How and to what extent do sea lice affect the performance of juvenile Pacific salmon? A systematic review protocol

Wild Pacific salmon are a culturally, ecologically, and economically important group of fishes. Unfortunately, several distinct lineages have already been lost. The abundance of these species varies over interdecadal and centennial time scales due to climatic and local ecosystem complexity and dynamics. Sea lice from net-pen salmon farms (traditional flow-through containment systems) have been linked to negative effects on wild salmon. However, there is debate over the quality of evidence for these claims. To gain a better understanding of this host–parasite system, we completed a systematic map to provide a summary of the existing literature base on the effects of sea lice (in the genera Lepeophtheirus or Caligus) on wild-caught, hatchery-sourced, and farmed Pacific (Chinook salmon Oncorhynchus tshawytscha, coho salmon O. kisutch, chum salmon O. keta, sockeye salmon O. nerka, or pink salmon O. gorbuscha) and Atlantic salmon (Salmo salar). This approach was intended as a first step, with the goal to later conduct a systematic review on one or more evidence clusters relating to Pacific salmon identified from the mapping approach. Based on the map findings, studies investigating sea lice effects on individual-level performance metrics (e.g., osmotic function and homeostasis, immune function, and survival) in Pacific salmon were identified as subtopics (i.e., knowledge clusters) that had sufficient coverage for further review. Here we present a protocol for a subsequent systematic review that will estimate how and to what extent sea lice affect the performance of juvenile Pacific salmon. This systematic review will use evidence identified during a systematic map process that included commercially published and grey literature available from 1900 to March 2025. This evidence was identified from English-language searches using four publication databases, Google Scholar, 25 specialist websites, hand-searching reference sections of 98 relevant reviews, and networking tools and calls for evidence in English and French to target grey literature (accepting suggestions until November 2025). Studies that evaluate the effect of sea lice (in the genera Lepeophtheirus or Caligus) on individual-level performance metrics in the five Pacific salmon species mentioned above found anywhere in the world will be included. Specifically, we will include measures of change related to: (1) a stress response (e.g., glucose, cortisol, heat shock proteins), (2) osmotic function and homeostasis (e.g., osmolality, Na+, haematocrit), (3) immune function (e.g., hypertrophy, macrophage function, immune-related genes), (4) injuries (e.g., visible injuries, tissue damage), (5) growth (e.g., length, mass, condition, specific growth rate), (6) behaviour (e.g., feeding, activity patterns, migration timing/route, swimming ability), (7) survival (number died or consumed by predator), (8) reproduction (e.g., number of eggs laid, estradiol, testosterone), (9) cardio-respiratory function (e.g., cardiac output, heart rate, critical swimming speed), or surrogates thereof. Included studies will undergo critical appraisal of internal and external validity. We will build off the coded and extracted information from the mapping exercise by extracting quantitative information on measured outcomes and further exposure and comparator details, as well as effect modifiers (e.g., sea lice infestation level, time since infestation, size and age of salmon). A narrative synthesis will be used to describe the quantity and characteristics of the available evidence, while quantitative syntheses (i.e., meta-analyses) will be conducted to estimate an overall mean and variance of effect for each outcome category separately (e.g., outcome groups 1-9 listed above) when sufficient numbers of similar studies are available. Further, we will attempt to identify sea lice exposure thresholds which could yield valuable information to help inform management for Canadian stakeholders.