Wednesday, March 26, 2014

Nocturnal moths shine light on dark taxa

Aside from probing the efficacy of DNA Barcodes as a tool for species identification, the present study has examined the correspondence between sequence clusters recognized by the BIN system and known species. The results of this analysis indicate the strong capacity of the BIN system to estimate species diversity (1 515 BINs versus 1 541 species), supporting the conclusion of an earlier investigation. These results suggest that DNA barcoding is poised to resolve a long-standing question – how many animal species are there on the planet? Moreover, the BIN system has the capacity to do more than just to deliver a species count when it is coupled with a well-parameterized barcode reference library. In this situation, in most cases, each BIN can be automatically assigned to a higher-level taxon. Automated phylum-level assignments are now secure and class and ordinal placements are correct in more than 90% of cases for terrestrial animals (pers. obs.). Further parameterization of the barcode library will undoubtedly lead to robust familial assignments. Although Ekrem et al. correctly pointed out that DNA Barcodes can only deliver a species-level assignment when a fully parameterized reference library is in place, the BIN system will provide a species count for each major compartment of biodiversity long before all species gain description.

I decided to start today's post with the end of a publication. The first part of the above paragraph summarizes the results of a new study published yesterday on PLoS ONE. Part two discusses BINs and their potential. It took the liberty to highlight two parts in the text that I find very promising especially in the light of this new paper as it makes a strong case for them.

The study is based on a very strong dataset - Some 30 000 DNA Barcodes of Canadian owlet moths (noctuoids) representing 99.1% of all known species. That alone is impressive enough: 1 555 noctuoid species occur in Canada and 1 541 of them have a DNA Barcode. However, this publication goes much further and uses the dataset to test the concordance between BIN assignment and species boundaries in Canadian noctuoids in order to evaluate utility and constraints of the BIN system for species delineation.

The study provides two different numbers on this. The first reflects the actual concordance between taxonomic names and sequence clusters delineated. 1 082 species (70%) were assigned to a unique BIN, while the total number of BINs estimated for the dataset is 1 515. The latter is very close to the actual number of morphospecies used for the study but it should not be considered an estimate for congruence. There are a variety of reasons for discordance - 158 species sharing their barcode sequence with at least one other taxon, and 189 species with low, but diagnostic COI divergence. A very few cases (13) involved species whose members fell into both categories. Most of the remaining 140 species show a split into two or three BINs per species, while Virbia ferruginosa was divided into 16.

The exciting result is how close the BIN estimate is to the species numbers determined by conventional methods. I am sure that colleagues working on DNA Barcoding will start using similar approaches to test if this holds true for other groups, regions or settings but something tells me they will end up with similar results. Actually I would like to encourage everyone to do put this to the test also with respect to completeness of libraries and in case you don't find this publication worthy I'd be more than happy to offer a guest post in this blog (sorry, no impact factor, but much less work and word gets out to the community).

This study is really good news especially when you think of all the data records on BOLD and other data repositories that have no species designation (and lacking perhaps even more). A BIN assignment will make those data more useful for a lot of biodiversity and ecology related questions. Rod Page once called those records without species ID 'dark taxa'. Perhaps they are not so dark anymore.

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