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:
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:|
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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.
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>.