Fish assemblages of two tropical estuaries are compared with regard to taxonomic structure and functional guilds using biomass data from different habitats of the Embley Estuary (north Australia) and the Caeté Estuary (north Brazil). First, the similarity of the habitats of the
two estuaries was compared using taxonomic classification of their respective ichthyofauna. Important taxonomic differences between the two estuaries emerged: the Neotropical fish species of the upper Caeté Estuary have no equivalents in the Embley Estuary, and the diverse chondrichthyan
fauna of the Embley have no equivalents in the Caeté Estuary. On the other hand, the more ubiquitous families Engraulidae, Sciaenidae, Ariidae, Carangidae, haemulidae, and Clupeidae, which were characteristic of the main channel and mangrove tidal creeks of the Caeté Estuary,
showed 70% similarity with the main channel of the Embley Estuary. Second, the similarity of the fish assemblages was compared in terms of ecological guilds (estuarine use and feeding mode). For the Embley Estuary, marine immigrants (mainly piscivorous and benthophagous) were the dominant
functional guild, whereas in the Caeté Estuary, the estuarine functional guild (mainly benthophagous) contributed to more than 50% of the biomass in each habitat. Factorial analysis of species functional guilds shows that the first factorial axis was formed positively by the dominant
fish species which spend part of their life cycle in Embley Estuary habitats, principally in the main channel, tidal channel (anadromous/piscivorous, marine immigrants/piscivorous, benthophagous, detritivorous, and marine stragglers/piscivorous), and negatively by dominant estuarine (planktivorous
and benthophagous) fish species which spend their life in the seagrass beds and in the mangrove intertidal creeks. The second factorial axis best represented the distribution of fish species in the estuary (upper, middle, and lower), which was evident in the Caeté than in the Embley
Estuary, where the freshwater and marine straggler guilds were most important in determining this second factorial axis.
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