DOI: 10.5061/dryad.np5hqc02d
title: Out of shape: Ocean acidification simplifies coral reef architecture and reshuffles fish assemblages

description: Climate change stressors are progressively simplifying biogenic habitats
 in the terrestrial and marine realms, and consequently altering the
 structure of associated species communities. Here, we used a volcanic CO2
 seep in Papua New Guinea to test in situ if altered reef architecture due
 to ocean acidification reshuffles associated fish assemblages. We observed
 replacement of branching corals by massive corals at the seep, with
 simplified coral architectural complexity driving abundance declines
 between 60-86% for an assemblage of damselfishes associated with branching
 corals. An experimental test of habitat preference for a focal species
 indicated that acidification does not directly affect habitat selection
 behaviour, with changes in habitat structural complexity consequently
 appearing to be the stronger driver of assemblage reshuffling. Habitat
 health affected anti-predator behaviour, with P. moluccensis becoming less
 bold on dead branching corals relative to live branching corals,
 irrespective of ocean acidification. We conclude that coral reef fish
 assemblages are likely to be more sensitive to changes in habitat
 structure induced by increasing pCO2 than any direct effects on behaviour,
 indicating that changes in coral architecture and live cover may act as
 important mediators of reef fish community structures in a future ocean.
description: <strong>Data Collection:</strong>
 <strong>Study sites:</strong> data were
 collected from two coral reefs near Upa-Upasina, Papua New Guinea: one
 acidified by natural CO2 seeps and a nearby control reef with ambient pCO2
 levels. <strong>Benthic Habitat
 Cover:</strong> Photo quadrats (40
 control, 31 seep) were taken at 1 meter distance from the
 substrate. Coral cover was analysed using
 CoralPointCount software, categorising each point into live or dead coral
 and three morphologies (branching, massive, rubble).
 <strong>Fish
 Density:</strong> Visual surveys
 conducted on SCUBA using belt transects (10x4 m for larger species, 10x2 m
 for smaller species). Surveys recorded densities of
 five damselfish species. 
 <strong>Habitat Use:</strong> 
 In situ video recordings captured fish interactions with
 habitats. Videos analysed to determine time spent in
 each habitat type, categorised by health and morphology.
 <strong>Aquarium Habitat
 Choice</strong> <em>P.
 moluccensis</em> individuals placed in aquaria with paired habitat
 types. Time spent in each habitat was recorded to
 assess preference without external influences. 
 <strong>Flight Initiation Distance
 (FID):</strong> FID measured as the
 distance at which fish fled from an approaching artificial startle
 cue. FID data collected for five species across both
 sites, with additional detail for <em>P. moluccensis</em>
 regarding habitat type. 
 <strong> </strong><strong>Data
 Processing:</strong> <strong>1.    
 </strong><strong>Coral Cover
 Analysis:</strong> Digital
 images processed with CoralPointCount to calculate percentage cover for
 each category. <strong>Fish
 Surveys:</strong> Densities
 calculated per 10 square meters, with data recorded in Excel.
 <strong>Video
 Analysis:</strong> Videos analysed
 using VLC media player. Habitat use expressed as a
 percentage of total observations for each fish. 
 <strong>Aquarium Experiments:</strong>
 Time in each habitat type recorded and expressed as a
 proportion of total observation time. 
 <strong>Flight Initiation Distance
 measurements:</strong> Distances
 measured from video recordings using VLC, referencing a ruler for
 accuracy.
description: # Out of shape: ocean acidification simplifies coral reef architecture and
 reshuffles fish assemblages
 [https://doi.org/10.5061/dryad.np5hqc02d](https://doi.org/10.5061/dryad.np5hqc02d) This dataset originates from a study examining the effects of ocean acidification on coral reef structural complexity and associated impacts on damselfish assemblages at Upa-Upasina, Milne Bay Province, Papua New Guinea. The study focused on comparative analyses between a naturally acidified shallow coral reef and a control site with ambient pCO2 conditions. Data collection occurred in June 2018. ## Description of the data and file structure The dataset includes the following six spreadsheets: 1. **Benthic cover** - Contains data on the percentage cover of five broad habitat categories (live branching, dead branching, live massive, dead massive, rubble) across two treatment locations (control, seep). Data were collected from photo quadrats (40 control, 31 seep) taken at 1 meter distance from the substrate.  *Variables* *Treatment:* Location at which cover was analysed; control (ambient pCO2), seep (elevated pCO2). *Live branching:* Percentage cover of living coral with complex, branching structure *Live massive:* Percentage cover of living cover with simple, massive structure *Dead branching:* Percentage cover of dead corals with intact/minimally degraded branching structure *Dead massive:* Percentage cover of dead corals with intact/minimally degraded massive structure *Rubble:* Percentage cover of dead coral fragments  2. **Fish density** - Records densities (per 10 square meters) of five focal damselfish species in each treatment location. Data were obtained through visual surveys conducted on SCUBA using belt transects (10x4 m for species with a larger home range - *A. polyacanthus* and *A. curacao*, 10x2 m for species with a smaller home range). Data are presented as densities per 10m2.  *Variables* *Species:* Species name of each of five focal damselfishes (*A. polyacanthus, A. curacao, D. aruanus, P. adelus, P. moluccensis*) *Treatment*: Location at which densities were surveyed; control (ambient pCO2), seep (elevated pCO2). *Density (10m2*): Standardised measure (individuals per 10m2) to account for variation in transect belt widths 3. **Habitat use** - Details the proportion of time each of the five focal damselfish species spent in each of the five broad habitat categories, collected from in-situ video recordings at control and seep locations. Habitat use is expressed as a percentage of total observations (taken every 15 seconds) for each fish. This sheet is used to assess habitat selectivity and preference, contrasting proportion time spent in each habitat against proportion of habitat available.  *Variables:* *Treatment:* Location at which in situ video was recorded; control (ambient pCO2), seep (elevated pCO2). *Fish species*: Species identity of focal individual  *lb*: Proportion of observations recorded in live branching coral habitats *lm*: Proportion of observations recorded in live massive coral habitats *db*: Proportion of observations recorded in dead branching coral habitats *dm*: Proportion of observations recorded in dead massive coral habitats *r:* Proportion of observations recorded in coral rubble habitats 4. **Aquarium (habitat choice)** - Data from an aquarium experiment involving *Pomacentrus moluccensis*, showing the proportion of time spent in two available habitat types (equal availability), to assess habitat preference in controlled conditions. Time in each habitat type was derived from video recordings and expressed as a proportion of total observation time. *Variables:* *Treatment*: Location from which individual *P. moluccensis* were sourced before being introduced to the aquarium; control (ambient pCO2), seep (elevated pCO2). *Comparison*: List of two equally available habitats presented to the individual fish being tested (db/lm: dead branching/live massive; lb/db: live branching/dead branching; lb/lm: live branching/live massive; lm/dm: live massive/dead massive).  *Fish number*: Unique number assigned to each individual fish in each aquarium trial (individuals were not tested across multiple trials) *nc*: Proportion time spent without associating with either available habitat *lb:* Proportion time spent associating with live branching habitat *lm:* Proportion time spent associating with live massive habitat *db:* Proportion time spent associating with dead branching habitat *dm:* Proportion time spent associating with dead massive habitat 5. **FID (all species)** - Flight initiation distance (FID) data, indicating the distance at which each species responded to an artificial startle cue, for both control and seep locations. Distances were measured from video recordings using VLC, referencing a ruler for accuracy. *Variables:* *Treatment*: Location at which individual damselfishes were tested; control (ambient pCO2), seep (elevated pCO2). *Species:* Species identity of focal individual  *FID:* Distance in cm at which individual fled the approaching startle cue 6. **FID (moluccensis)** - Detailed FID data for *Pomacentrus moluccensis*, including the habitat type during testing, across both control and seep locations.  *Variables:* *Treatment:* Location at which individual *P. moluccensis* were tested; control (ambient pCO2), seep (elevated pCO2). *Habitat:* Habitat in which individual *P. moluccensis* were located at the time of testing - live branching, live massive, dead branching, dead massive *FID:* Distance in cm at which individual fled the approaching startle cue