The DNA Evidence for Evolution

February 8, 2009

The strongest pieces of evidence to support the fact of evolution come from studying genes and genomes of organisms.

 

 

 1. Sequence Similarities. DNA sequences of an organism’s genome can be compared to other species genomes to determine how related they are. These sequences consist of a linear chain of four ‘letters’ (known as bases) called A, T, C, & G. The more similar the sequences of these letters are, the more related the species containing those genomes are. These sequence similarities may reflect the similarities in morphology, physiology, biochemistry, behaviours, and many other traits within species; however it is also possible to have very similar DNA sequences and completely different morphological characteristics. After comparing genome sequences of many species, a phylogenetic tree is constructed, which is a tree that shows relationships between species. What is remarkable is that these trees almost always match trees constructed using other markers, including fossils, comparative anatomy, and aspects of molecular biology, thus further illustrating the fact that all living organisms are related.

 

2. Chromosome II. Studying evolution allows scientists to infer relationships using many pieces of evidence. One prediction made by evolution is that humans are related to, and essentially are, apes. To support this claim, there have been many fossil discoveries, molecular and physiological studies, and anatomical comparisons, that all point towards relatedness, but the most important and reliable way to test it is to look at the DNA of these organisms. Right away, we notice something strange; human genomes consist of 46 chromosomes, 23 from each parental genome. However, chimpanzees, gorillas, and orangutans, our three closest living (ape) relatives, all contain 48 chromosomes, 24 from each parent. It seems as if humans have lost a pair somewhere along their evolutionary path. However, losing a pair of chromosomes is not an option for any organism, and would prove to be lethal. If one were to build a computer from a manual containing 24 chapters, it would not work if one of the chapters were missing. So how is this paradox resolved? The beauty of science is that extraordinary questions require extraordinary answers, and in this case, we have an strikingly elegant one. By comparing the human and chimpanzee genomes, one observation becomes very apparant. One of the human chromosomes, chromosome 2, happens to be very large. On closer examination and comparison, the chromosome shows a striking resemblance of two chimpanzee chromosomes. In fact, so similar are these chromosomes to the human chromosome 2, that if one is to line them up alongside it, you would find that the banding pattern (the pattern of darkened lines that are visible on each chromosome, which serve as markers for observation) of the chromosomes match perfectly.

 

 

Similar banding patterns and DNA sequences leads scientists to conclude that human chromosome 2 was formed by a fusion between two ancestral ape chromosomes, that are separate in other extant ape species. (Figure taken from http://www.evolutionpages.com/images/hum_ape_chrom_2.gif).

 

 

Human chromosome 2 also reveals remnants of a second centromere (a structure found at the merging point of both ‘arms’ of the chromosome; normally, chromosomes only have a single centromere). These findings can only point to one conclusion; human chromosome 2 was formed by the fusion of two ancestral chromosomes that were once separate in our common ancestor with chimpanzees (it is a fusion of 2 ancestral human chromosomes, rather than a separation of a chimpanzee chromosome, because the other great apes also possess 24 pairs, so it is extremely improbably that a separation event took place in all three species independantly). It is also observable that some of the other human chromosomes are products of ancestral chromosomes that have undergone inversions and translocations themselves, and show massive similarities to chromosomes of other apes which have not undergone these processes. Thus, the fact that we are apes is even more strongly supported by these observations.

 

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An area of a human chromosome has been inverted comparted to its cousin species' counterpart (http://www.plyojump.com/courses/biology/images/chromosome_human_chimp.jpg).

 

 

3. Pseudogenes. These are genes which have become dysfunctional due to changes that have occured in them over time. This could be for several reasons, including random accumulations of mutations in genes which are no longer required by the organism, or genes which do not confer any fitness costs or benefits whatsoever for the individual. Over time, these ancient relics may still remain in genomes, and can provide some clues as to what the ancestors of modern day carriers were like, and what sorts of lifestyles they led. More importantly, they act as genetic fossils that can be used as powerful evidence for evolution, and are as important evidence as vestigial tissues/organs. Two powerful examples of pseudogenes are presented below:

 

–  L-gulono-γ-lactone oxidase (GLO) Pseudogene. One of the most powerful pieces of genomic evidence to support evolution is the L-gulono-γ-lactone oxidase (GLO) gene. GLO is an enzyme which is involved in the synthesis of vitamin C. However, in humans, the gene coding for this enzyme, found on chromosome 8, is dysfunctional, because over time, it has accumulated many mutations which have changed its sequence enough to stop it functioning. Thus, humans cannot synthesize vitamin C and instead have to obtain their requirement from their diet (i.e. consuming fruits such as oranges). So what is so interesting about this? Well, we also know that many other primates, including our closest living relatives, chimpanzees and gorillas, also lack the ability to synthesize vitamin C. When we closely examine the genomes of some of these species, we find that they too also carry a dysfunctional copy of the GLO gene. This is a very interesting find, however, one could put it down to coincidence, albeit an extremely unlikely and improbable one. But what cannot be put down to coincidence is a startling fact about the DNA sequence of this pseudogene in these species: Most of the mutations that have arisen to render this gene dysfunctional have occurred in the same locations in the genes in each of these individual species. The odds for these species independently accumulating the same mutations in the same locations in the gene are astronomical, given the sizes of these genomes and the probability of these mutations occuring and then becoming fixed in the population of each individual species. You would have better odds for winning the lottery at least three times in a row. So how can we explain this observed fact? Only one explanation can do so, perfectly and elegantly, and that is one of common ancestry; since many members of the primate order carry this defective gene with a similar dysfunctional sequence, the only logical deduction one can make is that the common ancestor of all of these species carried this gene, and all of its descendents inherited it. Scientists now estimate the loss of function of the gene in primates to have occurred approximately 70 million years ago. Any other explanations would either require astronomically high odds, or a deceptful designer who wanted to fool us into thinking evolution took place. Both of these are nonsensical, and hence this piece of evidence when examined properly provides powerful evidence for evolution.

 

 

–  Human Olfactory Receptor Genes. Olfactory receptor (Or) genes code for receptors in the nasal epithelium in humans, which give rise to our sense of smell. These receptors bind various odorant molecules, which triggers a signal generated and carried by neurons travelling to the brain. An odour sensation is then perceived by the organism. Human genomes contain approximately 1000 Or genes, forming the largest gene family. However, only around 400 actually work. The remaining 600 are dysfunctional. Why does the human genome contain such a large number of these dysfunctional genes? The answer is simple; they are a relic of our evolutionary past; these genes were once required by ancestors who relied upon their sense of smell more than humans do now. Over time, as the requirement for olfaction decreased, the genes coding for Ors that were not required became dysfunctional.

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4. Endogenous Retroviruses (ERVs). ERVs are retroviruses found in the genomes of organisms, which have been passed down to descendants of infected individuals. A retrovirus (e.g. HIV-1) is a virus which makes a DNA copy of its RNA genome, and randomly inserts it into its host’s genome. The process of making a DNA copy from RNA involves an enzyme called reverse transcriptase, and after the whole process has completed, the copy consists of the virus’s genome (a few genes which mediate replication in the host), and a series of DNA sequences known as long terminal repeats (LTRs), which help the insertion of the viral DNA copy into the host’s genome. These DNA copies can now multiply and generate more and more copies within the host. A retrovirus can infect most cells within the body, but it infects a germline cell (e.g. sperm/egg), the integrated DNA will be passed on to any descendants that the infected individual may have. These retroviruses are dubbed endogenous retroviruses (ERVs). The human genome contains around 100,000 ERVs and around 400,000 associated LTR-like sequences. What is remarkable however is that genome sequencing has revealed that almost every single one of these sequences is shared with our closest living relatives, the chimpanzees. There are only about 100 human-specific and 300 chimpanzee-specific ERVs from the 100,000 odd that we both share! When one considers the fact that these viruses insert themselves randomly into genomes, it is easy to see why the conclusion that both human and chimpanzee lineages independantly accumulated these sequences is extremely improbable! So how else could this observation be explained? By common ancestry. A common ancestor of humans and chimpanzees (who lived between 6-7 million years ago) would have possessed these ERVs in its genome, and hence all of its descendants too would have inherited this collection of ERVs.

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