Background & Summary

We describe here a unique long-term data set describing coral cover in a series of permanent photo quadrats established on Heron Island Reef since 1962. Heron Island (23o26′ S, 151o55′ E) is located at the southern end of Australia’s Great Barrier Reef, around 65 km offshore from the mainland, and is surrounded by a broad platform reef. A series of quadrats were established by JH Connell at four intertidal or shallow subtidal locations across the reef (Fig. 1), representing different environments and levels of exposure to cyclones. These quadrats were monitored close to annually up until 2018, and in some early years sub-annually, although some sites were lost earlier due to loss of marker stakes. Photographs from one survey in each year up until 2012 have been orthorectified, and manually digitised to map the outline of each coral colony present, thus allowing the area of each colony to be calculated. The data set thus includes both percent cover, by coral species, as well as the size distribution of colonies. Full data for the exposed and protected crests are presented here, these being the two sites still extant. The exposed pools and protected inner flat sites have been lost, and the data sets for these have not been through full QA/QC, so only the images and shapefiles are included.

Fig. 1
figure 1

Map showing the location of Heron Island (red circle on inset), and the study sites described here. Colour coding indicates subsites grouped together as a single site, stars indicate sites still extant in 2019 and circles indicate site where the marker stakes had been lost prior to 2019. Main image source: Google Earth.

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At each site, different numbers of permanent quadrats were established. At most sites, the quadrats were contiguous, so do not constitute independent replicates. However, this should be viewed in the context of the unique temporal replication and taxonomic resolution1, and the difficulties in collecting data such as this prior to the advent of digital cameras.

Observations and data derived from earlier parts of this study have been influential in the development of ecological theory. In particular, they featured in the formalisation of the intermediate disturbance hypothesis2, as well as the Connell-Slatyer model of ecological succession3. More detailed analysis of earlier parts of these, and related data sets, explore the role of disturbance4,5 and competition6 in coral dynamics. Data from the study have also been used in a number of modelling studies of coral community dynamics7,8,9,10,11. These previous analyses were based on an independent extraction of data from the images using hand drawn paper maps. An analysis of the exposed and protected crest data sets presented here suggests that full recovery in both species composition and size distribution can occur over decadal time scales after a major cyclonic disturbance despite the removal of all corals and the alteration of the drainage pattern of the reef flat. However, if environmental factors don’t return to pre-disturbance conditions, then recovery will not necessarily occur1.

Given that this is the only study of coral communities with such temporal length and resolution, as well species level taxonomic resolution, the data are likely to be valuable in helping to place more recent studies with higher geographic resolution and/or extent into a better historical context. Full documentation of the data set will also allow others to continue the study on into the future, further building on Prof. Connell’s legacy.

Methods

Study site and field data collection

Permanent 1 m2 photoquadrats were established on Heron Reef in 1962/63, using 9 mm diameter mild steel (rebar) pegs, which were replaced over time. From the 1990’s, replacement pegs were stainless steel for greater longevity. Four sites were established, the protected (south) crest, inner flat, exposed (north) crest and exposed pools. Co-ordinates for each site are presented in Table 1, the layout shown in Fig. 2, and sites have been well described previously5,6. At each census, a 1 m2 frame divided into a 5 × 5 grid using string was placed over the pegs, and the quadrat photographed from directly above at low tide. From 1963 until 2003, a 35 mm camera and colour slide film were used. The camera was attached to a tripod affixed to the 1 m2 frame, and captured around 2/3 of the quadrat. The frame (and camera) were then rotated 180 degrees to capture the remainder of the quadrat. After 2003, a hand-held digital camera was used, with the entire quadrat being captured in a single image. Concurrent with each census, mud maps of each quadrat were hand drawn in the field, and all colonies identified in situ by someone with expertise in coral taxonomy.

Table 1 Coordinates of the study sites on Heron Island Reef (WGS84).
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Fig. 2
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Quadrat layouts for each of the four sites respectively, noting that the north crest and north ridge have been treated as a single north crest site in previous publications. Underlining indicates original 1962/63 quadrats. Other quadrats were added in or after 2008, as indicated in the text. Contiguous quadrats are pictured bordering each other. Spacing between separate quadrats or groups of quadrats is not shown to scale. Note that up until 2005, NRNW was known as NR. The acronyms in each quadrat represent its name.

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At the protected (south) crest, a set of six contiguous quadrats were established in 1963 in a 2 × 3 arrangement parallel to the waterline, and about 420 m southeast of the island. This site is exposed at low tide, and was photographed once all water had drained off it. Images of quadrats A, C & E (the shoreward row) from 1963 to 2012 have been fully processed, and the data have been through QA/QC. Data after 2012 exist as images only. These quadrats form the basis of previous analyses1,4,5,6 for this site. Photographs are available for quadrats B, D & F, but apart from 2003–2010, have not been processed. In 2010, an additional two quadrats were established either side of the original six, leading to a 2 × 5 arrangement. Again, only imagery is available for these additional quadrats.

At the inner flat, two pairs of contiguous quadrats were established in 1962, 44 m apart, about 70 m south of the island. This site is covered by ~10 cm of water at low tide, so could only be photographed on a still day. Imagery for this site is only available to 2012, after which the marker stakes appear to have been removed in a cleanup of the area. Images for one quadrat in each pair have been processed, but have not been subject to full QA/QC.

At the exposed (north) crest main site, a set of four contiguous quadrats was established about 1100 m northeast of the island in 1963. An additional single quadrat (north ridge) was established 326 m to the east. Images from 1963 to 2012 have been fully processed, and the data have been through QA/QC. Data after 2012 exist as images only. In 2005, the single north ridge quadrat was expanded to 4 m2, and in 2008, both subsites were expanded to six quadrats in a 2 × 3 arrangement. These additional quadrats have been digitised up to 2012, but have not been through full QA/QC.

The exposed pools are two individual quadrats about 5 m apart about 30 m north of the eastern (north ridge) exposed crest site. These are on the edge of a natural pool, and range from ~5–50 cm deep at low tide, and so could only be photographed on a calm day. Imagery for this site is only available until 2005, after which the marker stakes could not be relocated. Images from 1963 to 1998 have been processed, but have not been through full QA/QC.

Retrieval of coral composition data from the photoquadrats

Processing of the images involved scanning the colour slides to produce digital images, and then orthorectifying each image to a 1 m2 basemap in ArcGIS (ESRI Ltd). The corners of the frame, and the holes for the string grid, were used as control points for the orthorectification. For images that originated as colour slides, each half of the quadrat was individually orthorectified to the same basemap, producing a single image of the entire quadrat (see Fig. 3). While contiguous quadrats were orthorectified individually, they were done so against a basemap containing all quadrats in the group, meaning that the resulting images can be easily merged to create a single image of the group. The outlines of all visible coral colonies (>~1 cm2), and other benthic organisms such as algae and clams, were then digitised in ArcGIS to create a single shapefile for each quadrat for each year. Each colony was represented as an individual feature within the shapefile, and was assigned a unique colony number and species based on the mud maps drawn in the field. Colony numbers were consistent across years, allowing individual colonies to be tracked over time. If a colony underwent fission, the original colony number was retained for each, with the addition of a unique identifier after a decimal point. For example, if colony 35 split in two, the resultant colonies were identified as 35.1 and 35.2. If 35.2 later split again, the resultant colonies were identified as 35.2.1 and 35.2.2. If the colony overlapped the edge of the quadrat, only the area within the quadrat was digitised, and a flag was applied to indicate that only part of the colony was included (edgestatus = 1 in the data). Upon completion of digitisation, ArcGIS was used to calculate the area and perimeter of all colonies. While multiple census were conducted in 1963, 1971 and 1983, only a single census in each year has been processed. There are currently no plans to undertake further digitisation or QA/QC of this data set.

Fig. 3
figure 3

Example orthorectified and stitched (prior to 2001) images from the NCNE quadrat, showing the effects of a cyclone that removed all colonies in 1972, and slow recovery over subsequent decades.

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Data Records

The data are available on figshare12 and are detailed in Tables 2–5. All scanned and digital slides are provided as jpeg files (.jpg) along with accompanying files created during the orthorectification process (.jgwx,.jpg.aux.xml, and.ovr). The results of the digitisation process are provided as shapefiles (.shp) and their accompanying files (.dbf, .shn, .sbx and .shx). File names include the quadrat name (as per Fig. 2), the year, and sometimes the month and day the image was taken. For scanned slides, there are generally two images for each date, labelled N and S, or E and W, indicating the cardinal direction of each half of the quadrat. For any images not orthorectified, shapefiles for the basemaps are also provided. The final processed data set is provided as a single csv file for each quadrat, with the fields detailed in Table 6. The shapefiles also contain colony perimeter, and several other parameters that were used for internal processing that can be ignored.

Table 2 Data availability for the protected (south) crest12.
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Table 3 Data availability for the inner flats12.
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Table 4 Data availability for the exposed (north) crest12.
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Table 5 Data availability for the exposed pools12.
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Table 6 Description of data present in the final processed data set.
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Technical Validation

The first step of the data validation occurred in the field, with the taxonomic expert present double-checking each mud map to ensure that all colonies had been included and were consistently identified. Data for the protected and exposed crests have also been through a number of computer-based quality control steps described below to ensure that they are reliable. This quality control process has not been completed for the inner flat or the exposed pools, and hence only images and shapefiles are presented for these two sites. It is strongly recommended that before any data is extracted from these files, the steps described below are followed.

All digitising and taxonomic identifications were checked, and where necessary, refined by the lead author to remove inconsistencies between the multiple operators who undertook the initial image processing. The initial step involved closely checking each quadrat to ensure colony outlines were correctly located, and that all colonies had been included both according to what was visible in the image, and what was recorded in the field on the mud map. Sequential pairs of digitised images were then compared side-by-side to ensure any colonies recorded as lost were not present in the later image, that all new colonies were not present in the earlier image, and that species identifications were consistent. A second taxonomic check involved creating a pivot table of colony number against year, using the sum of species number. The average of the sum of species number across years was then subtracted from the species number. Any difference from zero indicated either changes in the species assigned to the colony over time, or multiple colonies assigned the same number. The digitised images were then carefully checked to resolve discrepancies. In the process, all coral taxonomy was updated to that presented by Veron13. There has been no revision to incorporate recent taxonomic changes. This validation has only been undertaken for corals and other benthic invertebrates. No validation has been done for algae, and thus data for these should not be relied upon without further work.

As species level taxonomy could be difficult to distinguish in the images for some species, to ensure that changes in community composition over time were not related to changes in taxonomy, the data set has been analysed by pooling species into groups that could potentially be mistaken for each other. This produced identical ordination plots to those produced for the species level taxonomy at both the exposed and protected crests1, providing evidence that there are no major taxonomic inconsistencies across the data set for these two sets of quadrats.