was created to validate assignments using a character‐based discrimination approach (using diagnostic SNPs as in Jaén‐Molina et al. ). The script was applied to validate clupeid assignments (herring, sardine, sprat, and anchovy) in our metabarcoding data.…”

“…As a sole base change in the 18S V9 could imply a species miss-assignment between anchovy and the predator species (one nucleotide variation between anchovy and sprat, two between anchovy and sardine and three when comparing both predator species; Fig. S1), a custom script (Aguirre 2015) was created to validate assignments using a character-based discrimination approach (using diagnostic SNPs as in Ja en- Molina et al 2015). The script was applied to validate clupeid assignments (herring, sardine, sprat, and anchovy) in our metabarcoding data.…”

How DNA barcoding can be more effective in microalgae identification: a case of cryptic diversity revelation in Scenedesmus (Chlorophyceae)

“…It has been proposed that P ID, GMYC and PTP approaches could be as complementary analysis to the phylogenetic tree identification of traditional DNA barcoding262728. For distance-based barcoding approach, due to the absence of a “barcoding gap”, the specimen identification based on intraspecific variation vs. interspecific divergence has already been shown to be impossible for some taxonomic groups, especially for the plants293031. Recently, a new distance method, called Automatic Barcode Gap Discovery (ABGD), is proposed as 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 species32.…”

“…Another new barcoding method, the character-based barcoding which is different from phylogenetic tree and distance analysis, is based on the fundamental concept that members of a given taxonomic group share diagnostic characters that are absent from comparable groups3334. It can provide better resolution in species identification and cryptic species revelation of some organisms (including some plants) in several cases where distance-based methods fail to distinguish species1231.…”