Between-Group and Within-Group PCA

#1
Hi all,

I'm running a PCA with two species (one fossil and one extant) divided into multiple geographic groups.

The program I'm using is called PAST (PAlaeontological STatistics).

Anyhow, I'm a little confused about within-group and between-group PCAs and how they differ from a PCA that disregards groups. Specifically, when is it appropriate to use a 'normal' PCA as opposed to, say, a between-group PCA? The scatterplot result for a between-group PCA obviously maximizes group difference and thus looks very different from a PCA that disregards group.

I appreciate it if someone can clarify all this for me. :)