Introduction to Molecular Phylogenetics - PowerPoint Presentation

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Introduction to Molecular Phylogenetics

Xuhua Xiaxxia@uottawa.cahttp://dambe.bio.uottawa.caSlide2

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Convergent Evolution

Placental mammals

MarsupialsSlide3

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German Farmer:

Strong and Robust

The elder son of the

German Farmer:

Strong and Robust

The younger son of the

German Farmer:

Weak and unmanly

Immunological &

Electrophoretic

Diagnosis

The Story of the German FarmerSlide4

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Branching pattern & Branching time

Colugos (flying lemurs): the Closest Living Relative of Primates

Janecka, JE et al. 2007 Science 318:792Slide5

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Gray

PNAS

86: 2267, 1989

Phylogenetic tree based on

SSU ribosomal RNA data

chloroplast

mitochondrial

How do you interpret the

data in this figure?

Dot = divergence point of

a

-proteobacterial and mitochondrial

lineages

Origin of organellesSlide6

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Associate structure with function

Compare parts lists

Two watches from same maker:

one with date, other without

Reveals parts likely to function in date mechanismSlide7

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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 genomeEach 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. 1982. Plasmid-mediated invasiveness of "Shigella-like" Escherichia coli. Ann Microbiol (Paris). 133(3):351-5.Slide8

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.

--Ronald A. Fisher

(1926). Journal of the Ministry of Agriculture of Great Britain 33: 503–513Slide9

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. 1986. Br Med J (Clin Res Ed) 292 (6524): 879–882

Treatment A: all open procedures

Treatment B: percutaneous nephrolithotomy

Question: which treatment is better?Slide10

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Methylation and CpG deficiency

5’-

C

G-3’

3’-G

C

-5’

5’-CA-3’

3’-GT-5’

5’-TG-3’

3’-AC-5’Slide11

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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

Sample #11

Sample WS4

Fin whaleSlide12

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Where have all the turtles gone?

Rookery

Adult Feeding Grounds

Rookery

Rookery

Rookery

Rookery

Rookery

Rookery

Rookery

Rookery

leatherback turtle swims from Indonesia to Oregan.Slide13

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Conservation of the Green Turtle

Rookery

1

Rookery

2

Rookery

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Adult Feeding Grounds

Adult Feeding Grounds

From Avise (1994, p 372)

(

a) Rookeries

demographically

independent

(

b) Rookeries

demographically

dependentSlide14

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Ind1

Ind2

Ind3

Ind4

Ind5

Ind6

Ind7

Ind8

Ind9

Ind10

Ind11

Ind12

Ind13

Ind14

Ind15

Ind16

Ind17

Ind18

Mitochondrial DNA Variation

Rookery 1

Rookery 2

Rookery 3

Rookery 4

(

The original data set is far more extensive and complicated)Slide15

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

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Comparative methodsSlide16

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Ochman

Nature

405: 299, 2000

“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

”.

Lateral gene transferSlide17

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Recombination in HIV-1

Robertson, D. L., P. M. Sharp, F. E. McCutchan, and B. H. Hahn. 1995. Recombination in HIV-1. Nature

374

:124.Slide18

Mouse

,

A3

Alligator

,

A4

Chicken

,

A5

Mouse,



3

Alligator,



4

Chicken,



5

Fish, A1

Frog, A2

Frog, A2

Alligator, A4

Chicken, A5

Mouse, A3

Alligator,

α

4

Chicken,

α

5

Mouse,

α

3

Fish, A1

Frog, A2

Alligator, A4

Chicken, A5

Mouse, A3

Alligator,

α

4

Chicken,

α

5

Mouse,

α

3

Fish, A1

(a)

(b)

(c)

Gene duplication and lineage sortingSlide19

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 treeBayesian inference: the tree with the largest posterior probability is the best treeGeneral assumptions:Different lineages evolve independentlyDifferent sites evolve independentlyModel-based methods:Distance Methods: Commonly used genetic distances from molecular sequences are all based on substitution modelsMaximum Likelihood Methods and Bayesian inferenceNon-model-based methods:Maximum Parsimony Methods: implicitly assumeMolecular sequences evolve slowly with few multiple substitutions at the same site.The evolutionary rate is relatively constantThe evolutionary process is stationary