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Historical records of terrestrial sediment and flood plume inputs to the Whitsunday Island region from

coral skeletons: 1861-2017

Neal Cantin, Yang Wu, Stewart Fallon and Janice Lough

Project Milestone Report prepared for CSIRO and DOEE

May 2019

Australian Institute of Marine SciencePMB No 3Townsville MC Qld 4810

PO Box 41775Casuarina NT 0811

The UWA Oceans Institute (M096)Crawley WA 6009

This report should be cited as:Cantin NE, Wu Y, Fallon S and Lough JM (2019) Historical records of terrestrial sediment and flood plume inputs to the Whitsunday Island region from coral skeletons: 1861-2017. Australian Institute of Marine Science, Townsville, Qld. (30pp).

© Copyright: Australian Institute of Marine Science (AIMS) [2019]All rights are reserved and no part of this document may be reproduced, stored or copied in any form or by any means whatsoever except with the prior written permission of AIMS

DISCLAIMERWhile reasonable efforts have been made to ensure that the contents of this document are factually correct, AIMS does not make any representation or give any warranty regarding the accuracy, completeness, currency or suitability for any particular purpose of the information or statements contained in this document. To the extent permitted by law AIMS shall not be liable for any loss, damage, cost or expense that may be occasioned directly or indirectly through the use of or reliance on the contents of this document.

Vendor shall ensure that documents have been fully checked and approved prior to submittal to clientRevision History: Name Date Comments

1Prepared by: Neal Cantin & Janice

Lough2 May 2019

Approved by: Britta Schaffelke 7 May 2019Reviewed by: Mark Baird 13 May

20192

Revised Final Neal Cantin 16 May

draft 2019

CONTENTS

1 EXECUTIVE SUMMARY..................................................................................61.1 PURPOSE...................................................................................................61.2 PROJECT SUMMARY...................................................................................61.2.1 KEY FINDINGS........................................................................................7

2 INTRODUCTION............................................................................................82.1 Massive corals as historical archives of growth rates and the marine environment.......................................................................................................82.2 Coral luminescence as a recorder of freshwater impacts..........................82.3 Geochemical proxies of river discharge and terrestrial sediment inputs

to the reef............................................................................................................93 MATERIALS and METHODS...........................................................................9

3.1 Coral core collection....................................................................................93.2 Preparation of core slices and measurement of coral growth rates and

luminescence.....................................................................................................103.3 Data Quality...............................................................................................123.4 Geochemical trace element analysis.........................................................123.4 Environmental data...................................................................................133.5 Analyses....................................................................................................14

4 RESULTS.....................................................................................................144.1 Climate variation and change: sea surface temperatures, tropical cyclones

and river flows...................................................................................................144.2 Coral growth rates.....................................................................................174.3 Coral luminescence as a recorders of freshwater flood plumes.................194.4 Geochemical tracers of terrestrial input....................................................19

5 References.................................................................................................28

Coral luminescence records freshwater impacts from the Fitzroy River Basin

LIST OF FIGURES

Figure 1: Site map showing reef locations within the Mackay-Whitsunday Islands region where long cores have been collected for this study. Cores from South Molle Island (SMI01 and SMI81) were collected from the same colony in 1984 and for this project in 2018. Icons in purple are Porites colonies used for both geochemistry analyses, growth and luminescence, icons in green are cores that were collected and used for only growth and luminescence.

Figure 2: a) average annual SST anomaly (from 1961-1990 mean) for Whitsundays (coloured bars) and global land and sea temperatures (grey line), 1871-2018, and b) Whitsundays maximum, annual and minimum SST, 1950-2018, with linear trend lines.

Figure 3: Annual (October-September) river flows for a) Pioneer River 1917-2018, and b) Fitzroy River 1915-2018. Also shown (dashed lines) are 90th percentile, median and 10th percentile flows. Extreme high flow years (>90th percentile) are highlighted in green and extreme low flow years (<10th percentile) are highlighted in orange. The dark blue line is 10-year Gaussian filtered data emphasising decadal variability.

Figure 4: a. observed Burdekin River flow (Oct-Sept) 1922-2018. b. reconstructed Burdekin River flow extended beyond the observational record from 1648-2011 using the calibration of luminescence intensity from coral cores against the instrumental record (Lough et al. 2015).

Figure 5: (a) Annual average Ba/Ca ratios within the coral skeleton from South Molle Island (SMI01 and SMI81). Also shown (dashed lines) are 90th percentile, median and 10th percentile Ba/Ca ratios. Extreme Ba/Ca years (>95th percentile) are highlighted in red, high Ba/Ca years (>90th percentile) are highlighted in green and extreme low Ba/Ca years (<10th percentile) are highlighted in orange. (b) Scatterplot of annual average Ba/Ca ratios within the coral skeleton from South Molle Island (SMI01 and SMI81) vs Pioneer river flow 1917-2017 showing positive trend in increased Ba/Ca with increasing river flow.

Figure 6: Annual luminescence range for seven coral cores. Also shown (dashed lines) are 90th percentile, median and 10th percentile values. Extreme high years (>90th percentile) are highlighted in green and extreme low years (<10th percentile) are highlighted in orange. The dark blue line is 10-year Gaussian filtered data emphasising decadal variability. Note different y-axis scale for SMI01C.

Figure 7: Annual average coral skeleton Ba/Ca (mol.mol-1) ratios throughout the Whitsunday Region to explore spatial patterns in sediment transport: a. Hook Island, b. Stonehaven, c. Whitsunday Island, d. Shaw Island, e. Scawfell Island. Also shown (dashed lines) are 90th percentile, median


and 10th percentile values. Extreme high years (>95th percentile) are highlighted in red, high years (>90th percentile) are highlighted in green and extreme low years (<10th percentile) are highlighted in orange. Note: Start years of each record are different and a function of time available on ICPMS and the length of each individual core.

Figure 8: Annual calcification anomalies (from 1959-1984 mean) for seven coral cores. Thick line is 10-year Gaussian filter emphasising decadal variability.

Figure 9: Relationships between a) calcification rate, b) linear extension rate, and c) density for massive Porites spp. vs annual average SST. Grey symbols and regression line for 49 Indo-Pacific sites; coloured symbols for seven Whitsunday coral cores.

LIST OF TABLES

Table 1: Porites spp. coral cores used in Whitsunday water quality project.Table 2: Average annual skeletal growth and luminescence characteristics for

the base period, 1959-1984 (growth) and 1960-1983 (luminescence), ± 1 sd.

Table 3: (a) Correlations between annual luminescence range and Pioneer and Fitzroy River flows (October-September) for a) 7 coral cores, (1960-1983), (b) 5 coral cores (1949-2015) and (c) annual skeletal Ba/Ca concentrations with luminescence range, Pioneer, Fitzroy and Burdekin River observed flows. Shaded values are significant at 5% level, locations are in order of perceived distance from River mouth and inshore influence.

Appendices

Appendix 1: X-ray and UV images Whitsundays 2019Appendix 2: Whitsunday data setsAppendix 3: density and extension time series


1 EXECUTIVE SUMMARY

1.1 PURPOSE

This technical report is the milestone report submitted to CSIRO for the Department of the Environment and Energy as part of the project “Scoping study to address poor water quality in the Whitsunday Region”. The AIMS contribution in this report seeks to provide indicative long-term records of sediment and freshwater flood plume transport patterns within the Mackay-Whitsunday Island region. The analysis provides evidence that freshwater flood plumes from the Pioneer and Fitzroy Rivers are reliably recorded as luminescent lines in coral cores of massive Porites colonies and the cores collected during this project span a time period from 1853-2017. This study will explore geochemical tracers (Ba/Ca, Y/Ca and Mn/Ca) of terrestrial sediment inputs to the region to determine, on decadal to century time-scales, if the recent decade of declining water clarity is significantly different than in the past.

1.2 PROJECT SUMMARY

The Whitsunday Island region is an important gateway for tourism for the Great Barrier Reef (GBR). Recent water quality monitoring in the region and anecdotal reports from local tourist operators have reported an apparent decline in water clarity and increased turbidity in recent years, since ~2007, which is degrading the quality of the coral reef sites in the region. This study uses new coral core collections and existing Porites coral core material from the Australian Institute of Marine Science (AIMS) Coral Core Archive, to determine if the recently reported periods of reduced water quality in the Mackay-Whitsunday region is unprecedented on decadal to century time-scales, to contextualize recent reports on longer-term timescales.

When viewed under ultra-violet light, core slices from massive Porites colonies at inshore reefs of the GBR show luminescent lines of varying intensity. These lines are a result of freshwater from river flood plumes reaching a reef and terrestrially-derived humic and fulvic acids being incorporated into the calcium carbonate coral skeleton. The intensity of luminescence can be measured, dated and calibrated against instrumental river flow measurements. This reveals a robust relationship between the occurrence and intensity of luminescence and the magnitude of river flows. This is clearly demonstrated on annual frequency for coral cores from South Molle Island (20.25878°S, 148.82834°E), Shaw Island (20.4796°S, 149.06908°E) and Whitsunday Island (20.17447°S, 148.97525°E). The coral luminescence time series extended back to the mid-19th century for South Molle Island, covering a time period from 1860-2017. This considerably extends the observational record of river flow into the region and spatial occurrence of freshwater flood plumes affecting nearshore reefs within the Whitsunday Islands. Coral cores from Hook Reef (19.81582°S, 149.17664oE), a


mid-shelf reef ~70 km from land, which extend back to the late 1950’s, provide a ‘control’ record as this reef is only rarely affected by very large freshwater flood plumes.

The dated coral luminescence records, combined with targeted geochemical proxies for terrestrial sediment transport, provides a long-term perspective on whether recent water quality declines in the Whitsunday region are significantly different than in previous decades. The core from South Molle Island revealed the strongest correlation with river flow patterns both in terms of luminescent freshwater inputs and associated cycles in Ba/Ca concentration within the coral skeleton. Temporal patterns in Ba/Ca terrestrial inputs to South Molle Island reflect the decadal patterns in river flow with significant increases in Ba/Ca during periods of higher flow.

The time-period from 1992-2006 represents the driest era in the instrumental record with 11 of the 15 years falling below median river flow, which is also captured in the SMI01_81 Ba/Ca signal. Concentrations of Ba:Ca within the coral skeleton are positively correlated with riverflow (Figure 5b) and increased during periods of high river flow in the years 2007-2011, but the observed Ba/Ca ratios during this recent decade are not higher than any of the previous major flood events throughout the 20th century (Figure 5a).

1.2.1KEY FINDINGS Porites cores from South Molle Island and Shaw Island consistently capture annual flood

plumes as luminescent lines and positive anomalies in skeletal Ba/Ca ratios, which are positively correlated with major river flow events through time from the Pioneer and Fitzroy Rivers.

Geochemical signals of Ba/Ca within the skeletons of long-lived Porites corals at South Molle Island provide strong signals of river flow and possible associated increase in sediment inputs to the region that correlate with decadal variations in drought and flood phases. The Ba/Ca ratios indicate, significant inputs of new terrestrial material only during major flood years (eg. 2007-2011, 2017, 1991, 1974).

The recent period of concern, from 2007-2017, represents a wet phase which follows the driest two decades (1992-2006) over the period examined, 1853-2017.

Ba/Ca ratios within the coral skeleton at South Molle Island, which is influenced by riverflow events, from 2007-2017 have not increased compared to past flooding events dating back to 1861. Recent observations of high turbidity and concerns of degrading water quality are likely the result of increased flood plume inputs during this time period, not dramatic changes to sediment transport into the region

Ba/Ca time series at South Molle Island is the only positively correlated location within the region with both luminescence and river flows

Ba/Ca concentrations from 1956-2017 at Scawfell Island indicate that a significant change in terrestrial Ba to this location from 2011-2015 has occurred with maximum annual skeletal Ba/Ca concentrations during this recent decade


Unlike the Ba/Ca ratios, Y and Mn/Ca, which have also been used as terrestrial sediment proxies previously, are not correlated with flood events at any of the study sites, which likely suggests that these terrestrial proxies have desorbed out of the seawater prior to reaching the corals throughout the Whitsunday Islands

Complex hydrodynamics throughout the Whitsunday Islands indicate that all of the sites except South Molle Island, appear to be influenced more strongly by marine resuspension events than direct flood plume inputs

Three measures of coral health: calcification rate, skeleton density and depth of the living tissue layer, all indicate that the 7 corals sampled were all at, or above, average condition compared to corals from other GBR and Indo-Pacific sites.

2 INTRODUCTION

2.1 Massive corals as historical archives of growth rates and the marine environment

Massive corals, such as Porites spp., are colonial animals that spend an entire lifetime in the same location and record inputs to the marine environment within the calcium carbonate skeleton they build from the surrounding seawater. Seasonal variations in skeletal density (high density bands form in the summer and low density bands in winter on the GBR) produce annual growth bands, similar to tree rings, made visible in X-ray images of core slices (Knutson et al 1972; Lough and Cooper 2011; Lough and Cantin 2014). These annual bands can be measured to derive annual linear extension rate, annual skeletal density and, the product of these two variables, annual calcification rate (the mass of calcium carbonate skeleton deposited each year). Some colonies grow to be several metres in height and thus provide long-term coral growth rates over decades to centuries and historical perspectives on coral growth responses to changes in the physio-chemical characteristics of surrounding waters. Having established an annual chronology, trace metals and rare-earth elements can be measured in coral skeletons using geochemical analyses and are good indicators of anthropogenic contaminants in the marine environment. Massive corals are thus historical archives of both the marine environment and coral growth responses to changes in that environment (Lough 2010).

2.2 Coral luminescence as a recorder of freshwater impacts

This study focuses on freshwater tracers in massive coral skeletons that can link flood plume events with terrestrial sediment inputs to the marine environment. Luminescent lines in inshore corals of the central GBR were first reported by Isdale (1984) and their occurrence and intensity linked to the magnitude of Burdekin River flows. The luminescent lines are made visible by viewing a coral slice under ultra-violet (UV) light and have been demonstrated to be a result of terrestrial humic substances, transported by freshwater river flows into nearshore waters of the GBR (Boto and Isdale 1985). Subsequently, Isdale et al (1998) produced an initial reconstruction of Burdekin River flow back to the


mid-17th century, considerably extending the gauged river flow record which started in the 1920s. Further support for the robustness of this freshwater tracer on the GBR was provided by Lough et al (2002). They examined the occurrence and intensity of luminescent lines in multiple Porites colonies from 30 reef sites throughout the length and breadth of the GBR. The reef sites varied from <1 km to >170 km from the mainland. This study demonstrated that the intensity of luminescence decreased with increasing relative distance across the shelf and divided the reefs into three groups: inshore reefs that recorded river runoff of varying intensity annually, midshelf reefs that only occasionally recorded river runoff during extreme river flood years and offshore reefs that never recorded river runoff events. AIMS’ custom-built gamma densitometer for measuring skeletal growth parameters (Chalker and Barnes 1990) was subsequently modified to measure the intensity of luminescence in coral slices using fibre optics (Barnes et al 2003). Since then AIMS has used this instrument to routinely quantify the intensity of luminescence in coral slices and developed robust reconstructions of rainfall and river flows for past centuries from living corals (Lough 2007a, 2011a; Lough et al 2015) and for a well-dated window of the mid-Holocene (6,000 years BP) from fossil corals (Lough et al 2014). The annual range of measured luminescence between the summer maximum (wet season) and preceding winter minimum (dry season) has been shown to be the most robust measure of the magnitude of freshwater reaching a reef (Lough 2011b). The annual luminescence range record for a core from Havannah Island, central GBR was used in combination with a network of tree-ring width records to develop the Australia-New Zealand Drought Atlas (ANZDA) – an annual reconstruction of drought severity across eastern Australia for the period 1500-2012. This reconstruction shows, for example, that the extreme wet La Niña summer of 2010-2011 was likely the wettest year in coastal Queensland since at least 1500 A.D. (Cook et al 2016).

Luminescent lines in massive coral skeletons, therefore, provide a robust historical context for when, where and the magnitude of freshwater flood plumes (and whatever land-based contaminants these waters may contain) affecting reefs on the GBR. These coral proxy records thus extend the modern, but short, flood plume maps derived from satellite ocean colour data (e.g. Devlin et al 2015; Petus et al 2016) which provide insights into contaminant pollution on the GBR (e.g. Bartley et al 2017) and contribute to strategies to improve GBR water quality (e.g. Kroon et al 2016).

2.3Geochemical proxies of river discharge and terrestrial sediment inputs to the reef

Growing evidence suggests that the water quality gradient in the Whitsunday Island group has been degraded by increased sediment and nutrient loads delivered from adjacent river catchments following expansion of grazing and cropping industries in the region (Lewis et al. 2012, Cooper et al. 2007, Fabricius et al. 2016, Thompson et al. 2014). Coral-based geochemical proxies from long-lived massive corals are valuable tools for reconstructing the timing and variability of water quality due to terrestrial sediment runoff to coastal marine


environments (Saha et al. 2016). Barium to calcium (Ba/Ca) ratios in coral skeletons correlate well with flood events (McCulloch et al. 2003, Sinclair and McCulloch 2004, Saha et al. 2016, Lewis et al. 2018). Combined with luminescent peaks visible in the coral skeleton (Lough et al. 2002), we can provide a long-term record of river discharge events reaching corals within the GBR. The Ba/Ca peaks are indicative of terrestrial inputs of both dissolved Ba transported with freshwater flows and terrestrial Ba bound to particulate matter entering the marine environment as the Ba desorbs from the suspended particulates by ion-exchange with seawater (see review by Saha et al. 2016).

Here we examine the luminescence records in 6 coral cores collected during this project and an additional existing long core from South Molle Island within the AIMS’ Coral Core Archive, which extends the skeletal record for the Whitsunday Island region to 1853. We have also conducted geochemical analyses targeting trace elements (Ba, Y and Mn) previously linked to terrestrial sediment inputs and flood plume transport (Saha et al. 2016). Through the combination of luminescent signals of humic and fluvic acids within freshwater flood plumes and geochemical concentrations of terrestrial sediment tracers, we will explore the historical patterns of terrestrial sediment inputs to the Mackay-Whitsunday region to determine if recent shifts in water clarity from 2007-2017 are different to previous historical periods of major flooding throughout the region.

3 MATERIALS AND METHODS

3.1 Coral core collectionIn February 2018, 29 coral cores were collected from shallow-water (< 10m depth) massive Porites bommies in and around the Whitsunday Island group. The cores came from 15 colonies at seven reef sites, which contained suitable large coral colonies throughout various locations of the Whitsunday-Mackay Island region (Figure 1).


Figure 1: Site map showing reef locations within the Mackay-Whitsunday Islands region where long cores have been collected for this study. Cores from South Molle Island (SMI01 and SMI81) were collected from the same colony in 1984 and for this project in 2018. Icons in purple are Porites colonies used for both geochemistry analyses, growth and luminescence, icons in green are cores that were collected and used for only growth and luminescence.

3.2 Preparation of core slices and measurement of coral growth rates and luminescence

Nineteen of the 29 cores were selected for further analyses. This selection was based on the overall quality of each core with bio-erosion and bore holes being the primary reasons for not analysing a core further.

Coral slices from the 19 selected coral cores were prepared using standard techniques (Lough and Barnes 1990a, b): cores were air dried, mounted on aluminium trays using dental casting plaster and three ~6.5 mm thick slices removed using a customised milling machine. Each slice was X-rayed and the X-ray converted to a positive print to reveal the annual skeletal density bands. Core slices were also photographed under ultra-violet (UV) light in a darkened room to reveal luminescent lines (Lough et al 2002). Based on the quality along each core length of consistent annual density banding and luminescence, six of the 19 cores from six reefs were selected for geochemical analyses and for which Coral luminescence records freshwater impacts from the Fitzroy River Basin

the growth and luminescence analyses are presented here. A long core from South Molle Island (SMI01C) in AIMS’ Coral Core Archive, collected in the 1980s, was also analysed as it provided data back to the mid-19th century (Table 1). Positive prints of the X-rays and photographs under UV light of analysed core slices are presented in Appendix 1.

Table 1: Porites spp. coral cores used in Whitsunday water quality project.

Skeletal density was measured using gamma densitometry along the slice and track from each core that displayed the clearest annual density bands (Chalker and Barnes 1990). At the same time the intensity of luminescence was measured along each core slice (Barnes et al 2003). Simultaneous measurements of skeletal density and luminescence were obtained at 0.254 mm steps along each core slice and core section. The year of annual density band formation was dated for each selected core slice from the measured distance vs density data, the X-ray positive prints and the assumption that the annual high density band forms in summer and the annual low density band in winter. Successive density bands were thus dated to provide an annual chronology from the outer edge of the core which corresponded with the date of collection. Luminscent lines were also dated working back from the outer edge of the core with particularly large flood events (e.g. 2011, 1991)


providing good chronological control both for luminescence and skeletal density (Hendy et al 2003). With the exception of the core (HOO81A) from Hook Reef, all core slices showed luminescent lines indicating that freshwater from river flood plumes were affecting those sites. Samples from Stonehaven Bay (SNH84A) and Scawfell Island (SCF81B) were characterised by background luminescent banding (Barnes et al 2003) and occasional more intense luminescent lines, indicating that freshwater sometimes affected these sites. Samples from Whitsunday Island (WHI84A), South Molle Island (SMI81A and SMI01C) and Shaw Island (SHW82C) all showed regular luminescent lines of varying intensity, indicating that these sites were affected by freshwater annually (Lough et al 2002).Once each density band and luminescent line was dated, the following variables were extracted for each core (Barnes and Lough 1992; Lough and Barnes 2000; Lough 2011):

annual linear extension rate (cm.yr-1), measured as the linear distance between adjacent low density minima;

annual average skeletal density (g.cm-3), measured as the average skeletal density between adjacent low density minima;

annual calcification rate (mass of calcium carbonate deposited per unit of time; g.cm-2.yr-1), calculated as the product of annual linear extension and annual average skeletal density;

annual luminescence range (no units), measured as the difference between peak luminescence of the current summer and the minimum luminescence of the preceding winter;

average depth of the living tissue layer at the outer edge of the coral slice (mm).

These data are provided in Appendix 2 – data for the seven analysed coral cores.

3.3 Data QualityNot all slices clearly presented annual density bands suitable for extracting annual growth and luminescence parameters along the full length of the core (see images in Appendix 1). This is due to some corals displaying quite complex skeletal architecture through the thickness of the coral slice leading to convoluted and off axis growth patterns (Barnes et al 1989; Barnes and Lough 1990; Lough and Barnes 1992). Such complex growth patterns are quite common in inshore corals living in often turbid waters (e.g. Nelly Bay, Magnetic Island in Cantin and Lough 2014). The years of dated annual growth and luminescence records are provided in Table 1, along with some general observations about the quality of the material. We also note that there was no evidence in the X-ray positive prints of growth hiatuses (high density stress bands) or partial mortality that are often linked with thermal stress and coral bleaching events (Cantin and Lough 2014).

3.4 Geochemical trace element analysis

Geochemical analyses were conducted at the Research School of Earth Sciences, The Australian National University in March and April 2019. Laser ablation–inductively coupled plasma–mass spectrometry (LA–ICP–Coral luminescence records freshwater impacts from the Fitzroy River Basin

MS) was used to measure the abundance of the major trace elements (B, Mg, Sr, Ba and U) and minor trace elements (Li, Al, P, Cl, Ti, V, Mn, Fe, Ni, Cu, Zn, As, Se, Y, Zr, Sn, La, Ce, Pb). An ArF Helex MkII excimer laser, with 193 nm wavelength, was used to ablate coral slices. A quadrupole ICPMS (iCAP RQ) was used to detect the concentrations of analytes sent from Laser chamber. All raw counts were normalizsed to 43Ca using LAtools based on Python (Branson et al., 2019). This technique provides relatively fast and high spatial resolution analysis of seasonal to decadal changes in coral growth.

Following coral slicing methods and X-ray analysis, coral skeletons were cut along the maximum growth axis into continuous ~95 x 25 mm pieces to fit sequentially into the laser holder on the LA-ICP-MS. The sections were cut using a bandsaw from the back side of the skeleton, with the blade entering half the depth of the skeleton at which point the pieces were fractured by hand to ensure that each piece fits together continuously down core for analysis. Coral pieces were cleaned by an ultrasonic probe to remove any loose dust or external material from the sample preparation procedures and then air dried before analysis. Analysis tracks are selected by following the main axis of growth identified from the X-ray imagery (Alibert and McCulloch 1997). Before analysis, samples were cleaned twice by the laser using a slit 200 μm wide parallel to the growth axis and 600 μm wide perpendicular to the growth axis with 10 Hz repetition rate. This removed ~10 μm of exposed coral skeleton from the surface. This pre-ablation process was shown to aid in increasing the reproducibility of repeat runs in the same track. Scan speed for pre-ablation was set to 200 μm/s. For analysis, a rectangular slit with 100 μm wide parallel to the growth axis and 500 μm wide perpendicular to the growth axis was used with a laser pulse repetition rate of 5 Hz. Scan speed for the analysis was 100 μm/s. This corresponds to approximately weekly sampling resolution. Before data smoothing, each data point corresponds to a sampling interval of ~0.059 mm along the maximum growth axis of the coral skeleton. After data smoothing (10 points average), each data point corresponds to a sampling interval of ~0.59 mm along the maximum growth axis of the coral skeleton. A NIST 614 glass standard, containing 61 elements (Horn et al. 1997; Pearce et al. 1997) was used for calibrating minor trace elements, and a coral standard from Davies Reef (GBR) was used for calibrating major trace elements (Fallon et al. 1999; Fallon et al. 2002). The entire sampling routine consists of ~150 s of background with the laser off, ~150 s of analysis of the NIST 614, ~150 s of analysis of the NIST 612, ~150 s of analysis of the coral standard, the track along the coral, then a second analysis of the coral standard, the NIST 612, the NIST 614 and a further 150 s of background.

3.4 Environmental dataMonthly sea surface temperature (SST, oC) were obtained from the HadiSST1 data set (Rayner et al 2003; UK Meteorological Office Hadley Centre: www.metoffice.gov.uk/hadobs/hadisst/index.html) for the 1-degree latitude by longitude box centred on 20.5oS, 148.5oE. Data are available for the period


http://www.metoffice.gov.uk/hadobs/hadisst/index.html

1871-2018, though are most reliable, due to increasing observational coverage, from 1950 (Deser et al 2010; see Appendix 2 – data). Annual global land and sea temperatures, 1871-2018, were obtained from the UK Meteorological Office Hadley Centre (Morice et al 2012; HadCRUT4; www.metoffice.gov.uk/hadobs/hadcrut4/).Climatological rainfall statistics were obtained from the Australian Bureau of Meteorology for Proserpine Airport, site # 033247, 1978-2019 and Mackay Aero, site # 033045, 1950-2019 (www.bom.gov.au/climate/data/). Details of tropical cyclones in the vicinity of the Whitsundays were obtained from the Bureau of Meteorology Southern Hemisphere Tropical Cyclone data Portal (www.bom.gov.au/cyclone/history/tracks), for the period 1969/1970 through 2017/2018. For each year the number of tropical cyclones were recorded within 50 km, 100 km and 200 km of 20.25oS, 149.00oE.Daily river flows (megalitres) were obtained from the Queensland Department of Natural Resources, Mines and Energy (DNRME) Water Monitoring Portal (https://water-monitoring.information.qld.gov.au) for the Pioneer and Fitzroy Rivers. Data were totalled for the October – September water year and expressed as km3. Data were obtained for the Pioneer River at Pleystowe Mill, 1917-1978 (catchment area 1430 km2, ~20 km from river mouth, now closed) and Pioneer River at Mirani Weir, 1979-2018 (catchment area 1,211 km2, ~46 km from river mouth). For four overlapping years (1979-1982) Mirani October –September river flow = (0.8343 * Pleystowe) + 1,3638 km3, r2 = 0.99. Pleystowe October – September flows prior to 1979 were, therefore, adjusted on the basis of this relationship between flows at the closed and currently open river gauging sites. River flow data were also obtained for the Fitzroy River at Yaamba for the period 1915-1969. This gauging station, now closed, is located ~109 km from the river mouth with a catchment area of ~136,400 km2. Data were obtained for the Fitzroy River at The Gap for the period 1965-2018. This gauging station is located ~142 km from the river mouth with a catchment area of 135,800 km2. River flows for Yaamba were adjusted to those for The Gap, based on linear regression for the 5 years of overlap. Yaamba flow = (0.9692 * The Gap) + 0.0633, r2 = 0.99). This provided Pioneer River flows for 1917-2018 and Fitzroy River flows for 1915-2018.

3.5 AnalysesTo provide a climatological backdrop for the study region, we examined long-term variations of SST and river flows. We also considered the impact of El Niño-Southern Oscillation (ENSO) extremes (El Niño and La Niña events) on regional river flows as these are one of the strongest drivers of rainfall variability, and hence river flows, in northeastern Australia (Risbey et al 2009). To examine river flows typical of El Niño and La Niña years, October-September flows were averaged for 13 El Niño events, 13 La Niña events and 13 ENSO-neutral years over the period 1949-2017. The years were identified from the Niño 3.4 SST index of ENSO (www.cpc.ncep.noaa.gov/data/indices/sstsoi.indices) and were: 1957-58, 1965-66, 1969-70, 1972-73, 1982-83, 1986-87, 1987-88, 1991-92, 1994-95, 1997-98, 2002-03, 2009-10, 2015-16 (El Niño); 1949-50, 1951-51,


http://www.cpc.ncep.noaa.gov/data/indices/sstsoi.indices

https://water-monitoring.information.qld.gov.au/

http://www.bom.gov.au/cyclone/history/tracks

http://www.bom.gov.au/climate/data/

http://www.metoffice.gov.uk/hadobs/hadcrut4/

1954-55, 1955-56, 1970-71, 1973-74, 1975-76, 1984-85, 1988-89, 1998-99, 1999-00, 2007-08, 2010-11 (La Niña); and 1952-53, 1959-60, 1960-61, 1966-67, 1978-79, 1980-81, 1981-82, 1989-90, 1996-97, 2001-02, 2003-04, 2005-06, 2013-14 (ENSO-neutral).

Annual total concentrations of the geochemical element ratios (Ba, Y, Mn to Ca) from the coral skeleton were calculated from the monthly resolution data and correlated with both annual riverflow data and coral luminescence to determine if historical terrestrial inputs to the Whitsunday region have increased in recent years compared to the past.

To examine and compare temporal variations in coral growth among cores with different average growth characteristics, annual linear extension, skeletal density and calcification were converted to percentage anomalies from the base period common to all seven cores, 1959-1984 (see Cooper et al 2012). Cross-correlation analysis was used to test for relationships between coral luminescence and river flows. There is a strong linear relationship (~84% explained variance) between average Porites linear extension and calcification rates and average annual SST, based on data from 49 coral reef sites throughout the Indo-Pacific (Lough and Barnes 2000; Lough and Cantin 2014). This allowed us to test whether average growth characteristics for massive Porites in the Whitsundays were what would be expected given the regional average SST (i.e. are corals performing as expected in the region?).

4 RESULTS4.1 Climate variation and change: sea surface temperatures, tropical

cyclones and river flowsGlobal and regional climate is changing rapidly due to human interference in the Earth’s energy balance as a consequence of increasing levels of greenhouse gases in the atmosphere (Stocker et al 2013). We, therefore, considered it informative to understand how the marine environment in the Whitsundays is responding to this global-scale stressor. SST in the Whitsundays have significantly warmed since the late 19th century, largely in step with global land and sea temperatures (Figure 2a). Over the period 1871-2018, Whitsunday SST warmed by 0.75oC (linear trend, r2 = 0.36), and global temperatures warmed by 0.90oC (linear trend, r2 = 0.73). Since 1950 (when these data are most reliable), average annual SST have warmed by 0.73oC with greater warming of annual minimum SST (+0.98oC) than annual maximum SST (+0.54oC; Figure 2b).


Figure 2: a) average annual SST anomaly (from 1961-1990 mean) for Whitsundays (coloured bars) and global land and sea temperatures (grey line), 1871-2018, and b) Whitsundays maximum, annual and minimum SST, 1950-2018, with linear trend lines.


The Whitsundays are within the Australian tropics with wet summers associated with the Australian summer monsoon and low winter rainfall (Lough 2007). Average annual total rainfall is ~1,449 mm at Proserpine and 1,561 mm at Mackay. Between 74% (Mackay) to 80% (Proserpine) of annual rainfall occurs in the summer half year (October – March). The summer monsoon also can bring tropical cyclones into the region. Over the period 1969-1970 through 2017-2018, 11 tropical cyclones were recorded within 50 km of the Whitsundays, 19 within 100 km and 38 within 200 km. These include severe Tropical Cyclone Debbie (Category 4), a large and damaging storm, which made landfall near Airlie Beach in March 2017.

Along with high seasonality, rainfall and river flows in north-eastern Queensland show high inter-annual variability (Figure 3). Median flow of the Pioneer River (1917-2018) is 0.52 km3 with maximum flow of 3.28 km3 in 2011 and minimum flow of 0.04 km3 in 1992. Median flow of the much larger Fitzroy River is 2.97 km3, with maximum flow of 36.84 km3 in 2011 and minimum flow of 0.10 km3 in 1969. Despite the disparity in total flows of the two rivers, they show very similar variations through time with years of extreme high and low flows similar for the two rivers as is decadal variability. The correlation between the two river flow series, 1917-2018, is 0.81 (significant at the 1% level). Both rivers have significantly higher flows in La Niña years compared to ENSO-neutral years but no significant difference with El Niño years.


Figure 3: Annual (October-September) river flows for (a.) Pioneer River 1917-2018, and (b.) Fitzroy River 1915-2018. Also shown (dashed lines) are 90 th

percentile, median and 10th percentile flows. Extreme high flow years (>90th

percentile) are highlighted in green and extreme low flow years (<10 th

percentile) are highlighted in orange. The dark blue line is 10-year Gaussian filtered data emphasising decadal variability.

4.2 Coral growth ratesAverage skeletal growth characteristics (Table 2) were compared to the expected growth characteristics based on the strong linear relationship between


average Indo-Pacific Porites growth and average annual SST (Lough and Cantin 2014). Interestingly, all 7 cores have calcification rates higher than would be expected for the average annual SST in the Whitsundays (25.6°C; Figure 9a). Across the 7 cores, calcification rates average 34% higher than expected (ranging from +20% SMI81C to +56% SCF81B). Similar results were found for linear extension rate (Figure 9b) which averaged 24% higher than expected (ranging from +12% SHW82C to +54% SCF81B). Average skeletal density, which shows a weaker relationship with average annual SST (Figure 9c) was closer to expected values, averaging 3% higher (ranging from -6% SMI01C to +16% SNH84A). Linear extension rate is the primary driver of calcification rate in massive Porites corals and linear extension rate tends to vary inversely with skeletal density (Lough and Barnes 2000). These relationships were evident across the 7 cores with correlations between calcification and extension of 0.73, calcification and density of 0.08, and density and extension of -0.62.

Table 2: Average annual skeletal growth and luminescence characteristics for the base period, 1959-1984 (growth) and 1960-1983 (luminescence), ± 1 sd.

Annual calcification anomalies for the seven cores are shown in Figure 8 (similar graphs for skeletal density and linear extension anomalies are provided in Appendix 3). Calcification rates integrate both skeletal density and linear extension and are, therefore, a useful measure of how coral growth varies through time. All seven cores show marked variations in calcification rates over their respective record periods. There is no obvious common trends to all seven cores. Calcification rates appear, however, to have increased in recent decades at Hook, South Molle and Shaw Island, whereas they decreased at Stonehaven, Whitsunday and Scawfell Islands.

The depth of the living tissue layer (TTL) at the outer edge of coral colonies can be a measure of the ‘health’ of the colony, with a thicker TTL indicating that the coral has more stored energy reserves to draw upon (Barnes and Lough 1992). In a study of the impact on Porites growth characteristics of a gold mine and ore-processing facility at Misima Island, Papua New Guinea, for example, only TTL showed a response (thinning) with increased exposure to mining disturbance (Barnes and Lough 1999). TTL for the seven Whitsunday cores varied from 4.13 mm at Scawfell to 10.35 mm at South Molle Island (SMI01C). We note that this core was collected in September 1985 whilst the other six cores were all


collected in February 2018. Although seasonal variations in TTL are not clear (Barnes and Lough 1999), TTL shows marked variations in relation to the monthly lunar cycle – typically declining by ~20% after the full moon (Rotmann and Thomas 2012). This difference in sampling could account for the unusually high TTL in the long South Molle Island core. The average TTL for the other 6 cores, all collected at the same time of year and within days of each other, was 5.53 mm. Based on multiple colonies throughout the Great Barrier Reef, TTL averages 5.43 mm (2.13-10.2 mm range; Barnes and Lough 1992). The Whitsunday cores are thus within this range and do not appear to be unusual.

4.3 Coral luminescence as a recorders of freshwater flood plumesAnnual luminescence range time series for all 7 cores are presented in Figure 6. Over the period common to all 7 cores, 1960-1983, annual luminescence range for the Hook and Shaw Island cores were not well correlated with any other core nor with Pioneer and Fitzroy River flows (Table 3a). The lack of relationship for Hook Island is unsurprising as under UV light there was no evidence of intense luminescent lines that are typically associated with freshwater flood plumes, given its mid-shelf distant location from inshore flood events. Shaw Island did, however, show marked luminescent lines characteristic of flood plumes and was significantly correlated with South Molle Island and the Pioneer and Fitzroy River flows over the longer period, 1949-2015 (Table 3b). Conversely, Stonehaven luminescence range was significantly correlated with other cores over the period 1960-1983, but only with South Molle Island over the longer period, 1949-2015. Somewhat mixed relationships between the two time periods were also evident for Whitsunday, Shaw and Scawfell Island cores. The strongest and most consistent relationships with river flows were for the two cores from South Molle Island. Although there are potential dating problems which could be confounding some of these results, it would also seem likely that the complex oceanography in the Whitsundays may also be playing a role. Based on these results and the UV images of the core slices, it would seem that the strongest freshwater signal is evident in cores from South Molle Island and that there is no evidence of freshwater flows influencing Hook Island. For the other five sites, UV images of luminescence indicates that they are certainly affected by freshwater plumes but this is not translating to a clear signal in the measured luminescence. It is also not possible to distinguish between the Pioneer and Fitzroy Rivers as being more or less dominant in affecting the six reef sites, due to the strong relationship between flows of these two rivers.

4.4 Geochemical tracers of terrestrial inputAnnual skeletal Ba/Ca ratios within the cores collected from the Porites colony at South Molle Island (SMI01_81) reveal significant positive correlations with annual river flow from the Pioneer River and the Fitzroy River (Figure 5b & Table 3c). Corresponding minimum and maximum ratios of Ba/Ca in the coral skeleton correlate strongly with periods of minimum and maximum river flow over the entire record from 1861-2017 (Figure 5), indicating that this site is influenced by river flood inputs to the region. Ba/Ca ratios peaked in 2011 over the recent decade, but the ratios are not significantly higher than historical Ba/Ca ratios


that correspond to other major flood events (Figure 5, eg. 1991, 1971-72). Maximum Ba/Ca ratios were actually detected in the late 1800’s (1898, 1896, and 1890, Figure 5). The long-term Ba/Ca record suggests that sediment inputs to South Molle Island are largely dominated by variations in river flow. Recent reports of declining water clarity are likely a result of the transition from a period of significantly dry, low river flow (1992-2006) to heavy rainfall and high river flow increasing the inputs to the region in 2007-2011 (Figures 3, 4 and 5), although these inputs are not higher than they have been previously.


Figure 4: a. observed Burdekin River flow (Oct-Sept) 1922-2018. b. reconstructed Burdekin River flow extended beyond the observational record from 1648-2011 using the calibration of luminescence intensity from coral cores against the instrumental record (Lough et al. 2015).


Figure 5: (a) Annual average Ba/Ca ratios within the coral skeleton from South Molle Island (SMI01 and SMI81). Also shown (dashed lines) are 90th percentile, median and 10th percentile Ba/Ca ratios. Extreme Ba/Ca years (>95th percentile) are highlighted in red, high Ba/Ca years (>90th percentile) are highlighted in green and extreme low Ba/Ca years (<10th percentile) are highlighted in orange. (b) Scatterplot of annual average Ba/Ca ratios within the coral skeleton from South Molle Island (SMI01 and SMI81) vs Pioneer river flow 1917-2017 showing positive trend in increased Ba/Ca with increasing river flow.


Figure 6: Annual luminescence range for seven coral cores. Also shown (dashed lines) are 90th percentile, median and 10th percentile values. Extreme high years (>90th percentile) are highlighted in green and extreme low years (<10th percentile) are highlighted in orange. The dark blue line is 10-year Gaussian filtered data emphasising decadal variability. Note different y-axis scale for SMI01C.


Annual skeletal Ba/Ca ratios within the coral skeletons from the other 5 reef locations throughout the Mackay-Whitsunday region do not correlate significantly with river flow trends (Figure 7 and Table 3c). This suggests that similar to the spatial patterns in luminescent signals of freshwater transport, the complex oceanography in the Whitsundays is likely playing a role in the spatial distribution of Ba and that these reef locations are influenced more strongly by the marine environment (resuspension of marine sediments and Ba) than the annual flood plume intensity. Historical patterns in Ba/Ca for Shaw Island suggest that abrupt increases in Ba/Ca ratios occurred for this location from 1966-1970 (Figure 7d). The distant reef at Scawfell Island does show a recent increase in Ba/Ca within the skeleton from 2011-2016 that is significantly higher than the past, suggesting that an increase in terrestrial transport to this location has occurred that is different than previous decades (Figure 7e).


Table 3: (a) Correlations between annual luminescence range and Pioneer and Fitzroy River flows (October-September) for a) 7 coral cores, (1960-1983), (b) 5 coral cores (1949-2015) and (c) annual skeletal Ba/Ca concentrations with luminescence range, Pioneer, Fitzroy and Burdekin River observed flows. Shaded values are significant at 5% level, locations are in order of perceived distance from River mouth and inshore influence.


Figure 7: Annual average coral skeleton Ba/Ca (mol.mol-1) ratios throughout the Whitsunday Region to explore spatial patterns in sediment transport: a. Hook Island, b. Stonehaven, c. Whitsunday Island, d. Shaw Island, e. Scawfell Island. Also shown (dashed lines) are 90th percentile, median and 10th percentile values. Extreme high years (>95th percentile) are highlighted in red, high years (>90th percentile) are highlighted in green and extreme low years (<10th percentile) are highlighted in orange. Note: Start years of each record are different and a function of time available on ICPMS and the length of each individual core.

Annual skeletal Y/Ca and Mn/Ca ratios did not correlate with river discharge patterns and have not been used further in this study to reflect terrestrial sediment inputs to the region.


Figure 8: Annual calcification anomalies (from 1959-1984 mean) for seven coral cores. Thick line is 10-year Gaussian filter emphasising decadal variability.


Figure 9: Relationships between a) calcification rate, b) linear extension rate, and c) density for massive Porites spp. vs annual average SST. Grey symbols and regression line for 49 Indo-Pacific sites; coloured symbols for seven Whitsunday coral cores.

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