A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

<div><p>Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to presumptive species, called operational taxonomic units (OTUs), these systems speed investigations into the patterning of biodiversity and enable studies that would otherwise be impossible. Although OTUs have conventionally been separated through their morphological divergence, DNA-based delineations are not only feasible, but have important advantages. OTU designation can be automated, data can be readily archived, and results can be easily compared among investigations. This study exploits these attributes to develop a persistent, species-level taxonomic registry for the animal kingdom based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome <i>c</i> oxidase I (COI) gene. It begins by examining the correspondence between groups of specimens identified to a species through prior taxonomic work and those inferred from the analysis of COI sequence variation using one new (RESL) and four established (ABGD, CROP, GMYC, jMOTU) algorithms. It subsequently describes the implementation, and structural attributes of the Barcode Index Number (BIN) system. Aside from a pragmatic role in biodiversity assessments, BINs will aid revisionary taxonomy by flagging possible cases of synonymy, and by collating geographical information, descriptive metadata, and images for specimens that are likely to belong to the same species, even if it is undescribed. More than 274,000 BIN web pages are now available, creating a biodiversity resource that is positioned for rapid growth.</p></div

BIN page for <i>Danaus plexippus</i> (Linnaeus, 1758), the monarch butterfly.

<p>BIN page for <i>Danaus plexippus</i> (Linnaeus, 1758), the monarch butterfly.</p

The correspondence between the species present in eight datasets and OTUs recognized through single linkage clustering with sequence divergence thresholds ranging from 0.1–6.0%.

<p>Green indicates the number of OTUs whose members perfectly match species; yellow shows those that merge members of two or more species; orange indicates cases where a species was split into two or more OTUs and red represents a mixture of splits and merges.</p

Computational time required by the ABGD, CROP, jMOTU, and RESL algorithms to generate OTUs for eight datasets.

<p>Computational time required by the ABGD, CROP, jMOTU, and RESL algorithms to generate OTUs for eight datasets.</p

A comparison of the performance of the ABGD, CROP, jMOTU, and RESL algorithms in OTU assignments for eight datasets.

<p>Each bar consists of four categories: green – percent of MATCHES, yellow – percent of MERGES, orange – percent of SPLITS, red – percent of MIXTURES.</p

Eight datasets used to test the performance of algorithms for OTU delineation.

<p>Eight datasets used to test the performance of algorithms for OTU delineation.</p

Computational time required by the GMYC and RESL algorithms to generate OTUs for eight datasets.

<p>Computational time required by the GMYC and RESL algorithms to generate OTUs for eight datasets.</p

Correspondence between OTUs generated by RESL and the number of species in eight datasets.

<p>Correspondence between OTUs generated by RESL and the number of species in eight datasets.</p

A comparison of the performance of the GMYC and RESL algorithms in OTU assignments for eight datasets.

<p>Side by side comparisons for MATCHES, LUMPS, SPLITS, and MIXTURES.</p

Comparison of BIN and species boundaries in eight datasets.

<p>Each inner ring partitions species, based on their assignment to BINs as MATCHES (green), MERGES (yellow), SPLITS (orange) or MIXTURES (red). Each outer ring categorizes BINs into those that MATCHED species, MERGED species, SPLIT species or MIXTURES using the same colour scheme. The number below each chart is the OTU count while the percentage indicates the incidence of OTUs that were not MATCHES.</p