[Pharmboy]

I understand that...but it still makes NO sense that two populations considered VERY old would be VERY distant from each other.

[Varda]

One is the founding population and the other is maybe the first daughter population. Both populations continue evolving, accumulating mutations. Over time they become more and more different. Because of the early split, this first daughter population doesn't contain the entire catalog of mutations of the founder population. The population with the most unique mutations compared to another population is the most distant from that population.
More recent daughter populations will contain the recent mutations and will not have had enough time to accumulate many unique mutations of it's own. These populations are considered closer in genetic distance.