Which is exactly what we'd expect. Now, if we look at the differences and similarities in detail, that tells a story.
Genesis and the Genome (pdf)
One protein used as a yolk component in egg-laying vertebrates is the product of the vitellogenin gene. (18) Since placental mammals are proposed to be descended from egg-laying ancestors, researchers recently investigated whether humans retained the remnants of the vitellogenin gene sequence in pseudo-gene form. To assist in their search, this group determined the location of the functional vitellogenin gene in the chicken genome, noted the identity of the genes flanking the vitellogenin sequence, and located these genes in the human genome. They found that these genes were present side-by-side and functional in the human genome; then they performed an examination of human sequence between them. As expected, the heavily mutated, pseudogenized sequence of the vitellogenin gene was present in the human genome at this precise location. (19) The human genome thus contains the mutated remains of a gene devoted to egg yolk formation in egg-laying vertebrates at the precise location predicted by shared synteny derived from common ancestry.
While the vitellogenin pseudogene is compelling, it is but one example of thousands that could be given. (20) For example, there are hundreds of genes used for the sense of smell (olfactory receptor genes) in the human genome that have become pseudogenes. (21) Moreover, many of these pseudogenes have identical inactivating mutations shared among humans, chimpanzees, and gorillas. (22) Furthermore, determining degrees of relatedness solely based on genomes that share identical inactivating mutations in olfactory receptor pseudogenes, independently arranges humans as most closely related to chimpanzees (most errors in common), and less so with gorillas (fewer errors in common), and even less with orangutans (fewer still errors in common). (23) Additionally, no "out of place" pseudogenes were found in this study: pseudogenes with identical inactivating mutations common to humans and gorillas were also present with the identical mutation in chimpanzees; mutations common to humans and orangutans were present in chimpanzees and gorillas.
This pattern is precisely what common ancestry predicts for these species, since an identical mutation present in two species is most readily explained by its presence in the common ancestor of both species. The common ancestor of humans and gorillas is also the common ancestor of chimpanzees, hence inactivating mutations present in humans and gorillas are also predicted to be present in chimpanzees. In short, the existence of shared pseudogenes between primate genomes, their syntenic locations, and their patterns of inactivation and distribution all coherently support the same model of common ancestry based on comparative sequence homology criteria alone.
