Floodplain river function in Australia s wet/dry tropics, with specific reference to aquatic macroinvertebrates and the Gulf of Carpentaria

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1 Floodplain river function in Australia s wet/dry tropics, with specific reference to aquatic macroinvertebrates and the Gulf of Carpentaria Catherine Leigh Bachelor of Science (Hons) Australian Rivers Institute Griffith School of Environment Science, Environment, Engineering and Technology Griffith University, Nathan, Queensland, Australia Submitted in fulfilment of the requirements of the degree of Doctor of Philosophy July 2008

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3 Abstract This thesis provides significant insight into our understanding of river function in highly seasonal systems. In north Australia s vast wet/dry tropics, large rivers and associated wetlands are regarded among the continent s most biologically diverse and ecologically healthy. Until recently however, research on the hydrology, biodiversity and function of Australian rivers has focussed on the south. My thesis investigates floodplain river function in Australia s wet/dry tropics, more specifically in the Gulf of Carpentaria drainage division, and is the first to present a dynamic conceptual model of river function for these systems. Three major themes reside within riverine ecology: flow, pattern and process. These themes feature within existing conceptual models of large river function, for example, the River Continuum Concept, the Flood Pulse Concept and the Riverine Productivity Model. These themes and models were used as a template to explore river function in the study region: flow, as broad-scale hydrology and more localised hydrological connectivity; patterns, as spatiotemporal variation in aquatic macroinvertebrate biodiversity; and processes, as organic carbon flow through aquatic macroinvertebrate food webs. The flow regime is major driver of river function, and as such, a multivariate analysis of daily flow data from large, Gulf of Carpentaria rivers was conducted. Two major classes of river were found, each with a distinct flow regime type: tropical rivers were characterised by flow regularity and permanent hydrological connection, dryland rivers by high levels of flow variability and ephemerality, similar to rivers in Australia s central and semi-arid zones. However, both river types experienced seasonal change, associated with higher flow magnitudes in the wet and lower flow magnitudes in the dry, with dryland rivers typified by greater numbers of zero flow days. These features flow regularity and permanence for tropical rivers, flow variability and absence for dryland rivers, and wet/dry seasonality for both river types were proposed as the broad-scale hydrological drivers of river function in the Gulf region and are expected to be found as important drivers throughout the wet/dry tropics. Along with the flow regime, spatiotemporal patterns of variation in biotic assemblages, and in biophysical and chemical characteristics, are an important aspect of river i

4 function and its conceptual description. To this end, a spatial study of main channel and floodplain waterbodies in the lower catchments of the tropical Gregory and dryland Flinders Rivers (southern Gulf of Carpentaria) was conducted during the 2005 dry season and repeated on a smaller scale the following year. Waterbodies were either lotic or lentic at the time of sampling, representing their hydrological state of connection (lotic) or disconnection (lentic). In addition, wet season characteristics and temporal change between wet and dry seasons were explored for the Gregory River during the 2007 wet season. Spatiotemporal patterns were investigated using univariate and multivariate analyses, with emphasis on macroinvertebrate structure (taxonomic abundances), function (functional feeding group proportions), and diversity (calculated metrics). A diverse fauna was found: forty-five samples were represented by 124 morphotaxa, over individuals, and dominated by gatherers and the Insecta. In particular, the analyses demonstrated a robust association between hydrological connectivity and the macroinvertebrate biota. Specifically, assemblages from waterbodies with similar hydrological connection histories and states of flow were most alike, in both structure and function, the effect of hydrological connectivity outweighing effects directly associated with catchment. In addition, beta-diversity was maximal between lotic and lentic waterbodies, and tended to increase with increasing spatial separation. At smaller spatial scales, a number of environmental factors like biophysical habitat and water physicochemistry were also important for explaining variation in assemblage structure. Characteristics associated with primary productivity potential and habitat diversity were important for explaining variation in assemblage function. However, much of the smallscale environmental variation across the study region was related to broad-scale variation in hydrological connectivity, which thus had both direct and indirect effects on the macroinvertebrate assemblages. Food webs describe the movement of energy through ecosystems, and this process, like patterns of variation in biotic assemblages, is a key component of river function. However, debate exists about the relative importance of different sources of organic carbon fuelling aquatic food webs in floodplain rivers. Therefore, the major basal sources of organic carbon fuelling macroinvertebrate food webs in the study region were explored, via the analysis of stable carbon and nitrogen isotopes. Potential subsidy ii

5 from the aquatic food webs to the terrestrial zone was also investigated by analysing the dietary guilds of terrestrial consumers observed at study sites. Algae, associated with phytoplankton and biofilm, were the primary source of organic carbon in the macroinvertebrate food webs, commonly contributing over 55% of organic carbon to the consumer biomass. Consumers were also shown to rely on additional contribution from other sources of organic carbon, e.g. terrestrial detritus derived from local C 3 riparian vegetation. In addition, food webs were characterised by substantial flexibility in source importance (generalism) and the assimilation of organic carbon across trophic levels (omnivory). These key characteristics may impart a degree of resilience against natural disturbances like flow regime seasonality, flow variability and variation in hydrological connectivity, such that the aquatic food webs display dynamic stability through space and time. Furthermore, the majority of vertebrate taxa identified in and around riparian zones were known consumers of aquatic fauna (invertebrates and fish). The aquatic food webs therefore represented a potentially large source of organic carbon for these terrestrial-zone consumers. Together, the analyses of flow, patterns and processes were used to develop a new and dynamic conceptual model of function specific to floodplain rivers in the study region, and more broadly to similar systems across Australia s wet/dry tropics. The new model highlighted three key aspects: 1. Large-scale hydrological drivers tropical rivers: flow permanence and regularity; dryland rivers: flow variability and absence; all rivers: wet-dry seasonality are important for overall river function in the region 2. Multi-scale spatiotemporal variation in macroinvertebrate assemblage composition and diversity is driven both directly and indirectly by hydrological connectivity, connectivity potential and connection history 3. Links between organic carbon sources and macroinvertebrate consumers, and the factors that influence them specifically, algal production, local riparian litterfall, food web flexibility and omnivory support aquatic food webs that show resilience against natural hydrological disturbance, and represent a large potential subsidy to the terrestrial environment. Using this conceptual model, Bayesian Belief Network scenarios provided a novel way of exploring potential impacts of two water resource development options (flow iii

6 regulation and water abstraction) on the composition and diversity of macroinvertebrate assemblages and on macroinvertebrate food web dynamics in the study region. Scenarios clearly showed that unmitigated flow regulation, via damming of rivers or other control methods, has the potential to alter and adversely impact upon the ecosystem function of these floodplain river systems, perhaps most significantly affecting their biodiversity. Consequently, flow regulation must be considered with great caution as a broad-scale water resource development option for rivers in Australia s wet/dry tropics. In summary, this thesis adds greater depth to our understanding of river function in Australia s wet/dry tropics and offers potential insight into the function of highly seasonal systems elsewhere. Ultimately, we must continue to improve our knowledge and understanding of river function in these important riverine ecosystems. iv

7 Declaration This work has not previously been submitted for a degree or diploma in any university. To the best of my knowledge and belief, the thesis contains no material previously published or written by another person except where due reference is made in the thesis itself. Catherine Leigh July 2008 Gregory River, September Photograph by Terry Reis. Cloncurry River, September Photograph by Terry Reis. v

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9 Table of Contents Abstract... i Declaration... v Table of Contents... vii List of Tables... xi List of Figures... xiv List of Appendices... xix Acknowledgements... xxi Chapter 1. General introduction Introduction Large rivers, floodplains and function The River Continuum Concept The Flood Pulse Concept The Riverine Productivity Model Australia: an outlier in conceptual model development Conceptual models united? Key aspects for understanding floodplain river function in Australia s wet/dry tropics Thesis aims Implications for future management and protection Thesis outline Chapter 2. Study region and design Introduction to northern Australia s wet/dry tropics Gulf of Carpentaria drainage division Southern Gulf of Carpentaria Study design and sampling regime Overall study design Site location Temporal sampling Notes on design, sampling and aims of thesis Chapter 3. Hydrological drivers of river function in the Gulf of Carpentaria drainage division and potential impacts of water resource development Preamble Classification of flow regimes and hydrological drivers of river function Introduction Methods Study region Classification of flow regimes Results Set aspects and variability of magnitude Set aspects of duration Comparison with other Australian rivers Multivariate analysis: separation among river types Discussion Flow regime classifications Proposed hydrological drivers of large river function vii

10 Conceptual model applicability Applied issues Hydrological changes and ecological impacts potentially associated with water resource development Introduction Methods Study region Assessment of post-wrd impacts Results Pre-WRD flow metrics Pre- to post-wrd changes Variation among rivers and directions of change due to flow modification Discussion Conclusion Chapter 4. Spatiotemporal variation in hydrological connectivity and the biophysical and chemical characteristics within and among waterbodies in the lower Gregory and Flinders River systems Introduction Methods Study area and sampling regime Waterbody-scale morphology Within-waterbody-scale morphology Dry season sample collection and laboratory analyses Water physicochemistry Chlorophyll a concentration and suspended solids Benthic organic material Wet season sample collection and laboratory analyses Data analysis Results Waterbody-scale morphology Within-waterbody scale morphology Physicochemical parameters, chlorophyll a concentration and benthic organic material Dry season, Dry season, Wet season, Discussion Spatiotemporal variation and hydrological connectivity Conceptual model applicability Extent and effects of human-induced disturbance Conclusion Chapter 5. Spatiotemporal variation in the structure, function and diversity of macroinvertebrate assemblages within and among waterbodies in the lower Gregory and Flinders River systems Introduction Methods Study area and sampling regime Macroinvertebrate samples Environmental characteristics Data analysis Results Environmental characteristics viii

11 5.3.2 Macroinvertebrate assemblages Spatial variation in assemblage structure, 2005 dry season Spatial variation in assemblage function, 2005 dry season Spatial variation in assemblage diversity, 2005 dry season Temporal variation in assemblage composition Discussion Assemblage biodiversity Spatial variation and hydrological connectivity Temporal variation Conceptual model applicability Conclusion and recommendations Chapter 6. Sources of organic carbon fuelling macroinvertebrate food webs in waterbodies within the lower Gregory and Flinders River systems and potential subsidy to terrestrial-zone consumers Introduction Stable isotopes analysis (SIA) Chapter objectives, questions and hypotheses Methods Study area and sampling regime Stable isotopes: sample collection, preparation and analysis Basal sources Aquatic-zone consumers Terrestrial-zone consumers Preparation and analysis Supplementary analyses Data analysis Variation within and among basal sources and consumers Trophic enrichment estimation Trophic levels (TL) and omnivory Mixing models and basal source contribution to consumer biomass Aquatic-terrestrial subsidies Conceptual model applicability Results Basal source origins and variation among sources and consumers Stable carbon isotope ratios (δ 13 C) Stable nitrogen isotope ratios (δ 15 N) Origins and quality of basal sources Temporal variation Food webs Consumer trophic levels and omnivory Basal source contribution to macroinvertebrate food webs: mixing model solutions Aquatic subsidy to the terrestrial food web Discussion Basal source origins and conceptual model applicability Sources of organic carbon fuelling macroinvertebrate consumers Dry season food webs Temporal variation Aquatic subsidies to the terrestrial environment and implications for aquatic food webs SIA: issues, assumptions and considerations Conclusion ix

12 Chapter 7. Floodplain river function in Australia s wet/dry tropics: a new and scenariodriven conceptual model Introduction Floodplain river function in the study region and Australia s wet/dry topics: a thesis summary Flow Patterns: biophysical and chemical characteristics Patterns: macroinvertebrate assemblages Processes River function in the study region Perspective: a new conceptual model of floodplain river function in Australia s wet/dry tropics Introduction The conceptual model as diagrammatic The conceptual model as dynamic and probabilistic The conceptual model as scenario-driven Flow regimes Macroinvertebrate assemblages Macroinvertebrate food webs Summary, caveats and limitations of the conceptual model Recommendations and future research directions Appendices References x

13 List of Tables Table 2.1: Waterbodies sampled in the study region, with site codes used throughout this thesis, and detail on catchment, river section, lateral position in relation to the main channel, flow status at the time of sampling Table 3.1: Continuous daily flow records from gauging stations in the Gulf of Carpentaria drainage division used to classify the flow regimes of large rivers Table 3.2: Flow metrics used to classify flow regimes of rivers in the Gulf of Carpentaria and categories used in multivariate analysis, including the ecologically relevant description of a river s flow regime (facet); aspect of these facets described by the metric; and the relevant period of record described by the metric Table 3.3: Calculated flow metrics, standardised per km 2 upstream catchment area, used to classify flow regimes of rivers in the Gulf of Carpentaria Table 3.4: Comparison of flow variability metrics among large rivers in the Gulf of Carpentaria drainage division and other previously studied Australian rivers Table 3.5: Characteristics of Murray-Darling Basin (MDB) gauging stations and flow data used to assess potential post-water resource development impacts on selected Gulf of Carpentaria (GC) rivers Table 3.6: Ecologically relevant hydrological measures used in the assessment of postwater resource development impacts on southern Gulf of Carpentaria rivers, calculated from mean annual flow data standardised by upstream catchment area Table 3.7: Eigenvectors for the PCA on pre- and post-water resource development flow metrics, as described by Figure 3.7, with the variance explained by the first two principal component axes, PC1 and PC2, given in parentheses Table 3.8: Potential ecological impacts of predicted hydrological changes associated with water resource development in large floodplain rivers of Australia s wet/dry tropics, adapted to different flow regimes as represented by three key hydrological drivers of ecosystem function Table 4.1: Waterbody-scale morphology (biophysical features) of sites sampled in the study region during the 2005 and 2006 dry seasons Table 4.2: Conductivity, salinity, ph and Secchi depths (Z SD ) of water sampled from a mid-channel location for eleven sites in the study region during the 2005 dry season.. 72 Table 4.3: Eigenvectors for the PCA on the physicochemical characteristics of sites sampled during the 2005 dry season, with variation explained by each of the first two principal components axes (PC1 and PC2) given in parentheses Table 4.4: Conductivity, salinity, ph, turbidity and Secchi depths (Z M ) of waterbodies sampled during the 2006 dry season, measured at mid-channel and littoral zone locations, compared with 2005 dry season data (given in parentheses) when appropriate Table 4.5: Diel (24 h) minima and maxima for temperature ( C) and dissolved oxygen (% saturation) in waterbodies sampled during the 2006 dry season, measured at the midchannel and littoral zone locations Table 4.6: Physicochemical characteristics of water collected from GWm in the 2007 wet season (spot measures and medians; inter-quartile ranges in parentheses) xi

14 Table 5.1: Abundance (N) and richness (S) data (absolute and relative) for the major taxonomic groups (plus Orders within Insecta) and functional feeding groups (FFGs) of macroinvertebrates collected from the study region in the dry seasons of 2005 and Table 5.2: Results of ANOSIM on assemblage structure (based on Bray-Curtis dissimilarities using log-transformed abundance data) between groups within aprioridefined factors. Results are presented with taxa identified by SIMPER as contributing to more than 50% of the difference between statistically different groups Table 5.3: Correlations between assemblage composition of macroinvertebrate samples (based on taxonomic abundances, structure ; and functional feeding group proportions, function ) and combinations of environmental variables (BIOENV results) for the study region during the 2005 dry season Table 5.4: Results of ANOSIM based on assemblage function (based on Bray-Curtis dissimilarities using log-transformed FFG proportions) between groups within aprioridefined factors. Results are presented with FFGs identified by SIMPER as contributing to more than 50% of the significant difference between groups within factors Table 5.5: Mean values of diversity measures for groups within apriori-defined factors with significant differences (ANOVA), based on macroinvertebrate abundance data for samples collected in the study region during the 2005 dry season Table 6.1: Differences in δ 13 C values between catchments and states of flow for the major basal sources (FBOM, CBOM, seston and biofilm) collected from the study region during the 2005 dry season (results of Mann-Whitney U tests of difference) Table 6.2: Mean trophic levels (TLs) calculated for the major groups of secondary consumers (with TLs > 1) collected from the study region, based on a 1.0 enrichment in δ 15 N per trophic step above basal sources Table 6.3: Ranked importance of basal sources to macroinvertebrate consumers within the study region based on the frequency that each source made high max (> 55%), high min (> 40%) or low max (< 35%) contributions to consumer diets Table 6.4: Significant differences in min and max source contributions to consumer diets between groups of waterbodies in the study region (Mann-Whitney U test results) Table 6.5: Vertebrate fauna* observed in and around the riparian zones of waterbodies sampled in the 2006 dry season, with information on their feeding habits and potential proportional reliance on aquatic fauna as a food source Table 6.6: Summary of likely origins of basal sources sampled from within waterbodies in the study region during the 2005 and 2006 dry seasons Table 7.1: Floodplain river function (drivers, patterns and processes) in the study region (in Australia s wet/dry tropics), based on analyses of the flow regimes of large rivers in the Gulf of Carpentaria and macroinvertebrate assemblages of waterbodies in the lower Gregory and Flinders River systems (Chapters 3-6), presented with relevant aspects of existing concepts of large river function Table 7.2: Key conceptual features of two major, but contrasting, types of undisturbed, floodplain river systems (in terms of flow, biodiversity patterns and food web processes) in comparison with the studied river systems in Australia s wet/dry tropics Table 7.3: States within nodes that represent the key drivers, patterns and processes depicted in Figure 7.2, under current conditions (states are relative to each other within xii

15 the range of these conditions), and the potential factors of concern with respect to land and water resource development options or climate change Table 7.4: Sensitivity of response nodes to input nodes states and probabilities within the BBN as depicted in Figure 7.2 and Table 7.3, when Season and Flow regime nodes are unselected (all season and flow regime states equally likely) Table 7.5: Posterior probabilities for states within response nodes of the BBN, modelled on the conceptual diagram of river function in the study region (see Figure 7.2), for different seasons (dry or wet) and flow regime types ( tropical or dryland ) Table 7.6: Posterior probabilities for states within response nodes of the BBN modelled on the conceptual diagram of macroinvertebrate assemblages (structure, function and diversity) in the study region (Figures 7.2 and 7.3), for a dryland or tropical flow regime in the dry or wet season, given current conditions, under water abstraction or flow regulation scenarios Table 7.7: Posterior probabilities for states within response nodes of the BBN modelled on the conceptual diagram of macroinvertebrate food web dynamics in the study region (Figures 7.2 and 7.4), for a dryland or tropical flow regime in the dry or wet season, given current conditions, under water abstraction or flow regulation scenarios xiii

16 List of Figures Figure 2.1: The Australian tropics (north of the Tropic of Capricorn) with detail on the Gulf of Carpentaria drainage division, southern Gulf of Carpentaria sub-catchments as referred to in the text, and in relation to Griffith University in southeast Queensland.. 13 Figure 2.2: Study area in the southern Gulf of Carpentaria, showing location of sites sampled in the lower Gregory and Flinders River systems during the 2005 and 2006 dry seasons, and the 2007 wet season, as described in the text (see also Appendices A-B). 18 Figure 3.1: Map of Australia showing major drainage divisions (Gulf of Carpentaria, Timor Sea, Lake Eyre Basin and Murray-Darling Basin) and sub-catchments of interest to this study Figure 3.2: Group average dendrogram, using a normalised Euclidean distance similarity matrix, of flow metrics calculated for 15 large rivers in the Gulf of Carpentaria, indicating differentiation (dashed line) between Type 1 rivers (higher flow magnitudes and less skew) and Type 2 rivers (higher variability and zero flow days).. 31 Figure 3.3: MDS plots of two-dimensional solutions for 15 large rivers in the Gulf of Carpentaria, based on normalised Euclidean distance similarity matrices of: a) set aspects of flow magnitude with bubble-plot of the median dry season flow (lower flow magnitudes top right); b) variability of flow magnitude with bubble-plot of the coefficient of variation of annual flows (higher variability to the right); and c) set aspects of zero flow duration with bubble-plot of the median number of annual zero flow days (higher numbers of zero flow days to the right) Figure 3.4: Twenty year hydrographs of annual discharges (ML) standardised per km 2 catchment area for 15 large rivers in the Gulf of Carpentaria drainage division Figure 3.5: Group average dendrogram, using a normalised Euclidean distance similarity matrix, of dry and wet season flow metrics calculated for 15 large rivers in the Gulf of Carpentaria drainage division. Groups (indicated by dashed lines) separate rivers with dry-wet seasonality based on changes in flow magnitude (Group 1) or changes in zero flow days (Group 3). Group 2 represents rivers either with flow metrics in between the extremes of Group 1 and 3 or a combination of both Figure 3.6: Flow metrics for two Murray-Darling Basin (MDB) and five southern Gulf of Carpentaria (SGC) rivers, based on 20 years of mean annual discharges (ML d -1 ) standardised by upstream catchment area (km 2 ) Figure 3.7: PCA bi-plot of the first two principal component axes (PC1 versus PC2) for pre- and post-wrd flow metrics calculated for five southern Gulf of Carpentaria (G, C, FG, FR and J) and two Murray-Darling Basin (DB and DW) rivers. Solid arrows indicate gradients of change in flow metrics that have dominant eigenvector loadings on PC1 and PC2. Broken arrows indicate direction of change defined in two-dimensional PCA space between pre- and post-wrd conditions Figure 4.1: Number and diversity of aquatic macroinvertebrate habitat types within the study region: a) relative proportions of macroinvertebrate habitat types present within each site sampled during the 2005 and 2006 dry seasons; b) relative proportions of woody debris size classes present in sites sampled during the 2006 dry season Figure 4.2: Depth of waterbody (m) compared with calculated euphotic (Z EU ) and surface mixed layers (Z M ), for sites sampled from a mid-channel location in the 2005 dry season xiv

17 Figure 4.3: Median nutrient concentrations (mg L -1 ) and dissolved molar N:P ratios of water sampled from a mid-channel location for waterbodies in the study region during the 2005 dry season Figure 4.4: PCA bi-plot for physicochemical characteristics of sites sampled during the 2005 dry season, presented as site centroids (mean ± 1 standard error bars) and with eigenvectors for each physicochemical variable included in the analysis Figure 4.5: Median chlorophyll a (Chl) and total suspended solids (TSS) concentrations and organic TSS to chlorophyll a ratios (OTSS:Chl) of sites sampled during the 2005 dry season Figure 4.6: Comparison of coarse (CBOM) and fine (FBOM) fractions within benthic organic material (BOM; mean dry weights and relative proportions, n = 3) collected from sites sampled during the 2005 dry season Figure 4.7: Mean depth (n=3, standard error 0.1 m) of waterbodies sampled during the 2006 dry season, at mid-channel (MC) and littoral zone (LZ) locations, compared with calculated euphotic depths (Z EU ) and surface mixed layers (Z M ) Figure 4.8: Median nutrient concentrations (mg L -1 ) and dissolved molar N:P ratios of water sampled from a mid-channel location for four sites in the study region during the 2006 dry season, presented with inter-quartile ranges as bars (n = 3) and compared with 2005 dry season data where available Figure 4.9: Median concentrations (mg L -1 ) of organic and inorganic fractions of particulate (< 75 µm) carbon (C) and dissolved (< 0.45 µm) carbon (C), nitrogen (N) and phosphorus (P) in the water column of sites sampled from a mid-channel location during the 2006 dry season Figure 4.10: Median chlorophyll a (Chl) and total suspended solids (TSS) concentrations and organic TSS to chlorophyll a ratios (OTSS:Chl) of sites sampled during the 2006 dry season, compared with Figure 4.11: Median concentrations (mg L -1 ) of total particulate nitrogen (TN) and phosphorus (TP) in the Gregory River between dry seasons (2005 and 2006) and within a wet season (2007) Figure 5.1: Historical hydrographs of mean daily flow standardised by upstream catchment area (ML d -1 km -2 ) at gauging stations (open squares) near waterbodies (closed circles) sampled in the Flinders and Gregory study regions Figure 5.2: a) Agglomerative dendrogram with group-average linking and b) MDS ordination with sites as centroids (mean ordination co-ordinates for n = 3 samples with ± 1 standard error bars), based on Bray-Curtis sample dissimilarities from logtransformed abundance data of 33 samples of macroinvertebrates collected from 11 waterbodies in the study region during the 2005 dry season Figure 5.3: TWINSPAN dendrogram of 33 samples collected from the study region in the dry season of 2005, with two-way table of species group fidelities (F) to sample groups Figure 5.4: Spatial variation among assemblages at different scales of resolution and as measured by pair-wise Bray-Curtis dissimilarities within and between waterbodies for the 11 sites sampled during the 2005 dry season, based on log-transformed a) abundance data or b) FFG proportion data Figure 5.5: Bubble plots of important variables identified by BIOENV in explaining patterns of variation in macroinvertebrate assemblages of waterbodies sampled in the xv

18 2005 dry season, overlain on the MDS ordination plot (lower left) of sample assemblages Figure 5.6: Mean relative abundances of taxa within functional feeding groups for waterbodies sampled in the 2005 dry season Figure 5.7: MDS ordination with sites as centroids (mean ordination co-ordinates for n = 3 samples) with ± 1 standard error bars, based on Bray-Curtis sample dissimilarities from log-transformed FFG proportion data of 33 samples of macroinvertebrates collected from 11 waterbodies in the study region during the 2005 dry season Figure 5.8: Bubble plots of important variables identified by BIOENV in explaining patterns of variation in functional organisation of macroinvertebrate assemblages sampled in the 2005 dry season, overlain on the MDS ordination plot (lower right) of sample assemblages Figure 5.9: Diversity measures (mean +1 standard error bars), based on macroinvertebrate abundance data and habitat types for waterbodies sampled in the study region during the 2005 dry season Figure 5.10: (a) Agglomerative dendrogram with group-average linking and (b-c) MDS ordination with sites as centroids (mean ordination co-ordinates for n = 3 samples with ± 1 standard error bars), based on Bray-Curtis sample dissimilarities from logtransformed abundance data (a and b) and FFG proportions (c) of macroinvertebrate samples collected from the study region during the 2005 and 2005 dry seasons Figure 5.11: Spatial variation among assemblages at different scales of resolution, measured by pair-wise Bray-Curtis dissimilarities (based on log-transformed abundance data in the upper figure, and FFG proportion data in the lower figure) within and between waterbodies, and between years, for the 4 sites sampled in both the 2005 and dry seasons Figure 5.12: Conceptual diagram of beta-diversity between macroinvertebrate assemblages of sites in the study region, shown in relationship with the hydrological connectivity potential between any two waterbodies Figure 6.1: Box-plots of δ 13 C values for basal sources and all consumer groups (as listed in Appendix Q) sampled from the study region during the 2005 dry season Figure 6.2: Comparison of mean site δ 13 C values between potential end-member basal sources and other sources collected during the 2005 dry season, showing linear correlation trendlines and R 2 values: C 3 riparian vegetation versus CBOM, FBOM, seston and biofilm; biofilm versus CBOM, FBOM and seston; and CBOM versus FBOM Figure 6.3: Correlation in site mean δ 13 C values ( ) between basal sources and macroinvertebrate consumers in the study region during the 2005 and 2006 dry seasons, showing linear correlation trendlines and R 2 values: a) seston, b) biofilm, and c) FBOM versus primary and secondary consumers Figure 6.4: Box-plots of δ 15 N values for basal sources and all consumer groups (as listed in Appendix S) sampled from the study region during the 2005 dry season Figure 6.5: Bi-plot of mean site δ 13 C and molar C:N ratios of sources collected from the study region during the 2005 dry season, with the two most distinct sources encircled (biofilm representing aquatic sources, and CBOM representing terrestrial sources) Figure 6.6: Mean C:N molar ratios (with ± 1 standard error bars) of CBOM, FBOM and seston (sources with the potential to originate and be transported from elsewhere), in xvi

19 comparison with local riparian vegetation, for sites that follow a downstream continuum and were linked by flow at the time of sampling (during the 2005 dry season) Figure 6.7: Comparison of mean δ 13 C values (presented with ± 1 standard error bars) of basal sources with their potential end-member sources and among sites sampled during the 2005 and 2006 dry seasons: a) CBOM versus C 3 riparian vegetation, b) FBOM versus CBOM and biofilm, c) seston Figure 6.8: Comparison among mean δ 13 C values of seston sampled from the Gregory River during the 2005 and 2006 dry seasons (at site GUm) and during the 2007 wet season (at site GWm) Figure 6.9: Minimum and maximum feasible contributions from basal sources (excluding FBOM) to consumer diets within waterbodies (11 sampled in 2005, 4 resampled in 2006) in the study region during the dry season, calculated with IsoSource mixing models on δ 13 C data Figure 7.1: Initial conceptual model (influence diagram) of important components of floodplain river function in the study region (in Australia s wet/dry tropics), across large and small spatiotemporal scales and with particular reference to hydrology and aquatic biota Figure 7.2: Simplified influence diagram (conceptual model) of the key drivers, patterns and processes operating within macroinvertebrate assemblages and food webs within floodplain rivers in the study region (in Australia s wet/dry tropics) at various spatiotemporal scales (modified from Figure 7.1) Figure 7.3: Influence diagram (conceptual model) of the links between the most important drivers of river function for macroinvertebrate assemblage composition and diversity within floodplain rivers in the study region (in Australia s wet/dry tropics) under current dry season conditions Figure 7.4: Influence diagram (conceptual model) of the important links between common organic carbon sources and macroinvertebrate consumers within floodplain rivers in the study region (in Australia s wet/dry tropics), along with other important drivers of river function for macroinvertebrate food webs, under current conditions. 216 Figure 7.5: Example BBN and posterior probabilities given a dryland river flow regime during the dry season (cf. Table 7.4) for the key drivers, patterns and processes operating within macroinvertebrate assemblages and food webs within floodplain rivers in the study region (in Australia s wet/dry tropics) at various spatiotemporal scales Figure 7.6: Example BBN, given a flow regulation scenario in a dryland river during the dry season, showing the potential effect (represented by posterior probabilities) of water resource development options on the composition (structural and functional) and diversity of macroinvertebrate assemblages within floodplain rivers in the study region (in Australia s wet/dry tropics) Figure 7.7: Two-dimensional MDS ordination of current and modified macroinvertebrate composition and diversity within floodplain rivers in the study region (in Australia s wet/dry tropics) given a water abstraction or flow regulation scenario, based on a normalised Euclidean distance matrix of posterior probabilities from the BBN as described in the text (see Table 7.5) Figure 7.8: Example BBN, given a flow regulation scenario in a dryland river during the dry season, showing the potential effect (represented by posterior probabilities) of water resource development options on macroinvertebrate food web dynamics within floodplain rivers in the study region (in Australia s wet/dry tropics) xvii

20 Figure 7.9: Two-dimensional MDS ordination of current and modified macroinvertebrate food web dynamics within floodplain rivers in the study region (in Australia s wet/dry tropics) given a water abstraction or flow regulation scenario, based on a normalised Euclidean distance matrix of posterior probabilities from the BBN as described in the text (see Table 7.6) xviii

21 List of Appendices Appendix A: Streamflow gauging stations in the lower reaches of the Nicholson and Flinders sub-catchments and study region Appendix B: Catchment, river section and waterbody-scale description of sites sampled in the study region during the 2005 dry season Appendix C: Conditions observed at GWm during the 2007 wet season for the January, March and April sampling periods Appendix D: Aquatic macrophytes and macroalgae (aquatic vegetation) and most common or dominant terrestrial plants (riparian vegetation) present (p) at sites sampled in the study region during the 2005 and 2006 dry seasons Appendix E: TRARC scores for sites sampled in 2006, assessed following methods outlined in Dixon et al. (2006) Appendix F: Spot measures for various physicochemical properties of waterbodies sampled in the study region during the 2005 and 2006 dry seasons and the 2007 wet season Appendix G: Median chlorophyll a concentration and physicochemical characteristics of waterbodies sampled in the study region during the 2005 and 2006 dry seasons and the 2007 wet season Appendix H: Mean chlorophyll a concentration and physicochemical characteristics of waterbodies sampled in the study region during the 2005 and 2006 dry seasons and the 2007 wet season Appendix I: Keys and guides used for taxonomic and functional feeding group identification of macroinvertebrates collected from the study region Appendix J: Datasets used to explore relationships between patterns of variation in macroinvertebrate assemblages and their biophysical and chemical environment, at different scales of resolution Appendix K: Biophysical and chemical characteristics of waterbodies in the dry season of 2005, described by variables used in the correlation analyses with macroinvertebrate assemblage data (BIOENV), with data for waterbodies re-sampled* in the 2006 dry season Appendix L: Taxa identified from samples collected from waterbodies in the Gregory and Flinders study region during the 2005 and 2006 dry seasons, associated functional feeding groups (FFG) and species groups identified by TWINSPAN (for samples collected in 2005 only) Appendix M: Box-plots of δ 13 C and δ 15 N values, and organic carbon to chlorophyll a (mass C:Chl) and to nitrogen (molar C:N) concentration ratios for seston collected from littoral zones and mid-channel (pelagic-zone) locations of waterbodies during the 2006 dry season Appendix N: Live versus detrital fractions within seston and biofilm Appendix O: Trophic enrichment within the study region Appendix P: Vertebrate species (mammals, birds, terrestrial reptiles and amphibians) observed ( o ) at sites sampled in the study region during the 2006 dry season and their main dietary guild classification, presented with detail on their potential consumption xix

22 ( yes ) of aquatic food sources (fish, crustaceans, invertebrates, and emergent adult insects) Appendix Q: Mean δ 13 C ( ) of basal sources and consumers for samples collected from the study region during the 2005 dry season Appendix R: Common or dominant C 3 plants found in the riparian zones of sites sampled during the 2005 dry season and those C 3 riparian plants used in SIA as well as taxa identified from CBOM samples Appendix S: Mean δ 15 N ( ) of basal sources and consumers for samples collected from the study region during the 2005 dry season Appendix T: Mean molar C:N ratios of basal sources and consumers for samples collected from the study region during the 2005 dry season Appendix U: Mean δ 13 C and δ 15 N values for zooplankton and primary consumers collected from the study region during the 2005 and 2006 dry seasons Appendix V: Mean δ 13 C and δ 15 N values for secondary consumers collected from the study region during the 2005 and 2006 dry seasons Appendix W: Mean δ 13 C ( ) of basal sources collected from the study region during the 2005 and 2006 dry seasons Appendix X: Mean molar C:N ratios of basal sources collected from the study region during the 2005 and 2006 dry seasons Appendix Y: Mean δ 15 N ( ) of basal sources collected from the study region during the 2005 and 2006 dry seasons Appendix Z: Site bi-plots of mean δ 13 C and δ 15 N values ( ) for basal sources and consumers collected from the Gregory River study region during the 2005 dry season Appendix AA: Site bi-plots of mean δ 13 C and δ 15 N values ( ) for basal sources and consumers collected from the Flinders River study region during the 2005 dry season Appendix BB: Site bi-plots of mean δ 13 C and δ 15 N values ( ) for basal sources and consumers collected from the Gregory and Flinders Rivers study regions during the 2006 dry season Appendix CC: 1 st -99 th percentile ranges of the contribution (%) of basal sources (excluding FBOM) to primary consumer diets in the study region during the 2005 and 2006 dry seasons, produced using IsoSource mixing models based on δ 13 C data Appendix DD: 1 st -99 th percentile ranges of the contribution (%) of basal sources (excluding FBOM) to secondary consumer diets in the study region during the 2005 and 2006 dry seasons, produced using IsoSource mixing models based on δ 13 C data Appendix EE: Conditional probability tables (priors) for Bayesian Belief Networks (BBNs) formulated in Chapter 7 (Tables EE.1-3) xx

23 Acknowledgements Throughout my PhD candidature, I have received help and support from many people and organisations, for which I am very grateful. I apologise to anyone I may have missed: all who have contributed are greatly appreciated. In particular, I thank my supervisors, Drs Fran Sheldon and Michele Burford and Prof. Stuart Bunn, for their encouragement, guidance and supervision, without which the work presented in this thesis would not have been possible. The PhD project was funded by a Land & Water Australia Postgraduate Research Scholarship (GRU35), administrated by Griffith University, and a Griffith School of Environment Completion Assistance Postgraduate Research Scholarship. I also received funding and in-kind support for conference attendance, travel, field work, sample analysis and mentorship from: the Australian Rivers Institute / Centre for Riverine Landscapes at Griffith University; the Australian Society for Limnology; the Griffith School of Environment / Australian School of Environmental Studies at Griffith University; Southern Gulf Catchments (SGC) in Mt Isa; and the Wentworth Group of Concerned Scientists through a 2007 Wentworth Group Science Program Scholarship award. The Australian wet/dry tropics and the Gregory and Flinders River systems are stunning places to have studied. I am very grateful for the opportunity to visit and study them, and, I hope, to assist in their future protection. My warmest regards and thanks extend to the traditional owners of this country, as represented through Moungibi and the Carpentaria Land Council, and to the pastoral leaseholders and station managers in the region, all for granting permission to access and study these river systems and for the on-site assistance they all provided. In addition, SGC, Shire Councils and a number of colleagues with experience in the region (especially James Fawcett and Joel Huey) were instrumental in helping me to establish these local contacts. Many people assisted me with field trip preparation, equipment and analytical methods. I thank them all, including: Jeff Argo, Andrew Brooks, Peter Brunner, Stuart Bunn, Michele Burford, Scott Byrnes, Chengrong Chen, Andrew Cook, Rene Diocares, Noreen Dejoras, Michael Douglas, James Fawcett, Christy Fellows, Vanessa Fry, Jane Gifkins, Susie Green, Wade Hadwen, Stephen Hamilton, Courtney Henderson, Mark xxi

24 Kennard, Jason Kerr, Priyanesh Muhid, Kylie Pitt, Carolyn Polson, Amanda Posselt, Jim Puckridge, Fran Sheldon, Terry Reis, David Roberts, Kate Smolders, John Spencer, and Loretta Young. Everyone at the Australian Rivers Institute and the Griffith School of Environment, especially Fran Sheldon, Lacey Shaw, Deslie Smith, Heidi Millington, Michele Burford and her RnR group, have been very helpful throughout my candidature. They have offered support, advice, and constructive criticism. Additionally, I was assisted in the field by wonderful volunteers. These people gave their time and worked amazingly hard. I cannot thank them enough: Erika Alacs, Jim McGuire, Ben Cook, Tim Page, Joel Huey and James Fawcett for their help during my first trip to Australia s great north in 2005, Terry Reis and Brett Taylor for their fantastic help and company during the 2006 field trip. Wet season sampling in 2007 would not have been possible without volunteers: Jo from the Gregory Downs Hotel, Murray from the Gregory Downs general store, and especially Megan Munchenberg from Gregory Downs, along with the assistance I received from SCG, in particular from Matthew Vickers and Mark van Ryt. Two volunteers also helped sort the seemingly endless detritus and sediment from my bug samples: thank you Jane Ogilvie and Jennifer Sanger. Flow data for Gulf of Carpentaria rivers were provided in 2005 by the Queensland Department of Natural Resources and Mines, which gives no warranty in relation to the data (including accuracy, reliability, completeness or suitability) and accepts no liability (including without limitation, liability in negligence) for any loss, damage or costs (including consequential damage) relating to any use of the data. Integrated Quantity and Quality Model (IQQM) flow data for the Darling River gauges were provided to Fran Sheldon, my principal supervisor, from the New South Wales Department of Land and Water Conservation (1995). The project was given ethical clearance by Griffith University s Animal Ethics Committee and research was conducted in accordance with the requirements of this Committee. I attended and presented components of research detailed in this thesis at national and international conferences. I learned much from these experiences, from other presentations and from discussions with other attendees, for which I am very appreciative. These conferences are the Australian Society for Limnology (ASL) conference in Hobart, Tasmania, 2005; the Third International Symposium on Riverine xxii

25 Landscapes (TISORL) on South Stradbroke Island, Queensland, 2007; the 10 th International RiverSymposium and Environmental Flows Conference in Brisbane, Queensland, 2007; and the joint ASL and New Zealand Freshwater Sciences Society (NZFSS) conference in Queenstown, New Zealand, In addition, I have published work arising from this thesis as principal author. The main body of Chapter 3 forms the basis of an original research paper, published as: Leigh C, Sheldon F Hydrological changes and ecological impacts associated with water resource development in large floodplain rivers in the Australian tropics. River Research and Applications. DOI: /rra The main body of Chapter 5 forms the basis of the following journal manuscript: Leigh C, Sheldon F. In review. Hydrological connectivity drives patterns of macroinvertebrate biodiversity in floodplain rivers of the Australian wet/dry tropics. Freshwater Biology. I conducted and produced the work outlined in these articles under supervision from Dr Fran Sheldon during my PhD candidature. Overall, the support of friends and family throughout my candidature has been paramount. These people have seen me through the low troughs. They have got me out and about and enjoying life. Thank you! Special thanks to my gorgeous friends Meg, Angie and Lynette, and my dear sister, Rachel. I dedicate this thesis to my parents, Eileen ( ) and Robert Leigh ( ). xxiii