A Large-scale, Hierarchical Approach for Assessing Habitat Associations of Fish Assemblages in Large Dryland Rivers

Multiple-scale assessments of fish-habitat associations are limited despite the fact that riverine fish assemblages are influenced by factors operating over a range of spatial scales. A method for assessing fish-habitat assemblages at multiple scales is proposed and tested in a large Australian dryland river, the Barwon–Darling River. Six discrete mesohabitat types (large wood, smooth bank, irregular bank, matted bank, mid-channel and deep pool) nested within 10 km long river reaches were sampled. Individual reaches were, in turn, nested within four larger geomorphological zones, previously identified along the river. Fish assemblages varied significantly between mesohabitat types and at different spatial scales. Golden perch (Macquaria ambigua), Murray cod (Maccullochella peelii peelii) and common carp (Cyprinus carpio) were strongly associated with large wood, but golden perch and Murray cod exhibited higher habitat specificity than carp. Bony herring (Nematalosa erebi) were more common in shallow edgewater habitats. At the river-scale, regional differences in the fish assemblage occurred at scales closely corresponding to geomorphological zones and these differences were associated with changes in the relative abundance of species rather than the addition or replacement of species. The proposed hierarchical framework improves the efficiency of fish surveys in large rivers by viewing meso-scale fish-habitat associations in the context of larger-scale geomorphological processes.     

Differential responses by two closely related native fishes to restoration actions

Globally, river degradation has decimated freshwater fish populations. To help reverse this trend in a southeastern Australia river, we used multiple restoration actions, including reintroduction of instream woody habitat, riparian revegetation, removal of a weir hindering fish movement, fencing out livestock, and controlling riparian weeds. We monitored the responses of native fish at the segment scale (20 km) and reach scale (0.3 km) over 7 years to assess the effectiveness of the different restoration strategies. Two closely related species, Murray cod Maccullochella peeli and trout cod Maccullochella macquariensis, increased at the restored segment compared with the control segment. However, inherent differences between river segments and low sample size hampered assessment of the mechanisms responsible for segment‐scale changes in fish abundance. In contrast, at the reach scale, only M. peeli abundance significantly increased in reaches supplemented with wood. These differential responses by 2 closely related fish species likely reflect species‐specific responses to increased habitat availability and enhanced longitudinal connectivity when the weir improved passage around a fishway. Changes in M. peeli abundance in segments supplemented with and without wood suggest an increase in carrying capacity and not simply a redistribution of individuals within the segment, facilitated the observed expansion. Our findings confirm the need to consider individual fish species' habitat preferences carefully when designing restoration interventions. Further, species‐specific responses to restoration actions provide waterway managers with precise strategies to target fish species for recovery and the potential to predict fish outcomes based on ecological preferences.     

Comparative movements of four large fish species in a lowland river

A multi‐year radio‐telemetry data set was used to comparatively examine the concurrent movements of the adults of three large‐bodied Australian native freshwater fishes (Murray cod Maccullochella peelii, trout cod Maccullochella macquariensis and golden perch Macquaria ambigua) and the introduced carp Cyprinus carpio. The study was conducted over a reach scale in the regulated Murray River in south‐eastern Australia. Differences were identified in the movements among these species. The predominant behaviour was the use of small movements (<1 km) for all species, and although larger‐scale movements (>1 km) did occur, the frequency varied considerably among species. Large‐scale movements were least evident for M. macquariensis and more common for M. ambigua and C. carpio with these two species also having a greater propensity to change locations. Macquaria ambigua displayed the largest movements and more M. ambigua moved on a ‘continual’ basis. Although a degree of site fidelity was evident for all species, the highest levels were exhibited by M. macquariensis and M. peelii. Homing was also evident to some degree in all species, but was greatest for M. peelii.     

Habitat preferences and habitat restoration options for small‐bodied and juvenile fish species in the northern Murray–Darling Basin

Degradation of instream habitats in the northern Murray–Darling Basin has occurred through numerous stressors, including siltation, clearing of bankside vegetation, intrusion of livestock and impacts of pest species. A better understanding of habitat preferences of native fish species could help guide future instream habitat restoration actions. The habitat choices of seven native fish species, juvenile Murray Cod (Maccullochella peelii), juvenile Golden Perch (Macquaria ambigua ambigua), juvenile Silver Perch (Bidyanus bidyanus), adult Murray–Darling Rainbowfish (Melanotaenia fluviatilis), adult Olive Perchlet (Ambassis agassizii), adult Un‐specked Hardyhead (Craterocephalus stercusmuscarum fulvus) and adult carp gudgeons (Hypseleotris spp.) were tested in preference troughs to help inform potential habitat restoration actions in the Condamine catchment. Each species was given a choice between pair combinations of open sandy habitat, submerged macrophytes, emergent plants and rocky rubble. Habitat preferences varied between species. Murray Cod, Golden Perch, carp gudgeons and Olive Perchlets preferred structure over open sandy habitat, whilst juvenile Silver Perch, Un‐specked Hardyhead and Murray–Darling Rainbowfish did not avoid open sandy habitats. Juvenile Murray Cod preferred rocky rubble habitat over all other habitat choices. Use of complex rock piles to provide nursery habitat for Murray Cod populations is a potential restoration option. Introduction of rock could also benefit Golden Perch and carp gudgeons. Use of emergent plants, submerged macrophytes and rocky rubble for habitat restoration all appear to have merit for one or more species of small‐bodied fishes or juvenile stages of larger sized fishes. Rocky rubble or floating attached macrophytes could be viable restoration options in areas too turbid to establish submerged macrophytes. These habitat interventions would complement existing actions such as re‐snagging and provision of fish passage to assist with sustainable management of native fish populations.     

Morphological variation in diadromous and landlocked populations of the spotted galaxias,Galaxias truttaceus,in Tasmania,south-eastern Australia

Synopsis A comparison of a suite of morphometric measurements and meristic counts of individuals of two landlocked lacustrine and two diadromous riverine populations of Galaxias truttaceus was carried out utilising both univariate and canonical variate analyses. Lacustrine fish had fewer dorsal and anal fin rays than did riverine fish. Differences were not as clear for gill rakers and vertebrae. Comparisons of serial counts were made with two derived lacustrine species, G. auratus and G. tanycephalus, also from Tasmania. Lacustrine G. truttaceus varied in the same direction as the derived species, relative to riverine G. truttaceus. From an analysis of 12 body measurements, the first canonical variate clearly separated lacustrine fish from riverine fish largely based on measurements associated with fins (pre-anal fin length, length of anal base, pre-dorsal fin length, maximum length of dorsal fin and inter-orbital width). An overall value for the correct classification of fish into groups based on locality was 84%. The percentage of fish classified into the wrong habitat (lake or stream) was much less than the percentage classified between localities within habitats. Overall morphological variation was greater between than within habitats. It is suggested that the differences in water movement and food type may in part account for the differences shown and that selective pressures peculiar to the lacustrine environment may be causing the lake populations to diverge from the riverine populations.     

Recovery from a fish kill in a semi‐arid Australian river: Can stocking augment natural recruitment processes?

Localized catastrophic events can dramatically affect fish populations. Management interventions, such as stocking, are often undertaken to re‐establish populations that have experienced such events. Evaluations of the effectiveness of these interventions are required to inform future management actions. Multiple hypoxic blackwater events in 2010–2011 substantially reduced fish communities in the Edward‐Wakool river system in the southern Murray‐Darling Basin, New South Wales, Australia. These events led to extensive fish kills across large sections of the entire system following a period of prolonged drought. To expedite recovery efforts, 119 661 golden perch Macquaria ambigua and 59 088 Murray cod Maccullochella peelii fingerlings were stocked at five locations over 3 years. All fish stocked were chemically marked with calcein to enable retrospective evaluation of wild or hatchery origin. Targeted collections were undertaken 3 years post‐stocking to investigate the relative contribution of stocking efforts and recovery via natural recruitment in the system. Of the golden perch retained for annual ageing (n = 93) only nine were of an age that could have coincided with stocking activities. Of those, six were stocked. The dominant year‐class of golden perch were spawned in 2009; before the stocking programme began and prior to blackwater events. All Murray cod retained (n = 136) were of an age that coincided with stocking activities, although only eight were stocked. Among the Murray cod captured, the dominant year‐class was spawned in 2011, after the blackwater events occurred. The results from this study provide first evidence that natural spawning and recruitment, and possibly immigration, were the main drivers of golden perch and Murray cod recovery following catastrophic fish kills. Interpreted in the context of other recent examples, the collective results indicate limited benefit of stocking to existing connected populations already naturally recruiting in riverine systems.     

Fish habitat modelling as a tool for river management

This paper presents an integrated modelling approach to simulate and assess ecological effects of physical habitat changes in rivers. An ecohydraulic simulation tool was created by combining a 1D hydraulic model based on HEC-RAS software and the fish habitat module of CASiMiR, a fuzzy logic-based ecohydraulic modelling system. This tool was applied on a river stretch commonly occurring in Belgium and elsewhere in Europe. In particular the effect of weir removal on habitat suitability for bullhead (Cottus gobio L.) was simulated. Physical conditions of the studied stretch after weir removal were simulated with a hydraulic model. CASiMiR linked these conditions to ecological expert knowledge to calculate habitat suitability for three life stages of bullhead at four different flow rates based on fuzzy logic. Results indicated that after weir removal, habitat suitability increased significantly for all life stages and all flow rates. The presented approach is promising regarding fish community assessment and ecological river engineering.     

Emergence of epizootic ulcerative syndrome in native fish of the Murray-Darling River System, Australia: hosts, distribution and possible vectors

Epizootic ulcerative syndrome (EUS) is a fish disease of international significance and reportable to the Office International des Epizootics. In June 2010, bony herring Nematalosa erebi, golden perch Macquaria ambigua, Murray cod Maccullochella peelii and spangled perch Leiopotherapon unicolor with severe ulcers were sampled from the Murray-Darling River System (MDRS) between Bourke and Brewarrina, New South Wales Australia. Histopathology and polymerase chain reaction identified the fungus-like oomycete Aphanomyces invadans, the causative agent of EUS. Apart from one previous record in N. erebi, EUS has been recorded in the wild only from coastal drainages in Australia. This study is the first published account of A. invadans in the wild fish populations of the MDRS, and is the first confirmed record of EUS in M. ambigua, M. peelii and L. unicolor. Ulcerated carp Cyprinus carpio collected at the time of the same epizootic were not found to be infected by EUS, supporting previous accounts of resistance against the disease by this species. The lack of previous clinical evidence, the large number of new hosts (n = 3), the geographic extent (200 km) of this epizootic, the severity of ulceration and apparent high pathogenicity suggest a relatively recent invasion by A. invadans. The epizootic and associated environmental factors are documented and discussed within the context of possible vectors for its entry into the MDRS and recommendations regarding continued surveillance, research and biosecurity are made.     

Hypoxia,Blackwater and Fish Kills: Experimental Lethal Oxygen Thresholds in Juvenile Predatory Lowland River Fishes

Hypoxia represents a growing threat to biodiversity in freshwater ecosystems. Here, aquatic surface respiration (ASR) and oxygen thresholds required for survival in freshwater and simulated blackwater are evaluated for four lowland river fishes native to the Murray-Darling Basin (MDB), Australia. Juvenile stages of predatory species including golden perch Macquaria ambigua, silver perch Bidyanus bidyanus, Murray cod Maccullochella peelii, and eel-tailed catfish Tandanus tandanus were exposed to experimental conditions of nitrogen-induced hypoxia in freshwater and hypoxic blackwater simulations using dried river red gum Eucalyptus camaldulensis leaf litter. Australia''s largest freshwater fish, M. peelii, was the most sensitive to hypoxia but given that we evaluated tolerances of juveniles (0.99±0.04 g; mean mass ±SE), the low tolerance of this species could not be attributed to its large maximum attainable body mass (>100,000 g). Concentrations of dissolved oxygen causing 50% mortality (LC₅₀) in freshwater ranged from 0.25±0.06 mg l⁻¹ in T. tandanus to 1.58±0.01 mg l⁻¹ in M. peelii over 48 h at 25–26°C. Logistic models predicted that first mortalities may start at oxygen concentrations ranging from 2.4 mg l⁻¹ to 3.1 mg l⁻¹ in T. tandanus and M. peelii respectively within blackwater simulations. Aquatic surface respiration preceded mortality and this behaviour is documented here for the first time in juveniles of all four species. Despite the natural occurrence of hypoxia and blackwater events in lowland rivers of the MDB, juvenile stages of these large-bodied predators are vulnerable to mortality induced by low oxygen concentration and water chemistry changes associated with the decomposition of organic material. Given the extent of natural flow regime alteration and climate change predictions of rising temperatures and more severe drought and flooding, acute episodes of hypoxia may represent an underappreciated risk to riverine fish communities.     

Polymorphic microsatellite loci for species of Australian freshwater cod, <Emphasis Type="Italic">Maccullochella</Emphasis>

The Australian freshwater cod genus, Maccullochella is represented by three species: Murray cod, M. peelii peelii, eastern freshwater cod, M. ikei, and trout cod, M.macquariensis. Seven novel microsatellite loci from M. ikei and six previously published loci from M. peelii peelii were tested on wild populations of Murray, eastern and trout cod. Levels of polymorphism varied between species with 13 loci polymorphic in Murray cod, 9 in trout cod and 7 in eastern cod. Observed heterozygosities ranged from 0.053 to 0.842. This suite of microsatellite loci will facilitate future studies of the genetic status of wild and hatchery bred populations of Maccullochella.     

Variation in habitat use along the freshwater–marine continuum by grey mullet Mugil cephalus at the southern limits of its distribution

In this study, habitat use by Mugil cephalus was investigated in the waters of the west coast of the North Island of New Zealand by analysing microchemical composition of otoliths (laser‐ablation inductively coupled plasma mass spectrometry) obtained from individuals from commercial fish stocks and research surveys. Results of this study show that M. cephalus at the southern limits of its distribution display highly flexible migratory behaviour with extensive use of freshwater and brackish habitats, potentially enabling them to maximize foraging opportunities. Mugil cephalus can tolerate a wide range of salinities and can therefore utilize higher productivity areas, such as estuaries and eutrophic riverine lakes. Finally, M. cephalus populations across a range of climates and latitudes appear to differ in the extent to which they utilize freshwater and brackish habitats, possibly with increasing penetration of fresh waters with increasing latitude.     

Changes of river morphology and physical fish habitat following weir removal

Gongneung Weir-2 was built in the 1970s to supply water for irrigation. For a long time, the weir was left untended due to the land-use changes that were made to a nearby area. This weir was removed completely on April 4, 2006. The present study investigated the effect of the resultant flow-regime changes on river morphology and fish habitat. Observed changes in the grain size distribution, bed elevation, and cross-section pre- and post-weir removal are provided and discussed in this paper. Various bed zones such as a sand island and a vegetated marshy zone, which can diversify an aquatic habitat, formed after the removal. In fact, changes in the number of observed fish species post-removal also were investigated. Finally, specific changes to the physical habitat of Zacco platypus were numerically simulated using the River2D model. The results indicated that habitat suitability post-removal was enhanced for all flow discharges. The WUA values increased 32.3-53.4% for all life stages in the flow discharge of 1.5 m³ s⁻¹. The numerical results also showed that after the removal of the weir, the distribution of the physical habitat changed to reflect continuity near the weir.     

Clarifying an ambiguous evolutionary history: range‐wide phylogeography of an Australian freshwater fish,the golden perch (Macquaria ambigua)

Aim We conducted a range‐wide phylogeographic study of a common Australian freshwater fish, the golden perch (Macquaria ambigua), to investigate the relationship between environmental processes and evolutionary history in drainage basins. Location Inland [Lake Eyre (LEB), Murray–Darling (MDB) and Bulloo (BULL)] and coastal basins [Fitzroy (FITZ)] of eastern Australia. Methods A total of 590 samples were collected from across the entire species’ distribution and a section of the mitochondrial DNA control region was sequenced. In order to reconstruct the evolutionary history of M. ambigua a comprehensive suite of phylogeographic analyses was conducted, including nested clade phylogeographic analysis, mismatch analysis and isolation‐with‐migration model simulations. Results Three major lineages corresponding to the major drainage basins, FITZ, MDB and LEB/BULL, were identified (Φ_ST = 0.92). Lineages from the coastal basin (FITZ) were highly divergent from those of the inland basins (up to 6%). Levels of genetic diversity in the inland basins were relatively low and our analyses indicate that these populations experienced both demographic and range expansions during the Pleistocene. Main conclusions Investigation of the range‐wide phylogeography of M. ambigua has revealed new insights into the biogeography of the Australian arid zone, particularly with regard to evolutionary events chronologically associated with cyclical moist and dry conditions. We propose that M. ambigua originated on the east coast (FITZ) and crossed a major geographic barrier, the Great Dividing Range (GDR), to colonize the inland basins (MDB, LEB and BULL). We infer a series of demographic and range expansion events for M. ambigua consistent with a scenario of moister Pleistocene conditions and increased connectivity of freshwater environments, both within and among drainage basins. Major lineages then diversified following isolation of freshwater environments under increasingly arid climate conditions. We suggest that management priorities for M. ambigua should include the resolution of taxonomic uncertainties and the maintenance of genetic diversity of both stocked populations in the MDB and native populations of the LEB that may be at risk of further isolation and reduced gene flow due to increased aridification under future climate change scenarios.     

小瓜虫在澳洲龙纹斑鳃器官上的分布及其影响

【目的】小瓜虫病是澳洲龙纹斑苗种阶段危害巨大的寄生虫病。探究小瓜虫在澳洲龙纹斑鳃器官上的分布及其影响可以丰富小瓜虫的致病性及病理学方面的研究内容,也可以为渔业生产中小瓜虫病的防治提供参考。【方法】采用光镜及扫描电镜技术确定病原,并观察小瓜虫在澳洲龙纹斑鳃丝、鳃小片及鳃盖上的分布情况及这些器官的变化情况。【结果】小瓜虫侵染澳洲龙纹斑的鳃器官后,分布在鳃丝、鳃小片及鳃盖的表面,上皮细胞之下及鳃小片之间,或是包裹在黏液细胞里,但侵染后期在鳃丝及鳃小片上的数量明显少于鳃盖。侵染后期,鳃丝、鳃小片及鳃盖出现一定程度的膨胀变形,黏液细胞分泌增多,鳃小片末端膨大变形甚至黏连融合,顶端充血呈球状或棒状。【结论】对于鳃部而言,侵染后期小瓜虫主要分布在澳洲龙纹斑的鳃盖上。小瓜虫主要通过侵染引发澳洲龙纹斑鳃部器官的变形膨大,使其丧失正常的功能,造成血液循环受阻、渗透压调节失衡,最终导致鱼体缺氧死亡。     

Novel insights into habitat suitability for Amazonian freshwater mussels linked with hydraulic and landscape drivers

Novel insights into habitat suitability for two Unionida freshwater mussels, Castalia ambigua Lamarck, 1819 (Hyriidae) and Anodontites elongatus (Swainson, 1823) (Mycetopodidae), are presented on the basis of hydraulic variables linked with the riverbed in six 500‐m reaches in an eastern Amazonian river basin. Within the reaches, there was strong habitat heterogeneity in hydrodynamics and substrate composition. In addition, we investigated stressors based on landscape modification that are associated with declines in mussel density. We measured hydraulic variables for each 500‐m reach, and landscape stressors at two spatial scales (subcatchment and riparian buffer forest). We used the Random Forest algorithm, a tree‐based model, to predict the hydraulic variables linked with habitat suitability for mussels, and to predict which landscape stressors were most associated with mussel density declines. Both mussel species were linked with low substrate heterogeneity and greater riverbed stability (low Froude and Reynolds numbers), especially at high flow (low stream power). Different sediment grain size preferences were observed between mussel species: Castalia ambigua was associated with medium sand and Anodontites elongatus with medium and fine sand. Declines in mussel density were associated with modifications linked to urbanization at small scales (riparian buffer forest), especially with percent of and distance from rural settlements, distance to the nearest street, and road density. In summary, the high variance explained in both hydraulic and landscape models indicated high predictive power, suggesting that our findings may be extrapolated and used as a baseline to test hypotheses of habitat suitability in other Amazonian rivers for Castalia ambigua and Anodontites elongatus and also for other freshwater mussel species. Our results highlight the urgent need for aquatic habitat conservation to maintain sheltered habitats during high flow as well as mitigate the effects of landscape modifications at the riparian buffer scale, both of which are important for maintaining dense mussel populations and habitat quality.     

Influence of streamflow on spawning‐related movements of golden perch Macquaria ambigua in south‐eastern Australia

In this study, linkages were examined between movement and spawning behaviour for golden perch Macquaria ambigua in a lowland river by integrating acoustic telemetry and egg and larval drift sampling over 4 years. Movement was strongly seasonal, being most prevalent during the spawning season (spring to early summer), and occurred primarily downstream into the lower river reaches during elevated flows. A very strong association was found between the occurrence of spawning and long‐distance M. ambigua movement. The results also revealed that targeted environmental water allocation can promote movement and spawning of this species. By integrating multiple analytical approaches and focusing on key life‐history events, this study provides an improved picture of the life history and flow requirements of M. ambigua. The findings can help guide the development of effective environmental flow recommendations.     

Linking fish population dynamics to habitat conditions: insights from the application of a process-oriented approach to several Great Lakes species

One of the major challenges facing fishery scientists and managers today is determining how fish populations are influenced by habitat conditions. Many approaches have been explored to address this challenge, all of which involve modeling at one level or another. In this paper, we explore a process-oriented model approach whereby the critical population processes of birth and death rates are explicitly linked to habitat conditions. Application of this approach to five species of Great Lakes fishes including: walleye (Sander vitreus), lake trout (Salvelinus namaycush), smallmouth bass (Micropterus dolomieu), yellow perch (Perca flavescens), and rainbow trout (Onchorynchus mykiss), yielded a number of insights into the modeling process. One of the foremost insights is that processes determining movement and transport of fish are critical components of such models since these processes largely determine the habitats fish occupy. Because of the importance of fish location, an individual-based model appears to be a nearly inescapable modeling requirement. There is, however, a paucity of field-based data directly relating birth, death, and movement rates to habitat conditions experienced by individual fish. There is also a paucity of habitat information at a fine temporal and spatial scale for many important habitat variables. Finally, the general occurrence of strong ontogenetic changes in the response of different life stages to habitat conditions emphasizes the need for a modeling approach that considers all life stages in an integrated fashion.     

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

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Distribution status and habitat characteristics of the endangered freshwater fish,Microphysogobio rapidus (Cyprinidae)

To investigate distribution, habitat characteristics, and current conservation status of the endangered endemic species, rapid small gudgeon Microphysogobio rapidus (Cyprinidae), we surveyed a total of 79 sites from the historic records (20 sites) plus additional sites (59 sites) with good habitat conditions, analyzed their sites, and compared them with historic recorded sites to reveal the factors of extinction threats and causes. We found only eight out of 79 sites in the Nam River areas. The habitats were greatly reduced and restricted compared with the historic sites, which mainly cause from habitat modification, such as various types of river renovations at the main stream and tributary streams of the Nakdong River. The present habitats are higher water temperature and more number of fish species than the absent ones, but conductivity, total nitrogen, and number of weir are lower. In addition, the present sites are lower low velocity at pool and higher mean substrate at pool. From this study, we suggest that maintaining good water quality and preventing anthropogenic impacts greatly aid conservation of the M. rapidus in South Korea.     

Habitat and Fish Fauna Structure in a Subtropical Mountain Stream in Taiwan before and after a Catastrophic Typhoon

Habitats and fish populations of a subtropical mountain stream in Taiwan were surveyed before and after the hit of super-typhoon Herb in July 1996. There was a significant decrease in total pool area and an increase in total riffle area. Upper stream habitat was more susceptible to the disturbance. Relative abundance of the species was significantly correlated before and after the typhoon (rs=0.89, p<0.001). Morisita's index of similarity for the fish communities in June 1996 and October 1997 ranged between 0.82 and 1.02 for seven out of nine stations. Most common cyprinids decreased in densities after Herb, but recovered seventeen months after the typhoon. There were only minor changes in fish community fourteen months after the typhoon. Cyprinids that are smaller in size, such as Candidia barbata and Abottina brevirostris alticorpus were affected the most. Gobiid Rhinogobius nantaiensis that is well adapted to riffle habitat was unaffected throughout the surveys. The results of this study suggested that in subtropical mountain stream, severe typhoon may significantly alter the habitats, but the impact on fish populations could be relatively small due to features of these mountain species.