Our understanding of the vertebrate immune system is dominated by a few model organisms such as mice. This use of a few model systems is reasonable if major features of the immune systems evolve slowly and are conserved across most vertebrates, but may be problematic if there is substantial macroevolutionary change in immune responses. Here, we present a test of the macroevolutionary stability, across 15 species of jawed fishes, of the transcriptomic response to a standardized immune challenge. Intraperitoneal injection of an immune adjuvant (alum) induces a fibrosis response in nearly all jawed fishes, which in some species contributes to anti-helminth resistance. Despite this conserved phenotypic response, the underlying transcriptomic response is highly inconsistent across species. Although many gene orthogroups exhibit differential expression between saline versus alum-injected fish in at least one species, few orthogroups exhibit consistent differential expression across species. This result suggests that although the phenotypic response to alum (fibrosis) is highly conserved, the underlying gene regulatory architecture is very flexible and cannot readily be extrapolated from any one species to fishes (or vertebrates) more broadly. The vertebrate immune response is remarkably changeable over macroevolutionary time, requiring a diversity of model organisms to describe effectively.

Department of Biology Texas State University San Marcos TX 78666 USA

Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT 06269 USA

Institute of Vertebrate Biology The Czech Academy of Sciences Brno 603 65 Czech Republic

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Alfaro M.E., Bolnick D.I. & Wainwright P.C., 2005. Evolutionary consequences of many-to-one mapping of jaw morphology to mechanics in labrid fishes. The American naturalist, 165(6), pp.E140–54. PubMed

Bolnick D.I. et al., 2024. The dominance of coinfecting parasites’ indirect genetic effects on host traits. The American naturalist, 204(5), pp.482–500. PubMed

Brownstein C.D. et al., 2024. Synergistic innovations enabled the radiation of anglerfishes in the deep open ocean. Current biology: CB, 34(11), pp.2541–2550.e4. PubMed

Bucchini F. et al., 2021. TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes. Nucleic acids research, 49(17), p.e101. PubMed PMC

Buchfink B., Xie C. & Huson D.H., 2015. Fast and sensitive protein alignment using DIAMOND. Nature methods, 12(1), pp.59–60. PubMed

Bushmanova E. et al., 2019. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. GigaScience, 8(9), p.giz100. PubMed PMC

Chen F. et al., 2023. Phylogenetic comparative analysis of single-cell transcriptomes reveals constrained accumulation of gene expression heterogeneity during clonal expansion. Molecular biology and evolution, 40(5), p.msad113. PubMed PMC

De Belle I. et al., 2003. In vivo cloning and characterization of a new growth suppressor protein TOE1 as a direct target gene of Egr1. The journal of biological chemistry, 278(16), pp.14306–14312. PubMed

De Lisle S.P. & Bolnick D.I., 2021. Male and female reproductive fitness costs of an immune response in natural populations. Evolution; international journal of organic evolution, 75(10), pp.2509–2523. PubMed PMC

Dubin A. et al., 2019. Complete loss of the MHC II pathway in an anglerfish, Lophius piscatorius. Biology letters, 15(10), p.20190594. PubMed PMC

Emms D.M. & Kelly S., 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome biology, 20(1), p.238. PubMed PMC

Emms D.M. & Kelly S., 2015. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome biology, 16(1), p.157. PubMed PMC

Emms D.M. & Kelly S., 2017. STRIDE: Species tree root inference from gene duplication events. Molecular biology and evolution, 34(12), pp.3267–3278. PubMed PMC

Fuess L.E. et al., 2021. Between-population differences in constitutive and infection-induced gene expression in threespine stickleback. Molecular ecology, 30(24), pp.6791–6805. PubMed PMC

Gilbertson S.E. & Weinmann A.S., 2021. Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis. Trends in immunology, 42(12), pp.1077–1087. PubMed PMC

Greenway R. et al., 2024. Integrative analyses of convergent adaptation in sympatric extremophile fishes. Current biology: CB, 34(21), pp.4968–4982.e7. PubMed

Haas B.J. et al., 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature protocols, 8(8), pp.1494–1512. PubMed PMC

Helfman G.S. et al., 2009. The diversity of fishes: Biology, evolution, and ecology 2nd ed., Chichester, England: Wiley-Blackwell.

Henderson N., Rieder F. & Wynn T., 2020. Fibrosis: from mechanisms to medicines. Nature, 587, pp.555–566. PubMed PMC

Hou X. et al., 2023. Transcriptome analysis reveals the neuroactive receptor genes response to Streptococcus agalactiae infection in tilapia, Oreochromis niloticus. Fish & shellfish immunology, 141(109090), p.109090. PubMed

Huang Y. et al., 2016. Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks. Molecular ecology, 25(4), pp.943–958. PubMed PMC

Hughes L.C. et al., 2018. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proceedings of the National Academy of Sciences of the United States of America, 115(24), pp.6249–6254. PubMed PMC

Hund A.K. et al., 2022. Population-level variation in parasite resistance due to differences in immune initiation and rate of response. Evolution Letters, 6(2), pp.162–177. PubMed PMC

Kool M., Fierens K. & Lambrecht B.N., 2012. Alum adjuvant: some of the tricks of the oldest adjuvant. Journal of medical microbiology, 61(Pt 7), pp.927–934. PubMed

Kuo C.-L. et al., 2020. APOE e4 genotype predicts severe COVID-19 in the UK biobank community cohort. The journals of gerontology. Series A, Biological sciences and medical sciences, 75(11), pp.2231–2232. PubMed PMC

Lohman B.K. et al., 2017. Gene Expression Contributes to the Recent Evolution of Host Resistance in a Model Host Parasite System. Frontiers in immunology, 8. Available at: https://www.frontiersin.org/articles/10.3389/fimmu.2017.01071. PubMed DOI PMC

Lohman B.K., Weber J.N. & Bolnick D.I., 2016. Evaluation of TagSeq, a reliable low-cost alternative for RNAseq. Molecular ecology resources, 16(6), pp.1315–1321. PubMed

Love M.I., Huber W. & Anders S., 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology, 15(12), p.550. PubMed PMC

Lyn Fortier A. & Pritchard J.K., 2024. The primate Major Histocompatibility Complex: An illustrative example of gene family evolution. bioRxiv.org: the preprint server for biology, p.2024.09.16.613318.

Malmstrøm M. et al., 2016. Evolution of the immune system influences speciation rates in teleost fishes. Nature genetics, 48(10), pp.1204–1210. PubMed

Matthews D.G. et al., 2023. Locomotor effects of a fibrosis-based immune response in stickleback fish. The journal of experimental biology, 226(23), p.jeb246684. PubMed

Meyer E., Aglyamova G.V. & Matz M.V., 2011. Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure: RNA-Seq EXPRESSION PROFILING CORAL LARVAE. Molecular ecology, 20(17), pp.3599–3616. PubMed

O’Connor E.A. et al., 2018. The evolution of immunity in relation to colonization and migration. Nature ecology & evolution, 2(5), pp.841–849. PubMed

Osborne M.J. et al., 2017. Spatio-temporal variation in parasite communities maintains diversity at the major histocompatibility complex class IIβ in the endangered Rio Grande silvery minnow. Molecular ecology, 26(2), pp.471–489. PubMed

Pasquier J. et al., 2016. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. BMC genomics, 17(1), p.368. PubMed PMC

Patro R. et al., 2017. Salmon provides fast and bias-aware quantification of transcript expression. Nature methods, 14(4), pp.417–419. PubMed PMC

R Core Team, 2024. R: A Language and Environment for Statistical Computing. Available at: https://www.R-project.org/.

Schiffman J.S. & Ralph P.L., 2022. System drift and speciation. Evolution; international journal of organic evolution, 76(2), pp.236–251. PubMed PMC

Singh K.K. et al., 2010. Human SAP18 mediates assembly of a splicing regulatory multiprotein complex via its ubiquitin-like fold. RNA (New York, N.Y.), 16(12), pp.2442–2454. PubMed PMC

Star B. et al., 2011. The genome sequence of Atlantic cod reveals a unique immune system. Nature, 477(7363), pp.207–210. PubMed PMC

Sun T. et al., 2023. Integrative mRNA-miRNA interaction analysis associated with the immune response in the head kidney of rainbow trout (Oncorhynchus mykiss) after infectious hematopoietic necrosis virus infection. Fish & shellfish immunology, 142(109140), p.109140. PubMed

Swann J.B. et al., 2020. The immunogenetics of sexual parasitism. Science (New York, N.Y.), 369(6511), pp.1608–1615. PubMed

True J.R. & Haag E.S., 2001. Developmental system drift and flexibility in evolutionary trajectories. Evolution & development, 3(2), pp.109–119. PubMed

Vrtílek M. & Bolnick D.I., 2021. Macroevolutionary foundations of a recently evolved innate immune defense. Evolution; international journal of organic evolution, 75(10), pp.2600–2612. PubMed PMC

Wainwright P.C. et al., 2005. Many-to-one mapping of form to function: A general principle in organismal design? Integrative and comparative biology, 45(2), pp.256–262. PubMed

Weber J.N. et al., 2022. Evolutionary gain and loss of a pathological immune response to parasitism. Science, 377(6611), pp.1206–1211. PubMed PMC

Weber J.N. et al., 2021. Evolution of a costly immunity to cestode parasites is a pyrrhic victory. Available at: https://www.biorxiv.org/content/10.1101/2021.08.04.455160.abstract. DOI

Wegner K.M., Reusch T.B.H. & Kalbe M., 2003. Multiple parasites are driving major histocompatibility complex polymorphism in the wild: Multiple parasites drive MHC polymorphism. Journal of evolutionary biology, 16(2), pp.224–232. PubMed

Wiley E.O. & Lieberman B.S., 2011. Phylogenetics: Theory and Practice of Phylogenetic Systematics 2nd ed., Hoboken, NJ: Wiley-Blackwell.

Wynn T.A. & Ramalingam T.R., 2012. Mechanisms of fibrosis: therapeutic translation for fibrotic disease. Nature medicine, 18(7), pp.1028–1040. PubMed PMC

Yang W. et al., 2022. Comparative immune-relevant transcriptome reveals the evolutionary basis of complex traits. iScience, 25(12), p.105572. PubMed PMC

Zapata A. et al., 2006. Ontogeny of the immune system of fish. Fish & shellfish immunology, 20(2), pp.126–136. PubMed