Why ignoring parasites in fish ecology is a mistake

The use of non-lethal sampling for transcriptomics to assess the physiological status of wild fishes

Fishes respond to different abiotic and biotic stressors through changes in gene expression as a part of an integrated physiological response. Transcriptomics approaches have been used to quantify gene expression patterns as a reductionist approach to understand responses to environmental stressors in animal physiology and have become more commonly used to study wild fishes. We argue that non-lethal sampling for transcriptomics should become the norm for assessing the physiological status of wild fishes, especially when there are conservation implications. Processes at the level of the transcriptome provide a "snapshot" of the cellular conditions at a given time; however, by using a non-lethal sampling protocol, researchers can connect the transcriptome profile with fitness-relevant ecological endpoints such as reproduction, movement patterns and survival. Furthermore, telemetry is a widely used approach in fisheries to understand movement patterns in the wild, and when combined with transcriptional profiling, provides arguably the most powerful use of non-lethal sampling for transcriptomics in wild fishes. In this review, we discuss the different tissues that can be successfully incorporated into non-lethal sampling strategies, which is particularly useful in the context of the emerging field of conservation transcriptomics. We briefly describe different methods for transcriptional profiling in fishes from high-throughput qPCR to whole transcriptome approaches. Further, we discuss strategies and the limitations of using transcriptomics for non-lethally studying fishes. Lastly, as 'omics' technology continues to advance, transcriptomics paired with different omics approaches to study wild fishes will provide insight into the factors that regulate phenotypic variation and the physiological responses to changing environmental conditions in the future.

Progress on Research Regarding Ecology and Biodiversity of Coastal Fisheries and Nektonic Species and Their Habitats within Coastal Landscapes

This paper aims to highlight the new research and significant advances in our understanding of links between coastal habitat quality/quantity/diversity and the diversity of fisheries species and other mobile aquatic species (hereafter nekton) that use them within coastal landscapes. This topic is quite diverse owing to the myriad of habitat types found in coastal marine waters and the variety of life history strategies fisheries species and nekton use in these environments. Thus, we focus our review on five selective but relevant topics, habitat templates, essential fish habitat, habitat mosaics/habitat connectivity, transitory/ephemeral habitat, and the emerging/maturing approaches to the study of fish-habitat systems as a roadmap to its development. We have highlighted selected important contributions in the progress made on each topic to better identify and quantify landscape scale interactions between living biota and structured habitats set within a dynamic landscape.

Do parasites influence behavioural traits of wild and hatchery-reared Murray cod, Maccullochella peelii?

This study aimed to investigate the links between parasites and behavioural traits of juvenile Murray cod (Maccullochella peelii). The Murray cod is an endangered Australian freshwater fish for which restocking programs are in place and there is a growing human consumption market. However, little is known about the parasites of these fish and how these parasites influence their behaviour and survival. Fingerlings and yearling fish were sourced from a hatchery and the wild, and after acclimatisation in the laboratory, variation in behavioural traits was examined using emergence, exploration and predator inspection tests. The fish were then euthanised to determine their age and examined for infection with parasites. Wild fish had more camallanid nematodes and lernaeid copepods than hatchery fish. An information theoretic approach using Akaike's Information Criterion (AIC) indicated that infection with protozoan cysts was an important factor for predicting the latency to emerge and explore a new environment, which was interpreted as reduced "boldness". In contrast, the presence of lernaeid copepods was included in two of the four best models predicting predator inspection, indicating that infected fish were less likely to inspect a predator. Source of fish (wild or hatchery) was found to be a strong influence on behavioural responses in all our tests. All parasites found in the present study are known to result in clinical signs of diseases in their fish hosts, raising the possibility that responses in tests of behavioural traits reflect side effects of infection. Additionally, the effect of host adaptation to not show signs of parasite infection, or more simply that the effects on behaviour are subtle and difficult to reveal with small sample sizes, is discussed. Nonetheless, we propose that it is important that infection with parasites is considered in fish behavioural studies both to assess survival behaviour and to avoid misinterpretation of behavioural tests of animal personality.