Publications by authors named "Marcus Sheaves"

16 Publications

  • Page 1 of 1

Evolutionary determinism and convergence associated with water-column transitions in marine fishes.

Proc Natl Acad Sci U S A 2020 12 16;117(52):33396-33403. Epub 2020 Dec 16.

Department of Biology, The University of Oklahoma, Norman, OK 73019;

Repeatable, convergent outcomes are prima facie evidence for determinism in evolutionary processes. Among fishes, well-known examples include microevolutionary habitat transitions into the water column, where freshwater populations (e.g., sticklebacks, cichlids, and whitefishes) recurrently diverge toward slender-bodied pelagic forms and deep-bodied benthic forms. However, the consequences of such processes at deeper macroevolutionary scales in the marine environment are less clear. We applied a phylogenomics-based integrative, comparative approach to test hypotheses about the scope and strength of convergence in a marine fish clade with a worldwide distribution (snappers and fusiliers, family Lutjanidae) featuring multiple water-column transitions over the past 45 million years. We collected genome-wide exon data for 110 (∼80%) species in the group and aggregated data layers for body shape, habitat occupancy, geographic distribution, and paleontological and geological information. We also implemented approaches using genomic subsets to account for phylogenetic uncertainty in comparative analyses. Our results show independent incursions into the water column by ancestral benthic lineages in all major oceanic basins. These evolutionary transitions are persistently associated with convergent phenotypes, where deep-bodied benthic forms with truncate caudal fins repeatedly evolve into slender midwater species with furcate caudal fins. Lineage diversification and transition dynamics vary asymmetrically between habitats, with benthic lineages diversifying faster and colonizing midwater habitats more often than the reverse. Convergent ecological and functional phenotypes along the benthic-pelagic axis are pervasive among different lineages and across vastly different evolutionary scales, achieving predictable high-fitness solutions for similar environmental challenges, ultimately demonstrating strong determinism in fish body-shape evolution.
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http://dx.doi.org/10.1073/pnas.2006511117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7777220PMC
December 2020

A realistic fish-habitat dataset to evaluate algorithms for underwater visual analysis.

Sci Rep 2020 09 4;10(1):14671. Epub 2020 Sep 4.

James Cook University, Townsville, Australia.

Visual analysis of complex fish habitats is an important step towards sustainable fisheries for human consumption and environmental protection. Deep Learning methods have shown great promise for scene analysis when trained on large-scale datasets. However, current datasets for fish analysis tend to focus on the classification task within constrained, plain environments which do not capture the complexity of underwater fish habitats. To address this limitation, we present DeepFish as a benchmark suite with a large-scale dataset to train and test methods for several computer vision tasks. The dataset consists of approximately 40 thousand images collected underwater from 20 habitats in the marine-environments of tropical Australia. The dataset originally contained only classification labels. Thus, we collected point-level and segmentation labels to have a more comprehensive fish analysis benchmark. These labels enable models to learn to automatically monitor fish count, identify their locations, and estimate their sizes. Our experiments provide an in-depth analysis of the dataset characteristics, and the performance evaluation of several state-of-the-art approaches based on our benchmark. Although models pre-trained on ImageNet have successfully performed on this benchmark, there is still room for improvement. Therefore, this benchmark serves as a testbed to motivate further development in this challenging domain of underwater computer vision.
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http://dx.doi.org/10.1038/s41598-020-71639-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7473859PMC
September 2020

Thermal exposure risks to mobile tropical marine snails: Are eco-engineered rock pools on seawalls scale-specific enough for comprehensive biodiversity outcomes?

Mar Pollut Bull 2020 Jul 7;156:111237. Epub 2020 May 7.

Marine Data Technology Hub, College of Science and Engineering, James Cook University, Queensland 4811, Australia; Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), College of Science and Engineering, James Cook University, Queensland 4811, Australia.

To test the model that eco-engineering plant boxes on seawalls sustain water temperatures within thermal tolerance to maximize tropical marine biodiversity, we conducted acute thermal effects (AET) experiments using intertidal gastropods (Nerita albicilla and Littoraria articulata). The AET (50th percentile) for N. albicilla (39.6 °C) was higher than L. articulata (32.8 °C). Loggers (Hobo) in boxes on a seawall positioned for full exposure to air temperature at mean sea level (<1.1 m) recorded temperature every 20 min during summer months. Temperature frequency distribution plots were generated for day and night, above and below 1.1 m (which is proximal to mean tide level for the region). Using the AET, N. albicilla would need to thermoregulate for a lower percentage of time compared to L. articulata regardless of day and night. It is likely that designing eco-engineering improvements to include microclimate refugia are particularly relevant in tropical areas, where extreme environmental conditions mean that scale-specific actions are important components for climate adaptation.
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http://dx.doi.org/10.1016/j.marpolbul.2020.111237DOI Listing
July 2020

Low redundancy and complementarity shape ecosystem functioning in a low-diversity ecosystem.

J Anim Ecol 2020 03 24;89(3):784-794. Epub 2019 Dec 24.

School of Science and Engineering, University of the Sunshine Coast, Maroochydore, Qld, Australia.

Ecosystem functioning is positively linked to biodiversity on land and in the sea. In high-diversity systems (e.g. coral reefs), species coexist by sharing resources and providing similar functions at different temporal or spatial scales. How species combine to deliver the ecological function they provide is pivotal for maintaining the structure, functioning and resilience of some ecosystems, but the significance of this is rarely examined in low-diversity systems such as estuaries. We tested whether an ecological function is shaped by biodiversity in a low-diversity ecosystem by measuring the consumption of carrion by estuarine scavengers. Carrion (e.g. decaying animal flesh) is opportunistically fed on by a large number of species across numerous ecosystems. Estuaries were chosen as the model system because carrion consumption is a pivotal ecological function in coastal seascapes, and estuaries are thought to support diverse scavenger assemblages, which are modified by changes in water quality and the urbanization of estuarine shorelines. We used baited underwater video arrays to record scavengers and measure the rate at which carrion was consumed by fish in 39 estuaries across 1,000 km of coastline in eastern Australia. Carrion consumption was positively correlated with the abundance of only one species, yellowfin bream Acanthopagrus australis, which consumed 58% of all deployed carrion. The consumption of carrion by yellowfin bream was greatest in urban estuaries with moderately hardened shorelines (20%-60%) and relatively large subtidal rock bars (>0.1 km ). Our findings demonstrate that an ecological function can be maintained across estuarine seascapes despite both limited redundancy (i.e. dominated by one species) and complementarity (i.e. there is no spatial context where the function is delivered significantly when yellowfin bream are not present) in the functional traits of animal assemblages. The continued functioning of estuaries, and other low-diversity ecosystems, might therefore not be tightly linked to biodiversity, and we suggest that the preservation of functionally dominant species that maintain functions in these systems could help to improve conservation outcomes for coastal seascapes.
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http://dx.doi.org/10.1111/1365-2656.13148DOI Listing
March 2020

Global spatial risk assessment of sharks under the footprint of fisheries.

Nature 2019 08 24;572(7770):461-466. Epub 2019 Jul 24.

Shark Research and Conservation Program, Cape Eleuthera Institute, Eleuthera, Bahamas.

Effective ocean management and the conservation of highly migratory species depend on resolving the overlap between animal movements and distributions, and fishing effort. However, this information is lacking at a global scale. Here we show, using a big-data approach that combines satellite-tracked movements of pelagic sharks and global fishing fleets, that 24% of the mean monthly space used by sharks falls under the footprint of pelagic longline fisheries. Space-use hotspots of commercially valuable sharks and of internationally protected species had the highest overlap with longlines (up to 76% and 64%, respectively), and were also associated with significant increases in fishing effort. We conclude that pelagic sharks have limited spatial refuge from current levels of fishing effort in marine areas beyond national jurisdictions (the high seas). Our results demonstrate an urgent need for conservation and management measures at high-seas hotspots of shark space use, and highlight the potential of simultaneous satellite surveillance of megafauna and fishers as a tool for near-real-time, dynamic management.
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http://dx.doi.org/10.1038/s41586-019-1444-4DOI Listing
August 2019

Patterns of fish utilisation in a tropical Indo-Pacific mangrove-coral seascape, New Caledonia.

PLoS One 2019 19;14(4):e0207168. Epub 2019 Apr 19.

College of Science and Engineering, James Cook University, Townsville, Queensland, Australia.

Mangrove forests are important habitats for fish. However, their utilisation by fish, and the specific values they confer, are still not fully understood. This study describes how fish use mangrove forests in an Indo-Pacific mangrove-coral reef seascape. Sampling was conducted using underwater video cameras (UVCs) to describe spatial and temporal variations in fish assemblages across a small-scale (~ 2.5 km2) system, and over the tidal and lunar cycle. UVCs were deployed in the two main component habitats of mangrove forests: at the mangrove forest edge, and inside the forest (5 m from the forest edge), to establish patterns of utilisation of fish across the tidal and lunar cycle. Proximity to coral reefs had a strong influence on the mangrove fish community, as most fish recorded were reef-associated. Juveniles of 12 reef species were observed, including two species classified as vulnerable on the IUCN list, and one endemic species. Fish assemblages on the mangrove edge differed significantly from those inside the forest. Most fish utilised the forest edge, with few species making regular use of in-forest habitats, supporting the contention that most fish species remain on the edge and potentially retreat into the forest for opportunistic feeding, or when threatened by larger predators. Species-specific patterns of utilisation varied across the tidal and lunar cycle. Small differences in depth profiles and substrate across the small-scale system had a significant effect on fish assemblages, highlighting the importance of accounting for spatial heterogeneity in these factors. These data provide important information for managers to implement adequate conservation strategies that include broader interconnected habitat mosaics.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0207168PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474647PMC
December 2019

Estimating the value of tropical coastal wetland habitats to fisheries: Caveats and assumptions.

PLoS One 2019 17;14(4):e0215350. Epub 2019 Apr 17.

College of Science and Engineering, James Cook University, Townsville, Queensland, Australia.

Habitat valuation can provide an objective basis for the prioritisation of conservation and restoration actions. The attribution of fisheries production to particular habitat units is an important measure of value, but is difficult to estimate. Using the case study of habitat use by juvenile banana prawns in a tropical estuary, we assessed the potential to produce valid value estimates at two spatio-conceptual scales: estuary reach and whole estuary. Additionally, we also explore the potential to produce meaningful value estimates at the scale of whole estuary contribution to the offshore fisheries stock. A diversity of potential and actual sources of error and logical problems means that quantification at any scale is at best of uncertain validity and produces estimates that are likely to produce unreliable results if treated as quantitative inputs to production models. Estimates for the whole estuary were the most viable, although still requiring substantial assumptions that may or may not be reasonable in particular situations. Estimates for individual habitats required the unreasonable assumption of limited prawn movement, while estimates of contribution of an estuary to the fishery required difficult-to-obtain and usually unavailable information. Because low occupancy habitats can have trophic value, we also used stable isotope analysis to assess the importance of mangroves and saltmarshes to prawn nutrition. No particular habitat was of critical trophic importance, again suggesting that the habitat-production link is most usefully assessed at the whole-of-estuary scale. While valuable and required to support targeted ecosystem management and protection and restoration efforts, valid estimates of the contribution of particular units to fisheries are likely to be unachievable in many situations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215350PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469798PMC
January 2020

Stable isotopes reveal opportunistic foraging in a spatiotemporally heterogeneous environment: Bird assemblages in mangrove forests.

PLoS One 2018 15;13(11):e0206145. Epub 2018 Nov 15.

College of Science and Engineering, James Cook University, Townsville, Queensland, Australia.

Environmental heterogeneity can foster opportunistic foraging by mobile species, resulting in generalized resource and habitat use. Determining species' food web roles is important to fully understand how ecosystems function, and stable isotopes can provide insight into the foraging ecology of bird assemblages. We investigated flexibility of food choice in mangrove bird assemblages of northeast Australia by determining whether species' carbon and nitrogen isotopic values corresponded to foraging group classification described in the literature, such as groups of species that are omnivorous or insectivorous. Subsequently, we evaluated foraging group isotopic niche size, overlap, degree of individual specialisation, and the probable proportions of coastal resources that contribute to their collective diets. We found that mangrove birds are more opportunistic when foraging than expected from previous diet studies. Importantly, relationships between the dietary diversity of species within a foraging group and isotopic niche size are spatially inconsistent, making inferences regarding foraging strategies difficult. However, quantifying individual specialisation and determining the probable relative contributions of coastal resources to the collective diet of isotope-based foraging groups can help to differentiate between specialised and generalised foraging strategies. We suggest that flexibility in mangrove bird foraging strategy occurs in response to environmental heterogeneity. A complementary approach that combines isotopic analysis with other dietary information (collated from previous diet studies using visual observation or gut content analyses) has provided useful insight to how bird assemblages partition resources in spatiotemporally heterogeneous environments.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0206145PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237324PMC
April 2019

Social capital plays a central role in transitions to sportfishing tourism in small-scale fishing communities in Papua New Guinea.

Ambio 2019 Apr 31;48(4):385-396. Epub 2018 Jul 31.

College of Science and Engineering, James Cook University, Building 142, Townsville, QLD, 4811, Australia.

Growing concerns about pressures of global change on small-scale fishing communities have resulted in a proliferation of livelihood diversification initiatives linked to tourism. Where the focus is often on the role of financial, physical, and human capital in influencing the uptake of new opportunities, we argue for more consideration of the role of social capital. We implemented 157 household-level surveys in small-scale fishing communities in Papua New Guinea and modelled the influence of social and other capital assets on people's perceptions of how easy it would be to become involved in sportfishing tourism. Social capital had a stronger influence relative to other forms of capital, with perceptions of reciprocity and satisfaction with leadership being the most influential aspects. Based on these results, we stress the importance of developing strategies aimed at understanding, building, and maintaining social capital and related social dynamics when implementing livelihood diversification initiatives.
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http://dx.doi.org/10.1007/s13280-018-1081-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411814PMC
April 2019

Phylogenetic analysis of trophic niche evolution reveals a latitudinal herbivory gradient in Clupeoidei (herrings, anchovies, and allies).

Mol Phylogenet Evol 2018 07 15;124:151-161. Epub 2018 Mar 15.

Bell Museum of Natural History, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, St. Paul, MN 55108, USA; Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, 135B Skok Hall, 2003 Upper Buford Circle, St. Paul, MN 55108, USA.

Biotic and abiotic forces govern the evolution of trophic niches, which profoundly impact ecological and evolutionary processes and aspects of species biology. Herbivory is a particularly interesting trophic niche because there are theorized trade-offs associated with diets comprised of low quality food that might prevent the evolution of herbivory in certain environments. Herbivory has also been identified as a potential evolutionary "dead-end" that hinders subsequent trophic diversification. For this study we investigated trophic niche evolution in Clupeoidei (anchovies, sardines, herrings, and their relatives) and tested the hypotheses that herbivory is negatively correlated with salinity and latitude using a novel, time-calibrated molecular phylogeny, trophic guilds delimited using diet data and cluster analysis, and standard and phylogenetically-informed statistical methods. We identified eight clupeoid trophic guilds: molluscivore, terrestrial invertivore, phytoplanktivore, macroalgivore, detritivore, piscivore, crustacivore, and zooplanktivore. Standard statistical methods found a significant negative correlation between latitude and the proportion of herbivorous clupeoids (herbivorous clupeoid species/total clupeoid species), but no significant difference in the proportion of herbivorous clupeoids between freshwater and marine environments. Phylogenetic least squares regression did not identify significant negative correlations between latitude and herbivory or salinity and herbivory. In clupeoids there were five evolutionary transitions from non-herbivore to herbivore guilds and no transitions from herbivore to non-herbivore guilds. There were no transitions to zooplanktivore, the most common guild, but it gave rise to all trophic guilds, except algivore, at least once. Transitions to herbivory comprised a significantly greater proportion of diet transitions in tropical and subtropical (<35°) relative to temperate areas (>35°). Our findings suggest cold temperatures may constrain the evolution of herbivory and that herbivory might act as an evolutionary "dead-end" that hinders subsequent trophic diversification, while zooplanktivory acts as an evolutionary "cradle" that facilitates trophic diversification.
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http://dx.doi.org/10.1016/j.ympev.2018.03.011DOI Listing
July 2018

Australian shellfish ecosystems: Past distribution, current status and future direction.

PLoS One 2018 14;13(2):e0190914. Epub 2018 Feb 14.

Centre of Excellence in Natural Resource Management, University of Western Australia, Albany, Western Australia, Australia.

We review the status of marine shellfish ecosystems formed primarily by bivalves in Australia, including: identifying ecosystem-forming species, assessing their historical and current extent, causes for decline and past and present management. Fourteen species of bivalves were identified as developing complex, three-dimensional reef or bed ecosystems in intertidal and subtidal areas across tropical, subtropical and temperate Australia. A dramatic decline in the extent and condition of Australia's two most common shellfish ecosystems, developed by Saccostrea glomerata and Ostrea angasi oysters, occurred during the mid-1800s to early 1900s in concurrence with extensive harvesting for food and lime production, ecosystem modification, disease outbreaks and a decline in water quality. Out of 118 historical locations containing O. angasi-developed ecosystems, only one location still contains the ecosystem whilst only six locations are known to still contain S. glomerata-developed ecosystems out of 60 historical locations. Ecosystems developed by the introduced oyster Crasostrea gigas are likely to be increasing in extent, whilst data on the remaining 11 ecosystem-forming species are limited, preventing a detailed assessment of their current ecosystem-forming status. Our analysis identifies that current knowledge on extent, physical characteristics, biodiversity and ecosystem services of Australian shellfish ecosystems is extremely limited. Despite the limited information on shellfish ecosystems, a number of restoration projects have recently been initiated across Australia and we propose a number of existing government policies and conservation mechanisms, if enacted, would readily serve to support the future conservation and recovery of Australia's shellfish ecosystems.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190914PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5812559PMC
April 2018

Expanding urban and industrial development in tropical seascapes necessitates green engineering and spatial planning thinking.

Environ Sci Technol 2015 Mar 20;49(5):2598-9. Epub 2015 Feb 20.

Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), Estuary and Coastal Wetland Ecosystems Research Group, James Cook University , Queensland 4811, Australia.

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http://dx.doi.org/10.1021/acs.est.5b00661DOI Listing
March 2015

Bimini Islands: a characterization of the two major nursery areas; status and perspectives.

Springerplus 2014 28;3:270. Epub 2014 May 28.

School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811 Australia ; Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER), James Cook University, Townsville, QLD 4811 Australia.

Bimini Islands (Bahamas, 25°44' N 79°16' W) are characterized by a unique tropical marine environment which provides critical nursery habitats and food resources for many important species of ecological and economical value. Two areas are particularly important in the function and dynamics of the local marine environment: North Sound and South Bimini. Since 1998 the northern part of the island has been subject to an intense urbanization process that involves the construction of an extensive touristic complex. Over the years this activity has radically modified a substantial portion of the land, and part of the underwater environment as well, threatening the fragile balance of the North Sound nursery ground. Effects on marine habitats and on local species have been reported, and although some measures to limit the damage have already been taken, the local ecosystem could ultimately suffer from continuation of the construction work on the area. In 2010, we performed surveys of both main nursery grounds to assess the current ecological status and the main differences between the two areas, investigating macrobenthic epifauna abundance, seagrass density and abiotic parameters. The results of this study indicate that the ecosystem still appears in reasonably healthy condition, although showing some concerning trends. These data provide baseline conditions to assess further changes, and possibly to support the development of plans for the conservation of the North Sound and South Bimini coastal ecosystems.
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http://dx.doi.org/10.1186/2193-1801-3-270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053571PMC
June 2014

Ecotone analysis: assessing the impact of vehicle transit on saltmarsh crab population and ecosystem.

Springerplus 2014 5;3:655. Epub 2014 Nov 5.

School of Marine and Tropical Biology, James Cook University, Townsville, Qld 4811 Australia ; TropWATER (Centre for Tropical Water & Aquatic Ecosystem Research), James Cook University, Townsville, Qld 4811 Australia.

The frequent transit of vehicles (recreational or not) through saltpans and saltmarsh fields has been recorded as one of the major causes of physical and ecological damage for these environments. While several studies have been carried out to assess the consequence of this anthropogenic activity on the different local plant species, little is known on its long-term impact on the faunal community. Invertebrates, such as crabs, provide several essential ecological services, and their presence and abundance are tightly connected to that of the saltmarsh plants. Decrease of vegetative cover due to vehicle transit is likely to cause alterations in the morphology and the composition of the saltmarsh ecosystem. In this study we evaluate presence and distribution of the main crustacean species in several impacted sites in Townsville area (Queensland, Australia), to determine possible correlation between vehicle tracks alterations and crab distribution, as well as investigate any possible habitat shift in the mid- and long-term. Results indicate that reduction of plant cover affects species composition and distribution, with different effects based on the unique characteristics of each crab species analysed, resulting in an overall alteration of the assemblage structure.
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http://dx.doi.org/10.1186/2193-1801-3-655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447770PMC
June 2015

Fish utilisation of wetland nurseries with complex hydrological connectivity.

PLoS One 2012 9;7(11):e49107. Epub 2012 Nov 9.

Estuary and Tidal Wetland Ecosystems, School of Marine and Tropical Biology, James Cook University, Townsville, Queensland, Australia.

The physical and faunal characteristics of coastal wetlands are driven by dynamics of hydrological connectivity to adjacent habitats. Wetlands on estuary floodplains are particularly dynamic, driven by a complex interplay of tidal marine connections and seasonal freshwater flooding, often with unknown consequences for fish using these habitats. To understand the patterns and subsequent processes driving fish assemblage structure in such wetlands, we examined the nature and diversity of temporal utilisation patterns at a species or genus level over three annual cycles in a tropical Australian estuarine wetland system. Four general patterns of utilisation were apparent based on CPUE and size-structure dynamics: (i) classic nursery utlisation (use by recently settled recruits for their first year) (ii) interrupted peristence (iii) delayed recruitment (iv) facultative wetland residence. Despite the small self-recruiting 'facultative wetland resident' group, wetland occupancy seems largely driven by connectivity to the subtidal estuary channel. Variable connection regimes (i.e. frequency and timing of connections) within and between different wetland units (e.g. individual pools, lagoons, swamps) will therefore interact with the diversity of species recruitment schedules to generate variable wetland assemblages in time and space. In addition, the assemblage structure is heavily modified by freshwater flow, through simultaneously curtailing persistence of the 'interrupted persistence' group, establishing connectivity for freshwater spawned members of both the 'facultative wetland resident' and 'delayed recruitment group', and apparently mediating use of intermediate nursery habitats for marine-spawned members of the 'delayed recruitment' group. The diversity of utilisation pattern and the complexity of associated drivers means assemblage compositions, and therefore ecosystem functioning, is likely to vary among years depending on variations in hydrological connectivity. Consequently, there is a need to incorporate this diversity into understandings of habitat function, conservation and management.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049107PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494659PMC
May 2013