Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility

peer reviewe

An assessment of otoliths, dorsal spines and scales to age the long-finned gurnard, Lepidotrigla argus, Ogilby, 1910 (Family: Triglidae)

Summary: Sagittal otoliths, dorsal spines and scales were critically assessed as structures to potentially determine the age of the long-finned gurnard, Lepidotrigla argus. Counts were made of opaque growth increments and a readability score was assigned to each structure. Comparisons of growth increment counts were made between structures and between readings. All three structures showed some degree of readability and quantifiable growth increments, but this varied within fishes and between structures. Initial results showed that whole otoliths were more suitable to determine age estimates than dorsal spines and scales. Scales were considered unsuitable due to between reading ageing bias, variation in age estimates between structures, low precision and poor readability for this species. Dorsal spines showed evidence of loss of growth increments due to hollowing of the vascular core, which resulted in underestimation of older individuals in comparison to whole otoliths. Further analysis showed that growth increment counts from whole otoliths were lower for older individuals in comparison to sectioned otoliths. It is suggested that this is because of decreased clarity of growth increments towards the outer margin of whole otoliths in older individuals; this problem was not present with sectioned otoliths. It was concluded that sectioned otoliths were a more suitable structure from which to estimate age of L. argus than were whole otoliths, dorsal spines and/or scales

Biophysical drivers of spawning dynamics in estuarine fish

Determining links among estuarine variability, habitat and spawning of estuary-dependent fish is essential for understanding population processes and directing conservation efforts. I used acoustic telemetry, habitat mapping and egg sampling, in the Shoalhaven and Clyde rivers (New South Wales, Australia), to examine biophysical drivers of habitat use and spawning dynamics in estuarine-dependent fish:, Estuary Perch, Percalates colonorum, Sand Whiting, Sillago ciliata , Yellowfin Bream, Acanthopagrus australis, Black Bream, Acanthopagrus butcheri and the Yellowfin Bream and Black Bream hybrid complex. Spawning activity of Estuary Perch was restricted to areas of structurally complex large wooden debris and a concrete ferry landing, adjacent to deep water. Eggs were released at night during the first 2 h of the run-out tide.Spawning movements of Sand Whiting were typified by regular, swift migrations from upstream resident sites to specific areas adjacent to river entrances and deep water. Spawning movements coincided with high water temperatures linked to coastal winds and down-welling oceanographic conditions. Similarly to Estuary Perch, spawning occurred after nocturnal high tides. This strategy increases offshore dispersal and exports eggs and larvae onto coastal waters. At upstream residences, Sand Whiting displayed small core home ranges and high site fidelity to habitat characterised by sediment containing benthic invertebrates. These locations are likely used to maintain reproductive growth between spawning movements.Large-scale tracking of Yellowfin Bream, Black Bream and their hybrids showed high levels of residency and site-fidelity, with peak distributions occurring in the lower and upper-middle estuary. Estuarine movements were correlated with freshwater flow, temperature, and genetic classification. Distinct repetitive spawning migrations were not observed. The data suggests that spawning may occur within estuaries, with inter-estuarine migrations playing a significant role in genetic dispersal and mixing.This study highlights the complex interrelationships between movement, spawning, physicochemical variation and habitat availability. Spawning and recruitment success may be dependent on the selection of spawning locations and the timing of spawning events, which influences dispersal of eggs and larvae within and between estuaries, and can act to isolate populations or facilitate inter-estuarine connectivity and genetic relatedness

Interactive Drivers of Activity in a Free-Ranging Estuarine Predator

Animal activity patterns evolve as an optimal balance between energy use, energy acquisition, and predation risk, so understanding how animals partition activity relative to extrinsic environmental fluctuations is central to understanding their ecology, biology and physiology. Here we use accelerometry to examine the degree to which activity patterns of an estuarine teleost predator are driven by a series of rhythmic and arrhythmic environmental fluctuations. We implanted free-ranging bream Acanthopagrus australis with acoustic transmitters that measured bi-axial acceleration and pressure (depth), and simultaneously monitored a series of environmental variables (photosynthetically active radiation, tidal height, temperature, turbidity, and lunar phase) for a period of approximately four months. Linear modeling showed an interaction between fish activity, light level and tidal height; with activity rates also negatively correlated with fish depth. These patterns highlight the relatively-complex trade-offs that are required to persist in highly variable environments. This study demonstrates how novel acoustic sensor tags can reveal interactive links between environmental cycles and animal behavior

Distribution and movement of catadromous fish: design and implementation of a freshwater-estuarine acoustic telemetry array

Movement patterns of two co-occurring catadromous fishes, estuary perch Macquaria colonorum and Australian bass Macquaria novemaculeata, were investigated in a large tidal river in southeastern Australia. Nineteen estuary perch and seventeen Australian bass were captured as mature adults from the Shoalhaven River, surgically implanted with electronic transmitters and released. Forty-nine Vem- co (VR2W) acoustic receivers were strategically placed throughout the river from the Tallowa Dam wall downstream to the sea (a distance of 75 km). Between September 2007 and February 2008, a total of 800,263 detection events were recorded with most fish detected in the middle (estuary perch) to upper (Australian bass) estuarine reaches of the river. Both species made extensive use of the estuary, with no estu- ary perch and only three Australian bass entering the freshwater, indicating that the freshwater residency phase of these catadromous fishes may not be obligatory. The data also suggests that estuary perch and Australian bass exhibit high site fidelity, which, along with their large scale movements may be influenced by factors such as river discharge and prey availability. This large freshwater-estuarine telemetry array combined with critical abiotic information (river discharge and salinity) has and will provide a greater understanding of catadromous fish movement, particularly in relation to habitat utilization and environmental flows

Fine-scale movements, site fidelity and habitat use of an estuarine dependent sparid

Abstract Space use and movement patterns are largely influenced by an animal’s size, habitat connectivity, reproductive mode, and foraging behaviours; and are important in defining the broader population biology and ecology of an organism. Acoustic telemetry was used to investigate the home range, habitat use and relative movement patterns of an estuarine dependant sparid (Acanthopagrus australis, Günther). Ten fish were internally tagged with acoustic transmitters and manually tracked in a riverine estuary for four, 3-day periods. Positional data was converted into a relative index of fish movement (Minimum Activity Index, MAI), and also used to estimate kernel density distributions which approximated areas of core and total space use for each fish. Space use for A. australis was not related to fish size; although movement of each fish (MAI) increased with fish length and a reduction in water conductivity. The distance between tagged fish and mangrove habitat was correlated with time-of-day and tide level with yellowfin bream moving closer to mangroves during the daytime and on high tides. Fish movements, residency and site fidelity revealed the nature of decision-making for fish, and the conservation value of small patches of estuarine habitats

Environmental influences on the spatial ecology and spawning behaviour of an estuarine-resident fish, Macquaria colonorum

Estuarine-resident fishes are highly susceptible to the effects of environmental and anthropogenic impacts on their assemblages and habitats. We investigated the distribution, movement and spawning behaviour of estuary perch, . Macquaria colonorum, in response to selected environmental variables using an acoustic telemetry array in a large tidal river in south-eastern (SE) Australia. Adult . M. colonorum were monitored for up to two years, covering two consecutive spawning periods between September 2007 and 2009. Salinity, water temperature and river flows all had a significant relationship with their estuarine distribution. In particular, large-scale movements were influenced by large freshwater inflow events and the resultant reduction in salinity levels, together with the seasonal cooling and warming trends in water temperatures associated with spawning behaviour. During the winter months, male and female . M. colonorum migrated from their upper estuarine home ranges to the lower estuarine spawning grounds in synchrony, with numbers of individual visits by both sexes consistently higher in the \u27wetter\u27 winter/spring period of 2008. Location, arrival, departure and occupation time within the spawning grounds were similar between sexes and years. Both resident and migrating . M. colonorum exhibited strong diel, and to a lesser extent, tidal behavioural patterns, with fish more likely to be detected at night and during the ebb tides. It is postulated that the effect of environmental fluctuations on the distribution and movement of . M. colonorum is influenced by behavioural mechanisms in response to osmoregulatory stress, predator-prey interactions and reproductive activity. The results also demonstrate the importance of accounting for autocorrelation inherent in telemetry data, and for developing management strategies that are more robust to the effect of future climate trends on estuarine fish populations