bioinformatics molecular phylogenetics lecture overview.ppt
- 2. A description of how sequences or species are related within families It assumes the objects under investigation are related through evolution The classical approach to phylogeny uses morphological characteristics to study the relationship between species Phenetic Vs Phylogenetic.
- 4. The use of molecular data to establish the relationship between species, organisms or gene families Data can be a variety of characteristics, such as: – Protein sequences – DNA hybridisation – Gene frequencies – Codon usage – DNA sequences – Immunological data – Restriction patterns – Gaps in sequences
- 5. Orthology vs Paralogy Orthologs: the sequences have diverged by speciations E.g. human, mouse and chicken α hemoglobin Paralogs: the sequences have diverged by gene duplication E.g. the α and β hemoglobin genes
- 6. Orthologs –genes in different species that evolved from the same ancestral gene. Paralogs – genes within an organism that have diverged due to gene duplication. So make sure that you are using orthologs, or at least be aware that your data set may contain a mixture of orthologs and paralogs!
- 7. What makes the reconstruction of evolutionary trees difficult, is the same thing that makes alignments difficult: The occurrence of substitutions, insertions and deletions On the other hand, this is also what makes it possible to reconstruct evolution: the differences between species (or sequences) Revisit mutations
- 8. Rooted: The tree reflects the branching pattern (order of evolutionary events) starting from the oldest common ancestor. Unrooted: The tree only shows the evolutionary relationships between the descendants
- 9. You can only reconstruct a rooted tree if there is a constant evolutionary clock present, i.e. if there is little variation between the rates of change in the branches This may not necessarily be true Most algorithms construct unrooted trees
- 10. The Newick (PHYLIP) bracket notation Diags…
- 11. The Goal Find the true evolutionary tree of -species evolution -gene evolution This information can be used to – predict the function of genes and proteins – design or alter protein function – study the origin of life on earth