Pseudogenes
Sean D. Pitman M.D.
© March 2002

Pseudogenes are DNA sequences that resemble functional genes but seem to have no purpose. It has beenproposed that similar pseudogenes in different species show a common ancestry. For example, the eta globin pseudogene in humans and chimps has been used as an argument for the common ancestry of the two species.

The first pseudogene was reported in 1977.(1) Since that time, a large number of these genes have been reported and described in humans and many other species. There are two types of pseudogenes: "unprocessed pseudogenes and processed pseudogenes."(2) Processed genes are found on different chromosomes from their functional counterparts. They lack introns and certain regulator genes, are often terminate in adenine series, and are flanked by direct repeats (which are associated with movable genetic elements). They may be complete or incomplete copies of genes or mixtures of several genes. They are believed to have occurred through a 3-step process: Copying DNA into RNA, editing the introns to make mRNA, and then mRNA back into DNA through a reverse transcription process. This process is thought to have created the "L1 family of pseudogenes."(2) Other theories include retroviruses as means of pseudogene transport between different organisms.

Unprocessed pseudogenes are usually found in clusters of similar functional sequences on the same chromosome. They usually have introns and associated regulatory sequences. The expression is usually prevented by a "misplaced" stop codon/codons. There may be other changes from the "original" as the result of deletions, insertions, and point mutations etc. Some form of mRNA may or may not be produced depending on the damage to the gene. These are believed to have arisen by gene duplication, which produced an extra copy of the gene. The extra copy could then accumulate mutations without harming the organism since it would still have a completely functional original copy.(2) (The evolutionary gene duplication hypothesis suggests that over time, random mutations may produce a new gene with new functions by using this gene duplicate while maintaining the original gene funtion5).

It is felt by many, especially evolutionary biologists, that shared pseudogenes, which have no function in any form in different species, are examples of common ancestry. Comparison of DNA sequences from humans, chimps, and other mammals shows a great number of shared pseudogenes. Humans and chimps have many similarities as well which is thought to be evidence of their relatively recent and common ancestry. The best-known example of a shared pseudogene is possibly the eta globin gene.

The eta gene is located on chromosome 11 in humans, fourth in a series of 6 beta globin genes (five are functional).(4) It has no start codon (AUG) and it has several stop codons… so obviously no mRNA is made and therefore no protein. Humans, chimps, and gorillas have the same number of beta globin genes arranged in the same sequence. The sequences of the exons of these genes are also similar… as well as the exons of the eta gene.(4) It is thought that the eta globin gene originated by a duplication of the gamma-A globin gene, because of the high similarity of the sequences. Both genes are present in primates. This pseudogene was thought to originate 140 million years ago in marsupials and placental mammals. After the "evolutionary divergence" of marsupials, the gamma globin gene formed by duplication of an existing gene in the beta globin family. Later, but before radiation of the orders of placental mammals, the eta globin gene formed from a duplication of the gamma globin gene. Gamma and eta genes must therefore have been present in ancestral placentals, but presumably gamma was lost by goats (which do not have gamma) and eta was lost by rabbits (which do not have eta). According to this scenario, the eta gene must have been functional at first, because it is functional in goats today.(2) It is non-functional in all primates, which is interpreted to mean it was already non-functional in ancestral primates 70-80 million years ago. This interpretation implies that the eta globin gene has been maintained for more than 70 million years without being converted to a useful new gene and without being eliminated through random mutations such as the vitamin-c gene must have been eliminated in primates and guinea pigs (who do not even have remnants of this very useful gene). The persistence of a non-functional DNA sequence in an entire lineage for such a supposed long period of time seems remarkable in the context of the gene duplication hypothesis. The very fact that pseudogenes are still present and recognizable after supposed tens of millions of years of nonfunction suggests that they serve some kind of purpose. Otherwise, they should have been removed or altered beyond recognition by the accumulation of mutations.

"The persistence of pseudogenes is in itself evidence for their activity. This is a serious problem for evolution, as it is expected that natural selection would remove this type of DNA if it were useless, since DNA manufactured by the cell is energetically costly. Because of the lack of selective pressure on this neutral DNA, one would expect that ‘old’ pseudogenes would be scrambled beyond recognition as a result of accumulated random mutations. Moreover, a removal mechanism for neutral DNA is now known."(6)

Given this, it is not known if all of what are currently thought of as pseudogenes have absolutely no function. In fact, some pseudogenes are believed to function as sources of information for producing genetic diversity. It is thought that partial pseudogenes are copied into functional genes during genetic recombination, producing variants of the functional gene. This phenomenon has been reported many times to include immunoglobulins of mice and birds, mouse histone genes, horse globin genes, and human beta globin genes. It is not known if this could be a possible role for the eta globin gene as well. However, the fact that the eta globin pseudogene is located between the fetal and adult genes suggests that it could play a role in gene switching… and there seems to be some preliminary evidence to this effect although the eta gene sequence’s part in this is still unknown.

Other pseudogenes and so-called transposons, such as the "Alu element" (once thought to be completely useless), are being found to have important functions.

"There is a growing body of evidence that Alu (a SINE — Short Interspersed Nuclear Element) sequences are involved in gene regulation, such as in enhancing and silencing gene activity, or can act as a receptor-binding site… This is surely a precedent for the functionality of other types of pseudogenes." (6,7)

Around 1998 Carl Schmid, a molecular biologist at the University of California at Davis, started advancing what seemed like a nutty idea to explain Alu’s unusual affinity for genes. Schmid suggested Alu sequences resided near genes because they are not really "junk" sequences, but are rather useful sequences involved with a mechanism that helps cells repair themselves. With the entire genome map in front of them, showing so many instances of Alu sequences around genes, scientists are beginning to take Schmid seriously. "It looks pretty convincing," Francis Collins said. Others such as M.I.T. geneticist Eric Lander agree.(8)

More recently in 2001, a team of molecular geneticists discovered two "hot spots" where the same SINEs inserted independently:

"Vertebrate retrotransposons have been used extensively for phylogenetic analyses and studies of molecular evolution. Information can be obtained from specific inserts either by comparing sequence differences that have accumulated over time in orthologous copies of that insert or by determining the presence or absence of that specific element at a particular site. The presence of specific copies has been deemed to be an essentially homoplasy-free phylogenetic character because the probability of multiple independent insertions into any one site has been believed to be nil. . . . We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry. Although independent insertions at the same locus may be rare, SINE insertions are not homoplasy-free phylogenetic markers."(9)

Another argument is of shared mistakes in pseudogenes, which "must have come from a common ancestor." However, there is some evidence that nucleotide changes may not be random in certain gene locations. Mutational "hotspots" have been identified in many genes as well as pseudogenes. In these locations, point mutations, even specific types of point mutations (i.e. a specific nucleotide pair switch) are much more common than elsewhere in the gene. What makes these hotspots, "hot"? Perhaps the answer is in the chemical nature of the hotspot region? The type of molecular bonds, their stability or instability, or other molecular interactions may lend themselves to specific nucleotide pair switches, especially given certain environmental changes. No one really knows for sure except to say that mutational hot spots do exist. So, given that they do exist, similar genes should be expected to function in similar ways and this includes having similar mutational "hotspots" and/or "shared mistakes."(3) In any case, it is interesting to note that there are no such examples of "shared errors" between mammals and other groups of animals (Although there are plenty of common "errors" that are shared by widely divergent mammalian groups).

"There are no examples of ‘shared errors’ that link mammals to other branches of the genealogic tree of life on earth. . . . Therefore, the evolutionary relationships between distant branches on the evolutionary genealogic tree must rest on other evidence besides ‘shared errors.’" (11)

Of course the argument used to explain this fact is that mammals split off from other groups of animals over 200 million years ago. Given this amount of time, random mutations would have obliterated any trace of common genetic errors.(11) This is a very good point. The question remains however, "Why are some identifiable genetic errors maintained as long as they are if they are in fact functionless?"

So far all proposed "foolproof" genetic markers of common decent have been shown to have significant flaws. The prediction that pseudogenes, transposons (SINEs and LINEs) and other shared mutational mistakes are conclusive evidence for common descent has not held up over recent years. Consider the following excerpt from Hillis:

"What of the claim that the SINE/LINE insertion events are perfect markers of evolution (i.e., they exhibit no homoplasy)? Similar claims have been made for other kinds of data in the past, and in every case examples have been found to refute the claim. For instance, DNA-DNA hybridization data were once purported to be immune from convergence, but many sources of convergence have been discovered for this technique. Structural rearrangements of genomes were thought to be such complex events that convergence was highly unlikely, but now several examples of convergence in genome rearrangements have been discovered. Even simple insertions and deletions within coding regions have been considered to be unlikely to be homoplastic, but numerous examples of convergence and parallelism of these events are now known. Although individual nucleotides and amino acids are widely acknowledged to exhibit homoplasy, some authors have suggested that widespread simultaneous convergence in many nucleotides is virtually impossible. Nonetheless, examples of such convergence have been demonstrated in experimental evolution studies."(10)