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Phylogeny

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  1. Phylogeny

  2. Phylogeny The history of organisms as they change through time

  3. Applications • Phylogenetics is used to assess DNA evidence presented in court cases to inform situations, e.g intentional transmission of HIV or hepatitis C From: EMBL-EBI

  4. Applications • Molecular sequencing technologies and phylogenetic approaches can be used to learn more about a new pathogen outbreak. • This includes finding out about which species the pathogen is related to and subsequently the likely source of transmission. • This can lead to new recommendations for public health policy From: EMBL-EBI

  5. Applications • Phylogenetics now informs the Linnaean classification of new species, i.e. kingdom, phylum, class etc. From: EMBL-EBI

  6. Applications • Conservation: Phylogenetics can help to inform conservation policy when conservation biologists have to make tough decisions about which species they try to prevent from becoming extinct. From: EMBL-EBI

  7. Applications • Many of the algorithms developed for phylogenetics, help in all those fields and many other From: EMBL-EBI

  8. Phylogenetic tree • Understanding a phylogeny is a lot like reading a family tree. • The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendants of that ancestor. • As you move from the root to the tips, you are moving forward in time. From: Berkeley

  9. Phylogenetic tree • When a lineage splits (speciation), it is represented as branching on a phylogeny. • When a speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages. From: Berkeley

  10. Phylogenetic tree • Phylogenies trace patterns of shared ancestry between lineages. Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages. From: Berkeley

  11. Phylogenetic tree • Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineages From: Berkeley

  12. Parsimony/Occam’s razor • The principle of preferring the simpler of two competing theories. • Another way of saying it is that the more assumptions you have to make, the more unlikely an explanation is. • William of Ockham, a Franciscan friar who studied logic in the 14th century, first made this principle well known.

  13. Parsimony/Occam’s razor • Example: A dog owner comes home to the trash can tipped over, and trash is scattered on the floor. There are 2 possible explanations • The dog tipped the trash can over • Someone broke into the house and sorted through the trash can • Since this second explanation needs several assumptions to all be true, it is probably the wrong answer. • Occam's razor tells us that the dog tipped the trash can over, because that is the simplest answer and therefore probably the right one.

  14. Parsimony Approach to Evolutionary Tree Reconstruction • Applies Occam’s razor principle to identify the simplest explanation for the data • Assumes observed differences resulted from the fewest possible mutations/changes • Seeks the tree that yields lowest possible parsimony score - sum of cost of all mutations found in the tree

  15. Example Tree a) is most parsimonious – fewer changes

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