Phylogenetic trees Flashcards
What do horizontal and vertical lines represent?
Phylogenetic tree starts at oldest known species of interest - also termed the root
Vertical - splitting of species into unique, distinct virus
Horizontal -
- each different species (leaf) are separate horizontal lines
- length of each line indicates time or represents the number of acquired mutations/ differences. e.g if one species of polio virus has developed more mutations, it will have a longer horizontal line than another polio virus
What is an inner node?
Inner node connects two daughter species with their parent
AKA - when a parent splits into two viral progeny
Inner node split point does not have a name. So we normally refer to the leaves
What is meant by term lineage?
Older parents viruses called ancestors
Younger viral progeny called daughters/ descendants
A group of species where they are all ancestors or descendants of one another, is termed a lineage
Can two different leaves (at tip of phylogenetic tree) belong to same lineage?
No, because two leaves are not ancestors or descendants of one another
Some phylogenetic trees ignore horizontal branch length
What are they called?
What is the benefit?
Cladogram
Useful for showing relative position of nodes in each lineage, mostly for readability purposes
Gives essential information - which viruses are closely related to each other
Cannot infer any information about genetic difference between each leaf
Cladograms show essential information about closely related viruses
What is a clade?
Clade covers an ancestor, and all of its descendants
Cladograms show essential information about closely related viruses
What is a clade?
Clade covers an ancestor, and all of its descendants
How do you interpret a radial phylogenetic tree?
branches are the long radii, moving from centre of tree
arcs are the splits (inner nodes)
In virology, what are phylogenetic trees used to show?
viral genomes - nucleotide sequences
viral proteins - amino acid sequences
Phylogenetic tree presentation is difficult for influenza viruses
Why is this?
Phylogenetic trees usually have one common ancestor
However recombinant viruses may have more than one parent
Most tree-building methods cannot identify a trees root - as viruses are million of years old, may not know the true root
Can produce an unrooted tree - this is not a true phylogenetic tree, as we do not know which node is the anscestor of which
What is a common methods of plotting a unrooted tree?
Mid-point rooting - take the two species with the largest distance of any pair of species, and set the root halfway between them.
longest-branch rooting - find the longest branch in the tree, and set the root at its middle.
outgroup rooting - add a related species (called the outgroup) to an analysis, and set the root at the middle of the branch that connects the outgroup with the rest (which is called the ingroup).
Takes the two species with the largest distance of any pair of species, and set the root halfway between them
