Cryptic Species in a Food Web Figure 3. Food web representation where nodes are described morphologically as in [9] (BEFORE), and where nodes were delineated using barcodes (AFTER). Diversity has increased (Nodes (N) increased from 110 to 156 (a 41% increase)) and links (L) from 336 – to 449) and the connectence (Connectance (L/N2)) has been reduced (from 0.03 to 0.02). Nodes are unlabelled, and the SBW is the center of the fan. Image produced with FoodWeb3D, written by R.J. Williams and provided by the Pacific Ecoinformatics and Computational Ecology Lab (www. foodwebs.org, [73]). doi:10.1371/journal.pone.0014424.g003 PD & MOTU It is important to note that our aim in using the neighbor- joining trees constructed here with a single marker is not to construct the most resilient nor accurate deep phylogeny. Rather, it was to use the PD approach parameterized with the standardized DNA marker to produce an estimate of ‘diversity’ independent of, but not unrelated to, the species question. Phylogenetic diversity (PD) [44] was measured as the evolutionary branch length spanned by a given set of species. In a more complete phylogeny, PD is expected to have important consequences for community assembly if close relatives exhibit greater ecological similarity than distant relatives [45]. As used here, a phylogenetically ‘close’ terminal is not necessarily the end result of the phylogenetic analysis – rather – the intended end result is to make transparent comparisons of diversity in a manner that is standardized (the accepted animal barcoding locus) in a fashion that is independent of species decisions. Such an analysis could be based on representative sequences – or all sequenced specimens (as here). When the conclusions of barcode based analyses have been compared between MOTU and PD [29,46,47] significant differences were not found between the two analyses. This was again the case here – while there were qualitative differences between the two results – they were not significant. Our results add to a growing literature demonstrating the power of using PD based on a standardized gene region (even a single marker) [46,47,48,49]. CBCs and species Recently, several papers presented evidence that strongly supported the hypothesis that the internal transcribed spacer region 2 (between 5.8S and the large subunit (LSU, 28S)) can be used as a species level identifier across broad taxonomic groups [50,51]. Specifically, the presence of even one CBC in ITS2 predicts a total lack of successful interbreeding [32]. An ITS2 pipeline has been suggested, similar to the Barcode of Life Datasystem (BOLD), which would make species identification very simple via the comparison of CBCs. Compensatory base changes (e.g. CG–AT), maintain pairing at corresponding sites and therefore secondary structures. Barcoding will have the greatest impact on food web ecology when the lineages it identifies equate as closely to independently evolving lineages as possible. PLoS ONE | www.plosone.org 6 July 2011 | Volume 6 | Issue 7 | e14424