Small-scale movement and migration cues of Australian bass (Percalates novemaculeata) in an urbanised river

Urban river catchments are often severely affected by human activities but may still retain significant biodiversity. Surprisingly little is known about the behaviour of urban fishes, even those popular with anglers. Key environmental variables that trigger fish behaviour, such as river flow, are highly affected by instream structures including weirs and changes in the natural flow regime. Here, we used acoustic telemetry to examine the movements of Australian bass in a river located in suburban Sydney, Australia. We found that fish tended to be nocturnally active, however, small-scale movements were highly idiosyncratic and less associated with river flow than other factors. Larger-scale movements associated with spawning migrations were strongly correlated with winter floods. Half of the tagged fish migrated to the confluence of the river with Sydney Harbour to breed. Their return migration was hampered by a weir, but the provision of a new fish way facilitated successful return to freshwater at high tide. Despite occupying a highly affected, urban catchment fish behaviour showed similarity to those occupying more natural drainages. Our results highlight the importance of maintaining natural river flows in urban catchments and sustaining fish movement and migration capabilities through the installation of appropriate fish passage devices

Multivariate analysis of biologging data reveals the environmental determinants of diving behaviour in a marine reptile

Diving behaviour of ‘surfacers' such as sea snakes, cetaceans and turtles is complex and multi-dimensional, thus may be better captured by multi-sensor biologging data. However, analysing these large multi-faceted datasets remains challenging, though a high priority. We used high-resolution multi-sensor biologging data to provide the first detailed description of the environmental influences on flatback turtle (Natator depressus) diving behaviour, during its foraging life-history stage. We developed an analytical method to investigate seasonal, diel and tidal effects on diving behaviour for 24 adult flatback turtles tagged with biologgers. We extracted 16 dive variables associated with three-dimensional and kinematic characteristics for 4128 dives. K-means and hierarchical cluster analyses failed to identify distinct dive types. Instead, principal component analysis objectively condensed the dive variables, removing collinearity and highlighting the main features of diving behaviour. Generalized additive mixed models of the main principal components identified significant seasonal, diel and tidal effects on flatback turtle diving behaviour. Flatback turtles altered their diving behaviour in response to extreme tidal and water temperature ranges, displaying thermoregulation and predator avoidance strategies while likely optimizing foraging in this challenging environment. This study demonstrates an alternative statistical technique for objectively interpreting diving behaviour from multivariate collinear data derived from biologgers

The functional role of biodiversity in ecosystems: incorporating trophic complexity

Understanding how biodiversity affects functioning of ecosystems requires integrating diversity within trophic levels (horizontal diversity) and across trophic levels (vertical diversity, including food chain length and omnivory). We review theoretical and experimental progress toward this goal. Generally, experiments show that biomass and resource use increase similarly with horizontal diversity of either producers or consumers. Among prey, higher diversity often increases resistance to predation, due to increased probability of including inedible species and reduced efficiency of specialist predators confronted with diverse prey. Among predators, changing diversity can cascade to affect plant biomass, but the strength and sign of this effect depend on the degree of omnivory and prey behaviour. Horizontal and vertical diversity also interact: adding a trophic level can qualitatively change diversity effects at adjacent levels. Multitrophic interactions produce a richer variety of diversity‐functioning relationships than the monotonic changes predicted for single trophic levels. This complexity depends on the degree of consumer dietary generalism, trade‐offs between competitive ability and resistance to predation, intraguild predation and openness to migration. Although complementarity and selection effects occur in both animals and plants, few studies have conclusively documented the mechanisms mediating diversity effects. Understanding how biodiversity affects functioning of complex ecosystems will benefit from integrating theory and experiments with simulations and network‐based approaches

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Respirometer in a box: Development and use of a portable field respirometer for estimating oxygen consumption of large‐bodied fishes

This study developed a portable, low‐cost field respirometer for measuring oxygen consumption rates of large‐bodied fishes..

New Host Record for the Marine Leech, Pontobdella macrothela (Hirudinida: Piscicolidae) from Sicklefin Lemon Sharks, Negaprion acutidens (Chondrichthyes: Carcharinidae) in St. Joseph Atoll, Republic of Seychelles, West Indian Ocean

Two specimens of the marine leech Pontobdella macrothela were found parasitizing the carcharhinid shark, Negaprion acutidens, at St. Joseph Atoll, Amirantes, Republic of Seychelles. This report presents the first record of this piscicolid leech from N. acutidens and is one of the few records of P. macrothela in the West Indian Ocean

Divergent field metabolic rates highlight the challenges of increasing temperatures and energy limitation in aquatic ectotherms

Environments where extreme temperatures and low productivity occur introduce energetically challenging circumstances that may be exacerbated by climate change. Despite the strong link between metabolism and temperature in ectotherms, there is a paucity of data regarding how the metabolic ecology of species affects growth and fitness under such circumstances. Here, we integrated data describing field metabolic rates and body condition of two sympatric species of ectotherms with divergent lifestyles, the benthic freshwater (or largetooth) sawfish (Pristis pristis) and the epipelagic bull shark (Carcharhinus leucas) occurring in the Fitzroy River, Western Australia, to test the implications of their differing metabolic ecologies for vulnerability to rising temperatures. Over a temperature range of 18–34 °C, sawfish had lower field metabolic rates (63–187 mg O2 kg−0.86 h−1) and lower temperature sensitivity of metabolic rates [activation energy (EA) = 0.35 eV] than bull sharks (187–506 mg O2 kg−0.86 h−1; EA = 0.48 eV). Both species lost body mass throughout the dry season, although bull sharks significantly more (0.17% mass loss day−1) than sawfish (0.07% mass loss day−1). Subsequent bioenergetics modelling showed that under future climate change scenarios, both species would reach potentially lethal levels of mass loss during dry season periods before the end of the century. These results suggest that ectotherms with low metabolic rates may be better suited to extreme environmental conditions, and that even small increases in temperature due to climate change could have substantial impacts on the ability of ectotherms to grow and survive in harsh conditions, including high temperatures and energy-limiting circumstances

Accounting for body mass effects in the estimation of field metabolic rates from body acceleration

Dynamic Body Acceleration (DBA), measured through animal-attached tags, has emerged as a powerful method for estimating field metabolic rates of free-ranging individuals. Following respirometry to calibrate oxygen consumption rate (MO2) with DBA under controlled conditions, predictive models can be applied to DBA data collected from free-ranging individuals. However, laboratory calibrations are generally performed on a relatively narrow size range of animals, which may introduce biases if predictive models are applied to differently sized individuals in the field. Here, we tested the mass dependence of the DBA-MO2 relationship to develop an experimental framework for the estimation of field metabolic rates when organisms differ in size. We performed respirometry experiments with individuals spanning one order of magnitude in body mass (1.74–17.15 kg) and used a two-stage modelling process to assess the intraspecific scale dependence of the MO2-DBA relationship and incorporate such dependencies into the coefficients of MO2 predictive models. The final predictive model showed scale dependence; the slope of the MO2-DBA relationship was strongly allometric (M1.55), whereas the intercept term scaled closer to isometry (M1.08). Using bootstrapping and simulations, we evaluated the performance of this coefficient-corrected model against commonly used methods of accounting for mass effects on the MO2-DBA relationship and found the lowest error and bias in the coefficient-corrected approach. The strong scale dependence of the MO2-DBA relationship indicates that caution must be exercised when models developed using one size class are applied to individuals of different sizes