Parsimony Process (Clad Anal 3)

Question 1

Define Exact Algorithms and name/define two types

Answer 1

Algorithim that constructs trees via sequential addition of taxa in all possible positions and calulated tree lenghts with the garantee of finding all shortest trees.

Two types are Exhaustive Search and Branch and Bound
Exhaustive is a straight foreward approach that evaluates all possibilities using a small amount of data, while branch and bound uses tilizes the concept of bounding to prune the search space and avoid unnecessary tree evaluations.

Question 2

Define Heuristic Algorithim

Answer 2

Algorithim that searches the subset of all possible trees. You may find the most parsimonous tree but w/out garantee to find all or any of the most parsimonious. After each taxa is added, neighboring treees are swapped to find shorter tree (BRANCH SWAPPING). Used for large scale data, and is much faster than exact algorithim.

Question 3

Define branch swapping

Answer 3

Branch swapping is a heuristic method used to explore variations of a tree believed to be close to the minimum length. It involves cutting and regrafting branches onto other parts of the tree to find potentially shorter trees, making it more efficient than examining a large number of trees with unknown lengths.

Question 4

In terms of tree lenght, L =

Answer 4

number of steps equivalent to number of
character transformations

remember:

Tree selected at the end of parsimony analysis
exhibiting the minimal length

Several shortest trees may be selected at the end of
parsimony analysis because of homoplasy

Several shortest trees with different topologies or
with different distributions in character states

Must take into account the evolutive and adaptative
context

Question 5

Parsimony Analysis will provide us with …

Answer 5

one shortest tree or
a number of shortest trees of equal length

remember:

MORE homoplasies, the less phylo information is good.

Question 6

What is the consistency Index? describe and provide formula.

Answer 6

It is the minimum possibe # of K changes (steps) divided by the actual # of k changes on current tree. For binary K, the min possible # of k changes is 1. So the CI will vary from one ( no homoplasy) and down towards 0 ( lots of homoplasy)

Question 7

Determine polarity and make the most parsimonious tree

Answer 7

Question 8

Define and explain and formulate the retention Index (RI)

Answer 8

Question 9

complete this table

Answer 9

Question 10

Define a consensus tree. Why do we use it?

Answer 10

a tree containing only clades found in all/most shortes trees. It is used in parsimony analysis to take into account all parsimonious trees.

Question 10

What is a polytomy?

Answer 10

unresolved clades in a consensus tree collapsed down to one node.

Question 11

Define a strict consensus tree and draw example. How are polytomy represented?

Answer 11

Clades supported by all shortest trees.

Question 12

Define a majority rule tree and draw example.

Answer 12

clades supported by >50% of shortest trees.

Question 13

In terms of tree rooting, what are two possibilities for the root?

Answer 13

1. CA (definition of plesiomorphic K)
2. one/several outgroup(s).

Question 14

When rooting with a CA, what are the four points to remember?

Answer 14

1. A is hypothetical
2. K state polarity is defined by the user
3. monophyly of groups are accepted
4. CA must only show plesiomorphic K.

Question 15

When rooting with an outgroup, what are five points to remember?

Answer 15

1. K state of outgroup must polarize k transformations
2. outgroup must be judiciously chosen
3. 1 outgroup = ingroup is monophyletic
4. several outgroups = needed to test monophyletic of ingroup
5. Allows sister group on ungroups

Question 16

Describe, compare and contrast PAUP and PAST

Answer 16

Paup shows shortest trees and evaluates branch strength by calc % of supporting branches.
not good with heuristic algorithms
recommend for serious work

evolution of k along trees
Kstate and status evaluated on each branch
polarity ( a posterior) evaluated and compared with polarity determined ( a prior)

Past packages lacks comprehensive functionality.

Question 17

In placement of phylo trees, fossils are considered…

Answer 17

as terminal taxa (OTU)

Question 18

Run the ‘ What is the sister group of birds’ exercise

Answer 18

Question 19

How do you place fossils on tree? (four pointers)

Answer 19

1. never place @ nodes of tree
2. cannot be ancestors from which have differentiated current species.
3. is not represented as CA
4. remains hypothetical.

Question 20

Step by step, how to you construct a phylogenetic classification with fossils?

Answer 20

1. define phylo problematic ( birds related to dinos?)
2. define ingroup (studied group)
3. chose rooting method (outgroup) and define in (comparisons).
4. define the characters
5. Code/ construct matrix
6. run data matrix with parsimony analysis software.
7. results = cladogram.
8. create phylo classification
9. names given to reliable clades.