GENETIC DISTANCES, DISTANCE-BASED PHYLOGENIES AND PHYLOGENETIC TREE CONSTRUCTION

Question 1

Genetic Distances

Answer 1

amount of dissimilarity between pairs of sequences.

Question 2

Phylogenies

Answer 2

It is the evolution of a genetically related group of organisms as distinguished from the development of the individual organism.

Question 3

Phylogenetic Tree

Answer 3

diagram that represents evolutionary relationships among organisms.

Question 4

Categories in building a phylogentic tree

Answer 4

1. Distance based
2. Character based

Question 5

TYPES OF DISTANCE BASED METHOD

Answer 5

Clustering type

Optimality based

Question 6

CLUSTERING TYPE

Answer 6

Compute tree based on a distance matrix starting from the most similar sequence .

Algorithms used include
•UPGMA – Unweighted Pair Group Method using Arithmetic Average
•NJ – Neighbour Joining

Question 7

NEIGHBOUR JOINING

Answer 7

used for creating phylogenetic (evolutionary) and phenetic (trait-based similarity) trees.

A neighbour joining tree aims to show the minimum amount of evolution needed to explain differences among objects, which makes it a minimum evolution method.

Question 8

PROS AND CONS OF UPGMA

Answer 8

Advantages

It is fast and simple.

Disadvantages

1. It assumes the same evolutionary speed on all lineage.
2. All leaves (terminal nodes) have the same distance from the root.
   In reality the individual branches are very unlikely to have the same mutation rate.

Question 9

PROS AND CONS OF DISTANCE-BASED METHOD.

Answer 9

ADVANTAGES

•Very fast

•Only one tree is derived.

•Topology and branch lenthg are calculated.

•Work with different substitution models of evolution.

Disadvantages

•Not gauranteed to find the best tree

•Dicards the primary character data thus actual sequence information is lost.

•Different sequence can yield the same matrix.

Question 10

Pros And Cons Of Neighbor-joining Trees

Answer 10

Advantages

1.It’s simple and easy to understand.

2.It’s fast and computationally inexpensive compared to other popular methods. It allows the use of an explicit model of evolution.

Disadvantages

•It reduces all sequences information into a single distance value.

•You only get one possible tree.

•Neighbor-joining can sometimes result in negative branch lengths. Note that this does not affect the topology of the tree, just branch lengths.