DOI: 10.5061/dryad.mw6m9062r
title: Depth variation in benthic community response to repeated marine heatwaves on remote Central Indian Ocean reefs

description: Coral reefs are increasingly impacted by climate-induced warming events.
 However, there is limited empirical evidence on the variation in the
 response of shallow coral reef communities to thermal stress across depth.
 Here we assess depth-dependent changes in coral reef benthic communities
 following successive marine heatwaves from 2015 to 2017 across a 5–25 m
 depth gradient in the remote Chagos Archipelago, Central Indian Ocean. Our
 analyses show an overall decline in hard and soft coral cover and an
 increase in crustose coralline algae, sponge, and reef pavement following
 successive marine heatwaves on the remote reef system. Our findings
 indicate that the changes in benthic communities in response to elevated
 seawater temperatures varied across depth. We found greater changes in
 benthic group cover at shallow depths (5–15 m) compared to deeper zones
 (15–25 m). The loss of hard coral cover was better predicted by initial
 thermal stress, whilst the loss of soft coral was associated with repeated
 thermal stress following successive warming events. Our study shows that
 benthic communities extending to 25 m were impacted by successive marine
 heatwaves, supporting concerns about the resilience of shallow coral reef
 communities to increasingly severe climate-driven warming events.
description: Study Sites The Chagos Archipelago is a
 remote archipelago located in the Central Indian Ocean. Situated at the
 southern end of the Laccadives-Maldives-Chagos ridge, it covers a total
 area of 640,000 km<sup>2 </sup>and consists of five islanded
 atolls. The archipelago has been uninhabited since the early 1970s, except
 for the US military base on the southern atoll, Diego Garcia (81). Benthic
 community data were collected with repeat sampling, in March–April
 2013/2014 (before) and 2018/2019 (after) following successive severe
 marine heatwaves in 2015–2017. The peaks of marine heatwave events
 occurred between May–June 2015 (4.2 ± 0.4 – 6.1 ± 0.3 °C-weeks) and
 April–June 2016 (12.1 ± 0.1 – 15.8 ± 0.1 °C-weeks) (Figure S1). Surveys in
 each period were carried out at 16 sites on forereef slopes across four
 atolls: Peros Banhos (PB), Salomon (SA), Great Chagos Bank (GCB), and
 Egmont (EG) (Figure 1), and conducted at four depth zones: 5–10 m, 10–15
 m, 15–20 m, and 20–25 m. For ease of interpretation, shallower depth zones
 in the text refer to benthic groups occurring between 5–15 m and deeper
 zones to benthic groups occurring between 15–25 m.
 Data collection and benthic community assessment
 Benthic community assessment was carried out using 10-minute
 continuous video swims conducted at a constant speed (0.1
 ms<sup>-1</sup>) at each site and depth zone. Equipped with
 two spotlights and two red laser pointers set at 10 cm apart, the camera
 set-up provided a scale of measurement of the benthos and adjustment for
 lower light levels at greater depth. During the survey, the camera was
 held approximately 0.5 m above the substrate and at a 45° angle to capture
 benthic organisms and substrate types under overhangs and canopies (82).
 Each video was converted into a sequence of still images (25 frames per
 second in Pinnacle Studio, v22.2.0). Thirty of these images were selected
 for analysis using Matlab (R2018a.Ink) (total across all sites,
 <em>n</em> = 5610). Selected images were separated by 80–100
 frames in each sequence to avoid re-sampling the same area of the
 reef. Benthic composition within each image was
 quantified using Coral Point Count with Excel extensions (CPCe) (83). To
 reduce observer bias, image analysis was equally distributed among SSP,
 RR, and LR (10 images per person per site). The percentage cover of
 benthic organisms and other substrate types was quantified at 15 randomly
 allocated points on each image, using a stratified random design (84). The
 broad classification of benthic groups was adapted from Denis et al.
 (2017) and the NOAA Coral Reef Information System (86). This study
 examined five benthic groups that have been found to undergo shifts in
 dominance and contribute to habitat building on coral reefs following
 thermal stress events: hard coral, soft coral, sponge, crustose coralline
 algae (CCA), and reef pavement (48,87–90). Despite being an important
 competitor to corals (47), macroalgae were not included as we only found
 small changes in macroalgal cover (turf and fleshy macroalgae) following
 marine heatwaves (pre-heatwaves: 6.5 ± 0.2 % and post-heatwaves: 6.0 ±
 0.1%). Estimating change in benthic groups following
 2015–2017 bleaching events The change in benthic group
 cover which occurred following the 2015–2017 warming events was calculated
 using: <em>δ = (</em>log(Vf) -
 log(V0))/t where <em>δ</em> is the
 geometric logarithmic change in cover, <em>V<sub>f 
 </sub></em>is the percentage cover of the benthic group
 collected at the end of the time series, i.e. 2018 or 2019
 and<sub> </sub><em>V<sub>0
 </sub></em> is the percentage cover of benthic groups at the
 beginning of the time series, i.e., 2013 or 2014 and<em>
 t</em> is the duration of the time in years between benthic surveys,
 i.e., before and after the successive marine heatwaves (91). This approach
 optimised the dataset by including surveyed sites that were monitored in
 different years before and after the heat stress event, i.e., to include
 pre-disturbance community data collected in 2013 or 2014 (hereinafter
 pre-heatwaves), and post-disturbance community data sampled in 2018 or
 2019 (hereinafter post-heatwaves). The geometric logarithmic change in
 cover metric allows the quantification and comparison of non-linear time
 series by taking into consideration the exponential decline and increase
 in cover of benthic communities over time (sensu 91) (for example 63,92).
 Compared to other metrics that measure ecological change over time (92),
 the geometric logarithmic rate of change preserves proportionality of
 change in cover (e.g. a 50% to 5% loss is proportionately similar to a 10%
 to 1% loss) and is symmetrical, i.e., produces similar rates of change for
 declines and matching increases (e.g. a 50% to 5% loss and a 5% to 50%
 increase yields the same rates (91).To summarise the geometric logarithmic
 change in cover metric, a negative value represents a loss in benthic
 group cover from pre- to post-heatwaves and a positive value indicates an
 increase in benthic group cover following thermal stress. Variation in the
 change in benthic group cover across depth zones was visualised using a
 forest plot (ggplot: ggplot2 package, (93)). For ease of interpretation,
 the log change in cover was back-transformed to the percentage change in
 cover (Figure S2), using: <em>i =
 (</em>e^<em>δ  - 1) x 100</em> where
 <em>δ</em> is the geometric logarithmic change in cover and ἱ
 is the percentage change in cover. Exposure to
 repeated thermal stress To determine how benthic
 groups were affected by thermal stress across depth zones during the
 2015–2017 marine heatwaves, maximum degree heat week (hereinafter maxDHW)
 was used to quantify thermal anomalies from 2015–2017. DHW is a proxy for
 accumulated thermal stress, represented by a 1°C increase above the local
 mean climatic temperature over a 12-week period at a given pixel and
 expressed as degree Celsius weeks (°C-weeks); and maxDHW is the annual
 maximum accumulated thermal stress in a year. Using the National Oceanic
 and Atmospheric Administration (NOAA) Coral Reef Watch 5 km resolution
 product (94), the annual maxDHW between January 2015 and December 2017 was
 extracted for each study site (using R packages: ncdf4 (95), raster (96),
 rgdal (97) and sp (98)). A DHW threshold of 4°C-weeks may be indicative of
 significant coral bleaching, and a DHW value of 8°C-weeks is a signal for
 severe and widespread bleaching with likely mortality (11,99–102).
 Local-scale hydrodynamics for e.g. upwelling and changes in mixed layer
 depth can influence temperature regime across depth gradients (103,104).
 However, in the absence of depth-specific temperature data from in-situ
 loggers across all study sites,  DHW that were derived from SST were used
 as a proxy of thermal stress experienced along the depth gradient at the
 study sites during the warming events (Figure S1). Here, initial thermal
 stress refers to maxDHW recorded in 2015 in the first year of the
 successive severe heatwaves (4.1–6.4 °C-weeks) and repeated thermal stress
 refers to the cumulative maxDHW recorded in all years from 2015–2017
 (17.1–21.1 °C-weeks, Table S1). Cumulative maxDHW has been shown to be a
 good predictor of bleaching in the Western Indian Ocean (105) and
 therefore the change in benthic group cover following repeated marine
 heatwaves. 
description: All data analyses were performed using R 3.5.1.
description: # Title: Depth variation in benthic community response to repeated marine
 heatwaves on remote Central Indian Ocean reefs This is a brief summary of
 all the datasets used to produce the plots and results for the above paper
 Description of data and structure 1. Percentage cover data of all benthic
 groups (categories): raw.broadcat.csv Dataset content: * Categories -
 refer to benthic groups surveyed: hard coral, soft coral, crustose
 coralline algae (CCA), sponge and reef pavement * Photo.Name - refer to
 each digital photo-quadrat * Year - 2013/2014 refers to data collected
 before the 2015-2017 marine heatwaves * 2018/2019 refer to data collected
 after the 2015-2017 marine heatwaves * Atoll - where data was collected
 EG: Egmont, GCB: Great Chagos Bank, SA: Salomon, PB: Peros Banhos * Site -
 refer to sites around each atoll where data was collected * Heatwaves -
 post refers to 2018/2019 when data was collected after 2015-2017 marine
 heatwaves, pre refers to 2013/2014 when data was collected before
 2015-2017 marine heatwaves * Depth - refer to 4 depth zones 5-10 m, 10-15
 m, 15-20 m, and 20-25 m. 2. Change in benthic group cover following
 2015-2017 marine heatwaves with initial and cumulative thermal stress
 data: broadcat_log_change_temp.csv * Columns of each benthic group - CCA,
 hard coral (hc), reef pavemnt (pavement), soft coral (sc), and sponge
 refer to log change in cover following marine heatwaves * dhw2015 - refers
 to initial thermal stress, the first years of 2015-2017 marine heatwaves *
 cum_dhw - refers to cumulative thermal stress, over the 3 years of the
 2015-2017 marine heatwaves 3. Mean predicted change in benthic group cover
 (%) across depth and atoll: pred_means_cca.csv, pred_means_hc.csv,
 pred_means_pavement.csv, pred_means_sc.csv, pred_means_sponge.csv *
 Predmean - refers to the mean predicted change in cover estimated from
 Bayesian models for each benthic group * predsd - refers to the standard
 deviation of the mean predicted change estimated from the Bayesian models
 for each benthic group * A .csv file is provided separately for each
 benthic group 4. Effects of depth on the change in benthic groups across
 atoll derived from Bayesian models: av_cca_depth_atoll_effects.csv,
 av_hc_depth_atoll_effects.csv, av_pavement_depth_atoll_effects.csv,
 av_sc_depth_atoll_effects.csv, av_sponge_depth_atoll_effects.csv * .value
 - refers to effects of depth * .lower and .upper - refer to lower and
 upper values at 50% (.width = 0.5) and 95% (.width = 0.95) credible
 intervals * .point - refers to the median estimate * .interval - refers to
 the highest density interval (hdi) * pred.change - refers to the predicted
 change in cover estimated from Bayesian models for each group * lower and
 upper - refer to the lower and upper values of predicted change at 50%
 (.width = 0.5) and 95% (.width = 0.95) credible intervals 5. Posterior
 distributions of the effects of thermal stress - initial and cumulative on
 the change in benthic group cover following 2015-2017 marine heatwaves:
 alldhw_postdist_cca.csv, alldhw_postdist_hc.csv,
 alldhw_postdist_pavement.csv, alldhw_postdist_sc.csv,
 alldhw_postdist_sponge.csv * dhw_2015_c and cum_dhw_c - refer to centered
 initial and cumulative thermal stress data * hw2015 and cumdhw - refer to
 initial and cumulative thermal stress data * .value - refers to the
 predicted thermal stress (initial and cumulative) effect values from 4000
 posterior draws (.draw) from Bayesian models for thermal stress