Lecture 23 - Phylogenetic's

Question 1

What do taxonomic ranks imply in phylogenetic trees?

Answer 1

They imply a tree structure, e.g., the order Nymphaeales contains families like water lilies.

Question 2

What is a phylogenetic tree?

Answer 2

A hypothesis about evolutionary ancestry reflecting the flow of genetic information through time.

Question 3

What are the main components of a phylogenetic tree?

Answer 3

Direction, branches (edges), nodes (taxa), and clades.

Question 4

What is UPGMA used for?

Answer 4

Clustering taxa based on pairwise distances to build phylogenetic trees.

Question 5

What is the limitation of UPGMA trees?

Answer 5

They might produce incorrect topology due to assuming constant rates of evolution.

Question 6

What is the principle of maximum parsimony?

Answer 6

It minimises the number of evolutionary changes needed to explain data.

Question 7

What issues arise with parsimony-based trees?

Answer 7

Not all changes are equally likely, and tree space is vast.

Question 8

What is maximum likelihood used for?

Answer 8

To find the tree that maximises the probability of the observed sequence data.

Question 9

Why is convergent evolution problematic in phylogenetics?

Answer 9

It causes unrelated species to appear similar, complicating evolutionary inferences.

Question 10

Why is tree space considered vast?

Answer 10

The number of possible trees increases exponentially with the number of taxa.

Question 11

What does the Kimura two-parameter model account for?

Answer 11

It differentiates between transitions and transversions in mutation rates.

Question 12

Why are transitions more frequent than transversions?

Answer 12

They involve changes between similar chemical structures (purines or pyrimidines).

Question 13

What do cladograms represent?

Answer 13

Phylogenetic trees without branch length information.

Question 14

What is the best guess for divergence time in phylogenies?

Answer 14

The average number of mutations observed.

Question 15

Why is substitution modelling critical in phylogenetics?

Answer 15

It predicts the likelihood of sequences given evolutionary processes.

Question 16

How can phylogenetic trees be represented differently?

Answer 16

The orientation of branches around nodes can vary, but the topology remains the same.

Question 17

Why does this variability not affect interpretation?

Answer 17

The evolutionary relationships are preserved regardless of branch orientation.

Question 18

What is the first step in UPGMA clustering?

Answer 18

Identify the pair of taxa with the smallest distance.

Question 19

How does UPGMA build a tree?

Answer 19

By iteratively combining pairs of taxa or groups based on their average distance.

Question 20

What is the significance of Darwin’s “I think” diagram?

Answer 20

It illustrates the branching nature of evolutionary history and shared ancestry.

Question 21

Why are molecular characters preferred over morphological ones?

Answer 21

They are more abundant, objective, and allow for precise distance calculations.

Question 22

Give an example of convergent evolution in animals.

Answer 22

Sharks and dolphins look similar but are distantly related.

Question 23

Why does convergence occur frequently at the molecular level?

Answer 23

Similar environmental pressures lead to the evolution of analogous traits.

Question 24

Why are some mutations not parsimoniously informative?

Answer 24

They occur in only one taxon and do not provide information about shared ancestry.

Question 25

What is a “parsimony-informative site”?

Answer 25

A site with at least two types of nucleotides, each shared by at least two taxa.

Question 26

How does maximum likelihood differ from parsimony?

Answer 26

It accounts for different probabilities of mutation types and branch lengths.

Question 27

Why do molecular sequences often provide better resolution?

Answer 27

They are less subjective and capture evolutionary changes at finer scales.

Question 28

What can phylogenies reveal about species?

Answer 28

Shared ancestry, divergence times, and rates of evolution.

Question 29

Why are branch lengths important in phylogenies?

Answer 29

They represent evolutionary time or the number of changes along a branch.

Question 30

What is the purpose of substitution models?

Answer 30

To estimate the likelihood of observed sequences given evolutionary parameters.

Question 31

Why might UPGMA produce inaccurate phylogenies?

Answer 31

It assumes a constant rate of evolution (molecular clock) across all taxa.

Question 32

Why are transitions more frequent than transversions?

Answer 32

Transitions involve changes within the same nucleotide type (purine to purine or pyrimidine to pyrimidine).

Question 33

How are mutation rates incorporated into phylogenies?

Answer 33

By calibrating branch lengths using fossil records or known divergence times.

Question 34

How is confidence in a phylogenetic tree measured?

Answer 34

By using bootstrap analysis to test the stability of tree topology.

Question 35

What is a “bootstrap value” in phylogenetics?

Answer 35

A measure of support for a given branch, expressed as a percentage.

Question 36

How do cladograms differ from phylograms?

Answer 36

Cladograms show relationships without branch lengths, while phylograms include evolutionary distances.

Question 37

Why is the root of a tree significant?

Answer 37

It represents the most recent common ancestor of all taxa in the tree.

Question 38

How do sister taxa help interpret trees?

Answer 38

They share a more recent common ancestor with each other than with other taxa.