Until arb-6.0.x species with more base positions were added before such with less bp.
Starting with arb-6.1 all species are added independently, i.e. there is no explicit insertion order (see exception below). The performance has been improved dramatically, especially when adding many species and/or when adding into big trees.
If multiple species are added to the same position in the tree, they form a subtree which will be optimized afterwards.
If the number of added species exceeds 50% of the size of the tree (e.g. if adding more than 1000 species to a tree containing 2000 sp.), the species will be devided into multiple sets and then these sets will be inserted one after each other. Longer sequences will be added earlier in this case.