Lecture 12 - 13 Flashcards Preview

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Flashcards in Lecture 12 - 13 Deck (27):
1

What is the root of a tree?

1 unique internal node that is the ancestor of all the sequences

2

What 2 types of data can be used in phylogenetic inference?

  • Character-based methods: Use aligned character (protein/DNA) directly during construction
  • Distance-based methods: Transform sequence into pairwise distances (dissimilarities) then use the matrix for construction

3

What is a tree?

A mathematical structure which represents a model of an actual evolutionary histiry of a group of sequences or organisms; ie an evolutionary hypothesis

3

What do internal nodes of a tree represent?

Hypothetical ancestors

4

Give 3 features of bootstrapping

  • Refers to distance method
  • Re-sample from original site
  • Repeat original analysis on each pseudoreplicate data set

5

What is the main step in the Neighbour Joining method?

At each step, each pair of possible neighbours are considered and the one producing the shortest tree is chosen

5

Give 2 strengths and 3 weaknesses of distance methods

Strengths:

  • Computationally simple and quick
  • Distance correction (Implies a model of evolution)

Weaknesses:

  • No insight about actual evolutionary changes
  • UPGMA (Not NJ) assumes molecular clock
  • For longer timescales distnces are non-linear and require correction

6

What is an additive tree?

A cladogram with branch lengths; also called phylograms and metric trees

7

What are the features of a tree when it is altrometric?

OTUs are equal distances from the root

9

What is the problem with numerical taxinomy?

Not entirely objective

10

What do terminal nodes represent?

Sequences or organisms for which there is data; typically called an Operational Taxonomical Unit (OTU)

10

What is an ultrametric tree?

A special kind of additive tree where the tips (OTUs) are all equidistant from the root

11

What is the fundamental step in the UPGMA method?

  • Choose the most similar pair
  • Cluster them together (Half the resulting value is attributed to the branch length)
  • Calculate the new distance matrix

13

What is a cladogram?

A tree showing relative order of common ancestry

14

What is included in the character-based method for tree construction?

  • The state of a specific (aa/nt) is considered
  • A tree that minimizes number of changes required to explain the data is chosen (maximum parisomy, minimum evolution)

15

What does a tree consist of?

Nodes connected by branches

16

Maximum parisomy is an example of what?

  • Occam's razor: simplest hypotheses are preferable to more complicated ones
  • ie finding a tree that requires the smallest number of evolutionary changes among the sequences

17

What assumptionabout speciation is made in tree construction?

That it is a rare event, occuring only once at a node,, generating only two branches (bifurcating) as opposed to multifurcating where there is polytomy at the node

17

Give 3 advantages of maximum parisomy

Advantages:

  • Doesn't reduce sequence information to a single number (might give info on specific changes in protein/regulatory sequence)
  • Tries to provide information on ancestral sequences
  • Evaluates different trees

19

What is an advantage of the UPGMA method?

It identifies the root of the tree

20

When phylogonies are used as analytical frameworks, what 3 things can be learned from character analysis?

  • When specific episodes of positive Darwinian selection occured during history
  • The genetic changes which are unique to human lineage
  • Likely geographical location of the common ancestor of African apes and Humans

21

What is a network?

More thanone path between any pair of nodes

22

List 3 things that can be inferred from phylogenetic trees built from DNA or protein sequence data

  • Species that are the closest living relative to humans
  • Forensics (Florida Dentist)
  • Origins of specific transposable elements

24

What is included in the distance method for tree construction?

  • Evolutionary distances are computed for all pairs of sequences (bases on number of substitutions)
  • The tree is based on a relationship among distances (ie UPGMA, Neighbour-joining)

25

What are neighbours?

When OTUs are connected through a single internal node

26

When does the UPGMA method fail?

When the rates of evolution are not constant; shown by distances between roots and OTUs varying; Neighbour joining usually gets the right tree

27

Give 4 disadvantages of maximum parisomy

Disadvantages:

  • Computationally expensive (exact searches increasinly impractical due to rapid increase in taxa)
  • Doesn't correct for multiple mutations (doesn't imply evolution model)
  • Evolution is not necessarily parasimonious
  • Doesn't provide onformation on branch lengths