BMP7 peripheral sequence evolution correlates with mammalian cloacal septation

Vertebrate evolution from a single multipurpose cloaca to separate urogenital and anal openings remains a central molecular question with relevance to reproductive diversification and anorectal malformations. We investigated BMP7, a critical regulator of cloacal formation, across 37 vertebrates from cartilaginous fish to mammals using phylogenetics, sequence alignment, physicochemical assessment, domain analysis, motif analysis and molecular docking. The BMP7 core TGF-beta domain was highly conserved (>90% identity), whereas peripheral regions showed significant habitat-associated divergence (p < 0.01), including shifts in isoelectric point between aquatic and terrestrial vertebrates (pI 6.22–6.97 to 6.98–8.98) and altered stability indices. A key finding was that placental mammals, in which cloacal septation produces distinct anorectal and urogenital outlets, showed lineage-specific amino-acid changes, including Pro111Ala, linked to predicted BMP7-FOXA1 regulatory refinement. MEME analysis identified mammal-bird GWQDWI conservation and amphibian-reptile RACGCH divergence, supporting peripheral BMP7 adaptation during cloacal evolution.