I am showing below yeast and neurospora cytochrome c alignment to explain an observation that is not covered in detail in my MGD paper but is covered in principle. The observation is that not all variant residues between two complex species are also variant between two simple species, when Table 1 of the paper seems to indicate that all variant residues between two complex species are also variant between two simple species. Table 1 is of course meant to express an idea in simplistic form and should not be taken to be literally exact.
Identities = 71/105 (67%), Positives = 88/105 (83%), Gaps = 0/105 (0%)
yeast 3 FKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNV 62
F AG +KKGA LFKTRC QCHT+E+GG +K+GP LHG+FGR +G +GY+YTDAN +K +
Neuro 3 FSAGDSKKGANLFKTRCAQCHTLEEGGGNKIGPALHGLFGRKTGSVDGYAYTDANKQKGI 62
yeast 63 LWDENNMSEYLTNPAKYIPGTAMAFGGLKKEKDRNDLITYLKKAT 107
WDEN + EYL NP KYIPGT MAFGGLKK+KDRND+IT++K+AT
neuro 63 TWDENTLFEYLENPKKYIPGTKMAFGGLKKDKDRNDIITFMKEAT 107
There are 10 of 22 residues differing between drosophila and human that are also different between yeast and neurospora.
So a major portion (about 50%) of variants between drosophila and human is also variant between yeast and neurospora. That portion can only be explained by the MGD but not by the molecular clock/neutral theory. Now, why not all?
As shown by Figure 2 of my paper, the MGD says that of all the conserved residues between two species at any time, there are a fraction of them that is due to adaptation to common environmental selection and may change from time to time. In our case, yeast and neurospora share 67% of all positions. Of these, maybe 20% is shared because of common selection (the two yeasts have very similar way of life). So, the absolutely non-neutral sequence may be 47% and the neutral region 53%. Human and drosophila share 80% positions, and 10% of these may be due to common environmental selection (they have very different life style and so the shared region due to common selection is less). So the neutral sequence is 30% in this case for the drosophila. The MGD says that this 30% region should completely overlap the 53% neutral region of yeast. But since only 20 of 30 in human/drosophila did actually vary and only 30 of 53 in yeast, the actual overlap residues are 20/30 x 30/53 x 30 = 11, which is very close to the actual number.
So, the exact numbers may not be real but the above is to illustrate in principle how the observation may be explained by the MGD. The key is to have a fraction of the shared residues as being neutral or changeable with environment, even when the distance is at maximum. This is a very reasonable and intuitively obvious point and is actually true in reality. So, when we see a maximum distance, it does not mean that all the shared residues are absolutely nonchangeable or nonneutral.