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 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

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

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

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

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. An evolutionary lineage is a series of organisms, populations, cells, or genes connected by a continuous line of descent from ancestor to descendent.[1][2] Lineages are subsets of the evolutionary tree of life. Lineages are often determined by the techniques of molecular systematics. From: Berkeley

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

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

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

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.

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.

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

Example Tree a) is most parsimonious – fewer changes