The non-metric multidimensional scaling (nMDS) analysis revealed substantial differences in nematode assemblages between connected and closed lagoons, but not between locations within the lagoons (Fig 5). The results of the PERMANOVA showed that the greatest variation in the data dissimilarities occurred due to differences in connectivity rather than between locations within lagoons (Table 3). The statistical tests confirmed that nematode assemblages of closed lagoons differed significantly from more connected ones (Table 3). The PERMANOVA tests also revealed that nematode assemblages of inner and outer portion of closed lagoons did not differ significantly, whilst in the ICOLLS and open they did (Table 3). The analysis of the average similarity between/within lagoons showed that nematodes assemblages from the open lagoons were more similar to each other than those from the closed ones (Table 3). As lagoons lose connectivity with the sea, nematode composition became more dissimilar. Internal similarities, conversely, were higher within closed lagoons, decreasing as lagoons gain connectivity. The results of these analyses were consistent whether analysed by means of presence/absence or relative abundances.