Neutrophil-monocyte progenitor trans-differentiation is a source of type 2 myelopoiesis and developmental basophil heterogeneity.

Basophils, eosinophils and mast cells (BEMs) are central to parasite immunity and play important roles in bacterial infection control and cancer. This functional diversity is mirrored by molecular heterogeneity, but whether BEM heterogeneity arises in resident tissues or through developmental specification remains to be understood. We here develop transition state capture using combined Gata1 reporting and lineage tracing to identify transitional progenitors (TPs) undergoing BEM commitment. We found that Gata1 -expressing TPs showed heterogeneity orthogonal to the commitment trajectory, with molecularly and functionally distinct megakaryocytic-erythroid-biased, myeloid-biased and oligo-potent states crossing the fate boundary. Myeloid-biased TPs arose via trans-differentiation of neutrophil-monocyte progenitors (NMPs) to a BEM fate. This fate switch occurred when the NM and BEM differentiation trajectories gained molecular proximity, opening a “wormhole” traversed by TPs up-regulating the BEM master regulators Lmo4 and Gata2 . Elane -Cre lineage tracing of NMP-derived BEMs showed eosinophil lineage bias compared to the oligo-potent erythroid-primed multi-potent progenitor (EMPP) pathway. Furthermore, basophils generated from EMPPs were molecularly primed for the early phase of the parasite response, while NMP-derived basophils expressed higher levels of chemoattractants involved in subsequent neutrophil and monocyte recruitment. Analogous molecular heterogeneity was observed in human basophils. These results demonstrate orthogonal functional heterogeneity of fate-transitioning progenitors, identify trajectory switching as a mechanism of blood cell specification, and show that TP heterogeneity is transmitted to mature cell types, with separate developmental pathways of type 2 myelopoiesis generating distinct basophil populations primed for successive phases of the infection response.