Abstract. Environmental degradation is reducing the variability of living assemblages at multiple spatial scales, but there is no a priori reason to expect biotic homogenization to occur uniformly across scales. This paper explores the scale-dependent effects of recent perturbations on the biotic variability of lagoonal reefs in Panama and Belize. We used new and previously published core data to compare temporal patterns of species dominance between depth zones and between geographic locations. After millennia of monotypic dominance, depth zonation emerged for different reasons in the two reef systems, increasing the between-habitat component of beta diversity in both taxonomic and functional terms. The increase in between-habitat diversity caused a decline in geographic-scale variability as the two systems converged on a single, historically novel pattern of depth zonation.Twenty-four reef cores were extracted at water depths above 2 m in Bahía Almirante, a coastal lagoon in northwestern Panama. The cores showed that finger corals of the genus Porites dominated for the last 2000-3000 yr. Porites remained dominant as the shallowest portions of the reefs grew to within 0.25 m of present sea level. At intermediate depths of 5-10 m, however, declining water quality in the Bahía enabled the lettuce coral Agaricia tenuifolia to replace Porites during the last several decades. In Belize, the staghorn coral Acropora cervicornis dominated the rhomboid shoals of the central shelf lagoon for millennia. As the shallowest portions of the rhomboid shoals approached sea level around 500 years ago, Porites spp. replaced Ac. cervicornis in an intrinsically driven successional sequence. At intermediate depths, white-band disease killed Ac. cervicornis in the late 1980s, precipitating a transition to dominance by Ag. tenuifolia. Phase shifts between coral taxa and the emergence of coral zonation in both locations were mediated by the sea urchin Echinometra viridis, which controlled algal growth. Opposite trends in biotic variability at the habitat and geographic levels highlight the complex, scale-dependent nature of the response of coral reefs to intense perturbations.

As human activities have intensified along tropical coastlines, the anthropic influence on adjacent coral reefs has become increasingly deleterious. Changes in land use generally degrade water quality, but controversy persists over the degree to which reduced water quality affects the ecology of reef communities. We cored reef frameworks at 4 sites in Bahía Almirante, a semi-enclosed, coastal lagoon in northwestern Panamá, to explore the historical relationship between turnover in coral-species dominance and terrigenous input. The coral constituents of the cores were analyzed in tandem with lignin-phenol concentrations. Chronologies and sedimentation rates were determined from 210 Pb profiles in the cores. Increased terrigenous input from agricultural development and expansion of the human population degraded water quality in Bahía Almirante over the last century. Documented episodes of heavy rainfall after 1970 accelerated a phase shift from dominance by branching corals of the genus Porites to dominance by the lettuce coral Agaricia tenuifolia at water depths of 5 to 10 m by increasing runoff, increasing sediment and nutrient loads, and lowering light levels. The phase shift in coral dominance was unprecedented on a millennial time scale and the degree to which it occurred varied along a gradient of terrigenous input to the Bahía.