Phylogenetic Trees Flashcards
What is represented by the root of the tree?
The common ancestor.
What are represented by the internal nodes?
Hypothetical ancestors.
What are represented by the terminal nodes?
Operational taxonomic units.
What are the 3 main types of phylogenetic tree?
Cladogram, additive tree and ultrametric tree.
What is shown in a cladogram?
Relative ancestry.
What is shown in an additive tree?
It quantifies the amount of change between taxa using branch length.
What is shown in an ultrametric tree?
It quantifies the evolutionary time between taxa. Terminal nodes must be in line if organisms are around at the same time.
What is the benefit of using a rooted tree compared to an unrooted tree?
The root provides an evolutionary time axis which allows the ancestor-descendant relationships to be defined.
What are polytomies?
Unresolved nodes resulting from insufficient resolution.
Define an apomorphy.
A character trait that is different from the form found in the ancestor.
Define a plesiomorphy.
An ancestral character trait.
Define a synapomorphy.
A shared apomorphy in a single taxon.
Define an autapomorphy.
An apomorphy in a single taxon.
Define a homoplasy.
A character trait present in separate lineages.
What is a monophyletic taxa?
A group containing a common ancestor and all its descendants.
What is a paraphyletic taxa?
A group containing a common ancestor but does not contain all its descendants.
What is a polyphyletic taxa?
A group that does not contain the most recent common ancestor of all the members.
What is homoplasy?
A shared character between two or more animals that did not arise from a common ancestor.
What is DNA saturation and why is it a problem?
When multiple substitutions at the same site in a sequence. This can mean the apparent divergence rate is lower than the actual mutation rate.
What are the pros and cons of the clustering tree-building method?
Pros: inexpensive + fast + only a single tree produced.
Cons: can depend on the order sequences are added.
What are the pros and cons of the search tree-building method?
Pros: can evaluate tree quality + can compare how hypotheses fit the data.
Cons: expensive + slow.
What is the maximum parsimony tree-building method?
The programme searches for a tree that requires the least evolutionary changes to explain the differences among the sequences.
What is long branch attraction and how can it be avoided?
Long branches cluster together due to homoplasy, not recent ancestry but can be overcome by adding more taxa.
What is the maximum likelihood tree-building method?
The programme that makes the tree with the most likely evolutionary outcome.
What is an outgroup?
A lineage that falls outside the clade being studied but is closely related to that clade. It roots the tree.
