Evolutionary history of the α-Carbonic Anhydrase (αCA) gene family in the phylum Arthropoda, with a focus on the copepod Eurytemora affinis species complex

The -Carbonic Anhydrase (CA) gene family encodes an abundant and ancient metalloenzyme present in all animals. Found in both eukaryotes and prokaryotes, members of this gene family play vital roles in ionic regulation, acid-base regulation, and respiration. However, little is known regarding the evolutionary history and patterns of molecular evolution of this gene family in the phylum Arthropoda. Through phylogenetic reconstruction and subcellular localization prediction, we discovered that arthropod CA genes could be classified into three clades based on phylogenetic topology and predicted subcellular localization, as has been found in chordate CA. Within the three distinct arthropod CA clades, the Extracellular & Membrane-bound CA clade exhibited the highest rates of evolution, variation in predicted subcellular localization, and number of homologs. Intriguingly, while we found that the majority of arthropod CA homologs were classified in the Extracellular & Membrane-bound CA clade, the majority of chordate CA were within the Cytosolic CA clade. This result indicates divergence in CA expansion patterns between the two phyla. In addition, we found that CA12, a paralog that showed salinity-associated signatures of selection in the copepod Eurytemora affinis species complex in previous studies, also shows signatures of positive selection (based on dN/dS) in two of the three sister species of the copepod Eurytemora affinis species complex (E. carolleeae and E. gulfia), compared to the general arthropod CA background. Overall, our results indicate that the CA gene family shows signatures of selection at the macroevolutionary scale, across phyla, and between closely related sister species. Significance statementAlpha Carbonic Anhydrase (CA) is an essential enzyme that is particularly well-studied among certain metazoan lineages, such as chordates and poriferans, but not in arthropods. Here, we provide the first comprehensive analysis of the evolutionary history of CA, and uncover the signatures of selection across phylum and between species. Through phylogenetic reconstruction, predicted subcellular localization, and dN/dS-based selection tests, our study shed light on how the CA gene family has and continues to evolve in the largest animal phylum Arthropoda.