Phylogeny Flashcards
Learn vocabulary and concepts associated with phylogenies
What is a phylogenetic tree
A diagram that depicts the lines of evolutionary descent of different species from a common ancestor
What are terminal taxa?
The branches that occur at the tips of the tree
What are internal nodes?
Nodes within the tree identifying different common ancestors
What is a root node?
The node at the bottom of the phylogenetic tree usually the last common ancestor
What are internal branches?
Branches that occur between internal nodes
Cladogram?
A phylogenetic tree that only shows the ancestral history of the branches
Phylogram?
A phylogenetic tree in which the branch lengths represent the amount of evolutionary divergence
Chronogram?
A phylogenetic tree where the lengths of the branches are based on time (usually has a time scale)
What is a monophyletic group?
A clade that includes the most recent common ancestor and all of its descendants
What is a paraphyletic group?
A monophyletic group that excludes SOME of the descendants
What is a polyphyletic group?
A monophyletic group that excludes the most recent common ancestor
What is a synapomorphy?
A trait that is present in a ancestral species and is shared ONLY with its descendants
What is an ancestral trait?
A trait that comes from a distant common ancestor with that trait
What is a derived trait?
A trait that appears in one branch proabably from mutation
What is convergence?
It is when two separate branches on a tree independently evolve similar traits
What is reversal?
It occurs when a trait appears and disappears again and again on a tree
What is homology?
A similarity due to ancestry between two branches
What is a homoplasy?
A similar structure that has evolved independently in two species
Sister groups?
Two descendants of a speciation event, close relatives
Ingroups?
The group of taxa in a study that is actually being analyzed
Outgroups?
The taxa or group of taxa in a study that is acting as a control and is not being analyzed
What is the relationship between phylogeny and classification?
Phylogeny is a type of classification that includes organizing various groups based on similar/different characteristics
What is a rooted tree?
A tree where one branch corresponds to the common ancestor of all the species included in the tree
What is an unrooted tree?
A tree that portrays relationships among species, but doesn’t depict their common ancestor
What is the parsimony principle?
It states that the best tree is the one that requires the fewest evolutionary changes
What is the maximum likelihood model?
The process of developing a probabilistic model of character evolution and search for the most likely tree under that model (two trees that are both parsimonious)
What are parsimony-uninformative characters?
Character traits that will always have the same number of changes on any tree
What are parsimony-informative characters?
Character traits that vary in number of changes from tree to tree
What is an invariant character?
Parsimony uninformative
Same state in all species CCCC
ZERO CHANGE
What is a transition?
It is a change from purine to purine (A-T)
What is a transversion?
It is a change from purine to pyrimadine (A-G)
What are synonymous substitutions?
They don’t change the phylogenetic relationship (same amino acid)
What are non-synonymous substitutions?
They change the phylogenetic relationship (different amino acid)
What is a polytomy?
Uncertainty in the phylogeny demonstrated by 2+ branches meeting at one node
What is the molecular clock?
States that DNA and protein sequences evolve at a rate that is relatively constant over time
How old a recent common ancestor is based on genetic differences
How do you calculate internal nodes?
N = species
internal nodes = N-1
What are the different phylogenetic applications?
Studying temp and mode of evolution
Coevolution
Biogeography
Community phylogenetics
Conservation biology
How have phylogenies been applied to coevolution?
How and to what extent interacting organisms from different clades evolve together
How have phylogenies been applied to biogeography?
Use phylogenies to infer where taxa originated and history of dispersal to other areas
How can phylogenies be used in conservation biology?
identify previously unsuspected diversity
emphasize conservation of old lineages and/or multiple lineages
What is the best strategy for conservation?
Conserve old lineages
Preserve greatest diversity of lineages
