phylogenetics

Question 1

phylogenetics

Answer 1

• aims to infer ancestral relationships among sets of species
• requires some representation of uncertainty
• statistical problem
  
  • mathematical and computational techniques involved
• trees

Question 2

phylogenetic trees

Answer 2

• align similar sequences first
• rooted or unrooted
  
  • rooted shows a basal ancestral root
    
    • each node represents most recent common ancestor
    • direction of ancestral relationship implied
  • unrooted shows simialrity without asssuming ancestry
• when n>3, number of unrooted trees always fewer than rooted
• number of possible trees grows rapidly as species number increases

Question 3

distance

Answer 3

• distance between 2 sequences has to fulfil:
  
  • d(i,j) > 0 when i ≠ j
  • d(i,i) = 0
  • d(i,j) = d(j,i)
  • d(i,j) ≤ d(i,k) + d(k,j)

Question 4

UPGMA

Answer 4

• unweighted pair group method
• clustering method using arithmetic averages from a distance matrix
• each species assigned its own cluster
• 2 clusters amalgamated at each stage
  
  • combine minimally separated clusters
  • creates new node
  • continue until 1 cluster remains
• molecular clock tree
  
  • assumes constant evolutionary rate

Question 5

neighbour joining

Answer 5

• agglomerative clustering method
• uses distance matrix
• connect 2 leaves of minimum distance with a new node (leaf)
  
  • new node is common ancestral node
  • connect new node to central node
  • calculate distances and repeat
• recursive algorithm
• difficult when pairs of leaves have identical sequences
  
  • with high numbers of sequences
  • need heursitic method

Question 6

maximum parsimony

Answer 6

• if i and j differ by n nucleotides:
  
  • at least n changes must have occurred since they separated
• find tree that involves the minimum number of evolutionary events to have occurred
• strong assumption that this is the best tree
• invovles evaluating the evolutionary cost of each tree and searching through all possible trees

Question 7

evolutionary models

Answer 7

• probability models that specify either:
  
  • probability of a given sequence
  • probabilities of given mutations
• markov models
• used to calculate likelihood of a tree
• Jukes cantor, kimura

Question 8

jukes cantor

Answer 8

• continous-time markov processes to define transition probability matrix
• assumes equal base frequencies so each row sums to 1
• assumes equal mutation rates
• unrealistic
  
  • time-reversible

Question 9

kimura model

Answer 9

• distinguishes between transition and transversion
  
  • purine to purine and purine to pyrimidine etc
• assumes equal base frequencies

Question 10

phylogenetic footprinting

Answer 10

• using phylogenetic information to estimate how evolutionary rate varies along a sequence
• slowly evolving elements indicate conserved regulatory regions
• involves comparing small numbe rof distantly related species
• shadowing is a variation comparing panels of closely related species