Population‐specific plasma proteomes of marine and freshwater three‐spined sticklebacks ( Gasterosteus aculeatus )

Molecular phenotypes that distinguish resident marine (Bodega Harbor) from landlocked freshwater (FW, Lake Solano) three‐spined sticklebacks were revealed by label‐free quantitative proteomics. Secreted plasma proteins involved in lipid transport, blood coagulation, proteolysis, plasminogen‐activating cascades, extracellular stimulus responses, and immunity are most abundant in this species. Globulins and albumins are much less abundant than in mammalian plasma. Unbiased quantitative proteome profiling identified 45 highly population‐specific plasma proteins. Population‐specific abundance differences were validated by targeted proteomics based on data‐independent acquisition. Gene ontology enrichment analyses and known functions of population‐specific plasma proteins indicate enrichment of processes controlling cell adhesion, tissue remodeling, proteolytic processing, and defense signaling in marine sticklebacks. Moreover, fetuin B and leukocyte cell derived chemotaxin 2 are much more abundant in marine fish. These proteins promote bone morphogenesis and likely contribute to population‐specific body armor differences. Plasma proteins enriched in FW fish promote translation, heme biosynthesis, and lipid transport, suggesting a greater presence of plasma microparticles. Many prominent population‐specific plasma proteins (e.g. apoptosis‐associated speck‐like protein containing a CARD) lack any homolog of known function or adequate functional characterization. Their functional characterization and the identification of population‐specific environmental contexts and selective pressures that cause plasma proteome diversification are future directions emerging from this study.