Single-Cell RNA Sequencing Reveals Microevolution of the Stickleback Immune System

Abstract

The risk and severity of pathogen infections in humans, livestock, or wild organisms depends on host immune function, which can vary between closely related host populations or even among individuals. This immune variation can entail between-population differences in immune gene coding sequences, copy number, or expression. In recent years many studies have focused on population divergence in immunity using whole-tissue transcriptomics. But, whole-tissue transcriptomics cannot distinguish between evolved differences in gene regulation within cells, versus changes in cell composition within the focal tissue. Here we leverage single cell transcriptomic approaches to document signatures of microevolution of immune system structure in a natural system, the three-spined stickleback (Gasterosteus aculeatus). We sampled nine adult fish from three populations with variability in resistance to a cestode parasite, Schistocephalus solidus, to create the first comprehensive immune cell atlas for G. aculeatus. Eight broad immune cell types, corresponding to major vertebrate immune cells, were identified. We were also able to document significant variation in both abundance and expression profiles of the individual immune cell types among the three populations of fish. Furthermore, we demonstrate that identified cell type markers can be used to reinterpret traditional transcriptomic data: we re-evaluate previously published whole-tissue transcriptome data from a quantitative genetic experimental infection study to gain better resolution relating infection outcomes to inferred cell type variation. Combined our study demonstrates the power of single cell sequencing to not only document evolutionary phenomena (i.e. microevolution of immune cells), but also increase the power of traditional transcriptomic datasets.

Single Cell RNA Sequencing Provides Clues for the Developmental Genetic Basis of Syngnathidae’s Evolutionary Adaptations

“…In less traditional models, the majority of scRNAseq atlases are produced from adult tissues, allowing investigations into cell types, population differences, and genetic networks (e.g. Chari et al, 2021; Fuess & Bolnick, 2023; Hain et al, 2022; Hong et al, 2023; Koiwai et al, 2023; Parker et al, 2022; Potts et al, 2022; Royan et al, 2021; Songco-Casey et al, 2022; Vonk et al, 2023; Woych et al, 2022). Creation of developmental scRNA-seq atlases in non-model organisms is just beginning to accelerate, but many emerging models still lack such a resource, limiting our understanding of their development (e.g.…”

From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology

“…The evolution of complex body plans of multicellular organisms and their functions are intricately linked to tissue-specific transcriptomic differentiation (Barbosa-Morais et al, 2012;Brawand et al, 2011;Fukushima & Pollock, 2020;Mantica et al, 2024). For some types of research questions, a defined morphological structure or tissue may be of interest, in particular when specific target tissues responsible for the adaptive mechanism(s) have already been identified.…”

“…In another eco-evolutionary study, a scRNAseq analysis of three populations of three-spined stickleback fish (Gasterosteus aculeatus) that exhibit natural variation in parasite resistance revealed differences in the composition and cell-type specific expression profiles of immune cells. Moreover, immune cell-type specific marker genes identified using the scRNAseq data were used to re-analyse previous tissue-specific RNAseq datasets of F 2 crosses to show that the response of gene expression in antigen-presenting cells to infection is most likely the result of regulatory variation and not due to an increase in the number of antigen-presenting cells (Fuess & Bolnick, 2023).…”

“…Accordingly, evolutionary change in spatial and temporal patterns of gene expression is one of the main drivers of phenotypic differentiation (e.g. Barbosa-Morais et al, 2012;Brawand et al, 2011;Fukushima & Pollock, 2020;Gerhart & Kirschner, 2007;Mantica et al, 2024;Shapiro et al, 2004;Steiner et al, 2007). Gene expression analyses based on RNA sequencing (RNAseq) provide a powerful tool to study a wide range of ecological and evolutionary questions (reviewed e.g.…”

Unlocking the genome of perch – From genes to ecology and back again

“…In parallel with technological advances, the repertoire of RNA‐seq methodologies is constantly expanding. For example, single‐cell RNA‐seq that enables gene transcription analysis at single‐cell resolution (scRNA‐seq; Tang et al, 2009) has already been used to characterise the immune response at unprecedented resolution in several fish species (Athanasiadis et al, 2017; Attaya et al, 2022; Fuess & Bolnick, 2021; Wang et al, 2021). Most recently, scRNA‐seq was further developed to “live‐seq” to enable the temporal scanning of expression changes within the same cell (Chen, Guillaume‐Gentil, et al, 2022).…”