Supplement B. Here, we provide the results from using the methodology on the same food webs used in two seminal papers on compartments in empirical food webs [Pimm, S. L. & Lawton, J. H. Are food webs divided into compartments? J. Anim. Ecol. 49, 879-898 (1980); Raffaelli, D. & Hall, S. J. Compartments and predation in an estuarine food web. J. Anim. Ecol. 61, 551-560 (1992)] n Odds ratio P-value IC Askew (1961)a 62 5.63 <0.996 0.05 Bird (1930) Prairiea 15 5.21 <0.819 0.13 Bird (1930) Willowa 12 2.41 <0.940 0.14 Jones (1949)a 12 2.77 <0.922 0.20 Koepcke & Koepcke (1952)a 46 11.02 <0.967 0.04 Menge & Mauzey (1978)b 22 2.81 <0.998 0.11 Milne & Dunnet (1972) Mudflata 12 3.89 <0.945 0.14 Milne & Dunnet (1972) Mussel beda 10 5.93 <0.814 0.18 Minshall (1967)a 13 1.60 <0.991 0.23 Niering (1963)a 27 8.21 <0.544 0.06 Paine (1966) 13 2.11 <0.990 0.18 Summerhayes & Elton (1923)c 29 18.09 <0.001* 0.06 Tilly (1968)a 11 3.83 <0.820 0.18 Zaret & Paine (1974)a 13 9.03 <0.519 0.10 Name a These webs were taken from: Cohen, J. E. (compiler). 1989. Ecologists' Co-Operative Web Bank. Version 1.00. Machine-readable data base of food webs. New York: The Rockefeller University. b This web was taken from: Cohen, J.E. 1978. Food Webs and Niche Space. Princeton University Press, Princeton, New Jersey. c This web was taken from: Pimm, S.L. and J.H. Lawton. 1980. Are food webs divided into compartments? J. of Animal Ecology. 49:879-898 Our results for nine of these food webs sustained the same conclusion of Pimm and Lawton (1980) and Raffaelli and Hall (1992). That is, these nine food webs did not have odds ratios higher than what was expected by chance, and therefore they were not compartmentalized. The lack of compartmentalization is likely due to how these food webs were constructed rather than a lack of compartments in the actual food webs or limitations in the method. The interactions in all of these webs were unweighted and our analysis demonstrated the difficulty in identifying compartments in unweighted food webs. In addition, these food webs likely represented a fraction of the species within the actual food web or aggregated species in a way that might obscure compartments. For example, two species of fish may interact with ten species of zooplankton for a total of ten realized interactions. If the fish are aggregated into one taxanomic group and the zooplankton are aggregated into another, then the ten interactions are reduced to one interaction. The method would no longer have the same information for identifying compartments. Weighting the one interaction would help to alleviate this problem. Our conclusions diverge from the previous studies with the Menge & Mauzey (1978) and Paine (1966) food webs. Both of these food webs were found to be significantly compartmentalized with 2 compartments. In our analysis, these food webs did not have odds ratios higher than expected by chance. A similarity index was used in both of the Pimm and Lawton (1980) and Raffaelli and Hall (1992) analyses and similarity indices have been used to identify trophic levels. Thus these analyses may have picked up on trophic levels. Koepcke & Koepcke (1952), Niering (1963), and Summerhayes & Elton (1923) were food webs where Pimm and Lawton (1980) were a priori defined compartments. They compared realized interactions between two compartments against an estimate (based on the average number of interactions per species and number of species within each compartment) using a chi-square distribution. They found that all of these food webs had lower than expected realized interactions between compartments. Our results indicate that there are only significant compartments than by chance alone for Summerhayes & Elton (1923). The Askew (1961) food web was published in the Pimm and Lawton (1980) paper but Pimm and Lawton were unable to analyze it due to lack of computing power. The Summerhayes and Elton (1923) food web had an interactive connectance within compartments = 0.12 and interactive connectance between compartments = 0.0072. This food web was found to have two compartments (see table below). Pimm and Lawton (1980) reported a priori placement of the taxa from the Summerhayes and Elton food web into three separate compartments. In their study, one compartment contained marine taxa, a second contained terrestrial taxa, and a third contained freshwater taxa. In our arrangement, all of the marine taxa, four terrestrial taxa, and six freshwater taxa are in compartment A and thirteen terrestrial taxa and three freshwater taxa are in compartment B. Only three interactions are shared between the two compartments of the potential 416 interactions which produce a very low between interactive connectance. The density of interactions between and within our compartments produced an odds ratio lower than the Pimm and Lawton’s a priori assignments. In fact, the odds ratio of the original analysis was smaller than 983 of the simulated food webs of this web and therefore would not have been significant in our analysis. Summerhayes and Elton (1923) food web divided into compartments based on our analysis Compartment A Compartment B marine plankton Plants marine animals Worms Seals Geese Sea-birds Colembola ducks and divers Diptera (terrestrial) skua and glaucous gull Mites benthic algae (freshwater) Hymenoptera Protozoa snow-bunting Diptera (freshwater) purple sandpiper other invertebrates Ptarmigan Lepidurus Spiders polar bear arctic fox decaying matter planktonic algae (freshwater) Protozoa invertebrates (freshwater) dead plants Original Citations for the food webs: Askew, R. R.. On the biology of the inhabitants of oak galls of Cynipidae (Hymenoptera) in Britain. Trans. Soc. Brit. Entomol. 14:237-268 (1961) Bird, R. D. Biotic communities of the Aspen Parkland of central Canada, Ecology, 11:356-442 (1930). Bird, R. D. Biotic communities of the Aspen Parkland of central Canada, Ecology, 11:356-442 (1930). Jones, J. R. E. A further ecological study of calcareous streams in the "Black Mountain" district of South Wales, J. Anim. Ecol. 18:142-159 (1949). Koepcke, H. W. and M. Koepcke, Sobre el proceso de transformacion de la materia organica en las playas arenosas marinas del Peru, Zoologie Serie A, No. 8, Publ. Univ. Nac. Mayer, San Marcos (1952). Milne H. and G. M. Dunnet, Standing crop, productivity and trophic relations of the fauna of the Ythan estuary. In: The Estuarine Environment, R. S. K. Barnes and J. Green, Eds., Applied Science Publications, Edinburgh, Scotland (1972) Minshall, G. W. Role of allochthonous detritus in the trophic structure of a woodland springbrook community, Ecology 48(1):139-149 (1967). Niering, W. A. Terrestrial ecology of Kapingamarangi Atoll, Caroline Islands, Ecol. Monogr. 33(2):131-160 (1963). Paine, R. Food web complexity and species diversity. Am. Nat. 100:65-75 (1966) Summerhayes, V.S. and C.S. Elton. Contributions to the ecology of Spitsbergen and Bear Island. J. Ecology. 11:214-286 (1923) Tilly, L. J. The structure and dynamics of Cone Spring. Ecol. Monogr. 38(2):169-197 (1968). Zaret, T. M. and R. T. Paine, Species introduction in a tropical lake, Science 182:449-455 (1973)