Coral community composition database
Data on coral species composition from the pre-human period to the present were compiled from semi-quantitative, quantitative, and qualitative records from the primary peer-reviewed scientific literature, government reports, and historical literature. These data were collected via surveys of uplifted fossil reefs, analysis of coral fossils in reef matrix cores, qualitative field notes from boat-based or snorkel surveys, high-resolution aerial photographs, and underwater field surveys using SCUBA. Most of the coral species composition data since the 1980s were received directly from contributors or gleaned from peer-reviewed literature to construct the Global Coral Reef Monitoring Network (GCRMN) database that assessed trends in Caribbean reef benthic communities from 1970-2011 (Table S1; ref 2).
Temporal changes were tracked for 14 common coral taxonomic groups that were consistently recorded within each time bin (henceforth termed “species groups”: Acropora cervicornis , Acropora palmata , Agaricia spp., Montastraea cavernosa ,Colpophyllia spp., Diploria spp., Madracis spp.,Meandrina spp., Millepora spp., Orbicella spp., branching Porites spp., Porites astreoides ,Siderastrea spp., and Stephanocoenia spp.). To provide sufficient temporal resolution and ensure adequate sample sizes for assessing change over the full time series, data were grouped into eleven time bins: Late Pleistocene (~131,000-12,000 years ago, which we also refer to as the pre-human period), Holocene (~9,100 years ago-1500 AD), 1500-1959, 1960-1969, 1970-1979, 1980-1984, 1985-1989, 1990-1994, 1995-2000, 2001-2004, and 2005-2011. Bins were reduced to 5-year increments after 1980 (except for a six-year increment for the most recent bin) due to the large increase in reef survey effort following the mass die-off of the urchinDiadema antillarum . The pre-human bin encompasses a period of high-magnitude fluctuations in sea level and climate (during whichAcropora coral dominance persisted in the Caribbean; ref 18), whereas the pre-historic bin encompasses a period with relatively higher stability in climate and sea level [19].
Data were extracted from text, tables and figures, and maps. Qualitative data were included in the database if, in addition to presence/absence information for at least one coral species, the following information was also available: (1) age of fossil data or year of observation of modern data, (2) original source of data, (3) country and island, coastline, or reef site, and (4) water depth or reef zone. Data were recorded at the survey level, with a survey constituting a unique combination of reef site, depth zone, and year. For surveys which included multiple replicates (i.e., transects or quadrats) at the same site, depth zone, and year/period, an overall value was computed for all replicates. Surveys constituted individual reef “sites” and in some cases encompassed more extensive areas such as entire reef tracts, bays, or banks.
We analyzed data from ”reef crest” and ”midslope” reef zones separately. Generally, the reef crest data spanned 0-6m water depth and midslope data spanned between 6-20m, as 6m was the depth at which dominance typically transitioned from A. palmata to A. cervicornisin the semi-quantitative and quantitative data. However, the reef crest/midslope zone delineation was made on a location-by-location basis by first considering water depth and, when available, additional environmental characteristics such as wave exposure and reef morphology. For some offshore locations with presumably higher water clarity, the cutoff was closer to 10m. When a precise water depth was not available, we utilized Acropora species presence and/or dominance in addition to environmental characteristics to delineate between zones [13]. When not reported in the papers from which data were extracted, paleo water depths were determined using the procedure outlined in ref. 13. Surveys from backreef habitats, reef flats, and reef pavements were excluded from our database, as these reef zones are not the preferred environments for Caribbean Acropora [20].
Change in coral community composition was assessed using coral species presence/absence data, extracted from species rankings, presence/absence, percent living coral cover, number of individual colonies, and percent weight or volume of coral fossils. Only species included in the 14 commonly occurring species groups were considered in our analyses. Data recorded as “Porites spp.” were assumed to be branching Porites spp. (whereas records listing “Porites astreoides ” were assigned to a separate category) and data recorded as “Montastraea spp.” were assumed to beOrbicella spp. because species within these complexes are difficult to distinguish and were not recognized as separate species until 1992 [21]. Pseudodiploria clivosa , Pseudodiploria strigosa , and Diploria labyrinthiformis were assigned toPseudodiploria spp., as these species were placed within the same genus until 2012 [22].