Topic 15: Phylogenies Flashcards
What are phylogenetic systematics, phylogeny, and phylogenetic trees?
Phylogenetic systematics: study of evolutionary relationships between organisms
Phylogeny: evolutionary history of a group of organisms
Phylogenetic tree: used interchangeably with phylogeny, a branching diagram depicting the ancestor-descendent relationships among a group of organisms
What is a node? What is bifurcating or multifurcating?
A point at which a branch splits into two or more branches, they represent a hypothetical or real ancestor.
Bifurcating is when it splits into two and multifurcating is when it splits into more than 2 (polytomy)
Tips represent extant (living) taxa or OTU (operational taxonomic units)
What is a branch and a branching pattern?
Branch: a line depicting the ancestor-descendent relationship between two nodes
Branching pattern: topology or cladogram
Branch length can be used to represent number of changes that occured in that branch.
WHat is the difference between a rooted and an unrooted tree?
Rooted: a tree in which the direction of evolution through time is implied (required knowledge of ancestral state)
Unrooted trees: trees which indicate relationships among taxa, but with no directionality
What is rooting an unrooted tree like?
It is essentially picking a branch and pulling up by some point.
TRUE or FALSE
There are always more unrooted than rooted topologies for any given number of taxa
FALSE
There are more rooted than unrooted
To properly root a tree, what is necessary?
We need to know the common ancestor of the group of interest, and this requires an outgroup
Outgroup: taxon or group of taxa that are closely related to our group of interest but known not to belong to the group
What are characters?
Anything that can be assessed in the taxa
DNA sequences, morphological traits, behavioural traits
What are the three character classifications?
Invariant: character that is the same state in all taxa, NOT USEFUL
Uninformative: character that is variable in state but does not confer any phylogenetic or grouping information, one state may be shared by many taxa but no other state is present in more than one taxa
Informative: a character that has a minimum of two states where each state is shared by at least two taxa
What are cladistics? What are phenetics?
Cladistics: trees constructed on the basis of shared evolved characters (Max parsimony, max likelihood, Bayesian)
Phenetics: trees constructed on the basis of similarity, distance-based methods (UPGMA, and neighbour joining)
What is a clade?
The set of taxa/OTU derived from a common ancestor, includes all taxa descendent from a particular node but no other taxa (monophyletic)
Extant taxa in a clade,always form a monophyletic group
What is maximum parsimony? What are the three steps to finding the most parsimonious tree?
All things being equal, the simplest explanation is the best
- Construct every possible (unrooted) tree
- For each possible tree, count the # of changes required for each character and sum over all characters
- Select the best tree by choosing the tree with the fewest changes
How do you find the tree score on a maximum parsimony tree?
Character mapping (set theory )
What is set theory?
A set is a collection of elements
S= {A,C,G} is a set of three elements
The null set (circle with line through it) is the set containing no elements
The intersection between sets (upside down U) is the elements contained in both sets
The union (U) of both sets is all the elements in both sets, with doubles counted once
First move from tips to root and label with either the intersection or the union of them.
What is an apomorphy/ synapomorphy/ plesiomorphy/ symplesiomorphy?
Apomorphy: derived character state (different from ancestor)
Synapomorphy: apomorphy shared between two or more taxa
Plesiomorphy: ancestral character state (usually inferred from the group)
Symplesiomorphy: a shared plesiomorphy
What happens if there is more than one maximum parsimony tree?
They can be combined into a consensus tree. This is a way to illustrate the similarities between the MP trees
How does homoplasy affect a tree? What is it?
Homoplasy is when two or more taxa share a character state not through shared ancestry, but through independent events
May cause issues with character mapping
What are the three mechanisms of homoplasy?
Parallel evolution: both separately evolve the same state
Evolutionary reversal
Convergence
What is maximum likelihood?
Estimates the likelihood of all the character data, given the proposed tree
Likelihood is maximized over all possible topologies/branch lengths/ internal node assignments
Best tree is that in which the data has the highest likelihood of occuring, and branch lengths indicate the number of mutations that have occured on each branch
What is a Bayesian method?
Find the most probable tree based on the likelihood and the incorporation of prior information
Best tree is the most likely, given the data
What is Phenetics?
The study of relationships among a group of organisms, on the basis of the degree of similarity which may be molecular, phenotypic or anatomical.
Distinct from using character states in cladistic methods
Generally use genetic distances as the information for building trees
What is UPGMA? What are the steps?
Unweighted pair-group method with arithmetic mean, given a matrix of genetic distances between taxa
- Identify from among all OTU’s, which two are most similar (smallest distance apart
- Create a new node by joining the two most similar OTU’s with equal branch length to each terminal node
- Treat the two grouped OTU’s as a single OTU and calculate a new distance matrix
- Repeat steps 1-3 with the new genetic matrix
What are the two types of UPGMA ties? How do you deal with them?
When two or more pairs of taxa are the same genetic distance apart.
1. If one species is included in more than one of the shortest clades START TWO TREES
2. If both of the shortest clades contain completely different taxa sets CREATE MULTIPLE UNATTACHED CLADES FOR THE SAME TREE
What is entailed in neighbour joining?
Start with a star phylogeny, and minimize the total distance when each pair is pulled out.
This pair that is then joined together to form a new node and the procedure is repeated
What are the two methods to assess the statistical significance of a tree?
Consensus (complete and majority rule) as well as bootstrapping
What is involved in consensus trees?
Often there are more than one equally good trees, and a consensus tree combines a number of different possible trees to provide a summary of the information
Objective of making this tree is usually to identify groups that are monophyletic in all of the possible trees
What is monophyletic, paraphyletic and polyphyletic?
Monophyletic: a group that contains the most recent common ancestor and ALL descendents
Paraphyletic: group that contains most recent common ancestor and NOT ALL DESCENDENTS
Polyphyletic: group that does NOT contain the most recent common ancestor
What is the difference between a strict consensus tree and a majority rule consensus tree?
STRICT: only the taxa that are monophyletic in ALL trees are grouped together
MAJORITY RULE: only the taxa that are grouped together greater than 50% of the time are grouped together
What is involved in bootstrapping?
Re-sample original data set with replacement to construct a series of replicates of the same size as the original data set (characters)
Each replicate analyzed like the OG
Variation among replicates indicates the confidence we have in the result from the original dataset
Each replicate data set is subjected to parsimony analysis and one most parsimonious tree is maintained
Finally, majority rule consensus tree is constructed for all replicate trees, if a group appears in X percent of bootstrap trees, then the confidence we have with that group is X
