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 α-Carbonic Anhydrase (αCA) 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 αCA genes could be classified into three clades based on phylogenetic topology and predicted subcellular localization, as has been found in chordate αCA. Within the three distinct arthropod αCA clades, the Extracellular & Membrane-bound αCA 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 αCA homologs were classified in the Extracellular & Membrane-bound αCA clade, the majority of chordate αCA were within the Cytosolic αCA clade. This result indicates divergence in αCA expansion patterns between the two phyla. In addition, we found that αCA12, 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 αCA background. Overall, our results indicate that the αCA gene family shows signatures of selection at the macroevolutionary scale, across phyla, and between closely related sister species.