1 Basic concepts of molecular evolution

The phenotype of living organisms is always a result of the genetic information that they carry and pass on to the next generation and of the interaction with the environment. The genome, carrier of this genetic information, is in most organisms deoxyribonucleic acid (DNA), whereas some viruses have a ribonucleic acid (RNA) genome. Part of the genetic information in DNA is transcribed into RNA, either mRNA, which acts as a template for protein synthesis; rRNA, which together with ribosomal proteins constitutes the protein translation machinery; or tRNA, which offers the encoded amino acid. The genomic DNA also contains elements, such as promotors and enhancers, that orchestrate the proper transcription into RNA. A large part of the genomic DNA of eukaryotes consists of genetic elements, such as introns, alu-repeats, the function of which is still not entirely clear. Proteins, RNA, and to some extent DNA, through their interaction with the environment, constitute the phenotype of an organism. DNA is a double helix in which the two polynucleotide strands are antiparallelly oriented, whereas RNA is a single-stranded polynucleotide. The backbone in each DNA strand consists of deoxyriboses with a phosphodiester linking each 5 ′ carbon with the 3 ′ carbon of the next sugar. In RNA, the sugar moiety is ribose. On each sugar, one of the following four bases is linked to the 1 ′ carbon in DNA