jon c. herron, u of wa teaching tree thinking with

Jon C. Herron, U of WA

Teaching tree thinking withforensic applications

Outline1.A famous example

2.A software-based tutorial

3.Additional case studies

•http://faculty.washington.edu/~herronjc

Evolution Meeting © Jon C. Herron 2002

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The Florida dentist

• In 1986 dentist tested positive for HIV; later AIDS.

•Continued general dentistry for 2 years.

•Patient with no risk factors discovered she had HIV

•Dentist publicly urges other patients to take test

•10 of 1100 patients are HIV+

Did the dentist pass HIV to his patients?

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Objectives for students

•Describe the logic of a phylogenetic analysis that would answer the question

•Predict the results if the dentist did/did not infect his patients

•Use UPGMA to analyze small datasets

•Correctly interpret the published phylogeny

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Markham et al. 1998PNAS 95: 12568

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Leitner et al. 1996PNAS 93: 10864

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Dentist

Patient A

Patient BPatient C

Local Control

Local ControlLocal Control

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Dentist

Patient A

Patient B

Patient C

Local Control

Local Control

Local Control

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Dentist

Patient A

Patient B

Patient C

Local Control

Local Control

Local Control

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\

Branch length(number of single-letter

substitutions in thegenetic sequence)

0 5 10 15

Dentist-x

Patient B-x

Patient B-y

Patient A-x

Patient E-x

Patient E-y

Dentist-y

Patient C-x

Patient C-y

Patient A-y

Patient G-x

Patient G-y

LC02-x

LC03-x

LC02-y

LC09

LC35

Patient D-x

Patient D-y

LC03-y

Patient F-x

Patient F-y

HIVELI

Ou et al. 1992. Science 256: 1165

Hillis et al. 1994. Science 264: 671

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A recent issue of the Journal of Medical Virology contained a paper about a German surgeon who handled orthopedic cases in the emergency room. In July of 2000, the surgeon disclosed to his hospital that he was infected with Hepatitis C Virus (HCV). HCV infects the liver, and is spread by contact with the blood of an infected person. Although many infected individuals are asymptomatic, some patients suffer serious liver damage.

Upon learning of the surgeon’s infection, the hospital performed blood tests on 207 of the surgeon’s former patients. Three tested positive for HCV. The question: Did these patients get HCV from the surgeon, or from someone else?

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19650

20

40

60

80

100

120

Gen

etic

div

erge

nce

from

orig

inal

sam

ple

(nuc

leot

ide

sub

stitu

tions

in t

he h

emag

glut

inin

gen

e)

1970 1975 1980 1985 1990Year influenza virus sample was collected

Fitch, et al. 1991PNAS 88: 4270

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A) B) Tree:

C) D) Tree:

E) F) Tree:

6 26 35 2929 29 29

29 2929

B C D EABCD

A B

ABC D E

CD

28.5

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A

BC

D

E

H

G

F

A B

0

0

100

E

100

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\

A) B) Tree:

C) D) Tree:

E) F) Tree:

6 26 35 2929 29 29

29 2929

B C D EABCD

A B

ABC D E

CD

28.5

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Doc

Patient A

Patient B

Control

Control

Control

Control

Control

Control

Control

Control

Cody et al. 2002 Archives of Internal Medicine162: 345

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SIVcpz HIV-1Edward Hooper. 1999. The River.

Oral polio vaccineprepared in cultured

kidney cells fromchimpanzees

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0.10

Sabin-1

CHAT type I Wy4B

M. mulatta (India)

WCh 24CHATpool 13

M. mulatta

CHAT type I Wy4BCHAT pool 23CHAT pool 16

M. fascicularis CHAT pool 23

M. arctoïdes

CHAT pool 13

M. mulatta (Myanmar)

C. cephus

C. nictitansC. torquatus

C. atys

C. a. sabaeusC. a. sabaeus

E. patas

C. a. tantalus

C. a. aethiops

C. neglectus

P. paniscusP. t. troglodytesP. t. troglodytes

H. sapiensCHAT 1 FL

C. monaG. gorilla

Macaques

Gorillas, Chimps,Humans

Other primates

Blancou et al. 2002. Nature 410: 1045

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Read et al. 2002Science 296: 2028

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Acknowledgments

•Eli Meir, University of Washington

•Joel Kingsolver, University of North Carolina

•Susan Maruca, Derek Stahl