Phenetics Numerical Taxonomy (Phylo Phen)

Question 1

Define Phenetics numerical taxonomy

Answer 1

Method that does not account for ancesteral and derived K states into account, and does not attemp to reconstruct evolutionary relationships. Only goal is to produce groups based on number of shared K states, quantify similaritues between taxa and utalize similarity indices as equivilency to distance between taxa to produce a phenogram.

Question 2

What is a phenogram?

Answer 2

A tree like network that expresses phenetic relationships.

Question 3

What character data does phenetics use?

Answer 3

molecular and morphological charecters based on morphometry with (idealy) continous variables, but can include binary, multistate qualitive traits.

Question 4

Name four Analytical Approcahes within phenetics.

Answer 4

Cluster analysis –>similarity matrix

Principal component analysis –> original data set

Principal coordinate analysis (converts data on distances)–> dissimilarity matrix ( allows mixed data type)

Canonical variate analysis ( AKA one way multivariate analysis) —> original data set

Question 5

Phenograms represent what, but not what?

Answer 5

Phenograms represnet similarity between taxa but not relationships.

Question 6

Phenetics vs cladistics; explain the difference by comparing taxa a, b, c, and ancestor.

Answer 6

Question 7

Briefly describe how you would construct a phenogram using molecular data.

Answer 7

Question 8

What is UPGMA?

Answer 8

Unweighted Pair Group Method using Average.

Method used to create a tree (phenogram) that shows the relationships between taxa based on their average similarities, assuming a constant rate of evolution.

Question 9

What is the neighbor-joining method?

Answer 9

The Neighbor-Joining method starts with a distance matrix showing differences between organisms and begins with a simple star-like tree (unresolved tree). ​ It iteratively adjusts the tree to minimize the total branch lengths, finding the best arrangement of organisms. ​ The process continues until a fully resolved tree is created, showing the relationships and branch lengths between all organisms. ​uses topology

Question 10

In terms of the neighbor-joining method, define topology

Answer 10

A star network

Question 11

How do you construct a phenogram? (four steps)

Answer 11

1. Establish K/matrix
2. establish distance matrix (matrix of diff between each pair of taxa)
3. use calc algorithin (UPGMA, Neighbor-joining…)
4. Results: Phenogram (more K state taxa share, more morphologically close).

Question 12

Describe the Index of Dissimilarity using taxa A, B, and C and reconstruct graphically.

Answer 12

• Difference between A and B (A/B) = 0.7
• Difference between A and C (A/c)= 0.4
• Difference between B and C (B/C) = 0.9
• A and C share the highest number of similarities
• (A/C )= 0.4 => 0.4/2 = 0.2
• Then, (A/B) = 0.7 and (B/C) = 0.9
• What is the distance between A and (B,C)?
• Average distance of (A/B) and (B/C): (0.7 + 0.9)/2 = 0.8 and 0.8/2=0.4