Molecular Genetics and Primate Evolution

By David Layzell and Graeme Finlay

Background

This paper came out of two lectures run on 14th and 21st August 2010 by Graeme Finlay, Senior Lecturer in Scientific Pathology, University of Auckland, as part of the Continuing Education Programme of the University of Auckland. The lectures were entitled “The Human Genome, Evolution and Creation”. Graeme Finlay, a cancer researcher, has sought to demonstrate how genomic research has provided unprecedented evidence for evolution, and in particular, human evolution. David Layzell is a Biology teacher and coauthor with Meg Bayley of Continuing Biology, a write-on textbook for Year 13 Biology. The authors are Christians who are concerned that some churches teach that Christian belief and evolution are incompatible and that church young people sometimes avoid biology because they are afraid that biological evolution somehow opposes their faith. Both are concerned at the message that Creationists present. In non-professional contexts, the Creationist message sounds convincing, but the evidence introduced below demonstrates the ultimate inadequacy of their claims.

Introduction

Figure 1 below shows the generally accepted view of (simplified) primate classification. Evolutionary biologists accept that this is also a phylogenetic tree – that it shows the pattern of evolution of the primates. Creationists accept the classification on an anatomical basis, but not as a pattern of evolution.

In spite of what is thought about them, Creationists do accept a limited form of natural selection from “kinds”. They have no trouble in accepting that the four kaka species, kea and kakapo have developed by natural selection from a “parrot kind”. “Kind” is undefined, and may be just a species, or something more.

Figure 1. A simplified primate classification



The role of molecular genetics

Molecular genetics provide a powerful tool for analysing the evolutionary relationships of taxonomic groups of organisms such as the primates. It supports the present phylogenetic tree and enables scientists to decide between different pathways when other evidence is lacking or contradictory. The principle is very simple. It relies on mutations (particularly complex mutations that would be expected to arise in unique events) to act as markers of evolutionary descent.

The beauty of this new approach to working out evolutionary relationships is that genetic variants or rare mutations are already used widely for defining relationships of people or of cells. For example, in legal cases where paternity is disputed, panels of variant genetic loci are used to establish the identity of the father. The rigour of the legal system thus recognises the power of genetics to establish family relationships. Criminals have been identified on the basis of shared genetic variants with other family members. In medical genetics, particular mutations are often present in all the cells that comprise a cancer. These shared mutations indicate that all the cancer cells are descended from one delinquent progenitor cell – the cell in which the mutation arose.

Our genome possesses a large number of obvious mutations, many of which are shared by other species. It follows that we and those other species are descended from the unique reproductive cell in which each of these mutations arose. (This does not mean that there was only one progenitor organism alive at the time of the mutation. It simply means that over the vast evolutionary timescales that have elapsed since the mutation, all copies of the chromosome which lacked the mutation have been lost.)

Equivalent gene base sequences in related species are compared. If species A, B and C have an identical mutation at one gene locus that is absent from the locus of related species, then A, B and C share the one common ancestor in which that mutation occurred. On the other hand, if A and B have a sequence at another locus, and C does not have it, then A and B evolved after the lineage that led to species C diverged. This is because the mutation unique to A and B occurred after species C had formed. This is shown in Figure 2 below.

The genes used in evidence

Since structural genes code for proteins, mutations in these genes may well result in non-functional proteins. There are two main types of genetic markers referred to here and they are shown in Table 1 below.



A note on terminology

While High School biology texts refer to the DNA strand complementary to the template strand as the “non-template strand”, University texts and scientific papers use the term “coding strand”. While use of this term might lead High School students to think that mRNA is complementary not to the template strand, but the other one, this is not a problem at higher levels. The coding strand is identical to mRNA except that T’s are substituted for U’s. So it is easy to read the coding strand and use the code table to identify the amino acids, mentally substituting T’s for U’s. We have stuck to the University convention here.

Summary table of all genes referred to in this article

Table 2 summarizes all genes referred to in the article with the references. References are found at the end of the article.

Evidence for the separation of humans from the great apes

It is well known that while humans have 46 chromosomes, the great apes have 48. In particular, while humans have a long number 2 chromosome, chimpanzees, gorillas and orang-utans have two short chromosomes in its place. This is shown in Figure 3 below.



DNA sequencing has shown that in fact the chromosomes 2a and 2b of the great apes have actually joined to form the human chromosome 2.

While both chromosomes 2a and 2b of the great apes naturally have centromeres, chromosome 2 of humans has both a functional centromere, and also a fossil centromere located on the long arm at band 21. The fossil centromere is a relic of the centromere of one of the precursor chromosomes.

Further evidence of chromosome fusion is found in telomeric repeats. These are highly repeated sequences found at the ends of chromosomes. They protect the ends of the chromosome. The telomeric repeat unit is 5’TTAGGG- 3’. Figure 4 below shows a short stretch of telomeric repeat sequences at top left and bottom right (with their complementary opposite strands), somewhat degenerated, but in the middle of the human chromosome 2. These mark the site of the ancient telomeric fusion that formed human chromosome 2. The existence of these head-to-head telomeric sequences indicates that two chimp chromosomes were transformed into the human chromosome 2 by a familiar genetic mechanism, telomeric fusion.

Evidence from eye colour.

It is believed that the characteristic of having blue eyes arose once in human history. In the brown/blue eye colour locus (specifically the promoter of the OCA2 gene), one base separates blue-eyed humans from brown-eyed humans and other mammals in a critical site. This is shown in Figure 5 below. (2)

As can be seen a substitution mutation A . G occurred at base 10. This occurred after the formation of humans, perhaps several thousand years ago. It is believed that all people with blue eyes are descended from the one individual in whom this mutation occurred. This conclusion is based on the fact that blue-eyed people share a common haplotype, an expanse of DNA surrounding the mutation that is relatively homogeneous because it has not be shuffled by recombination.

Separation of humans and chimpanzees from other apes and monkeys

The ACYL3 pseudogene comes from an ancient gene coding for an enzyme. It is found in both pro and eukaryotes, but not in humans and chimpanzees. Amino acid sequences for part of the ACYL3 protein of several primate species are shown in Figure 6 below (3)

In place of tryptophan (symbolised by W, and coded by the base triplet TGG) humans and chimps have a stop codon (indicated by an asterisk, and encoded by TGA). A substitution mutation G . A has occurred to generate the stop codon. (Remember this is the coding strand). This results in termination of the peptide chain. Such a mutation must have occurred after the ancestors of chimps and humans separated from the primate line (because no other species has the mutation), but before humans and chimpanzees parted company (as both species have inherited the same mutation).

Separation of humans and African great apes from the orang-utan (Asian great ape), lesser apes and monkeys

Gaucher’s disease is caused by recessive mutations in the glucocerebrosidase gene on chromosome 1. Lipids accumulate in white blood cells and certain organs like the spleen, liver, kidneys, lungs, brain and bone marrow. Gauchers disease may arise when a section of a glucocerebrosidase pseudogene is pasted into the functional gene. In humans, chimpanzees and gorillas, the pseudogene possesses a deletion of precisely 55 bases. This deletion is not found in the corresponding pseudogene of orang-utans, or in the glucocerebrosidase genes of any other apes or monkeys. This is shown in Figure 7 below. The inference is that his unique mutation occurred in an ancestor of the African Great apes, and all species that now possess it received it by inheritance. (4)

As a second example we consider the ABCC13 pseudogene. (5) The ABC gene family codes for certain proteins that transport molecules across extra- and intracellular membranes. ABCC13 gene coding strand sequences are shown for a number of primates (Figure 8).The deletion of 11 bases occurs in humans and great apes, but not in lesser apes like gibbons, Old World or New World monkeys. This indicates that the unique mutation occurred in an ancestor of humans, chimps and gorillas, and that the species that now possess it received it by inheritance.

Separation of all great apes from lesser apes and monkeys.

Urate oxidase breaks down uric acid (a product of nucleic acid metabolism) into products that are excreted. The urate oxidase gene is non-functional in humans and all the great apes. In these species it is present only as a pseudogene. (6)

Figure 9 shows a segment of base sequences of the urate oxidase gene for some primates. As can be seen in the third codon, a C . T base change has occurred, so that CGA (arg) becomes TGA (stop). The same mutation is present in each of the four great ape species, indicating that they have inherited it for the one ancestor in which it occurred.

Separation of the apes from monkeys

As noted earlier, Alu elements are common in primate genomes and provide good material for elucidating phylogenetic pathways. They multiply to high numbers in their host genomes. Figure 10 shows an Alu insert found in the genomes of all apes and humans but not in Old World or New World Monkeys or prosimians (7). The Alu insert is about 300 bases long. It is bracketed between a duplication of the 12-base target site, (as indicated by shading). Such duplications reflect the mechanism of insertion. This Alu element represents a unique insertion event, that occurred in an ancestor of all ape species.

Separation of humans, apes and Old World monkeys from New World monkeys

The COX8H pseudogene provides evidence of the separation of New World monkeys from Old World monkeys, apes and humans (8). This pseudogene possesses a deletion of 14 base pairs that is found in humans, great apes (for which sequence data are not available) and baboons (which are OWMs), but that does not occur in NWMs or prosimians. Figure 11 shows a fragment of the gene sequence, including the site of the unique deletion. The deletion that is shared precisely by all apes and OWMs subjected to sequence analysis indicates that it occurred in an ancestor of the apes and OWMs, after the lineage leading to NWMs had split off.

Primates, tarsiers, lorises and lemurs

The position of tarsiers has been debated for a century. Regardless how they are classified, it is possible to show where they fit into the Primate order using Alu inserts as markers. Figure 12 below shows that Alu elements C7, C9, C12 & C14 are found in the genomes of anthropoid primates and tarsiers, but not in lorises or lemurs (9). This shows that the anthropoid primates and tarsiers must have evolved from a common ancestor after that common ancestor separated off from the prosimian lorises and lemurs.

Contrary arguments and conclusions

As noted at the beginning in Figure 2, the principle underlying the science described in this paper is that if the same mutation occurs in two related species, it indicates that they have a common ancestor. Creationists will argue that this is not the case. Two possible arguments and their counters are listed below.





We conclude that the development of comparative genomics, especially over the last ten years, is providing unambiguous evidence for the descent of humans and other primates from common ancestors. The study of pseudogenes and jumping genes such as Alu elements has established the evolutionary relationships of all major primate groups. These are empirical findings upon which all people should come to agreement. As such there is no reason why biological evolution should be pitted against belief in God. We regret that controversy has been fomented by groups with a metaphysical axe to grind. There is no reason why the created order should not have an evolutionary history.

David Layzell would like to acknowledge Fred Newton, ex Tauranga Boys’ College, Biology teacher extraordinaire

References

1. Yunis JJ and Prakash O (1982) Science 215, 1525

2. Eiburg H et al (2008) Human Genetics 123, 177

3. ZhuJ et al (2007) PLoS Computational Biology 3, e247

4. Martinez-Arias R et al (2001) Genome Res 11, 1071 and Wafaei JR and Choy FYM (2005) Blood Cell Molec Dis 35, 277

5. Annilo T and Dean M (2004) Genomics 84, 34

6. OdaM et al (2002) Mol Biol Evol 19, 640

7. Mola G et al (2007) J Mol Biol 366, 1055

8. Goldberg A et al (2003) Proc Natl Acad Sci USA 100, 5873

9. Schmitz J et al (2001) Genetics 157, 777

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Category: Four Questions, Human Origins, Scholarly Articles, Science and Evidence, Uncategorized