Coral reef populations of a variety of fish and invertebrate species are replenished by individuals that use inshore coastal habitats as temporary juvenile habitats. These habitats vary greatly in their architecture, and different characteristics of structure could play a role in their selection and utilization by resident fauna. To solely investigate the role of structural complexity in microhabitat selection, in situ habitat preference of 48 individuals of the early juvenile stage of a common reef fish (Haemulon flavolineatum) was studied for 4 structurally very different lagoonal microhabitats (i.e. mangrove, seagrass, rubble, coral), using a multiple-choice experiment in field enclosures. This fish species was selected as it utilizes these habitats during different parts of its life cycle. The structural complexity of each microhabitat was changed in each replicate experiment and assessed on the basis of 7 commonly used measures of structure using digitized photographs. We tested the hypothesis that in isolation of other factors, fish prefer the structurally most complex microhabitat that is available, independent of habitat type. However, fish always preferred seagrass and coral microhabitats even when offered at low complexity, and this choice was rather consistent over a 24 h time period. Structural characteristics appeared to be marginally important for the seagrass microhabitat only. Therefore, the differential preference for distinct lagoonal microhabitats does not appear to be driven by measures of structural complexity that are known to be important at the level of individual habitat types. In this light, continuing loss of coral and seagrass habitats in lagoonal environments due to anthropogenic effects is alarming as it affects preferential habitat of certain stages of the life cycle of fishes.
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