Perry 1 Perry et al. Data Repository Items Appendix DR1. Sedimentary Setting The main source of muddy terrigenous sediment to the central section of the GBR is the Burdekin River, located approximately 100 km south of Paluma Shoals. Flows in the Burdekin are highly seasonal (>90% of annual discharge typically occurs between January and April) and variable from year to year, but its mean annual discharge (~ 10 x 10 6 Ml) is the largest entering the Great Barrier Reef (GBR) lagoon. Estimates of mean annual sediment export to the GBR shelf vary from 2.7 Mt (Moss et al. 1983) to 9.0 Mt (Neil and Yu, 1996; Neil et al., 2002). The Ross, Bohle and Black Rivers are important sources of coastal sediment closer to Paluma Shoals, with an average combined annual sediment yield estimated at between 0.13 0.55 Mt (Belperio, 1983). Sediment is transported northwards by longshore wave- and wind-driven currents (Larcombe and Woolfe, 1999), but sediment accumulation rates decrease northwards from the river mouths with long-term accumulation rates of < 0.1 mm yr -1 calculated for Halifax Bay (Woolfe and Larcombe, 1998). The reefs in the vicinity of Paluma Shoals experience prolonged high turbidity events (up to 175 nephelometric turbidity units (NTU) and >40 NTU for more than 40 % of the time) driven by wavedriven resuspension of subtidal terrigenous sediment (Larcombe et al., 2001). This site is appropriate as a location to examine long-term records of coral community response to terrigenoclastic sediment influence and to test the effects of alleged post-european settlement deteriorations in water quality because: (1) The reefs occur within inner-shelf areas that have been a focus for terrigenous sediment accumulation through the mid-late Holocene (Larcombe and Woolfe, 1999), (2) Post-European settlement sediment yields for the proximal Ross and Black Rivers are estimated to be 3 times higher than during pre-european times (Neil et al., 2002),
Perry 2 (3) The reefs occur within inner-shelf areas that are episodically influenced by flood plumes (Devlin and Brodie, 2005) and within nearshore zones regarded as at risk from land-derived sediments and nutrients, (4) The site is near other reefs (Havannah and Pandora Reefs, located some 17 km further offshore) where Ba/Ca records in coral skeletons indicate marked increases in sediment influx post-european settlement (McCulloch et al., 2003), and (5) The reefs are located within areas where significant increases in nutrient enrichment in the post- European settlement period have been modelled (Woolridge et al., 2006). References: Belperio, A.P., 1983, Terrigenous sedimentation in the central Great Barrier Reef lagoon: a model from the Burdekin region. BMR Journal of Australian Geolology & Geophysics, v. 8, p. 179-190. Devlin, M. J. and Brodie, J., 2005, Terrestrial discharge into the Great Barrier Reef Lagoon: nutrient behaviour in coastal waters: Marine Pollution Bulletin, v. 51, p. 9-22. Larcombe, P. and Woolfe, K.J., 1999, Terrigenous sediments as influences upon Holocene nearshore coral reefs, central Great Barrier Reef, Australia: Australian Journal of Earth Sciences, v. 46, p. 141-154. Larcombe, P. Ridd, P.V., Prytz, A., and Wilson, B., 1995, Factors controlling suspended sediment on inner-shelf coral reefs, Townsville, Australia: Reefs, v. 14, p. 163-171. McCulloch M., Fallon, S., Wyndham, T., Hendy, E., Lough, J., and Barnes, D., 2003, record of increased sediment flux to the inner Great Barrier Reef since European settlement: Nature, v. 421, p. 727-730. Moss, A., Rayment, G.,Reilly, N., and Best, E., 1983, Sediment and nutrient exports from Queensland coastal catchments: a desk study. Department of Environment and Heritage, Brisbane. Neil, D. and Yu, B., 1996, in H. Hunter, A. Eyles, and G. Rayment, Downstream effects of land use change. Department of Natural Resources, Rockhampton. Neil, D. T., Orpin, A. R., Ridd, P. V., and Yu, B., 2002, Sediment yield and impacts from river catchments to the Great Barrier Reef lagoon: Marine and Freshwater Research, v. 53, p. 733-752. Woolfe, K.J., and Larcombe, P., 1998, Terrigenous sediment accumulation as a regional control on the distribution of reef carbonates, in Camoin, G.F., and Davies, P.J. (Eds.) Reefs and Carbonate Platforms in the Pacific and Indian Oceans. Blackwells, Oxford. pp. 295-310. Wooldridge, S., Brodie, J. and Furnas, M., 2006, Exposure of inner-shelf reefs to nutrient enriched runoff entering the Great Barrier Reef Lagoon: Post-European changes and the design of water quality targets: Marine Pollution Bulletin, v. 52, p. 1467-1479.
Perry 3 Appendix DR2. Materials and Methods 1. Fieldwork and core recovery Core sites were selected to achieve maximum coverage across the reef structure from landward to seaward reef flats. Cores (with the exception of Core PS1/2 recovered using a Jacro 100 system) were recovered using percussion techniques (using aluminium core piping with an internal diameter of 9.5 cm). Cores were up to 2.9 m in length and had 100 % recovery. Rates and depths of core penetration were recorded throughout to ensure a reliable depth chronology and to constrain for sediment compaction (typically ~20%, and which, based on core penetration rates, was uniform down-core). Cores were stored in a cold room after collection. 2. Core logging and sediment facies analysis Recovered cores were split in half using a circular saw to cut through the aluminium pipe, and digital photo composites of each core prepared. Cores were logged to record basic biosedimentary facies information. Data collected included; the ratio of coral clasts to matrix, description of framework fabrics (following Embry and Klovan, 1971), preliminary coral species identification (based on descriptions in Veron and Stafford-Smith, 2002), sediment textural characteristics using the Udden-Wentworth nomenclature, as well as a visual assessment of sediment composition. These criteria were used to delineate basic facies units within the cores (see Fig. 2). Subsequent and more detailed sedimentary analysis included assessments of sediment texture (mean grain size, sorting) and carbonate content based on sub-sampling matrix material at 10 cm downcore intervals. Sediment texture was determined by sieving the 8mm to 63µm size fractions (following the methods in McManus, 1994) and then further analysing the <63µm fraction using a Beckman Coulter Counter. The results of these analyses were combined using the computer programme GRADISTAT (Blott and Pye, 2001), from which values of mean grain size and sorting
Perry 4 were taken (descriptive nomenclature of Udden-Wentworth is used throughout). CaCO 3 content was determined from sub-samples of known weight that were treated in a 2M HCl solution until no discernible reaction with the carbonate could be detected. Samples were then filtered through preweighed Whatman 42 filter papers and oven dried. Replicate samples indicated that results were reproducible to within 3%. Carbonate content is reported as % dry weight of the dried original sample. 3. Modern Reef Community Surveys and Taxonomic Analysis of s in Core. Quantitative assessments of contemporary reef community structure were made on an across reef basis based on digital photograph quadrat surveys (10 images per station) undertaken at each of 21 equidistant sampling stations. s were identified to genus level and data grouped into landward, central and seaward zones on the basis of variations in the relative abundance of coral taxa. Data on coral abundance in cores were based on the recovery of all coral material (>1 cm in size) recovered from each 20 cm down-core unit. specimens were examined and grouped based on morphology and skeletal architecture. Each sample group was given a unique identifying code that was used as a basis for recording the composition of all coral material identified in core. samples were subsequently analysed under both binocular and Scanning Electron Microscope (SEM) to examine details of coral microarchitecture and skeletal structure. High-quality coral preservation allowed, in most cases, species-level discrimination (based on reference to taxonomic features in Wallace (1999) and Veron and Stafford-Smith (2002), and reference to the coral collections at the Museum of Tropical Queensland, Townsville). Using this taxonomy, species/genera names were related to material associated with each identifier code and used to examine species abundance down-core. abundance data were analysed in each down-core interval (excluding those that could not be accurately identified either due to size or preservation) and presented as percentage abundance data (see Fig. 2).
Perry 5 4. Statistical Treatment of Community Data. One-way Analysis of Similarity (ANOSIM) was used to explore variation in the fossil coral assemblages among depth and time intervals and to compare living communities with fossil assemblages. Because of the difficulty of producing accurate species-level determinations using photo transects, the living coral community data was collected at genus level. Species-level determinations are available for the core record, but except for Acropora (2 species identified), all genera identified were represented by a single species. The first Acropora species (A. muricata) was extremely rare (2 fragments from one sample), and the other species (A. pulchra) was by far the most common taxon in the analysis. Therefore, these two taxa have been merged to enable a genuslevel analysis that is more directly comparable to the composition of living communities. For fossil assemblages, Bray-Curtis dissimilarities were calculated among assemblages recovered from each 20 cm downcore interval using square-root transformed species abundances, rank species abundances, and presence/absence data. Living communities were compared with fossil assemblages calculated from rank abundance and presence/absence data only. All analyses were performed using the R statistical programming language (R_Development_Core_Team, 2006). Four sets of ANOSIM tests were performed. The first set tested the null hypothesis of no significant difference in coral assemblages prior to, and following, changes in land use associated with European settlement. Pre-and post impact cut-offs were placed to bracket a radiocarbon age of 150-200 cal years BP. This interval occurred at lower levels in landward than seaward cores because of different growth histories across the sampled part of the reef (120 cm in PSS-0 and PSPC1/2, 60 cm in PSS-1, and 40 cm in PSS-2, PS1/2, and PSPC3/4). Using these cut-off values, there was no significant difference among assemblages in the pre-impact and post-impact parts of the cores in analyses of root-transformed absolute abundance (p =0.645), rank abundances (p=0.565) or presence/absence (p=0.415) data. A second set of ANOSIMs were performed to test the null hypothesis of no significant difference of coral assemblages in the top 80 cm of the cores
Perry 6 from assemblages in core samples deeper than 80 cm. Tests using log-transformed abundance, rank abundance, or presence/absence data all provided insignificant evidence to reject the null hypothesis suggesting that there was no significant difference in community composition in lower and upper parts of the cores (log abundance p=0.465, rank abundance p=0.255, presence/absence p=0.37). We conclude that no significant change in coral community composition is apparent within the core record since reef initiation. The third and fourth sets of ANOSIMS were designed to compare the composition of the living assemblage with core data from post-impact samples as defined above and samples from the top 80 cm of each core. In each case, analyses performed using both rank abundance and presence/absence provided strong evidence to reject a null hypothesis of no difference between living communities and fossil communities with p-values < 0.001. Clear differences thus exist between the living reef-flat community and the record of communities preserved in core in both the post-european interval and the shallowest intervals (<80 cm depth) regardless of their age within core. References: Blott, S.J., and Pye, K., 2001, Gradistat: a grain size distribution and statistics package for the analysis of unconsolidated sediments: Earth Surface Processes and Landforms (Technical Communication), v. 26, p. 1237-1248. Embry, A.F., and Klovan, J.E., 1971. A Late Devonian reef tract on northeastern Banks Island, Northwest Territories. Bulletin of Canadian Petrolology and Geology, v. 33, p. 730-781. McManus, J., 1994, Grain size determination, in Tucker, M.E., ed., Techniques in Sedimentology, Blackwells, Oxford, p. 63-85. R_Development_Core_Team., 2006, R: A language and environment for statistical computing, version 2.4.1. R Foundation for Statistical Computing, http://r-project.org. Veron, J. E. N., and Stafford-Smith, M., 2002, ID Key to the zooxanthellate scleractinian corals of the world. CD-Rom, Australian Institute of Marine Sciences, Townsville. Wallace, C., 1999, Staghorn s of the World. CSIRO, Collingwood, Australia, 421 p.
Perry 7 Appendix DR3. Radiocarbon Dating of s. Samples selected for radiocarbon dating were sectioned and microsampled to remove surficial calcareous encrustation, washed in distilled water, subjected to ultrasonic agitation in distilled water to remove detrital particles, oven dried (40 o C) and then sealed in plastic bags. Reference is made in the text to a series of radiocarbon-dated cores presented by Smithers and Larcombe (2003), supplemented with a series of additional dates obtained in 2007 (Table 1). Dates were calibrated using Calib 5.0.2 and calibration curve Marine04 (http://calib.qub.ac.uk/marine). The conventionally employed Marine Reservoir Correction in Australian waters is 450 ± 35 years (Gillespie, 1977). However, various studies have indicated significant deviations in regional marine reservoir signatures. The geographically closest sites to Paluma Shoals are from Port Curtis and Gladstone where marine reservoir ages ranging from 240 ± 61 to 419 ± 61 14 C y BP are reported (Ulm, 2002). These combined give a weighted mean ΔR value of +10 ± 7, currently the best estimate of variance in the local open water marine reservoir effect for the central Queensland coast (Ulm, 2002). Core number and sample depth. Lab. code Material δ 13 C ratio Conventional 14 C age (years BP) Calibrated (68.2% probability) cal BP PSS1/B1 SUERC-9967-3.9 ± 0.1 1589 ± 35 1078-1185 PSS-0-A Wk 22132 0.6 ± 02 538 ± 50 98-247 PSS-0-B Wk 22133-2.1 ± 0.2 297 ± 54 <60 PSS-0-C Wk 22134-0.3 ± 0.2 1692 ± 61 1174-1291 PSS-1-A Wk 22129-0.3 ± 0.2 611 ± 43 147-163 PSS-1-B Wk 22130-1.5 ± 0.2 911 ± 44 477-542 PSS-1-C Wk 22131 1.0 ± 0.2 1530 ± 36 1023-1134 PSS-2-A Wk 22135 0.6 ± 0.2 725 ± 36 309-404 PSS-2-B Wk 22136-1.3 ± 0.2 1524 ± 37 1009-1123 PSS-2-C Wk 22141-0.8 ± 0.2 1731 ± 35 1241-1308
Perry 8 Table DR3. Dates from cores from the South Shoal at Paluma Shoals. Sample SUERC 9967 was dated at the NERC Radiocarbon Dating Laboratory at East Kilbride (UK), the remaining samples at the Waikato Radiocarbon Dating Laboratory in New Zealand. Conventional dates were calibrated using Calib 5.0.2 and calibration curve Marine04 (http://calib.qub.ac.uk/marine). References: Gillespie, R., 1977, Radiocarbon dating of marine mollusc shells: Australian Quaternary Newsletter v. 9, p. 13-15. Smithers, S. G., and Larcombe, P., 2003, Late Holocene initiation and growth of a nearshore turbidzone coral reef: Paluma Shoals, central Great Barrier Reef, Australia: Reefs, v. 22, p. 499-505. Ulm, S., 2002, Marine and estuarine reservoir effects in Central Queensland, Australia: Determination of the modern marine calibration curve: Geoarchaeology, v. 17, p. 319-348.
Perry 9 Appendix DR4 Contemporary Reef Flat Assemblages on the South Shoal at Paluma Shoals. taxa Landward reef flat Central reef flat Seaward reef flat Goniastrea sp. 23.8 22.8 20.0 Acropora sp. 10.0 39.3 17.0 Turbinaria sp. 7.5 7.8 2.0 Galaxea sp. 16.3 10.0 45.5 Symphyllia sp. 7.5 2.8 5.5 Lobophyllia sp. 1.3 1.4 1.0 Favia sp. 0.0 0.0 0.5 Montipora sp. 0.0 2.1 1.5 Porites sp. 28.8 10.0 4.0 Oulophyllia sp. 1.3 0.0 0.0 Platygyra sp. 0.0 0.7 1.5 Favites sp. 2.5 2.8 1.5 Fungia sp. 1.3 0.0 0.0 Mean live coral cover 18.6 23.6 52.5 Table DR4. community data (by coral taxa) and mean live coral cover for each of the distinct zones identified on the reef flat of the South Shoal at Paluma Shoals.
Perry 10 Fig. DR4. Contemporary reef flat coral assemblages on the South Shoal at Paluma Shoals. (A) Typical coral communities along the leeward margins of the reef flat that is dominated by extensive low-relief Porites rus pavements and Goniastrea aspera bommies. (B) Detail of leeward reef communities showing colonies of G. aspera, P. rus, Platygyra sp. and Acropora sp. (C) Typical coral communities across the central sections of the reef flat, with abundant G. aspera bommies and extensive carpets of Acropora pulchra. (D) Detail of A. pulchra and a tabular Acropora sp.,
Perry 11 both common across the reef flats. (E) Typical coral communities across the central-windward sections of the reef flats, with abundant G. aspera bommies and expansive colonies of Galaxea fascicularis. (F) Details of central-windward reef flat coral communities with colonies of G. fascicularis, Acropora sp., G. aspera and Turbinaria frondens.