1. Evolutionary Biology Concepts
“What is behind is not important!”-
or is it?
Molecular Evolution
Phylogenetic Inference
2/23/2019
Chuck Staben

2. Change in living organisms via reproduction
Evolution
Change in living organisms
via
reproduction
"Change over time"-Kentucky School Boards
2/23/2019
Chuck Staben

3. Levels of Evolution Species Population Organismal Molecular
gene frequencies
Organismal
genomic
Molecular
2/23/2019
Chuck Staben

4. Branching Descent
Evolutionary Tree
Family Tree
2/23/2019
Chuck Staben

5. FRAMEWORK for INFERENCE
Phylogeny
Branching diagram showing the ancestral relations among species.
“Tree of Life”
History of evolutionary change
FRAMEWORK for INFERENCE
2/23/2019
Chuck Staben

6. Phylogenetic Inference
Mom's hair color?
Which form of reproduction?
2/23/2019
Chuck Staben

7. courtesy, Ms. J. Rae Staben
Mom-Inferred vs Real
“Blonde” Phenotype
Recombination
Male/hair color
Multigenic hair color?
Potential Asexual Propagation
Date of vasectomy?
courtesy, Ms. J. Rae Staben
2/23/2019
Chuck Staben

8. Inferring the Framework
How do we describe phylogenies?
How do we infer phylogenies?
2/23/2019
Chuck Staben

9. DNA Inheritance RNA Protein Function Classical Phylogeny
Molecular Phylogeny
Classical Phylogeny
2/23/2019
Chuck Staben

10. Phylogenetic Trees Sister Taxa Terminal Taxa Node Internode AncestorB C D E F
Terminal Taxa
Internode
Node
Ancestor
Root
2/23/2019
Chuck Staben

11. More Trees Paraphyletic Group Clade Monophyletic Group A B C D E F
2/23/2019
Chuck Staben

12. Trees-3 A B C D E F
Polyphyletic Group
2/23/2019
Chuck Staben

13. Rooted vs Unrooted Trees
Add Root
2/23/2019
Chuck Staben

14. Extinction A B C D E F
2/23/2019
Chuck Staben

15. Speciation Poorly understood Reproductive isolation/divergence
“…the mystery of mysteries…”-Darwin
Reproductive isolation/divergence
2/23/2019
Chuck Staben

16. Population Genetic Forces
Hardy-Weinberg Paradigm
p+q=1
p2 + 2pq + q2 =1
Natural Selection (fitness)
Drift (homozygosity by chance)
much greater in small populations
Mutation/Recombination (variation)
Migration
homogenizes gene pools
2/23/2019
Chuck Staben

17. DNA, protein sequence change
Rate=1 change/6 aa sites per 108 yrs
Rate=0.16 x 10-9 yrs
(normal ~ 1 per 10-9 yrs per site)
2/23/2019
Chuck Staben

18. Multiple Changes/No Change
..CCU AUA GGG..
..CCC AUA GGG..
..CCC AUG GGG..
..CCC AUG GGC..
..CCU AUG GGC..
..CCU AUA GGC..
5 mutations
1 DNA change
0 amino acid changes (net)
Underestimate Evolution
2/23/2019
Chuck Staben

19. Mechanisms of DNA Sequence Change
Neutral Drift vs Natural Selection
For a 1000 base gene, sequences!
Selection
(Jukes)
Neutral
(Kimura)
2/23/2019
Chuck Staben

20. Rate varies Gene-to-Gene
2/23/2019
Chuck Staben

21. Rate varies Site-to-Site
Coding>Silent???
2/23/2019
Chuck Staben

22. Constraints on “Silent” Changes
Codon Biases-translation rates
Transcription elongation rates
polymerase ‘pause’ sites
“Silent” regulatory elements
select for or against presence/absence
Overall genome structure
2/23/2019
Chuck Staben

23. Coding/noncoding can be flexible?
Neutralism in Eukaryotes vs Prokaryotes- “Slightly deleterious mutations” Models
Most non-coding sites
are neutral?
Coding/noncoding can be flexible?
Reconsider evolutionary mechanisms?
2/23/2019
Chuck Staben

24. Evolutionary Genetic Forces
Hardy-Weinberg Paradigm
p+q=1
p2 + 2pq + q2 =1
Natural Selection (fitness)
Drift (homozygosity by chance)
much greater in small populations
Mutation/Recombination (variation)
Migration
homogenizes gene pools
Genome
Recombination?
2/23/2019
Chuck Staben

25. DNA, Protein Similarity
Similarity by common descent
phylogenetic
Similarity by convergence
functional importance
Similarity by chance
random variation not limitless
particular problem in wide divergence
2/23/2019
Chuck Staben

26. Homology-similar by common descent
2/23/2019
Chuck Staben

27. Inferring Trees and Ancestors
CCCAGG
CCCAAG->
CCCAAG
CCCAAA->
CCTAAA
CCTAAA->
CCTAAC
MANY traps, problems
2/23/2019
Chuck Staben

28. Homology, Orthology, Paralogy
Paralogs
Orthologs
2/23/2019
Chuck Staben

29. Paralogy Trap
2/23/2019
Chuck Staben

30. Improper Inference
Man is a mouse,
not a rat!
2/23/2019
Chuck Staben

31. Convergence Globin Common Ancestor Convergence Leghemoglobin 2/23/2019
Chuck Staben

32. Our Goals Infer Phylogeny Phylogenetic inference Optimality criteria
Algorithm
Phylogenetic inference
(interesting ones)
2/23/2019
Chuck Staben

33. Watch Out
“The danger of generating incorrect results is inherently greater in computational phylogenetics than in many other fields of science.”
“…the limiting factor in phylogenetic analysis is not so much in the facility of software applicaition as in the conceptual understanding of what the software is doing with the data.”
2/23/2019
Chuck Staben