TreeOfLife-jeopardy-2014
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This document contains questions from various categories related to phylogenetics including distances & substitution models, phylogenies, selection, and random processes. It asks about key concepts like p-distance, the Jukes-Cantor model, gene trees, synonymous and non-synonymous substitutions, the Last Universal Common Ancestor (LUCA), bootstrapping, and incomplete lineage sorting. The questions are from a game of Jeopardy! about phylogenetic trees and molecular evolution.
TreeOfLife-jeopardy-2014
- 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?
Editor's Notes
- #2: Created by Educational Technology Network. www.edtechnetwork.com 2009