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Phylogeny

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

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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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