Here is a full list of locations where you can find Runes to upgrade your Ancient Totem:

1) 1 Rune for 100% clearing Herra.

2) 1 Rune for 100% clearing Sanderra.

3) 1 Rune for completing the questline in Asher's Studio, the second part of the "Saving Granthill" story adventure (The icon is on the left side of your screen).

4) 1 Rune for completing all 3 parts of the "Saving Granthill" story adventure.

5) 1 Rune for 100% clearing the Sailors' Camp, the first part of the "Captain Paloma's Journey" story adventure.

6) 1 Rune for 100% clearing Libertalia, the second part of the "Captain Paloma's Journey" story adventure.

7) 2 Runes for completing all 3 parts of the "Captain Paloma's Journey" story adventure.

8) 1 Rune for 100% clearing the Ancestors' Land, the second part of the "Adventures of Ragnar" story adventure.

9) 1 Rune for 100% clearing the Land of Settlers, the third part of the "Adventures of Ragnar" story adventure.

10) 1 Rune for 100% clearing the Valley of Mirages, the second level of the Land of Settlers.

11) 1 Rune at the Sheriff’s Office in the Land of Settlers.

12) 2 Runes for completing all 3 parts of the "Adventures of Ragnar" story adventure.

Total: You can collect 14 Runes in the game, allowing you to upgrade your Ancient Totem 8 times.