DOI: 10.5061/dryad.x0k6djht1
title: Data from: Decadal-scale time series highlight the role of chronic disturbances in driving ecosystem collapse in the Anthropocene

description: These data support a publication in the Journal Ecology that describes 37
 years of change on the coral reefs of St. John, US Virgin Islands. In this
 paper, four decades of surveys from two coral reefs (9 and 14 m
 depth) off St. John, US Virgin Islands, are used to quantify the
 associations of acute and chronic events with the changes in benthic
 community structure. These reefs profoundly changed over 36 years, with
 coral death altering species assemblages to depress abundances of the
 ecologically important coral Orbicella spp. and elevating the coverage of
 macroalgae and crustose coralline algae/turf/bare space (CTB). Linear
 mixed models revealed the prominent role of chronic variation in
 temperature in accounting for changes in coverage of corals, macroalgae,
 and CTB, with rising temperature associated with increases in coral cover
 on the deep reef, and declines on the shallow reef. Hurricanes were also
 associated with declines in coral cover on the shallow reef, and increases
 on the deep reef. Multivariate analyses revealed strong associations
 between community structure and temperature, but weaker associations with
 hurricanes, bleaching, and diseases. These results highlight the
 overwhelming importance of chronically increasing temperature in altering
 the benthic community structure of Caribbean reefs.
description: The study began in December 1987 to evaluate the effects of coral
 bleaching. Three, 10-m long, permanently marked transects were established
 at 14-m depth at the Tektite reef, and at 9-m depth at Yawzi Point. These
 reefs were selected because of their high percentage cover of
 <em>Orbicella</em> spp. and ease of access from a field
 station with small boats. Each transect was sampled
 using 10 contiguous photoquadrats (1 × 1 m), recorded annually between May
 and December beginning in December 1987 and ending in July 2022. The reefs
 were sampled twice each year in 1988, 1989, and 2017 to evaluate the
 effects of hurricanes, and initially were recorded using color slide film,
 and from 2001, digitally. A strobe was used with all cameras, each image
 contained a scale bar, and slides were digitized (4000 dpi) for analysis.
 Images were analyzed using CPCe or CoralNET software, with 200
 randomly-located points image<sup>-1</sup> that were manually
 annotated to resolve coral (scleractinians and
 <em>Millepora</em>), macroalgae, and crustose coralline algae
 + algal turf + bare space (CTB). Objects to ~ 5 mm diameter were
 identified, although the taxonomic resolution was occasionally restricted
 by shadows, leading to a consensus list of 23 space holders that were
 quantified for percentage cover (mean ± SE).
 Environmental conditions (temperature, hurricanes, rainfall) were
 tested for their capacity to explain variation in coral community data,
 and these data are pusblished with the paper. 
 Differences over time in the cover of each benthic group were
 evaluated from contrasts of means and non-overlapping SEs. Linear mixed
 models (LMM) were used to test for the effects of time, average annual
 temperature (°C), rainfall (mm), hurricanes (0 or 1), disease (0 or 1),
 and bleaching (0 or 1) (fixed effect) on the percentage cover of corals,
 macroalgae, and CTB. Quadrats were averaged by transect within each site
 (n = 3) because transects were haphazardly selected and repeatedly
 surveyed; transects were introduced as a random factor. Models were fit
 using restriction maximum likelihood methods (REML), and were also run in
 simplified forms with non-significant fixed effects excluded. Models were
 evaluated using the Akaike Information Criterion corrected for small
 sample sizes (AIC<sub>c</sub>). Interaction terms were not
 included because of the potential for multicollinearity among predictors.
 The influence of the fixed effects was evaluated through the model
 estimates and 95% confidence interval about these values.
 Multivariate changes were displayed with 2-dimensional
 ordinations using non-metric multidimensional scaling (MDS) with
 Bray-Curtis dissimilarities based on square-root transformed data and 999
 permutations until stress stabilized. MDS plots were prepared for
 community structure (coral, macroalgae, and CTB), and coral taxa, with
 significance tested using SIMPROF. To test for
 associations between the environment and multivariate benthic community
 (by both functional groups and coral genera) environmental conditions were
 screened for collinearity using Pearson correlations, and where a
 significant association was detected (at P ≤ 0.05 with r &gt; 0.341
 and 35 years of data), one member of each pair was excluded based on weak
 clarity of interpretation of the environmental condition. The association
 of biological and environmental ordinations was tested using the BEST
 routine in Primer 7.0 software, in which Spearman rank correlation (ρ)
 identified the best match within a permutational framework. One analysis
 was completed with the biological and environmental data calculated by
 year, and one using a centered 3-year running mean to smooth variation.
 Environmental data were square-root transformed and converted to a
 resemblance matrix using Gower distances. BIO-ENV detects multiple
 associations, sometimes with different combinations of variables, among
 which the relative role of each variable in causing changes in community
 structure was evaluated using distance based linear modeling (DISTLM).
 This procedure distinguishes among associations identified through the
 BEST routine using AIC, and it attributes variance to components in the
 model. Descriptive statistics and LMMs were completed
 using Systat 13 (Inpixon, San Jose, CA), and multivariate tests were
 completed using Primer 7.0 and PERMANOVA+. Statistical assumptions of LMM
 were evaluated through graphical analyses of residuals. Although MDS,
 SIMPROF, and DISTLM make no explicit assumptions about the distribution of
 the data, attention was paid to stress and avoidance of collinearity in
 the DISTLM.
description: # Data from: Decadal-scale time series highlight the role of chronic
 disturbances in driving ecosystem collapse in the Anthropocene
 [https://doi.org/10.5061/dryad.x0k6djht1](https://doi.org/10.5061/dryad.x0k6djht1) The data managed here describe how coral community structure at two sites (Yawzi Point and Tektite) have changed over 37 years based on mostly annual samplings. The data originated form 1 x 1 m quadrats recorded photographically at fixed positions on the reef.  Ten quadrats are recorded along each of three transect lines, each ~ 10 m long and 5 m apart at each site. Images are analyzed using a grid of 200 randomly-located dots and analyses are completed with (a) functional group resolution, and (b) by coral genus ## Description of the data and file structure **File 1: Yawzi_Point_Functional_Groups_1987_2022** This files contains functional group data for Yawzi Point: These data support Figures 1A and 3A, and describe how the community structure at Yawzi Point has changed with functional group resolution Site = location where work was completed, Yawzi Point, 9 m depth Year = time of sampling with mostly year resolution. A decimal notation is used in rare cases to denote sampling in multiple months each year. For example, 2017.07 = July 2017 Transect = Transect along which sampling occurred, 1, 2 or 3 Quadrat = photoquadrat from which data were obtained, values 1–10 reflecting contiguous photoquadrats along one of the transect lines % All Coral = percentage cover of all corals combined in each quadrat % Macroalgae = percentage cover of all macroalgae in each quadrat % CTB = percentage cover of crustose coralline algae + algal turf + bare space in each quadrat nd = 999 **File 2: Tektite_Functional_Groups_1987_2022** This files contains functional group data for Tektite: These data support Figures 1B and 3B, and describe how the community structure at Tetite has changed with functional group resolution Site = location where work was completed, Yawzi Point, 9 m depth Year = time of sampling with mostly year resolution. A decimal notation is used in rare cases to denote sampling in multiple months each year. For example, 2017.07 = July 2017 Transect = Transect along which sampling occurred, 1, 2 or 3 Quadrat = photoquadrat from which data were obtained, values 1–10 reflecting contiguous photoquadrats along one of the transect lines % All Coral = percentage cover of all corals combined in each quadrat % Macroalgae = percentage cover of all macroalgae in each quadrat % CTB = percentage cover of crustose coralline algae + algal turf + bare space in each quadrat nd = 999 **File 3: Yawzi_Point_Genus_1987_2022** This files contains coral genus data for Yawzi Point: These data support Figure 3C and describe how the coral community structure at Yawzi Point has changed with genus resolution Site = location where work was completed, Yawzi Point, 9 m depth Year = time of sampling with mostly year resolution. A decimal notation is used in rare cases to denote sampling in multiple months each year. For example, 2017.07 = July 2017 Transect = Transect along which sampling occurred, 1, 2 or 3 Quadrat = photoquadrat from which data were obtained, values 1–10 reflecting contiguous photoquadrats along one of the transect lines Columns entitled with coral genera report percentage cover by genus for each quadrat for taxa shown below: Orbicella Montastrea Agaricia Colpophyllia Dichocoenia Diploria Eusmilia Favia Madracis Meandrina Porites Stephanocoenia Siderastrea Manicina Mycetophyllia Acropora Isophyllastrea Scolymia Solenastrea Millepora nd = 999 **File 4: Tektite_Genus_1987_2022** This files contains coral genus data for Tektite: These data support Figure 3D and describe how the coral community structure at Tektite has changed with genus resolution Site = location where work was completed, Yawzi Point, 9 m depth Year = time of sampling with mostly year resolution. A decimal notation is used in rare cases to denote sampling in multiple months each year. For example, 2017.07 = July 2017 Transect = Transect along which sampling occurred, 1, 2 or 3 Quadrat = photoquadrat from which data were obtained, values 1–10 reflecting contiguous photoquadrats along one of the transect lines Columns entitled with coral genera report percentage cover by genus for each quadrat for taxa shown below: ``` Orbicella Montastrea Agaricia Colpophyllia Dendrogyra Dichocoenia Diploria Eusmilia Favia Madracis Meandrina Mussa Porites Stephanocoenia Siderastrea Manicina Mycetophyllia Scolymia Helioseris Solenastrea Millepora ``` nd = 999 ## Sharing/Access information Data also hosted here: [https://coralreefs.csun.edu/data/](https://coralreefs.csun.edu/data/) ## Code/Software Commercial statistical software was used: Primer 7.0 software (Clarke and Gorley 2015) Systat 13 (Inpixon, San Jose, CA)