Lecture 33 Flashcards
1
Q
Phylogenetic trees:
A
- Used for many reasons
- Provide a representation of the relationship between species
2
Q
Linnean taxonomy:
A
- Classifying organisms into various ranks: phylum, kingdom, class, order, genus, species
3
Q
Phenetics:
A
- Classifying organisms on how similar they are
4
Q
Cladists:
A
- Classifying organisms on their evolutionary history
5
Q
Molecular phylogenetics:
A
- Protein electrophoresis
- DNA:DNA hybridisation
- Sequences
6
Q
How is phylogeny determined?
A
- Identify homologous characters (derived from a common ancestor)
- We must ensure a good alignment of sequences
7
Q
Terminal branch:
A
- The group of organisms at the end of of a branch
8
Q
Clade:
A
- A group of sequences that share a common internal branch
9
Q
Terminal node:
A
- The point where the line stops (present)
10
Q
Internal node:
A
- The points where the tree branches
11
Q
Root:
A
- Ancestral sequences for all the other taxa
- By asserting a root we are putting a time axis on the tree
- Without a root we just have a topology
- Changing the root can change the interpretation of the topology
- Either assert an out group OR invoke a molecular clock
12
Q
Trees:
A
- Networks without cycles
- Usually bifurcating (splitting into two)
- Occasionally polytomies, or star phylogenies indicatin failures to resolve the nodes into bifurcations
13
Q
Clagogram
A
- Shows which groups are related to each other
14
Q
Ultrametric tree:
A
- Terminal branches line up at the end
- We have a root
- We have a time axis allow determination of divergence points
15
Q
Phylogram:
A
- Branch length is proportional to the number of changes or the distance between different organisms
16
Q
The parsimony principle:
A
- When consider all pssible evolutionary scenarios, the one that takes the fewest steps is most likely to be the real scenario
17
Q
Homoplasy:
A
- You have to invoke multiple changes for a single character on a phlyogenetic tree
18
Q
Small parsimony problem:
A
- For a given tree, what is the minimal number of steps required to explain the data
19
Q
The large parsimony problem:
A
- For a given tree which of all possible trees has the smallest minimum number of steps?
- Increasing number of taxa and increasing number of topologies (2N-5)!
20
Q
Searching tree space:
A
- ‘Branch and bound’
- An exact method will find the shortest trees, some data sets will be too complex for it
21
Q
Heuristics method:
A
- Branch swapping
- Remember the metaphor.. Find the highest point on a map, so walk uphill, if you’re lucky enough you may find the highest point and find the global optimum, but you will more likely walk up a local optimum
22
Q
Tree bisection and reconnection:
A
- All possible bisections and re-attachment points are evaluated
- Cut point is not necessarily the reattachment point
23
Q
Subtree pruning and re-grafting:
A
- All possible subtree removals and re-attachment points are evaluated but the cut point is the re-attachment point
24
Q
Nearest neighbour interchange:
A
- There are two rearrangements per interior branch
25
Does evolution always work in the most parsimonious way?!
- Not sure
- But can form consensus trees to show the majority rule consensus (70% show this branch) or the strict consensus (all trees show this branch)
26
Distance methods:
- Lose info by reducing the data set to the distance matrix
- Compare every sequence to every other sequence and summarise the number of differences as a matrix
- Group the ones together will the smallest differences,
27
Bootstrap approach
- Sample from the original dataset, and generate a pseudo replicate (some characters are represented twice, and some are not represented at all)
- Do this 1000 times, draw a consensus of the pseudo replicates and figure out how often certain ends are grouped together
- A measure of confidence of grouping, below 70% is less confident
- Consensus tree, so branch lengths will be distorted
28
Assumptions:
- Sites evolve independently
| - All changes are equally likely
