One of the many evidences for macroevolution, or speciation. Briefly explained here by Douglas Theobald Phd in Biochemistry-
The amino acid sequences of proteins are often used to establish the phylogenetic relationships of species. Sequence studies with functional genes have centered on genes of proteins (or RNAs) that are ubiquitous (i.e. all organisms have them). This is done to insure that the comparisons are independent of the overall species phenotype.
For example, suppose we are comparing the protein sequence of a chimpanzee and that of a human. Both of these animals have many similar anatomical characters and functions, so we might expect their proteins to be similar too, regardless of whether they are genealogically related or not. However, we can compare the sequences of very basic genes that are used by all living organisms, such as the cytochrome c gene, which have no influence over specific chimpanzee or human characteristics.
Cytochrome c is an essential and ubiquitous protein found in all organisms, including eukaryotes and bacteria (Voet and Voet 1995, p. 24). The mitochondria of cells contain cytochrome c, where it transports electrons in the fundamental metabolic process of oxidative phosphorylation. The oxygen we breathe is used to generate energy in this process (Voet and Voet 1995, pp. 577-582).
Using a ubiquitous gene such as cytochrome c, there is no reason to assume that two different organisms should have the same protein sequence or even similar protein sequences, unless the two organisms are genealogically related. This is due in part to the functional redundancy of protein sequences and structures. Here, “functional redundancy” indicates that many different protein sequences form the same general structure and perform the same general biological role. Cytochrome c is an extremely functionally redundant protein, because many dissimilar sequences all form cytochrome c electron transport proteins. Functional redundancy need not be exact in terms of performance; some functional cytochrome c sequences may be slightly better at electron transport than others.
Decades of biochemical evidence have shown that many amino acid mutations, especially of surface residues, have only small effects on protein function and on protein structure (Branden and Tooze 1999, Ch. 3; Harris et al. 1956; Lesk 2001, Chs. 5 and 6, pp. 165-228; Li 1997, p. 2; Matthews 1996). A striking example is that of the c-type cytochromes from various bacteria, which have virtually no sequence similarity. Nevertheless, they all fold into the same three-dimensional structure, and they all perform the same biological role (Moore and Pettigrew 1990, pp. 161-223; Ptitsyn 1998).
Even within species, most amino acid mutations are functionally silent. For example, there are at least 250 different amino acid mutations known in human hemoglobin, carried by more than 3% of the world’s population, that have no clinical manifestation in either heterozygotic or homozygotic individuals (Bunn and Forget 1986; Voet and Voet 1995, p. 235). The phenomenon of protein functional redundancy is very general, and is observed in all known proteins and genes.
With this in mind, consider again the molecular sequences of cytochrome c. Cytochrome c is absolutely essential for life - organisms that lack it cannot live. It has been shown that the human cytochrome c protein works in yeast (a unicellular organism) that has had its own native cytochrome c gene deleted, even though yeast cytochrome c differs from human cytochrome c over 40% of the protein (Tanaka et. al 1988a; Tanaka et al. 1988b; Wallace and Tanaka 1994). In fact, the cytochrome c genes from tuna (fish), pigeon (bird), horse (mammal), Drosophila fly (insect), and rat (mammal) all function in yeast that lack their own native yeast cytochrome c (Clements et al. 1989; Hickey et al. 1991; Koshy et al. 1992; Scarpulla and Nye 1986). Furthermore, extensive genetic analysis of cytochrome c has demonstrated that the majority of the protein sequence is unnecessary for its function in vivo (Hampsey et al. 1986; Hampsey et al. 1988). Only about a third of the 100 amino acids in cytochrome c are necessary to specify its function. Most of the amino acids in cytochrome c are hypervariable (i.e. they can be replaced by a large number of functionally similar amino acids) (Dickerson and Timkovich 1975). Importantly, Hubert Yockey has done a careful study in which he calculated that there are a minimum of 2.3 x 1093 possible functional cytochrome c protein sequences, based on these genetic mutational analyses (Hampsey et al. 1986; Hampsey et al. 1988; Yockey 1992, Ch. 6, p. 254). For perspective, the number 1093 is about one billion times larger than the number of atoms in the visible universe. Thus, functional cytochrome c sequences are virtually unlimited in number, and there is no a priori reason for two different species to have the same, or even mildly similar, cytochrome c protein sequences.
In terms of a scientific statistical analysis, the “null hypothesis” is that the identity of non-essential amino acids in the cytochrome c proteins from human and chimpanzee should be random with respect to one another. However, from the theory of common descent and our standard phylogenetic tree we know that humans and chimpanzees are quite closely related. We therefore predict, in spite of the odds, that human and chimpanzee cytochrome c sequences should be much more similar than, say, human and yeast cytochrome c - simply due to inheritance.
Confirmation:
Humans and chimpanzees have the exact same cytochrome c protein sequence. The “null hypothesis” given above is false. In the absence of common descent, the chance of this occurrence is conservatively less than 10-93 (1 out of 1093). Thus, the high degree of similarity in these proteins is a spectacular corroboration of the theory of common descent. Furthermore, human and chimpanzee cytochrome c proteins differ by ~10 amino acids from all other mammals. The chance of this occurring in the absence of a hereditary mechanism is less than 10-29. The yeast Candida krusei is one of the most distantly related eukaryotic organisms from humans. Candida has 51 amino acid differences from the human sequence. A conservative estimate of this probability is less than 10-25.
