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Background  Species distribution models are commonly used tools to describe diversity patterns and support conservation measures. There is a wide range of approaches to developing SDMs, each highlighting different characteristics of both the data and the ecology of the species or assemblages represented by the data. Yet, signals of species co-occurrences in community data are usually ignored, due to the assumption that such structuring roles of species co-occurrences are limited to small spatial scales and require experimental studies to be detected. Here, our aim is to explore associations among marine sandy-bottom sediment inhabitants and test for the structuring effect of seagrass on co-occurrences among these species across a New Zealand intertidal sandflat, using a joint species distribution model (JSDM).    Results  We ran a JSDM on a total of 27 macrobenthic species co-occurring in 300,000 m 2  of sandflat. These species represented all major taxonomic groups, i.e. polychaetes, bivalves and crustaceans, collected in 400 sampling locations. A number of significant co-occurrences due to shared habitat preferences were present in vegetated areas, where negative and positive correlations were approximately equally common. A few species, among them the gastropods  Cominella glandiformis  and  Notoacmea scapha , co-occurred randomly with other seagrass benthic inhabitants. Residual correlations were less apparent and mostly positive. In bare sand flats shared habitat preferences resulted in many significant co-occurrences of benthic species. Moreover, many negative and positive residual patterns between benthic species remained after accounting for habitat preferences. Some species occurring in both habitats showed similarities in their correlations, such as the polychaete  Aglaophamus macroura,  which shared habitat preferences with many other benthic species in both habitats, yet no residual correlations remained in either habitat.    Conclusions  Firstly, analyses based on a latent variable approach to joint distributions stressed the structuring role of species co-occurrences beyond experimental scales. Secondly, results showed context dependent interactions, highlighted by species having more interconnected networks in New Zealand bare sediment sandflats than in seagrass meadows. These findings stress the critical importance of natural history to modelling, as well as incorporating ecological reality in SDMs.

Co-occurrence patterns and the large-scale spatial structure of benthic communities in seagrass meadows and bare sand