Phylogenetic relationship of vertebrate carbonic anhydrases

Carbonic anhydrases (CAs, EC 4.2.1.1) are zinc-dependent metalloenzymes that catalyze the reversible hydration of carbon dioxide, a reaction essential for acid-base regulation, respiration, and metabolic integration in vertebrates. In animals, CA activity is exclusively encoded by the α-CA family, which has undergone extensive expansion during vertebrate evolution. This chapter presents a phylogenetic synthesis of vertebrate α-CAs, integrating sequence-based analyses with comparative genomics, structural constraints, and patterns of subcellular localization. Phylogenetic evidence indicates that the modern vertebrate CA repertoire originated early in the evolution of life, and was shaped by ancient whole-genome duplication events, followed by differential retention, divergence, and lineage-specific gene loss. Cytosolic, mitochondrial, membrane-associated, and secreted CAs form well-supported evolutionary lineages that primarily reflect diversification in regulation, cellular targeting and physiological roles, rather than changes in catalytic mechanism. Catalytically inactive CA-related proteins (CARPs) constitute a distinct evolutionary branch derived from gene duplication and functional divergence of catalytically active CAs. Molecular analyses reveal strong evolutionary constraints on residues essential for zinc coordination and proton transfer, whereas surface-exposed and regulatory regions show greater evolutionary flexibility. Comparative analyses across vertebrates highlight the broad conservation of major CA clades, together with lineage-specific differences in isoform repertoires. By embedding functional interpretation within a phylogenetic framework, this chapter provides an evolutionary basis for comparative and biomedical studies of vertebrate CAs.