Conservation of Human IgSF Proteins Throughout Eukaryotic Evolution

The human immunoglobulin superfamily (IgSF) encompasses hundreds of proteins involved in cell-cell adhesion, neural connectivity, junctional organization, and immune regulation, with many serving as key checkpoint proteins. To elucidate the evolutionary history of human IgSF members, we systematically analyzed all available eukaryotic reference genomes to determine when each IgSF subfamily first appeared. The human IgSF was partitioned into six major evolutionary timeframes: Metazoa, Vertebrata, Gnathostomata, Tetrapoda, Amniota, and Mammalia. Although proteins were grouped solely by their conservation across eukaryotes, their biological functions clustered naturally, reflecting how new physiological systems create selective pressures that drive the appearance, retention, and diversification of protein architectures suited to those functions. Conservation and functional analyses indicate that human IgSF members arising in tetrapods and amniotes primary regulate the strength and duration of immune responses and form many of the critical components of the immune synapse, while IgSF genes that appear first in mammals have evolved to fine-tune immune activation thresholds to support maternal-fetal tolerance. Case studies are provided to illustrate three key evolutionary themes: (i) highly conserved yet catalytically inactive proteins retain essential regulatory functions, (ii) functional convergence among evolutionarily distinct IgSF families, and (iii) compensatory evolution within adaptive immunity following a lineage-specific loss of an IgSF member. Together, these findings establish an evolutionary framework for organizing the human IgSF by both ancestry and function, providing a foundation for assessing IgSF importance. Notably, this study facilitates the identification of conserved but understudied proteins that emerged alongside the development of the adaptive immune system, highlighting them as promising candidates for future experimental investigation.