The utility of transcriptomics in fish conservation

Abstract

There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers.

Applying a gene-suite approach to examine the physiological status of wild-caught walleye (Sander vitreus)

“…This difficulty in distinguishing the physiological responses due to the 64 environmental conditions prior to capture from those induced by capture and handling techniques 65 is a challenge facing conservation physiologists. 66 framework of conservation physiology (Connon et al, 2018). As the initial step in gene 68 expression, gene transcription is a key regulator of physiological status and may provide insights 69 into phenotypic plasticity and responses to environmental factors in wild fish (Alvarez et al, 70 2015;Oomen and Hutchings, 2017), constituting an important tool in the conservation 71 physiology toolbox (Madliger et al, 2018).…”

Genomic signals found using RNA sequencing support conservation of walleye (Sander vitreus) in a large freshwater ecosystem

“…To take effective action, conservation practitioners require research on the environmental 35 stressors a population faces, as well as population structure and evolutionary patterns to 36 determine a species' adaptive potential (Connon et al 2018; Russello et al 2011;Waples & 37 Gaggiotti 2006). Transcriptomics has been discussed in the context of differential gene 38 expression, for identifying important physiological thresholds in species of conservation concern 39 that can support risk assessments and setting management thresholds, thus, ultimately benefiting 40 species conservation (Connon et al 2018). An advantage of using RNA sequencing for 41 conservation research is that it provides information about both genetics and molecular 42 physiology by returning transcript abundances and single nucleotide polymorphisms (SNPs) 43 3 allowing researchers to gather a diverse array of information within one data set.…”

Salmonid gene expression biomarkers indicative of physiological responses to changes in salinity, temperature, but not dissolved oxygen

“…Therefore, examining individual salmon is a more direct and integrative approach to assessing the magnitude of the effect different stressors are having on the fish (Wikelski and Cooke, 2006). For example, using panels of gene expression biomarkers associated with transcriptional responses to specific environmental stressors (Connon et al, 2018). A similar biomarker approach is being used for exam-ining the relationship among Pacific salmon viral disease status and survival in the natural environment (Miller et al, 2017a).…”

“…Few studies have specifically documented the association between gene expression and other physiological measures or fitness-related traits important to the conservation of fishes (e.g. Connon et al, 2018;Oomen and Hutchings, 2017). Hence, beyond measurements of mortality, we also collected measures of salmon fitness-related traits such as behaviour, skin pigmentation, body morphology, as well as physiological biomarkers of stress and seawater tolerance such as plasma lactate, glucose, chloride concentrations (Barton, 2002) and gill Na + /K + ATPase activity (McCormick, 1993).…”