Molecular Phylogenies

1
Molecular Phylogenies

• Interesting,
• Intriguing,
• Exciting,
• Practical,
• Useful

2
Molecular phylogeny goes to court!
3
(No Transcript)
4
male, homosexual
female, heterosexual
male, heterosexual
female, heterosexual
female, heterosexual
female, heterosexual
male, homosexual
male, homosexual
5
(No Transcript)
6
1998 Criminal trial State of Louisiana
vs Richard J. Schmidt
1st ruling in a U.S. court on admissability of
phylogenetic analyses...
7
(No Transcript)
8
On August 4, 1994, Janice Trahan of Lafayette, LA
was lying in bed alongside her young son when her
ex-lover, a Louisiana physician, Dr. Richard J.
Schmidt, jammed a needle in her arm. Dr. Schmidt
told Trahan he was giving her an injection of
vitamin B-12, but she later told friends she
sensed immediately that something was wrong. In
January 1995, Trahan tested positive for HIV-1.
9
The victims risk factors for HIV-1 were
determined. From 1984 to 1995, the victim had
sexual contacts with seven men, including the
doctor, all of whom were found to be HIV-1
negative. The victim had donated blood, for
which she was tested and found negative for HIV-1
in 1992, 1993, and 1994. In subsequent
investigation, law enforcement agents identified
an HIV-1-infected male patient of Dr. Schmidt
whose blood was drawn on August 4, 1994. The
patient became infected with HIV-1 in 1990. A
vial containing the patient blood was discovered
in the doctors home refrigerator.
10
(No Transcript)
11
Phylogeny for HIV (env gp120)
50 HIV clones from alleged SOURCE
50 HIV clones from VICTIM
HIV from 28 individuals (pop. sample)
12
Phylogeny for HIV (reverse transcriptase)
HIV clones from VICTIM
HIV from 25 individuals (pop. sample)
13
The State of Louisiana versus Richard J. Schmidt
went to trial on Thursday, October 15, 1998.
The jury had to decide on the basis of
evolutionary relatedness rather than similarity
(as in disputed paternity or criminal presence
cases. The trial lasted eight days. At 835 PM
on Friday, October 23, 1998, after taking 10
votes, the nine-woman, three-man jury came back
with a 10-2 guilty verdict. At the close of the
hearing, District Judge Durwood Conque sentenced
Dr. Schmidt to 50 years at hard labor, the
stiffest penalty possible. "In the final
analysis, the punishment must fit the crime,"
said the judge.
14
His victim's medical outlook is uncertain, but in
an ironical way remains a topic of paramount
concern to Dr. Schmidt. Under the doctrine of
double jeopardy, a defendant can only be tried
once for a criminal act. So if Janice Trahan were
to die from her viral infections, Dr. Schmidt
could not be retried for her murder. However, if
any of Dr. Schmidt's appeals succeed, his case
would be remanded to the original court in
Lafayette, where prosecutors will have the option
of re-indicting and re-trying him. If in the
meantime Janice Trahan dies from AIDS or
hepatitis C, then the DA will be free to consider
homicide charges carrying the death penalty.
15
(No Transcript)
16
Species in which polio vaccines were tested.
Mandrillus sphynx
Cercopithecus lhoesti
17
(No Transcript)
18
Species from which HIV-1 were transferred to
humans.
Chimpanzee Pan troglodytes
Sooty mangabey Cercocebus atys
19
Bushmeat AIDS as a Zoonosis
20
Molecular phylogeny and the cold war!
21
(No Transcript)
22
MOLECULAR PHYLOGENETIC ARCHEOLOGY
23
(No Transcript)
24

• Michael Crichton's fantasy about cloning
  dinosaurs, Jurassic Park, contains a putative
  dinosaur DNA sequence.
• What organism is this dinosaur related to?

25
The sequence

• gtDinoDNA from JURASSIC PARK p. 103 nt 1-1200
• GCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACA
  AAAATCGACGC GGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCG
  TTTCCCCCTGGAAGCTCCCTCG TGTTCCGACCCTGCCGCTTACCGGATA
  CCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGC
  TGCTCACGCTGTACCTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCT
  GGGCTGTGTG CCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATC
  GTCTTGAGTCCAACCCGGTAA AGTAGGACAGGTGCCGGCAGCGCTCTGG
  GTCATTTTCGGCGAGGACCGCTTTCGCTGGAG
  ATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGC
  CTTCGTCACT CCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCA
  TGGCGGCCGACGCGCTGGGCT GGCGTTCGCGACGCGAGGCTGGATGGCC
  TTCCCCATTATGATTCTTCTCGCTTCCGGCGG
  CCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCATCAGGG
  ACAGCTTCAA CGGCTCTTACCAGCCTAACTTCGATCACTGGACCGCTGA
  TCGTCACGGCGATTTATGCCG CACATGGACGCGTTGCTGGCGTTTTTCC
  ATAGGCTCCGCCCCCCTGACGAGCATCACAAA
  CAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTT
  CCCCCTGGAA GCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCT
  GTCCGCCTTTCTCCCTTCGGG CTTTCTCAATGCTCACGCTGTAGGTATC
  TCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTG
  ACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGT
  CTTGAGTCCA ACACGACTTAACGGGTTGGCATGGATTGTAGGCGCCGCC
  CTATACCTTGTCTGCCTCCCC GCGGTGCATGGAGCCGGGCCACCTCGAC
  CTGAATGGAAGCCGGCGGCACCTCGCTAACGG
  CCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAAC
  CAACCCTTGG CCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCA
  TCTCGGGCAGCGTTGGGTCCT

26

• NCBI scientist Mark Boguski noticed this obvious
  "contaminant" and supplied Crichton with a better
  sequence, for the sequel book, The Lost World.
  Identify the most likely source of this sequence
  using translating BLAST (blastx) and nr database

27

• gtDinoDNA from THE LOST WORLD p. 135
• GAATTCCGGAAGCGAGCAAGAGATAAGTCCTGGCATCAGATACAGTTGGA
  GATAAGGACG GACGTGTGGCAGCTCCCGCAGAGGATTCACTGGAAGTGC
  ATTACCTATCCCATGGGAGCC ATGGAGTTCGTGGCGCTGGGGGGGCCGG
  ATGCGGGCTCCCCCACTCCGTTCCCTGATGAA
  GCCGGAGCCTTCCTGGGGCTGGGGGGGGGCGAGAGGACGGAGGCGGGGGG
  GCTGCTGGCC TCCTACCCCCCCTCAGGCCGCGTGTCCCTGGTGCCGTGG
  GCAGACACGGGTACTTTGGGG ACCCCCCAGTGGGTGCCGCCCGCCACCC
  AAATGGAGCCCCCCCACTACCTGGAGCTGCTG
  CAACCCCCCCGGGGCAGCCCCCCCCATCCCTCCTCCGGGCCCCTACTGCC
  ACTCAGCAGC GGGCCCCCACCCTGCGAGGCCCGTGAGTGCGTCATGGCC
  AGGAAGAACTGCGGAGCGACG GCAACGCCGCTGTGGCGCCGGGACGGCA
  CCGGGCATTACCTGTGCAACTGGGCCTCAGCC
  TGCGGGCTCTACCACCGCCTCAACGGCCAGAACCGCCCGCTCATCCGCCC
  CAAAAAGCGC CTGCTGGTGAGTAAGCGCGCAGGCACAGTGTGCAGCCAC
  GAGCGTGAAAACTGCCAGACA TCCACCACCACTCTGTGGCGTCGCAGCC
  CCATGGGGGACCCCGTCTGCAACAACATTCAC
  GCCTGCGGCCTCTACTACAAACTGCACCAAGTGAACCGCCCCCTCACGAT
  GCGCAAAGAC GGAATCCAAACCCGAAACCGCAAAGTTTCCTCCAAGGGT
  AAAAAGCGGCGCCCCCCGGGG GGGGGAAACCCCTCCGCCACCGCGGGAG
  GGGGCGCTCCTATGGGGGGAGGGGGGGACCCC
  TCTATGCCCCCCCCGCCGCCCCCCCCGGCCGCCGCCCCCCCTCAAAGCGA
  CGCTCTGTAC GCTCTCGGCCCCGTGGTCCTTTCGGGCCATTTTCTGCCC
  TTTGGAAACTCCGGAGGGTTT TTTGGGGGGGGGGCGGGGGGTTACACGG
  CCCCCCCGGGGCTGAGCCCGCAGATTTAAATA
  ATAACTCTGACGTGGGCAAGTGGGCCTTGCTGAGAAGACAGTGTAACATA
  ATAATTTGCA CCTCGGCAATTGCAGAGGGTCGATCTCCACTTTGGACAC
  AACAGGGCTACTCGGTAGGAC CAGATAAGCACTTTGCTCCCTGGACTGA
  AAAAGAAAGGATTTATCTGTTTGCTTCTTGCT
  GACAAATCCCTGTGAAAGGTAAAAGTCGGACACAGCAATCGATTATTTCT
  CGCCTGTGTG AAATTACTGTGAATATTGTAAATATATATATATATATAT
  ATATATCTGTATAGAACAGCC TCGGAGGCGGCATGGACCCAGCGTAGAT
  CATGCTGGATTTGTACTGCCGGAATTC

28
Results
What else can you see?
29
Results
What else can you see?
30
DNA is an unstable molecule that decays
spontaneously through hydrolysis and oxidation.
The chances of unprotected DNA surviving over
long periods of time are low. Calculations
suggest that DNA should not survive for more than
10,000-100,000 years, and then only in a highly
fragmented form. All records of ancient DNA
recovery from protected and unprotected sources
have been discredited.
31
(No Transcript)
32
(No Transcript)
33
Types of ancient biological material that may
contain DNA ______________________________________
____________ Sample Maximum age
(years) __________________________________________
________ Dry remains Hair 0.3 Herbarium
plant specimens 120 Feathers 130 Museum
skins 140 Charred seeds and
cobs 4,500 Human mummies 5,000 Naturally
preserved skins 13,000 Natural animal
mummies 13,000 Bones and teeth 30,000 Mumifie
d seeds 45,000 Frozen remains Muscle
tissue 53,000 Wet remains Pickled museum
specimens 100 Human remains preserved in
peat 8,000 _______________________________________
___________
34
Postmortem changes in DNA In a concatenated
229-bp sequence from a 140 years-old skin sample,
Higuchi et al. (1987) detected two postmortem
modifications. Both modifications were
transitions that could be attributed to the
postmortem deamination of C to U. Therefore, 1
of all the nucleotides in this sample have
changed postmortem.
35
Molecular Evolution of the Extinct Quagga
36
The female that died in Amsterdam Zoo on August
12, 1883, marked the extinction of the species
Equus quagga.
37
Plains zebra Equus burchelli
Grevys zebra Equus grevyi
Mountain zebra Equus zebra
38
Equus przewalskii
39
Equus asinus
40
Ceratotherium simum
Rhinoceros unicornis
41
(No Transcript)
42
(No Transcript)
43
(No Transcript)
44
Disextinction, Inc.
45
The dusky seaside sparrow Ammodramus maritimus
nigrescens
46
(No Transcript)
47
(No Transcript)
48
(No Transcript)
49
Conservation priorities
50
(No Transcript)
51
(No Transcript)
52
more likely
53
rampant morphological convergence
54
(No Transcript)