2Descent with modification At the most abstract level, evolution can be defined asdescent with modification. We have seen how DNAreplication ensures a mostly faithful passing of the genometo progeny. But if this replication were 100% accurate, nomodification whatsoever could occur in asexual species,the variability in sexually reproducing organisms would belimited to the possible recombinations of a fixed number ofalleles.
3Descent with modification However, the variety we see in nature is MUCH greaterthan what could be achieved by recombination alone.Most modifications in the course of evolution are due tocopying errors in the process of DNA replication calledmutations. These copying errors provide the raw materialthat natural selection acts on. Deleterious mutations tendto be eliminated by selection, favorable mutations tend tospread through the population and eventually replace theoriginal (wildtype) allele.
4Descent with modification Many mutations appear to be neither deleterious norfavorable. The change in frequency of individuals thatcarry such neutral mutations is largely determined bygenetic drift.It is not always clear whether a mutation is deleterious,favorable, or neutral. Due to epistatic interactions ofdifferent loci in the genome, a mutation on one locus canconfer a selective advantage when in the company of oneset of alleles and can confer a disadvantage when in thecompany of a different set of alleles.
5Types of mutations For the development of good models of molecular evolution it is useful to distinguish between different typesof mutations. I will make here the major distinctionbetween mutations on a local scale and mutations ona global scale, the former being ones that can be describedby looking at a stretch of a few thousand base pairs, thelatter being ones on the scale of the whole genome. Itshould be pointed out that the distinction is made formodeling purposes only and is clear cut in some andartificial in other cases.
6Mutations on a local scale On a local scale, there are for types of mutations:Point mutationsInsertions of a stretch of DNADeletions of a stretch of DNAInversions of a stretch of DNAIt is often difficult to decide whether a deletion or aninsertion has occurred relative to the genome of a commonancestor. Insertions and deletions are therefore oftenlumped together under the name indels.
7Tandem repeats Another effect of local mutations (most likely due to DNA-slippage or to unequal crossover) is the frequentoccurrence of tandem repeats, where the same fragmentof DNA is repeated in tandem, often many times.Dependent upon the length of the repeated stretch andthe number of repeats, geneticists distinguish satelliteDNA, minisatellites, and microsatellites.
8Point mutationsPoint mutations are the replacement of one nucleotide byanother. We distinguish transitions (the replacement ofone purine by another or one pyrymidine by another) fromtransversions (the replacement of a pyrymidine by a purineor vice versa). Transitions occur much more frequentlythan transversions.
9Point mutationsIf point mutations occur in a coding region, due to thedegeneracy of the genetic code, the mutation may or maynot alter the sequence of amino acids that is being coded.We distinguish between silent or synonymous mutationsand non-synonymous mutation. In the case of the former,a codon for an amino acid is being mutated to anothercodon for the same amino acid (or one STOP codon foranother STOP codon); in the case of the latter, thetranslation of the codon changes.
10Mutations on a global scale On the scale of the whole genome, several types ofmutations are known to have occurred. For our purposes,the most interesting phenomena are gene duplicationsand genome rearrangements.Another important effect of evolution on a global scale isthe existence of highly repetitive non-coding DNAproduced by transposable elements.
11Genome rearrangements Over the course of evolution, many large-scale genomerearrangements are known to have occurred. This involvesuch processes as large-scale inversions and transpositions(often involving the movement of genetic material fromone chromosome to another) as well as linking or breakingup chromosomes.
12Gene duplicationsGene duplication is a process by which two copies of aparental gene get passed on to the progeny. This processleads to several important phenomena. Some genes simplypersist in several copies. Other genes form gene familieswith each gene having somewhat different functions. Inother cases, one copy of the duplicated gene ceases tobe expressed and becomes a pseudogene.
13Orthologous vs paralogous genes In bioinformatics, we often study genes from differentorganisms that have evolved from a common ancestralgene. Such genes are called homologous genes. If thegenes have all evolved from the same copy of theancestral gene since the most recent duplication of thisgene, we speak of orthologous genes, otherwise wespeak of paralogous genes.