Comparison of techniques for correlating survival and gene expression data from wild salmon

Abstract

In laboratory and field studies of survival, one of two alternative analytical techniques is often used to estimate survival rates and identify covariates, namely parametric survival analysis or Cormack-Jolly-Seber models. These techniques differ in algorithms and assumptions of the data. They also tend to be used under different circumstances depending on whether the intention is to demonstrate group-specific differences or to predict survival variables. Here, we apply and compare both analytical techniques in a study that couples functional genomics with biotelemetry to ascertain the role of physiological condition on survival of adult sockeye salmon (Oncorhynchus nerka) migrating in the Fraser River, British Columbia, which builds on the growing concern over the decline in numbers of spawning fish. Herein, we show a high level of quantitative and qualitative agreement between the two analytical methods, with both showing a strong relationship exists between the genomic signature that accounts for the largest source of variance in gene expression among individuals and survival in one of the three populations assessed. This high level of agreement suggests the data and the approaches are generating reliable results. The novel approach used in our study to identify physiological processes associated with reduced fitness in wild populations should be of broad interest to conservation biologists and resource managers as it may help reduce the uncertainty associated with predicting population sizes.

A perspective on physiological studies supporting the provision of scientific advice for the management of Fraser River sockeye salmon (Oncorhynchus nerka)

“…low overall variance in survival explained) in the results ( Cooke et al ., 2006 ; Miller et al ., 2011 ). For example, in the study by Hammill et al . (2012) , individuals from one of the three populations examined had a different suite of gene expression profiles that could predict fate.…”

Factors influencing infectious agent communities and infection burden in free-ranging migratory adult salmonids across Canada

“…These patterns are consistent with senescence in Pacific salmon, including adult coho and suggest that transcriptional profiles represented by PC3 may be associated with senescence and/or spawning preparedness. Stress associated genes were also linked with the infectious agent community composition of tagged coho at release and recapture; however, the low variation explained by PC3 and small effect size of the relationship indicates a highly variable physiological (Cooke et al 2006) and/or transcriptional (Hammill et al 2012; cysticola (Teffer et al 2017). As semelparous fish undergo senescence and infection burdens increases, osmotic stress also increases.…”