Origin Of Life: Another reason the ToE does NOT predict nested hierarchy
The point being is that the ToE does not tell us that living organisms can arise from non-living matter only once. And it does not have any say in the number of ways that living organisms could arise from non-living matter. The ToE does not say there would be a universal genetic code for the same reason.
Therefore when evolution starts there could already be in place populations that could not be placed in any hierarchial arrangement. And when those original populations evolved we wouldn't expect to form a nested hierarchy with those descendants.