LAUSR

Significance Archaeal lipids are ubiquitous in marine sediments and are commonly used to infer past marine sea surface temperatures. However, these molecules can also be used to investigate the ecological and evolutionary history of marine archaea. Here we utilized data science techniques to identify two distinct patterns of archaeal lipid distribution from globally distributed seawater and surface sediments, indicative of shallow and deep ecotypes in the modern oceans. Further investigation of ancient marine sediments across the Mesozoic–Cenozoic suggests that deep water AOAs were suppressed in global oceans during greenhouse climates, which has not been observed by traditional molecular evolutionary models. This perspective carries important implications for marine nitrogen and carbon cycling and the reconstruction of past ocean temperatures.