Evidence for the Evolutionary Model

Pseudogenes

      A pseudogene is a former gene that has mutated to the point of inactivation. By comparing the polymorphism of pseudogenes in orthologous loci in other species, any nested hierarchies they fall into can be identified. This is aided by the identification of an orthologous active gene in other species, which the pseudogene is a deactivated copy of. The following is an example of how a pseudogene can be evidence of common ancestry:

                   

      L-gulono-γ-lactone oxidase (GULO) is the forth and final enzyme of the metabolic pathway that converts glucose to 2-keto-gulono-γ-lactone, witch spontaneously converts into L-ascorbic acid (vitamin C); a critical vitamin in biosynthesis; acting as a cofactor, substrate, or electron donor for numerous enzymes.

First, let's look at all the GULO data, without any presuppositions:

  1. Strepsirrhines and most other plants and animals have the GULO gene, and are immune to deadly vitamin C deficiency (scurvy).
  2. Haplorrhines (Inai, Ohta, & Nishikimi, 2003), the remaining primates, along with pigs (Hasan et. al., 1999), guinea pigs (Nishikimi, Kawai, & Yagi, 1992), and certain fish and birds are prone to vitamin C deficiency. Additionally, they posses an altered, inactive form of the GULO gene, as well as the genes for all the remaining enzymes in the metabolic pathway, such as UDP-glucose dehydrogenase (4p15.1) and glucuronic acid epimerase (15q23).
  3. Haplorrhine GULO inactivation is likely due to a missing base pair in the amino acid coding region of exon 10, which shifts its reading frame. This shift forms a stop codon several base pairs downstream of the missing base pair. Not only is this stop codon present, and is this base pair missing in all haplorrhine GULOs, but it is not found in the guinea pig GULO; which is likely inactivate due to one of 3 stop codons in exons 2, 3, and 6.
  4. There are many single nucleotide polymorphisms (SNPs) shared among haplorrhine GULOs, but not shared with the guinea pig GULO. And the shared haplorrhine SNPs fall in a hierarchical grouping, where each set falls within another set (a nested hierarchy).


      Notice how the proceedings were intentionally worded to make no assumptions about ancestry or mutation. So now let's look at the models of GULO deactivation and of common ancestry and see how well they fit the data:

 If humans, other haplorrhines, and guinea pigs share common ancestry: If they never shared common ancestry and were separately designed:
 
  1. Since they all would have once biosynthesized L-ascorbic acid, we should find the the GULO gene and all the remaining genes in the pathway. And we do.
  2. Deactivation:
    1. We should find deactivating mutations, which are mutations that render the GULO gene incapable of producing the GULO enzyme, or even activating in the first place, i.e. a GULO pseudogene (GULOP). And we do.
    2. If the deactivation occurred in an ancestor common to the haplorrhines, we should expect to find the same deactivating mutation in all haplorrhine GULOPs. And we do.
    3. Since there are many other species genetically closer to haplorrhines than guinea pigs, and since those species have active GULOs, the guinea pig GULOP deactivation should be lineage-specific; so we should expect to find its deactivating mutation in a different location. And we do.
  3. Since pseudogenes accumulate mutations from generation to generation, and since the haplorrhine GULOP would have to have been in pseudogene form across many speciation events (and in turn, many common ancestors), we should find shared mutations (again, manifesting as shared SNPs), and we should find that they are arranged in such a way that they give an unbroken line of inheritance for every species (a nested hierarchy). And we do.
 
  1. Since they would have been designed to lack the capability of biosynthesizing L-ascorbic acid, we should not find the GULO gene. Yet we do.
  2. Deactivation:
    1. Despite that we should not find GULO in the first place, if present, we should find deactivating mutations and/or designed-in alterations, i.e. GULOP. And we do.
    2. If the deactivation was designed into these separate creations, we should expect to find either the same deactivating mutation in every GULOP, or an arbitrary, disordered distribution of shared and unshared deactivating mutations. Yet we find neither.
    3. Since the majority of GULOP deactivations are in the same location, we should find that the guinea pig GULOP deactivation is likewise in the same location as it is in haplorrhines. Yet we do not.
  3. We should find little to no shared SNPs, and we should find that whatever few did arise are not arranged in any particular pattern. Yet we find neither.

                                                                             

 

 

     It is all these shared mutations that necessitate inheritance from ancestors common to each member of each species that shares them (common ancestral species), which have since diverged, and the nested hierarchy they fall into both corroborates this and necessitating a specific sequence of divergence that is consistent with that of the distributional and mutational nested hierarchies of ERVs (Ohta & Nishikimi, 1999).

From this, it is evident that the only model that parsimoniously fits all the data is that of common ancestry; where the shared SNPs are shared mutations.


 

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References

Hasan, L., P. Vogeli, S. Neuenschwander, P. Stoll, E. Meijerink, C. Stricker, H. Jorg, and G. Stranzinger. "The L-gulono-gamma-lactone oxidase gene GULO which is a candidate for vitamin C deficiency in pigs maps to chromosome 14." Animal Genetics 30.4 (1999): 309-12. <http://www.ncbi.nlm.nih.gov/pubmed/10467707>.

Inai, Y., Y. Ohta, and M. Nishikimi. "The whole structure of the human nonfunctional L-gulono-gamma-lactone oxidase gene--the gene responsible for scurvy--and the evolution of repetitive sequences thereon." Journal of Nutritional Science and Vitaminology (Tokyo) 49.5 (2003): 315-19. <http://www.ncbi.nlm.nih.gov/pubmed/14703305>.

 

Nishikimi, M., T. Kawai, and K. Yagi. "Guinea pigs possess a highly mutated gene for L-gulono-gamma-lactone oxidase, the key enzyme for L-ascorbic acid biosynthesis missing in this species." Journal of Biological Chemistryhttp://www.jbc.org/content/267/30/21967.long>. 267.30 (1992): 21967-1972. <

Ohta, Y., and M. Nishikimi. "Random nucleotide substitutions in primate nonfunctional gene for L-gulono-γ-lactone oxidase, the missing enzyme in L-ascorbic acid biosynthesis." Biochimica et Biophysica Acta 1472.1-2 (1999): 408-11. <http://www.ncbi.nlm.nih.gov/pubmed/10572964>.