Phylogenetic basis of systematics Linnaeus: Ordering principle is God. Darwin: Ordering principle is shared descent from common ancestors. Today, systematics is explicitly based on phylogeny.
Natural Selection: Darwin’s four postulates More young are produced each generation than can survive to reproduce. Individuals in a population vary in their characteristics. Some differences among individuals are based on genetic differences. Individuals with favorable characteristics have higher rates of survival and reproduction. Evolution by means of natural selection Presence of ”design-like” features in organisms: Quite often features are there “for a reason”
Real life example: Alignment Insulin from 7 different species Homo:ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAA Pan:ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGTGCTGCTGGCCCTCTGGGGACCTGACCCAGCCTCGGCCTTTGTGAA Sus:ATGGCCCTGTGGACGCGCCTCCTGCCCCTGCTGGCCCTGCTGGCCCTCTGGGCGCCCGCCCCGGCCCAGGCCTTCGTGAA Ovis:ATGGCCCTGTGGACACGCCTGGTGCCCCTGCTGGCCCTGCTGGCACTCTGGGCCCCCGCCCCGGCCCACGCCTTCGTCAA Canis:ATGGCCCTCTGGATGCGCCTCCTGCCCCTGCTGGCCCTGCTGGCCCTCTGGGCGCCCGCGCCCACCCGAGCCTTCGTTAA Mus:ATGGCCCTGTTGGTGCACTTCCTACCCCTGCTGGCCCTGCTTGCCCTCTGGGAGCCCAAACCCACCCAGGCTTTTGTCAA Gallus:ATGGCTCTCTGGATCCGATCACTGCCTCTTCTGGCTCTCCTTGTCTTTTCTGGCCCTGGAACCAGCTATGCAGCTGCCAA
Interpretation of Multiple Alignments Conserved features assumed to be important for functionality For instance: conserved pairs of cysteines indicate possible disulphide bridge
Darwin: all organisms are related through descent with modification Prediction: similar molecules have similar functions in different organisms Protein synthesis carried out by very similar RNA-containing molecular complexes (ribosomes) that are present in all known organisms Sequences are related
Sequences are related, II Related oxygen- binding proteins in humans
Gel electrophoresis DNA fragments are seperated using gel electrophoresis –Typically 1% argarose –Colored with EtBr or ZybrGreen (glows in UV light). –A DNA ”ladder” is used for identification of known DNA lengths. Gel picture: http://www.pharmaceutical-technology.com/projects/roche/images/roche3.jpg PCR setup: http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/gels/agardna.html + -
The Sanger method of DNA sequencing Images: http://www.idtdna.com/support/technical/TechnicalBulletinPDF/DNA_Sequencing.pdf } Terminator X-ray sequenceing gel OH
Automated sequencing The major break-through of sequencing has happended through automation. Fluorescent dyes. Laser based scanning. Capillary electrophoresis Computer based base- calling and assembly. Images: http://www.idtdna.com/support/technical/TechnicalBulletinPDF/DNA_Sequencing.pdf
Handout exercise: ”base-calling” Handout: Chromotogram Groups of 2-3. Tasks: –Identify “difficult” regions –Identify “difficult” sequence stretches. –Try to estimate the best interval to use.
Biological data on computers The GenBank database File formats –FASTA –GenBank
NCBI GenBank GenBank is one of the main internaltional DNA databases. GenBank is hosted by NCBI: National Center for Biotechnology Information. GenBank has exists since 1982. The database is public - no restrictions on the use of the data within.