Barcoding a Quantified Food Web: Crypsis, Concepts, Ecology and Hypotheses M. Alex Smith1*, Eldon S. Eveleigh2,4, Kevin S. McCann 3 , Mark T. Merilo1, Peter C. McCarthy2, Kathleen I. Van Rooyen2 1 Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada, 2 Natural Resources Canada, Canadian Forest Service, Atlantic Forestry Centre, Fredericton, New Brunswick, Canada, 3 Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada, 4 Population Ecology Group, Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada Abstract The efficient and effective monitoring of individuals and populations is critically dependent on correct species identification. While this point may seem obvious, identifying the majority of the more than 100 natural enemies involved in the spruce budworm (Choristoneura fumiferana – SBW) food web remains a non-trivial endeavor. Insect parasitoids play a major role in the processes governing the population dynamics of SBW throughout eastern North America. However, these species are at the leading edge of the taxonomic impediment and integrating standardized identification capacity into existing field programs would provide clear benefits. We asked to what extent DNA barcoding the SBW food web would alter our understanding of the diversity and connectence of the food web and the frequency of generalists vs. specialists in different forest habitats. We DNA barcoded over 10% of the insects collected from the SBW food web in three New Brunswick forest plots from 1983 to 1993. For 30% of these specimens, we amplified at least one additional nuclear region. When the nodes of the food web were estimated based on barcode divergences (using molecular operational taxonomic units (MOTU) or phylogenetic diversity (PD) – the food web became much more diverse and connectence was reduced. We tested one measure of food web structure (the ‘‘bird feeder effect’’) and found no difference compared to the morphologically based predictions. Many, but not all, of the presumably polyphagous parasitoids now appear to be morphologically-cryptic host- specialists. To our knowledge, this project is the first to barcode a food web in which interactions have already been well- documented and described in space, time and abundance. It is poised to be a system in which field-based methods permit the identification capacity required by forestry scientists. Food web barcoding provided an effective tool for the accurate identification of all species involved in the cascading effects of future budworm outbreaks. Integrating standardized barcodes within food webs may ultimately change the face of community ecology. This will be most poignantly felt in food webs that have not yet been quantified. Here, more accurate and precise connections will be within the grasp of any researcher for the first time. Citation: Smith MA, Eveleigh ES, McCann KS, Merilo MT, McCarthy PC, et al. (2011) Barcoding a Quantified Food Web: Crypsis, Concepts, Ecology and Hypotheses. PLoS ONE 6(7): e14424. doi:10.1371/journal.pone.0014424 Editor: Tamara Natasha Romanuk, Dalhousie University, Canada Received July 26, 2010; Accepted October 22, 2010; Published July 6, 2011 Copyright: 2011 Smith et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The field study was funded by the Canadian Forest Service to ESE and laboratory reagents were funded by Genome Canada through the Ontario Genomics Institute and through a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant to MAS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: salex@uoguelph.ca Introduction ‘What’s the use of their having names the Gnat said, ‘if they won’t answer to them?’ ‘No use to them,’ said Alice; ‘but it’s useful to the people who name them, I suppose. If not, why do things have names at all?’ ‘I can’t say,’ the Gnat replied. ‘Further on, in the wood down there, they’ve got no names. Lewis Carroll, Through the Looking Glass The spruce budworm (Choristoneura fumiferana, SBW) is the most economically important insect species in eastern North America. Every 30–40 years, the species undergoes population outbreaks [1] that can result in damage to over tens of thousands of hectares, affecting hundreds of communities and costing many millions of dollars. For example, consider an outbreak of the scale of the one that peaked in the mid-1970’s – where SBW defoliation peaked at approximately 57 million ha [2]. If the impending outbreak due to affect eastern North America within the next few years reaches this magnitude, it would cost billions of dollars (A value approximated by dividing the average value of forest land ($/ha) from the contribution of forests to GDP by the total forested area in Canada in 2009 multiplied by 57 million ha [3]). Despite being a disruptive ecological force on a continental scale with impacts comparable to forest fires, there is currently no consolidated plan for managing budworm outbreaks [4]. Clearly, there are gross economic factors that ought to reinforce how important an understanding of the food web of organisms that depend on, and interact with, the spruce budworm is to our environment and our economy. PLoS ONE | www.plosone.org 1 July 2011 | Volume 6 | Issue 7 | e14424