Challenges with assessing long-term trends
To track Caribbean coral community change prior to and since the arrival of humans, we used data from multiple sources, including uplifted fossil reefs, reef matrix cores, qualitative historical data, and underwater survey data. However, the prevalence of most of coral taxa are comparable across the paleo, historical, and early modern time bins, suggesting that overall trends were not artifacts of comparing differing data types (Figures 2, 3). Exceptions include (1) the conspicuously lower within-country community dissimilarity observed within the fossil versus non-fossil time bins, which is likely due to the greater time averaging within the former and (2) significant differences in the prevalence of multiple coral taxa between the Pleistocene and Holocene. Significant Pleistocene-Holocene differences included declining prevalence of A. cervicornis at the midslope zone and increased prevalence of a number of stress-tolerant and weedy taxa at both zones (Table 2, Figures 2,3). These differences could reflect declining rates of sea level rise during the late Holocene, which would favor increased dominance of more slowly growing species with massive colony forms [68]—a trend we observe in our data from the midslope zone (Figure 3b). Lower A. cervicornis prevalence in the Holocene compared to the Pleistocene could also be a result of inaccurate paleodepth estimates and/or underestimation of A. cervicornis abundance from the narrow-diameter core tubes which comprise most of the Holocene data. However, A. palmata dominance increased slightly at the reef crest between the Pleistocene and Holocene, demonstrating that there was no bias against sampling this coral in the Holocene reef cores [13]. Importantly, when data from the Pleistocene and Holocene periods are combined, overall trends in prevalence of coral functional and species groups are largely identical to those with these time periods separated–declines in Acropora prevalence first occurred in the 1960s, followed by increases in stress-tolerant and weedy species in the 1970s and 1980s (Table S6, Figures S3,S4).
Although abundance data allows for a more robust assessment of community composition than presence/absence data, the exceptionally broad temporal, taxonomic, and geographic scales covered in this study necessitated the utilization of the latter. Prevalence does not equal abundance; although we found that the prevalence of stress-tolerant and weedy corals has increased over the most recent decades, the total abundance of living coral has declined by 50-80% across the Caribbean since the initiation of quantitative surveys in the 1970s [1-2,8]. However, ecological studies show that, on large spatial scales,trends in prevalence (proportion of sites occupied) are correlated with trends in abundance [69-70]. This suggests that the long-term trends shown in this study are reliable proxies of qualitative trends in relative (but not absolute) abundance.