1. Tree of life
Jeopardy!

2. Distances &
Substitution models
Phylogenies Selection Random
10 10 10 10
10 10 10 10
20 20 20 20
20 20 20 20
30 30 30 30
30 30 30 30
40 40 40 40
40 40 40 40
50 50 50 50
50 50 50 50

3. FINAL QUESTION
This genetic event that occurred before LUCA
made rooting of the tree of life possible
What is a gene duplication?

4. Answer
Question
This is the number of differences
divided by the alignment length
DISTANCES & SUBSTITUTION MODELS
10 POINTS
What is p-distance?

5. Answer
Question
This distribution is used to describe
inhomogeneous substitution rates
DISTANCES & SUBSTITUTION MODELS
10 POINTS
What is Gamma (Γ) distribution?

6. Answer
Question
This term is used about the following nucleotide changes:
A ↔ G and C ↔ T
DISTANCES & SUBSTITUTION MODELS
20 POINTS
What are transitions?

7. Answer
Question
This term is used about changes between
purines and pyrimidines
DISTANCES & SUBSTITUTION MODELS
20 POINTS
What are transversions?

8. Answer
Question
This simple substitution model assumes
equal substitution rates for all nucleotides
DISTANCES & SUBSTITUTION MODELS
30 POINTS
What is Jukes Cantor model?

9. Answer
Question
This substitution model takes transitions/transversions
into account and assumes equal nucleotide frequencies
DISTANCES & SUBSTITUTION MODELS
30 POINTS
What is Kimura (2-parameter) model?

10. Answer
Question
When the Gamma (Γ) shape parameter takes this value,
all the sites have the same substitution rate
DISTANCES & SUBSTITUTION MODELS
40 POINTS
What is infinity?

11. Answer
Question
When the Gamma (Γ) shape parameter is smaller
than this value, many sites are invariable
DISTANCES & SUBSTITUTION MODELS
40 POINTS
What is 1?

12. Answer
Question
This distance measure has the lowest variance
DISTANCES & SUBSTITUTION MODELS
50 POINTS
What is p-distance?

13. Answer
Question
This substitution model takes transitions/transversions into
account and doesn’t assume equal nucleotide frequencies
DISTANCES & SUBSTITUTION MODELS
50 POINTS
What is Tamura-Nei/HKY model?

14. Answer
Question
This is a tree reconstructed from homologous sequences
from different species
PHYLOGENIES
10 POINTS
What is a gene tree?

15. Answer
Question
This is a tree representing the evolutionary history
of a group of species
PHYLOGENIES
10 POINTS
What is a species tree?

16. Answer
Question
This is a group consisting of all the descendants
of a node in a tree
PHYLOGENIES
20 POINTS
What is a monophyletic clade?

17. Answer
Question
This is a tree that shows the position of the MRCA
of all sequences in the leaves
PHYLOGENIES
20 POINTS
What is a rooted tree?

18. Answer
Question
This is the branching pattern of a tree
PHYLOGENIES
30 POINTS
What is a topology?

19. Answer
Question
This distance-based tree reconstruction method
returns a rooted tree
PHYLOGENIES
30 POINTS
What is UPGMA?

20. Answer
Question
This tree reconstruction method uses the idea that
the simplest explanation is the correct one
PHYLOGENIES
40 POINTS
What is Maximum Parsimony?

21. Answer
Question
This distance-based tree reconstruction method
returns an unrooted tree
PHYLOGENIES
40 POINTS
What is Neighbour Joining?

22. Answer
Question
This method uses an outgroup to find the position of
the MRCA of all sequences in the leaves
PHYLOGENIES
50 POINTS
What is 'rooting a tree'?

23. Answer
Question
This statistical tree reconstruction method seeks a tree
that maximizes the probability of observing the data
PHYLOGENIES
50 POINTS
What is Maximum Likelihood?

24. Answer
Question
This substitution doesn’t lead to a change in
the amino acid encoded by the codon in question
SELECTION
10 POINTS
What is a synonymous substitution?

25. Answer
Question
This substitution leads to a change in
the amino acid encoded by the codon in question
SELECTION
10 POINTS
What is a non-synonymous substitution?

26. Answer
Question
These symbols are used to denote the number of
potential synonymous and non-synonymous sites
of a sequence, respectively
SELECTION
20 POINTS
What are S and N?

27. Answer
Question
These symbols are used to denote the observed proportion
of synonymous and non-synonymous differences
between two sequences, respectively
SELECTION
20 POINTS
What are pS and pN?

28. Answer
Question
These symbols are used to denote the number of
synonymous / non-synonymous substitutions per
synonymous / non-synonymous site, respectively
SELECTION
30 POINTS
What are dS and dN?

29. Answer
Question
This type of evolution has a dN/dS ratio = 1
SELECTION
30 POINTS
What is neutral evolution?

30. Answer
Question
This type of evolution has a dN/dS ratio > 1
SELECTION
40 POINTS
What is positive selection?

31. Answer
Question
This type of evolution has a dN/dS ratio < 1
SELECTION
40 POINTS
What is purifying selection?

32. Answer
Question
This method for calculating dN and dS
assumes random nucleotide substitutions
SELECTION
50 POINTS
What is Nei-Gojobori method?

33. Answer
Question
This method for calculating dN and dS
takes the transition/transversion ratio (R) into account
SELECTION
50 POINTS
What is modified Nei-Gojobori method?

34. Answer
Question
This is the most recent common ancestor of all life
RANDOM
10 POINTS
What is LUCA (Last Universal Common Ancestor)?

35. Answer
Question
This footwear sounding method calculates
branch support for a given tree
RANDOM
10 POINTS
What is bootstrapping?

36. Answer
Question
These are genes whose ancestral sequence was split
by a speciation event
RANDOM
20 POINTS
What are orthologous genes?

37. Answer
Question
These are genes whose ancestral sequence was split
by a duplication event
RANDOM
20 POINTS
What are paralogous genes?

38. Answer
Question
This is the hypothesis that substitution is
approximately constant over evolutionary time
RANDOM
30 POINTS
What is molecular clock?

39. Answer
Question
This method re-samples the columns in an alignment,
for calculating variances
RANDOM
30 POINTS
What is bootstrapping?

40. Answer
Question
This is a way to compare non-nested models,
using their corresponding maximum likelihoods
and number of free parameters
RANDOM
40 POINTS
What is AIC/BIC?

41. Answer
Question
This is the hypothesis necessary for estimating
speciation times from trees
RANDOM
40 POINTS
What is molecular clock?

42. Answer
Question
This is a reason why gene trees may differ from
the underlying species tree
RANDOM
50 POINTS
What is incomplete lineage sorting?

43. Answer
Question
This is a way to compare two nested models,
using their corresponding maximum likelihoods
and number of free parameters
RANDOM
50 POINTS
What is likelihood ratio test?