Oxygen-sensing regulatory architecture structures mammalian diversification

The HIF oxygen-sensing pathway traces to the last metazoan common ancestor [~]800 million years ago and is conventionally viewed as a conserved cellular stress-response module. Whether this ancestral system has contributed to mammalian diversification at macroevolutionary timescales remains unexplored. We analyzed sequence-encoded TF-gene regulatory architecture for 34 transcription factors and 705 genes in 10 oxygen-sensing pathways across 239 mammalian species. Oxygen-sensing regulatory architecture carries strong clade-structured evolutionary signal. The primary axis of variation tracks a fast-slow life history gradient, marked by rewiring of growth-control and tumor suppressor hub genes. A second axis recovers the monotreme-marsupial-placental transition and aligns with the decline in atmospheric O2 from the Permo-Carboniferous maximum toward present-day levels1. Orthogonal axes encode distinct ecological regulatory strategies; two later axes separately resolve HIF-compatible binding-site architecture and dominant TF-family assignment, identifying regulatory strategies associated with powered flight and hibernation. This multidimensional space also informs Petos paradox, suggesting that relative cancer resistance tracks the combination of tumor-suppressor enrichment and coordinated HIF-complex assignment. Together, these results indicate that regulatory configurations arise at major evolutionary transitions and persist coherently across descendant lineages through a punctuated mode of regulatory evolution, providing genomic-level evidence for Simpsons adaptive zones and a mechanism for evolutionary stasis. These findings reframe oxygen sensing as a regulatory hub in mammalian diversification, with stable patterns of TF-family assignment configurations emerging as a structuring force in macroevolution. BriefAncient molecular processes such as oxygen-sensing, whose HIF-pathway dates to the origin of animals [~]800 million years ago, are typically regarded as conserved across lineages. How such deeply ancestral systems have contributed to mammalian diversification remains largely unexplored. By analyzing the oxygen-sensing regulatory architecture (which transcription factors regulate which genes) across 239 mammalian species, we find that oxygen-sensing regulatory rewiring tracks placental evolution, atmospheric O2, life history evolution, ecological specializations, and cancer resistance. Major radiations occupy discrete, heritable configurations established at key phylogenetic transitions and subsequently retained across descendant lineages through near-neutral within-regime drift, revealing regulatory architecture lock-in as a structuring force in macroevolution.