Phylogenetics

Question 1

What is a phylogeny?

Answer 1

The evolutionary history of a group of species, including when current species and past lineages speciated and the relatedness of extant species and even extinct species.

Question 2

What is a phylogenetic tree?

Answer 2

A graphical representation of a phylogeny.

Question 3

What is a clade?

Answer 3

A monophyletic group = Includes an ancestral taxon and all of its descendants

Question 4

What is the basic logic behind phylogenies?

Answer 4

More closely related taxa should share more traits/characters in common than distantly related taxa.

Question 5

What types of traits can phylogenies be based on?

Answer 5

• Morphology
• Behaviour
• Physiology
• Steps in development of an embryo or juvenile
• Nucleotides in a gene

Question 6

What two traits are most common today for basing phylogenies off of?

Answer 6

Morphology
Nucleotides

Question 7

Why is morphology useful for phylogenies?

Answer 7

especially skeletal morphology is often well-conserved through macroevolution, offering insights into the evolutionary history of group of species

Question 8

Why is DNA helpful to phylogenies?

Answer 8

large amounts of data can be generated
o Each nucleotide is a character
o Provides insight into homology when modeled appropriately

Question 9

For studies on phylogenies, how many species tend to be used?

Answer 9

50+

Question 10

What are the only characters that are useful in estimating phylogenetic trees?

Answer 10

Homologous characters

Question 11

What is a synapomorphy?

Answer 11

A synapomorphy is a homologous trait that represents a shared derived character

Question 12

What are the two reasons for why synapomorphies help to infer phylogenetic trees?

Answer 12

o They identify evolutionary branch points; All species formed after the origin of the synapomorphy share the trait
o Synapomorphies are nested; As you move through time and trace a tree from its root to its tips, each branching event adds one or more shared, derived traits

Question 13

What does identification of the best phylogeny rely on?

Answer 13

relies on finding a method that maximizes groups based on synapomorphies and reduces groups based on homoplasy

Question 14

What is homoplasy?

Answer 14

convergent evolution where two similar characteristics evolve independently

Question 15

Describe maximum parsimony.

Answer 15

• The “best” tree is the one that minimizes the total amount of evolutionary change in the characters
  o Thus, finds the simplest explanation

Question 16

Describe maximum likelihood.

Answer 16

The “best” tree is the one with the highest likelihood at explaining the data given a specific mathematical model that describes the probability that different types of character changes (e.g., nucleotide substitutions) occur

Question 17

What type of data does maximum likelihood usually use?

Answer 17

DNA sequence data

Question 18

How does maximum likelihood estimate lengths of brances?

Answer 18

Estimates lengths of branches according to number of substitutions between nodes

Question 19

Give the equation for determining the likelihood of a tree under maximum likelihood.

Answer 19

L(tree)=P(data|tree, branch lengths, model)

Question 20

Who introduced the Bayesian Markov Chain Monte Carlo method and when?

Answer 20

Thomas Bayes
1763

Question 21

Describe the Bayesian method.

Answer 21

• There is no single best tree
• There are many possible trees with variation in probability in explaining the observed sequence variation, given a statistical model of character evolution and prior assumptions about the values of the model

Question 22

What is the formula for determining the posterior probability of a tree?

Answer 22

P(tree|data)=P(data├tree)*P(tree)/P(data)

Question 23

How are the trees formed under the Bayesian method represented?

Answer 23

Operationally reported as a single tree, and probability of observing each node and corresponding monophyletic grouping of species based on its frequency among the posterior distribution of possible trees

Question 24

Differentiate between maximum likelihood and Bayesian methods.

Answer 24

Likelihood = What is the probability of seeing the observed data (D) given the phylogenetic tree?
Bayesian = What is the probability that the phylogenetic tree is correct given the data (D)?

Question 25

What method is best for determining a phylogenetic tree?

Answer 25

Hotly debated. Bayesian inference is preferred by many, but most purely phylogenetic papers will report results from all methods.

Question 26

Give examples of applications of phylogenetics. (6)

Answer 26

• Defining species
• DNA barcoding
• Classification, taxonomy and nomenclature
• When did events happen in the past?
• Where and how did a virus arise?
• What is the origin of whales?