The genome as a fossil, and the tree of life

Mutations, duplications, and evolutionary pressure

Adaptive evolution

Some genes evolve more quickly than other, for example, some histone genes are highly conserved whereas the immunoglobelin loci are extremely polymorphic. Why the difference? The answer is evolutionary pressure. In the first case evolutionary pressure preserves the adapted condition, a common feature for functionally important genes. In the other case with immunoglobelin, extensive variation in genes indicate that the gene product benefits from exchanging amino acids. Hence, evolutionary pressure works in two ways, either to preserve or to change. In either case evolutionary pressure leads to higher fitness of the organism at present environmental conditions.

The rate of evolutionary pressure can be detected by comparing the rates of silent and non-silent (amino acid changing) nucleotide substitutions in a phylogenetic tree:
• No selection (pressure), then the rate of silent and non-silent substitutions are equal.
• Selection for preserving an adapted gene shows a higher frequency of silent mutations.
• Positive selection induces highly adaptive gene products and shows a higher frequency of non-silent mutations.

A good example of positive selection are found in surface proteins of pathogens. These organisms benefits from changing the three dimensional structure of their surface proteins to avoid recognition by antibodies. In the influenza virus, two of the surface proteins have a very high frequency of non-silent mutations. This is also the case for the envelope protein of HIV 1.

Mutation rate

The mutations in a genome should not be looked at as something bad happening to it. If a bacteria is having a to good proofreading system where no errors occurs, the evolution would stop. A good reliable replication and repair is necessary to maintain a genome, however diversity among the genome lineage will improve the chance of survival of some members of a population if the environment changes. It is the survival a population that carries the genome forward in time.

The mutations in a genome is not evenly distributed, it is predicted that the addition and deletion of nucleotide bases in translated sequences are strongly excluded. But do this occur but the result is then often fatal? Even if addition/deletions are very rare, base substitution are more common. The mutations are not occurring at random, some sites in a gene, called hotspots are mutated more frequently then other locations within the gene. The difference in mutation rate between “hotspot” and “cold spots” is one to two orders of magnitude lower in the cold spots. The mutations at these so cold hotspots are occurring not at random, where some changes are occurring more frequently the others. Throughout the genome transition where pyrimidine are substituted by a pyrimidine is more common then transversions where the opposite is occurring (pyrimidine is changed to a pyrine).

The mutation rate are fairly constant when looking at the whole genome of different organisms and between prokaryotes, eukaryots and viruses when looking at the rate are expressed per cell division is roughly 0.01. However, when looking at the rate per sexual generation the rate varies highly.

Gene Duplication

Duplication of genetic material is an important mechanism for evolution of new genetic functions and expression patterns. Genes can be duplicated one by one, a whole chromosome and sometimes the whole genome (polyploidization). The following three alternative courses have been suggested for a duplicate gene pair:
• Nonfunctionalization, when one of the genes becomes silenced.
• Neofunctionalization, one copy acquires a new function.
• Subfunctionalization, both genes degenerate so that they together do the job of the original gene.

Given this it is interesting to know how often genes are duplicated and also how often duplication leads to a loss or a change in gene function respectively.

Some researchers have looked at number of duplicate genes retained a long time after a polyploidization event. These studies have estimated between 50-92% of the duplicates are lost. A more recent study by Lynch and Conery (2000) argue these studies are likely to be underestimates. They studied three whole and three partial genomes identifying duplicate genes and analysing the number of synonymous and nonsynonymous substitutions between the pairs. They estimated the half-life of duplicated genes to be 3 to 7 million years. Moreover, they concluded gene duplication to be very frequent. In the order of 10e-3 to 10e-2 duplications per gene over one million years. This is in the same order as the mutation rate per nucleotide site.