Talk:Evidence of common descent/Evidence from genetics (draft)

Although it has only recently become available, the best evidence for common descent comes from the study of gene sequences. Comparative sequence analysis examines the relationship between the DNA sequences of different species, producing several lines of evidence justifying common descent.

The simplest and most powerful is phylogenetic reconstruction. If the the hypothesis of common descent is true, then species that share a common ancestor will have inherited that ancestor's DNA sequence. Notably they will have inherited mutations unique to that ancestor. Gene sequences may thus be used to reconstruct the tree of life according to the assumption that closely-related species will have a greater fraction of identical sequence and will have sharedsubstitutions when compared to more distantly-related species.

Such reconstructions, especially when done using slowly-evolving protein sequences, are often quite robust and can be used to reconstruct a great deal of the evolutionary history of modern organisms (and even in some instances such as the recovered gene sequences of mammoths, Neanderthals or T. rex, the evolutionary history of extinct organisms). These reconstructed phylogenies recapitulate the relationships established through morphological and biochemical studies. The most detailed reconstructions have been performed on the basis of the mitochondrial genomes shared by all eukaryotic organisms, which are short and easy to sequence.

It is conceivable that genetic identity is not the result of common descent, but only the product of common functional or structural requirements: that is, there is one best way to produce a hoof, so all hoofed creatures share a common genetic basis. However, phylogenetic relationships also extend to a wide variety of non-functional sequence elements, including repeats, transposons, pseudogenes, and mutations in protein-coding sequences that do not result in changes in amino-acid sequence. While a minority of these elements might later be found to harbor function, in aggregate they demonstrate that identity must be the product of common descent rather than common function.

Finally, a deeper understanding of developmental biology shows that common morphology is, infact, the product of shared genetic elements. For example, although camera-like eyes are believed to have evolved independently on many separate occasions, they share a common set of light-sensing proteins (opsins), suggesting a common point of origin for all sighted creatures. Another noteworthy example is the familiar vertebrate body plan, whose structure is controlled by the homeobox (Hox) family of genes.