This study was conducted in two estuarine inlets (Saco da Mangueira and Saco do Arraial) at the Patos Lagoon estuary, southern Brazil. The changes in relative abundance and size of post-larvae and juvenile shrimp Farfantepenaeus paulensis and juvenile blue crab Callinectes sapidus were compared, considering the influence of salinity and the presence of submerged seagrass meadows. The analyses were performed using generalized linear models (GLM) for abundance variations and ANOVA for variations on the size of individuals. The pink shrimp was more abundant at Saco da Mangueira, in seagrass meadows and areas of higher salinity. The blue crab was more abundant at Saco do Arraial and in lower levels of salinity. The importance of submerged vegetation for the blue crab lies in a preference of smaller crabs of the species for the seagrass meadows. It has been shown that these species choose different habitats in the estuary, and both the salinity and the presence of submerged seagrass meadows influence the selection of habitat.
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