Lecture 33 Flashcards Preview

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Flashcards in Lecture 33 Deck (28):
1

Phylogenetic trees:

- Used for many reasons
- Provide a representation of the relationship between species

2

Linnean taxonomy:

- Classifying organisms into various ranks: phylum, kingdom, class, order, genus, species

3

Phenetics:

- Classifying organisms on how similar they are

4

Cladists:

- Classifying organisms on their evolutionary history

5

Molecular phylogenetics:

- Protein electrophoresis
- DNA:DNA hybridisation
- Sequences

6

How is phylogeny determined?

- Identify homologous characters (derived from a common ancestor)
- We must ensure a good alignment of sequences

7

Terminal branch:

- The group of organisms at the end of of a branch

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Clade:

- A group of sequences that share a common internal branch

9

Terminal node:

- The point where the line stops (present)

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Internal node:

- The points where the tree branches

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Root:

- 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

Trees:

- Networks without cycles
- Usually bifurcating (splitting into two)
- Occasionally polytomies, or star phylogenies indicatin failures to resolve the nodes into bifurcations

13

Clagogram

- Shows which groups are related to each other

14

Ultrametric tree:

- Terminal branches line up at the end
- We have a root
- We have a time axis allow determination of divergence points

15

Phylogram:

- Branch length is proportional to the number of changes or the distance between different organisms

16

The parsimony principle:

- When consider all pssible evolutionary scenarios, the one that takes the fewest steps is most likely to be the real scenario

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Homoplasy:

- You have to invoke multiple changes for a single character on a phlyogenetic tree

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Small parsimony problem:

- For a given tree, what is the minimal number of steps required to explain the data

19

The large parsimony problem:

- 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

Searching tree space:

- 'Branch and bound'
- An exact method will find the shortest trees, some data sets will be too complex for it

21

Heuristics method:

- 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

Tree bisection and reconnection:

- All possible bisections and re-attachment points are evaluated
- Cut point is not necessarily the reattachment point

23

Subtree pruning and re-grafting:

- All possible subtree removals and re-attachment points are evaluated but the cut point is the re-attachment point

24

Nearest neighbour interchange:

- 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