1. Introduction to Molecular Phylogenetics
Xuhua Xia

2. Convergent Evolution
Placental mammals
Marsupials
Slide 2

3. The Story of the German Farmer
The elder son of the
German Farmer:
Strong and Robust
Immunological &
Electrophoretic
Diagnosis
German Farmer:
Strong and Robust
The younger son of the
German Farmer:
Weak and unmanly
Slide 3

4. Branching pattern & Branching time
Colugos (flying lemurs): the Closest Living Relative of Primates
Janecka, JE et al Science 318:792
Slide 4

5. Origin of organelles chloroplast How do you interpret the
Dot = divergence point of
a-proteobacterial and mitochondrial
lineages
chloroplast
How do you interpret the
data in this figure?
Phylogenetic tree based on
SSU ribosomal RNA data
Gray PNAS 86: 2267, 1989
mitochondrial
Slide 5

6. Associate structure with function
Compare parts lists
Two watches from same maker: one with date, other without
Reveals parts likely to function in date mechanism
To identify an adaptive trait, imagine comparing two very similar watches made by the same manufacturer, one shows the date, while the other doesn’t. Comparison of the parts lists of these two watches would then focus on the parts found in the watch with the date display that are missing from the watch without the date display. These parts are likely to play critical roles in the date mechanism.
Slide 6

7. Shigella and Escherichia
Shigella species causes shigellosis, whereas strains of Escherichia coli are generally avirulent.
What is responsible for the difference?
Genomic differences between Shigella species and different E. coli strains are not greater than those between different E. coli species, i.e., a Shigella genome could be mistaken for an E. coli genome
Each of the Shigella genomes includes a virulence plasmid.
Some E. coli strains cause shigellosis-like diseases. They also contain essentially the same plasmid.
These strains become avirulent when the plasmid is taken away
An originally avirulent strain becomes virulent after acquiring the plasmid
Sansonetti et al Plasmid-mediated invasiveness of "Shigella-like" Escherichia coli. Ann Microbiol (Paris). 133(3):351-5.
Slide 7

8. Why a systems biology perspective?
No aphorism is more frequently repeated in connection with field trials, than that we must ask Nature few questions, or ideally, one question at a time. The writer is convinced that this view is wholly mistaken. Nature, he suggests, will respond to a logical and carefully thought-out questionnaire; indeed, if we ask her a single question, she will often refuse to answer until some other topic has been discussed.
... in his correct but somewhat awkward English: “”. In short, you should consider everything that is relevant.
Of course his statement did not come out of a vacuum. At that time, a lot of data involving unbalanced experimental designs and multi-factor interactions have accumulated, and one is prone to draw wrong conclusions if one does not use balanced factorial designs and does not think broadly and critically. Here is one real data set to illustrate this point – Simpson’s paradox.
--Ronald A. Fisher (1926). Journal of the Ministry of Agriculture of Great Britain 33: 503–513

9. Simpson’s paradox Treatment A Treatment B Small Stones 93% (81/87)
87% (234/270)
Large Stones
73% (192/263)
69% (55/80)
Pooled
78% (273/350)
83% (289/350)
C. R. Charig et al Br Med J (Clin Res Ed) 292 (6524): 879–882
Treatment A: all open procedures
Treatment B: percutaneous nephrolithotomy
Question: which treatment is better?
This example is from a study of the efficacy of two treatment for kidney stones. (pointing to the first cell). Here 87 is the total number of patients in this category and 81 is the number of successes. 93% is the percentage of the success in each group. As we can see clearly, treatment A is more efficacious than treatment B in both “Small stones” group and the “Large Stones” group. However, if we pool these two groups together, we see that treatment B has greater success rate than treatment B. We thus would draw a wrong conclusion if we fail to consider the confounding effect of stone size.
But can we now conclude that treatment A is better than treatment B? Such a conclusion would be highly significant because it can guide us in our choice of the treatment if we happen to have a kidney stone. Unfortunately, we cannot draw this conclusion because the success rate of both treatments changes over time. We can only say that treatment A is better than treatment B at the time of data collection and cannot provide us any guidance today. Such a conclusion, albeit scientifically correct, seems quite useless and trivial. You see that a correct conclusion is often trivial, and a potentially wrong generalization that treatment A is better than treatment B appears much more significant. So if you want your conclusions to be highly significant, don’t be too correct, because it will then be trivial.

10. Methylation and CpG deficiency
5’-TG-3’ 3’-AC-5’
5’-CG-3’ 3’-GC-5’
5’-CA-3’ 3’-GT-5’
Slide 10

11. Where have all the whales gone?
Facts:
North Atlantic minke whales were not taken for commercial purposes under IWC resolutions since 1986
Fin whales have not been hunted legally since 1986
Hunting of humpback whales has been prohibited since 1966
Birth rate was found to be higher than death rate
Why not more whales?
Illegal hunting?
Forensics
Minke whele (North Atlantic)
Sample #19a
Sample #9
Sample #15
Sample #19b
Humpback whale
Sample #41
Sample #3
Baker & Palumbi 1996
Sample #11
Sample WS4
Fin whale
Slide 11

12. Where have all the turtles gone?
Rookery
Rookery
Rookery
Rookery
Rookery
Sea turtles breed in beaches called rookeries. After breeding, they go back to the ocean to feed. It was believed that as long as sea turtles were abundant in some rookeries, it was alright to kill a large number, or even all turtles, in some other rookeries because these extirpated populations would be replenished by migrant individuals from other rookeries.
Turtles in a number of rookeries were hunted to such an extent that no turtle was seen to breed in these rookeries. People waited for a long time for the rookeries to be colonized by migrant indiduals from other rookeries, but this did not happen.
Adult Feeding Grounds
leatherback turtle swims from Indonesia to Oregan.
Slide 12

13. Conservation of the Green Turtle
(a) Rookeries
demographically
independent
Adult Feeding Grounds
Rookery 1
Rookery 2
Rookery 3
(b) Rookeries
demographically
dependent
Adult Feeding Grounds
From Avise (1994, p 372)
Slide 13

14. Mitochondrial DNA Variation
Ind1
Ind2
Rookery 1
Ind3
Ind4
Ind5
Ind6
Rookery 2
Ind7
Ind8
Ind9
Ind10
Ind11
Ind12
Rookery 3
Ind13
Ind14
Ind15
Ind16
Rookery 4
Ind17
Ind18
(The original data set is far more extensive and complicated)
Slide 14

15. Comparative methods Slide 15 20 25 30 35 40 45 50 55 60 65 70 0.35 0.4
0.45
0.5
0.55
0.6
0.65
0.7
0.75 X Y
Slide 15

16. Lateral gene transfer
“Bacterial speciation is likely to be driven by a high rate of horizontal
transfer, which introduces novel genes, confers beneficial phenotypic
capabilities, and permits the rapid exploitation of competitive environments”.
Ochman Nature 405: 299, 2000
Slide 16

17. Recombination in HIV-1
ZR-VI191 is a recombinant:
Its gap gene clusters it with type G HIV-1
Its env gene clusters it with type A HIV-1
Robertson, D. L., P. M. Sharp, F. E. McCutchan, and B. H. Hahn Recombination in HIV-1. Nature 374:124.
Slide 17

18. Gene duplication and lineage sorting
Chicken, A5
Frog, A2
Alligator, A4
Chicken, A5
Mouse, A3
Alligator, α4
Chicken, α5
Mouse, α3
Fish, A1
Frog, A2
Alligator, A4
Chicken, A5
Mouse, A3
Alligator, α4
Chicken, α5
Mouse, α3
Fish, A1
(a)
(b)
(c)
Chicken, 5
Alligator, A4
Alligator, 4
Mouse, A3
Mouse, 3
Frog, A2
Fish, A1

19. Phylogenetic Methods
There are four categories of phylogenetic methods currently in use:
Distance-based: the shortest tree is the best (minimum-evolution criterion)
Maximum parsimony: the tree with the fewest number of substitution events required to explain the sequence variation is the best
Maximum likelihood: the tree with the largest likelihood is the best tree
Bayesian inference: the tree with the largest posterior probability is the best tree
General assumptions:
Different lineages evolve independently
Different sites evolve independently
Model-based methods:
Distance Methods: Commonly used genetic distances from molecular sequences are all based on substitution models
Maximum Likelihood Methods and Bayesian inference
Non-model-based methods:
Maximum Parsimony Methods: implicitly assume
Molecular sequences evolve slowly with few multiple substitutions at the same site.
The evolutionary rate is relatively constant
The evolutionary process is stationary