Single-cell foundation modeling with species-native protein tokens links regenerative competence across frog and mouse

<jats:p>Appendage regenerative capacity varies dramatically across developmental stages and anatomical sites, yet comparing these functional transitions across species remains difficult because cell types and gene vocabularies diverge. Universal cell embedding (UCE) provides a shared coordinate space across diverse organisms. Here we demonstrate that an experimentally anchored Xenopus laevis tail-organizer contrast identifies a developmental limb transition from which we define a frozen cross-species competence ruler. Applied without refitting, this ruler distinguished regenerative and fibrotic library groups in adult mouse digit repair and resolved a repeatable aligned component within state-balanced macrophage repair populations. Universal cell embeddings thus convert source population contrasts into portable vector rulers, enabling zero-shot functional comparisons across species boundaries.</jats:p>