Molecular Evolution. Lectures Papers Lab. Dr. Walter Salzburger. Structure of the course: Structure i

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1 Dr. Walter Salzburger Molecular Evolution Herbstsemester 2008 Freitag 13:15-15 Uhr 2 Kreditpunkte Structure i Structure of the course: The Nature of Molecular Evolution Molecules as Documents of Evolutionary History Inferring Molecular Phylogeny! Models of Molecular Evolution The Neutral Theory and Adaptive Evolution Evolutionary Genomics From DNA to Diversity Lectures Papers Lab

2 Structure ii Lectures:! The Nature of Molecular Evolution! Molecules as Documents of Evolutionary History ! Inferring Molecular Phylogeny!!!!!!!! ! Models of Molecular Evolution! The Neutral Theory and Adaptive Evolution! Evolutionary Genomics! From DNA to Diversity ?.?. Structure iii Useful books: Page and Holmes (1998) Molecular Evolution A Phylogenetic Approach, Blackwell Publishing Nei and Kumar (2000) Molecular Evolution and Phylogenetics; Oxford University Press Avise (2004) Molecular Markers, Natural History, and Evolution; Sinauer Carroll, Grenier and Weatherbee (2005) From DNA to Diversity; Blackwell

3 Structure iv Examination: + Written Exam Report Goal v Learning targets: Introduction to the field of Molecular Evolution Key concepts and methods of Molecular Evolution Key players in the field of Molecular Evolution Key papers in Molecular Evolution Milestones in Molecular Evolution

4 Walter Salzburger The Nature of Molecular Evolution A brief history 1 Molecular evolution deals with the process of evolution at the scale of DNA, RNA and proteins

5 A brief history Charles R. Darwin publishes On the origin of species by means of natural selection and establishes the theory of evolution Charles R. Darwin ( ) A brief history Gregor Mendel publishes Experiments in plant hybridization. This paper established what eventually became formalized as the Mendelian laws of inheritance. Gregor Mendel ( )

6 A brief history Gregor Mendel publishes Experiments in plant hybridization. This paper established what eventually became formalized as the Mendelian laws of inheritance. A brief history Johann Friedrich Miescher extracts what comes to be known as DNA from the nuclei of white blood cells. Johann F. Miescher ( )

7 A brief history Independently of one another, Hugo de Vries ( ), Erich von Tschermak-Seysenegg ( ) and Carl Correns ( ) rediscover Mendel s published, but long neglected, paper outlining the basic laws of inheritance. Hugo de Vries Erich v. Tschermack Carl Correns A brief history Theodor Boveri and Walter Sutton propose that chromosomes bear heritary factors in accordance with Mendelian laws. Walter Sutton ( ) Theodor Boveri ( )

8 A brief history Thomas H. Morgan establishes the chromosomal theory of inheritance. He also discovered the recombination of homologous chromosomes during meiosis. Thomas Hunt Morgan ( ) A brief history Oswald T. Avery ( ), Maclyn McCarty ( ) and Colin MacLeod ( ) identify deoxyribonucleic acid (DNA) as the transforming principle. Oswald T. Avery ( )

9 A brief history Erwin Chargaff discovers regularity in proportions of DNA bases. In all organisms he studied, the amount of adenine (A) equaled that of thymine (T), and guanine (G) equaled cytosine (C). Erwin Chargaff ( ) A brief history James Watson and Francis Crick discover the double helical structure of the DNA and that this structure meets the unique requirements for a substance that encodes genetic information. James D. Watson (1928-) Francis H. C. Crick ( )

10 A brief history A brief history Discovery of messenger RNA (mrna) by Sydney Brenner (1927-), Francis Crick ( ), Francois Jacob (1920-) and Jacques Monod ( ).

11 A brief history Discovery of restriction endonucleases by Werner Arber (1929-), Hamilton O. Smith (1931-) and Daniel Nathans ( ). A brief history Frederick Sanger (1918-) and Walter Gilbert (1932) develop techniques for DNA sequencing Walter Gilbert Frederick Sanger

12 A brief history Kary B. Mullis (1944-) invents and helps to develop the polymerase chain reaction (PCR) Kary B. Mullis A brief history ,830,137 bp of Hamophilus influenzae sequenced: the first genome of a free living organisms determined

13 A brief history Caenorhabditis elegans sequenced 2000 Drosophila melanogaster sequenced A brief history Homo sapiens sequenced

14 Genetic Organization Genetic Organization 1 chromosome cell gene protein

15 Genetic Organization 2 desoxyribonucleic acid (DNA) Genetic Organization 3 DNA double helix pyrimidines purines

16 Genetic Organization 4 chromosome cell gene protein Genetic Organization 5 DNA mrna transcription translation protein

17 Genetic Organization 6 transcription Genetic Organization 7 translation

18 Genetic Organization 8 protein structure Genetic Organization 9 The genetic code* *Note that there is not just one universal genetic code!

19 Genetic Organization 10 The degenerated genetic code 4-fold degenerated 2-fold degenerated The Nature of Molecular Evolution

20 The Nature of Molecular Evolution 1 Molecular evolution deals with the process of evolution at the scale of DNA, RNA and proteins The Nature of Molecular Evolution 2! Natural populations show variation at all levels, from gross morphology to DNA sequences. Natural selection can only operate, if heritable variation exists.! Natural variation is generated by two processes: recombination reshuffling of genetic material by introducing or breaking up physical linkage mutation generation of new genetic variation by mistakes during the copying of a DNA strand

21 The Nature of Molecular Evolution 3! New mutations are only transmitted to the next generation, if they occur in germinal tissue! The Nature of Molecular Evolution 4 The primary cause of evolution is the mutational change of genes Nei and Kumar (2000) nucleoide substitution insertion/ deletion gene or genome duplication chromosome rearrangements

22 Nucleotide substitutions synonymous mutation: C > T CCG CTT GTC AAC TAG GLY GLU GLN LEU ILE non-synonymous mutation: A > C original DNA sequence: CCG CTC GTC AAC TAG GLY GLU GLN LEU ILE CCG CTC GTC C AC TAG GLY GLU GLN ILE ILE frameshift mutation: insert C CCG CCT CGT CAA CTA GLY GLY ALA VAL ASP stop mutation: G > A CCG CTC A TC AAC TAG GLY GLU STOP! Nucleotide substitutions TRANSITION TRANSVERSION TRANSVERSION TRANSITION Transition mutations outnumber transversions!

23 Genome duplication Hox gene clusters Swalla (2006) Chromosomal rearrangements A B C D E F G H A B C D E F G H deletion duplication A E F G H A B C D E F G H F G H A B C D E F G H A B C D E N O P Q R inversion A E D C B F G H reciprocal translocation A B C O N E D P Q R