Shamans in this game are loosely based on shamans in reality. They do not deny gods, but they are connected to their ancestry. They are guided not only by their tribe's shaman spirits, but their totem animal plays a huge role in their life, greater than that of their ancestry. It is their totem in which they gain their wisdom and insight, and it is their totem that can revoke its power to the shaman, leaving them bereft and inept. (At this point, I do feel that the spirit journey quest should play a greater role, perhaps even making it mandatory to complete for a shaman to receive access to further spells.) Far easier to have them gain their powers from that than to make an entire new pantheon of shaman based deities. Shamans are a mixture of nature revering and spirituality. They control weather because that is one of their functions. Not enough rain? They were expected to commune with the spirits, natural and spiritual, to find out why and to make it change to bring rain. Call lightning is a bit of a stretch, admittedly, and I don't recall reading any anthropology books in regards of voodoo, specifically, but there have been stories, as well as beliefs, that shamans could control natural events, which could be construed as calling lightning to show their strength, as well as inflicting spiritual damage to other, respectively.
Call lightning comes out of the sky, a natural event. It is not like lightning that is conjured and comes out of a warlocks fingertips, making them a direct vessel of the elements. If this were the case with shamans, then, yes, there would be issue. It is not, though.
A side note of the thread: Charisma should play a role in a shaman's life. Charisma has been found in many cultures to mean the shaman's mana, their power, or a sort of aura of energy that surrounds them.
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