The species have very different behaviours, are extremely difficult to mate, and with different allele frequency, consistent with genetic drift during a founder event.
Note also that the neutral theory does not assume the strict neutrality of alleles but that the allele frequency changes are dominated by genetic drift.
An initial genetic drift could have caused differences in allele frequency distribution that have not been re-established due to a certain level of geographic isolation.
Height indicates fitness, while each of the other dimensions may represent allele identity at one gene, allele frequency at one gene, or one phenotypic trait.