We examined the geographic distributions of 1135 species of resident shore fishes to assess biogeographic subdivision of the Tropical Eastern Pacific (TEP), which stretches from the Gulf of California to northern Peru. Using hierarchical clustering refined by Analysis of Similarity (ANOSIM), we determined geographic groupings in the distributions of the entire fauna, of regional endemics and of 3 functional (habitat) groups of species. We also examined the distributions of local endemics throughout the TEP and how differences in faunal size versus faunal composition among sites contribute to the subdivision pattern. Our results indicate that: (1) the continental coast contains 2 provinces, the Cortez (Gulf of California and lower Pacific Baja) and the Panamic (southward), each of which has a peak in abundance of local endemics and of overall species richness; (2) the northern and southern boundaries of the TEP are located near Magdalena Bay on Baja California (~25°N) and the southern shore of the Gulf of Guayaquil (~4°S), respectively; and (3) the 5 oceanic islands/archipelagos collectively represent a third, Ocean Island Province. Relative to mainland areas, the fauna of the ocean islands is smaller, has a different functional-group composition, and includes more transpacific species and more highly localized endemics. The 3-province pattern probably developed in response to the formation of the Gulf of California, the rise of the Isthmus of Panama, immigration from the north, south and west to the TEP, and differing environmental conditions between and within provinces. In contrast, barriers to dispersal within this geographically simple region are weak and likely had much less influence.

The Greater Caribbean biogeographic region is the high-diversity heart of the Tropical West Atlantic, one of four global centers of tropical marine biodiversity. The traditional view of the Greater Caribbean is that it is limited to the Caribbean, West Indies, southwest Gulf of Mexico and tip of Florida, and that, due to its faunal homogeneity, lacks major provincial subdivisions. In this scenario the northern 2/3 of the Gulf of Mexico and southeastern USA represent a separate temperate, “Carolinian” biogeographic region. We completed a comprehensive re-assessment of the biogeography of the Greater Caribbean by comparing the distributions of 1,559 shorefish species within 45 sections of shelf waters of the Greater Caribbean and adjacent areas. This analysis shows that that the Greater Caribbean occupies a much larger area than usually thought, extending south to at least Guyana, and north to encompass the entire Carolinian area. Rather than being homogenous, the Greater Caribbean is divided into three major provinces, each with a distinctive, primarily tropical fauna: (1) a central, tropical province comprising the West Indies, Bermuda and Central America; (2) a southern, upwelling-affected province spanning the entire continental shelf of northern South America; and (iii) a northern, subtropical province that includes all of the Gulf of Mexico, Florida and southeastern USA. This three-province pattern holds for both reef- and soft bottom fishes, indicating a general response by demersal fishes to major variation in provincial shelf environments. Such environmental differences include latitudinal variation in sea temperature, availability of major habitats (coral reefs, soft bottom shorelines, and mangroves), and nutrient additions from upwelling areas and large rivers. The three-province arrangement of the Greater Caribbean broadly resembles and has a similar environmental basis to the provincial arrangement of its sister biogeographic region, the Tropical Eastern Pacific.

Caribbean reef corals have declined precipitously since the 1980s due to regional episodes of bleaching, disease and algal overgrowth, but the extent of earlier degradation due to localised historical disturbances such as land clearing and overfishing remains unresolved. We analysed coral and molluscan fossil assemblages from reefs near Bocas del Toro, Panama to construct a timeline of ecological change from the 19th century-present. We report large changes before 1960 in coastal lagoons coincident with extensive deforestation, and after 1960 on offshore reefs. Striking changes include the demise of previously dominant staghorn coral Acropora cervicornis and oyster Dendrostrea frons that lives attached to gorgonians and staghorn corals. Reductions in bivalve size and simplification of gastropod trophic structure further implicate increasing environmental stress on reefs. Our paleoecological data strongly support the hypothesis, from extensive qualitative data, that Caribbean reef degradation predates coral bleaching and disease outbreaks linked to anthropogenic climate change.

Caribbean coral reefs have transformed into algal-dominated habitats over recent decades, but the mechanisms of change are unresolved due to a lack of quantitative ecological data before large-scale human impacts. To understand the role of reduced herbivory in recent coral declines, we produce a high-resolution 3,000 year record of reef accretion rate and herbivore (parrotfish and urchin) abundance from the analysis of sediments and fish, coral and urchin subfossils within cores from Caribbean Panama. At each site, declines in accretion rates and parrotfish abundance were initiated in the prehistorical or historical period. Statistical tests of direct cause and effect relationships using convergent cross mapping reveal that accretion rates are driven by parrotfish abundance (but not vice versa) but are not affected by total urchin abundance. These results confirm the critical role of parrotfish in maintaining coral-dominated reef habitat and the urgent need for restoration of parrotfish populations to enable reef persistence.