A more accurate rendering of Table 1 in the MGD paper

The following modification of Table 1 of the MGD paper take into account those positions that are shared between species due to common adaptation to a common environmental selection, depicted by ‘#’.   Variant positions are denoted by 'x'. This more realistic rendering explains both equidistance and overlap features. It explains why not all variants between Hs and Dm are also variants between Hs and Sc or between Nc and Sc. Also see the related post on May 1, 2009 titled 'more on the MGD interpretation of certain facts.'

Table 1. Alignment of a hypothetical 20 amino acid peptide.

Nc     1 2 3 4 5 6 7 8 # 1 x 3 4 # x # x # x x     N. crassa

Sc     1 2 3 4 5 6 7 8 # 1 2 x x # x # # # x x     S. cerevisiae

Dm     1 2 3 4 5 6 7 8 # 1 2 3 4 5 6 # # x x x     D. melanogaster

Hs     1 2 3 4 5 6 7 8 # 1 2 3 4 # 6 7 # 9 9 x     H. sapiens

Equidistance feature:

Identity

Nc-Sc, 65% (13/20)

Dm-Sc, 65%

Dm-Nc, 65%

Hs-Sc, 65%

Hs-Nc, 65%

Hs-Dm, 75%

Overlap feature:

Of 5 variants between Hs-Dm, four are variants between Hs-Sc.

Of 5 variants between Hs-Dm, four are variants between Hs-Nc.

Of 5 variants between Hs-Dm, two are variants between Sc-Nc.  

Actual alignment of the above four species for cytochrome c:

Dm              -GDVEKGKKLFVQRCAQCHTVEAGGKHKVGPNLHGLIGRKTGQAAGFAYTDANKA

Hs              -GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKN

 

Sc              -GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIK

Nc              -GDSKKGANLFKTRCAQCHTLEEGGGNKIGPALHGLFGRKTGSVDGYAYTDANKQ

                 *   **   *   * **** * **  * ** ***  **  *   *  ** ** 

 

Dm              KGITWNEDTLFEYLENPKKYIPGTKMIFAGLKKPNERGDLIAYLKSAT

Hs              KGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKAT

 

Sc              KNVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKAT

Nc              KGITWDENTLFEYLENPKKYIPGTKMAFGGLKKDKDRNDIITFMKEAT

                *   * *    *** *********** * * **   * * *   * **  

 

The existence of shared residues due to environmental selection is key to the adaptive survival of species over long evolutionary time.  The MGD predicts that while a simple organism may have great genetic diversity potential, only a fraction of the diversity is expressed at any one time due to natural selection to be the most optimal.  This view is fully consistent with one of the two most remarkable early results of molecular evolution: the levels of allozyme diversity vary by no more than a few fold across almost all species.  (the other result is of course the seemingly similar mutation rates in different species.)  This view is also fully supported by the work Eviatar Nevo on the ‘evolution canyon’ in Israel.

Nevo: “Natural selection in some form proved to be the major determinant of genetic population structure and differentiation. The parallel genetic patterns obtained across all geographical scales in nature were once again inconsistent with the neutral theory of molecular evolution.  Natural selection in its various forms appears to maintain genetic polymorphism and orient molecular evolution at both the protein and DNA level, as was also supported theoretically.”

Nevo E, Beiles A, Ben-Shlomo R (1984) The evolutionary significance of genetic diversity: ecological, demographic and life histroy correlates. In: Mani GS, editor. Evolutionary Dynamics of Genetic Diversity. Berlin: Spinger-Verlag. pp. 13–213.

Nevo E (2001) Evolution of genome-phenome diversity under environmental stress. Proc Natl Acad Sci U S A 98: 6233-6240.

Acknowledgements:

I thank my college classmate Dr. Wei Shen for providing the actual sequence alignment shown here and for the helpful discussion on Table 1 of the MGD paper.