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One of the issues that have drawn the attention of ecologists is how ecosystems that are both complex and stable are organized. It has been argued that ecosystems have regulatory mechanisms that optimize their structure and function. These mechanisms are known as self-organizing processes that are regulated by environmental forcing factors. In this way, ecosystems existence endures in the long-term in often-hostile environments. However, ecosystem dynamics change over time depending on environmental conditions. It has been observed that recovery of ecosystem is enhanced when hostile conditions end up. Graph theory suggests that cohesive structures play a relevant role in the resilience of networks (artificial or natural). Here, we use two marine food webs to analyse the existence of substructures that contribute to maintain and preserve the ecosystem. The first one is Terminos Lagoon (TL) in the southern Gulf of Mexico and the other is the Sinaloa Continental Shelf (SCS) at the Central Mexican Pacific. We use these as case studies because we have Ecopath trophic models for both of them representing periods with different environmental conditions. For TL we have three models representing 1980, 1998 and 2011 years. Differences in environmental conditions as indicated by climate variability at the southern Gulf of Mexico have been reported for those years (Del Monte-Luna 2012; Arreguín-Sánchez et al. 2008). For SCS we have two models 1995 and 2007 years that also represent different environmental periods (Hernández-Padilla, 2012). First, we compare summary trophic flows and network indices to identify differences in ecosystem function related with environmental conditions. Then, in order to search for cohesive substructures during different environmental conditions we use the clique concept. A clique is a set of nodes where every element of the set is connected to every other member. In this sense a clique is a substructure of functional groups that are more intensively related among them, than they are with other members of the food web. In the case of TL, most energy flows decreased by 40% in 1998 and 58% in 2011, when compared to 1980. There were also differences between years in transfer efficiency among trophic levels. Additionally, the ecosystem organization decreased, as measured by ascendency/development capacity, with 11% in 1998 and 7% in 2011, relative to 1980. In SCS, we found that the total system throughputs were decreased by between years. Conversely, the organization of the ecosystem was 14%higher in 2007 compared to 1995. These results suggest different functional status of both ecosystems during the periods analysed. The analysis of substructures, however, indicated that there are certain groups at different trophic levels that conform cohesive structures and remain constant over time for both ecosystems. In the case of TL, cliques conformed mainly by seagrasses, microcrustaceans, meiobenthos, echinoderms, and some fishes were prevailing during all the three years studied; the structure is maintained because there are substructures that have remained relatively stable, and which are associated with ecosystem stability. In the case of SCS, cliques were conformed by macrophytes, shrimps, zooplankton, some fish groups and seabirds. Finally, we discuss the relevance of substructures in marine food webs. Krause et al. (2003) indicates that compartments or substructures are related to stability in networks. Alon et al. (2007) suggest that the identification of recurrent network interconnections is important to understand network evolution because substructures perform relevant functions. Future work will address how climate forces affect ecosystem function and substructures through dynamic simulations.

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