Abyssal hydrothermal alteration drives the evolution from simple alkanes to prebiotic molecular complexity.

Abyssal hydrothermal vents are regarded as reactors for simple reduced carbon transforming into more complex forms of prebiotic organic chemistry. While the organic geochemical continuum and evolutionary transitions remain elusive, due to the intense hydrothermal alteration. We apply a metabolomics-inspired molecular fingerprinting strategy integrating mass spectral networking and hierarchical organization, to construct a molecular relatedness phylogenetic tree for vents from ultraslow-spreading Indian Ridge. Here we show that organic molecules from different vent fields and activity states share common molecular connection patterns. The observed progressive molecular evolution from alkanes through aromatics to complex heteroatom-bearing compounds reveals a systematic increase in molecular functionalization and polarity. This finding helps bridge the gap between simple reduced carbon and prebiotic molecular complexity, underscoring the role of hydrothermal systems in shaping life's essential feedstock on the primordial Earth. This framework may contribute to the search for life-markers on other astrobiological contexts, e.g., Mars, Enceladus, Callisto and Europa.