Phylogenetics Flashcards
Lesson 13
What is a phylogenetic tree?
The mathematical structure used to depict the evolutionary history of a group of organisms or genes
What does phylogenetic trees show?
Shows historical relationships, not similarities
What is systematics?
The discipline that focuses on inferring the phylogenetic relationships of organisms and creating classifications based on their evolutionary histories
What is the hierarchical classification (from broad to specific)?
domain -> kingdom -> phylum -> class -> order -> family -> genus -> species
What is a root?
The oldest point in the tree
What is an internal branch?
Connects two nodes together
What is an external branch?
Connects a tip (taxa) and a node
What is a node?
Represents a branching point from the ancestral population
What is a taxa?
It is a classification unit, representing a set or group of organisms
What is a polytomy?
An internal node of a phylogenetic tree that is linked to three or more subtrees in a rooted tree or 4 or more subtrees in a unrooted tree
What is a bifurcation?
An internal node that has exactly two descendants arising in a rooted tree and 3 descendants in an unrooted tree
What is resolution?
the amount of information we get from sequence comparisons
What does a hash mark mean in a phylogenetic tree?
represents a character shared by the groups to the right of the mark
What is a sister group?
a single ancestral lineage gives rise to two daughter lineages
What is the Newick standard?
((A,B,C), (D,E))
What does the vertical axis mean in trees?
Cladograms: nothing
Chronograms: time
Phylograms: amount of change
What does the horizontal axis mean in trees
nothing!!!
What is the difference between a rooted tree and a unrooted tree?
A rooted tree attempts to identify when various species diverge from a common ancestor
What are homologous characters?
characters present in a group of species due to shared ancestry
What are analogous/homoplastic characters?
characters present in certain species that have evolved independently (convergent evolution)
What are shared ancestral characters?
characters shared beyond a taxon we are trying to define
What are shared derived characters?
evolutionary novelties unique to a particular clade
clade- a monophyletic group
What is the differences between a monophyletic, polyphyletic, and paraphyletic groups?
Monophyly- based on shared derived characters
Paraphyly- based on shared ancestral characters
Polyphyly- based on convergent characters
What are phylogenetic trees made out of, and what are some assumptions that are made?
Built from characters that can be morphological, behavioral, physiological, or molecular
Two assumptions: homologous and evolve independently from each other
