DOI: 10.5061/dryad.0rxwdbs27
title: Functional divergence from ecological baselines on Caribbean coral reefs

description: Understanding how emergent ecological assemblages have diverged from
 natural states is fundamental in predicting future functioning and
 services of ecosystems. Coral reefs are of particular concern due to their
 high susceptibility to anthropogenic stressors. Yet, little is known about
 their pre-disturbance ranges of natural states, and most reports of
 decline are based on a limited number of sites and high levels of
 uncertainty. Here, we used a novel approach to estimate the physical
 functionality of reefs across marine ecoregions based on habitat
 suitability and morpho-functional traits for coral species. We calibrated
 ecological niche models for 49 reef-building corals of the Greater
 Caribbean based on occurrence records and environmental predictors, which
 we combined with species-specific functional coefficients derived from
 morpho-functional traits reflecting their contribution to the reef
 three-dimensional structure to estimate the reef functional potential
 (RFP). We then assessed the degree of divergence of western Caribbean
 reefs by comparing our physical functionality estimates against recent
 field data evaluations. We found spatial variability in RFP across the
 Caribbean, with the highest mean value in the western Caribbean and the
 lowest in areas with marginal environmental conditions. Hotspots of RFP
 exist along the coast of Belize and the southeast of Cuba. Overall, 84% of
 sites along the western Caribbean showed a substantial reduction in their
 physical functioning, with the highest reductions occurring within
 hotspots, implying that reefs displaying the greatest changes have high
 initial RFP. We conclude that combining niche models with species
 morpho-functional traits is a valuable and promising approach to estimate
 the large-scale functional potential of communities and the degree of
 change in the absence of ecological baselines. These findings have
 important implications and could be used to guide efforts to preserve
 coral reefs functionality and define priority conservation areas in the
 Caribbean.
description: Species occurrence
 records To create a
 geodatabase of occurrence records of Atlantic shallow-water reef-building
 corals we conducted a systematic search using the following sources: The
 Global Biodiversity Information Facilities (www.gbif.org/), the Ocean
 Biogeographic Information System (https://obis.org/), Biodiversity
 Information Serving Our Nation (https://bison.usgs.gov/#home), the Time
 Series Coral-cover from Florida and the Virgin Islands (Guest et al.
 2018), the Caribbean Coastal Marine Productivity Program database
 (CARICOMP 2000), the Atlantic and Gulf Rapid Reef Assessment database
 (Marks and Lang 2018), and data from the laboratory of Biodiversity and
 Reef Conservation, which was curated, systemized, and is now included in
 Caribbean Reefs Information System database. Additionally, we performed a
 literature search to incorporate occurrence data for reefs areas that
 appeared to be underrepresented when the pooled occurrences were plotted
 in the geographic space (i.e. none or very few records). The compiled
 occurrences were reviewed to exclude duplicated coordinates per species,
 data coming from the fossil record and data with georeferencing errors
 (i.e. records on land). We applied a spatial filter with a
 minimum nearest-neighbor distance between points in order to reduce
 spatial clumping of occurrences (Veloz 2009, Kramer-Schadt et al. 2013,
 Boria et al. 2014). To select the proper distance for the spatial thinning
 of occurrence data we tested models using ten coral species with different
 sample sizes and geographic range sizes as test examples. One group of
 models had no spatial thinning of the occurrence data; this yielded strong
 model overfitting coincident with a higher density of occurrences. A
 second group of models was run with a spatial filtering of 20 km applied
 to all data, and a third group was run with occurrences split in subsets
 according to different geographical clumping, where the data corresponding
 to the western Caribbean basin (higher clumping) was filtered with a
 distance of 40 km, and the rest of the data with a distance of 20 km. The
 resulting model outputs were converted to presence–absence maps using the
 minimum training presence threshold to cut off habitat suitability
 (Kramer-Schadt et al. 2013). We visually compared the two sets of
 presence–absence models with filtered occurrences against those generated
 with no thinning. As a result, we decided to use the 40–20 km filtering as
 these models showed a reduction in model overfitting, and better
 represented the known distribution of species. Once occurrence data were
 spatially filtered, the resulting subset was used as the training dataset,
 and the occurrences not included were used as testing dataset.
 Divergence analysis
 For this analysis we used
 published information on the estimation of the reef functional index (RFI;
 González-Barrios and Álvarez-Filip 2018), complemented with information
 obtained through the Caribbean Reefs Information System database. Data
 collection follows the AGRRA protocol point intercept (Lang et al. 2010)
 and ReefBudget (Perry et al. 2012) methodologies. A total of 242 sites were included
 in this analysis covering a period from 2010 to 2017. The RFI obtained
 from field data was plotted against the modeled RFP to which we added an
 equivalence line. To construct this line, we used 0 as the minimum value
 for both axes and as maximum, the highest value that could potentially be
 achieved in each case. In the case of the FRI, the highest value would
 correspond to a hypothetical site with 100% of coral cover of the species
 with the highest functional coefficient, corresponding to a RFI of 0.977.
 In the case of modeled RFP the highest value would correspond to a cell in
 which the suitability value was 1 for all the 49 modelled species, in this
 case the RFP would be of 10.568. On the plot, a site with a coherent RFI
 and RFP values would be close to the line, sites with a higher RFI than
 RFP would be above the line, and sites with lower RFI than RFP would be
 below the line. As a measure of divergence from the RFP, we used the
 distance of each point to the equality line that we further transformed
 into percentage values.