Transcript LIVE INTERACTIVE LEARNING @ YOUR DESKTOP NSDL/NSTA Web Seminar: Studying Genomes: From the Lab to the Classroom Tuesday, November 13, 2007

LIVE INTERACTIVE LEARNING @ YOUR DESKTOP
NSDL/NSTA Web Seminar:
Studying Genomes: From the Lab
to the Classroom
Tuesday, November 13, 2007
Today’s NSDL Expert:
Dr. Rob DeSalle,
Author and Curator in the Sackler
Institute for Comparative Genomics,
American Museum of Natural History
http://nsdl.org
• What do evolutionary trees tell us?
• How are evolutionary trees built from
genomic information?
• Some neat things about the trunk of
the tree of life
• Some even neater things about the
tips of the tree of life where we
humans reside
http://nsdl.org
vertebrae
4 limbs
watertight
eggs
hole in hip socket
Some tree terminology
BRANCH
NODE
ROOT
http://nsdl.org
Cast of Characters
F
C
D
L
P
If we have these four taxa and F is the root,
how many possible trees are there?
Write your answer in the chat
http://nsdl.org
C
D
P
L
F
L
D
C
P
I
P
D
C
L
F
III
F
II
C
D
P
L
F
IV
D
C
Where would you attach
these species on the tree?
(Bonobo, Marsupial, Bear)
Stamp your answer
a
b
c*
c
P
L
F
*d *a
b*
d
Not marked
C
Which
of
these
trees is
not like
the
others?
D
P
L
C
F
D
P
I
F
II
P
C
D
P
L
F
D
L
C
III
http://nsdl.org
L
F
IV
Poll Question!
P
D
C
L
F
A good root for the tree above would be:
a. Orangutan
b. Tiger
c. Snake
d. Sea urchin
http://nsdl.org
“This is a dinosaur DNA sequence.”
Dr. Wu, Ingen
http://www.ncbi.nlm.nih.gov/BLAST
>DinoDNA "Dinosaur DNA" from Crichton's JURASSIC PARK p. 103 nt 11200GCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCGGTG
GCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGTTCCGACCCT
GCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCTGCTCACGCTGTACCTATCT
CAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCCGTTCAGCCCGACCGCTGCGCCTTATC
CGGTAACTATCGTCTTGAGTCCAACCCGGTAAAGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTT
CGGCGAGGACCGCTTTCGCTGGAGATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGC
TCAAGCCTTCGTCACTCCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGC
GCTGGGCTGGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGG
CCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCATCAGGGACAGCTTCAACGGCTCTT
ACCAGCCTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCGCACATGGACGCGTTGC
TGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAACAAGTCAGAGGTGGCGAAACCCGA
CAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCGCTCTCCTGTTCCGACCCTGCCGCTTACCG
GATACCTGTCCGCCTTTCTCCCTTCGGGCTTTCTCAATGCTCACGCTGTAGGTATCTCAGTTCGGTGT
AGGTCGTTCGCTCCAAGCTGACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATC
GTCTTGAGTCCAACACGACTTAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCT
CCCCGCGGTGCATGGAGCCGGGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGGCCAA
GAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGGCCATCGCGTCCG
CCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCT
http://nsdl.org
Search
For
Eminem
http://nsdl.org
Building a Bikini
Bottom Phylogeny
http://nsdl.org
ENTREZ
http://www.ncbi.nlm.nih.gov/Entrez/
http://nsdl.org
http://nsdl.org
>spongebob
1 ggttgatcct
61 taagctttta
121 gtcactgcta
181 ttcgcagaag
241 gattcatgat
301 acctatcagc
361 ttagggtttg
421 aggcgcgcaa
481 gcatccatgt
541 agggcaagtc
601 gttgcggtta
661 tgtgcatctg
721 tgcggtattt
781 gaatacatta
841 ctgaggtaat
901 ttcttggatt
961 tcaagaacga
1021 ctatgccaac
1081 atcaaagtct
1141 cggaagggca
1201 accaggtcca
1261 gtggtgcatg
1321 gagaccttaa
1381 ggactttgtg
1441 atgtcctggg
1501 aatggccggg
1561 tcttcaacga
1621 cctttgtaca
1681 gacgcagtgc
1741 ggaaggagaa
gccagtagtc
cacggcgaaa
catggataac
ggttgtattt
aactcgatga
ttccgacggt
attccggaga
attacccaat
cttgtaattg
tggtgccagc
aaaagctcgt
gctcagcctt
aggacattta
gcatggaata
ggtcgatagg
tgttaaagac
aagttagggg
tagagattgg
ttgggttccg
ccaccaggag
gacatagtaa
gccgttctta
cctgctaaat
tgtctaacgc
ctgcacgcgc
taatcttttt
ggaattccta
caccgcccgt
tcagcttctg
gtcgtaacaa
atatgcttgt
ctgcgaatgg
tgtggtaatt
attagataca
atcgtgtggc
agggtatggg
gggagcctga
cctgacacag
gaatgagtag
agccgcggta
agttggattt
gacatcttcc
ccttgaggaa
ataagatagg
gatagttggg
ggactactgc
atcgaagacg
aggtcgttac
gggggagtat
tggagcctgc
ggattgacag
gttggtggag
agttacatgt
aaggaagttt
gctacactga
aaaatgcatc
gtaagcgcga
cgctcctacc
gacgttgcgt
ggtttccgta
ctcaaagatt
ctcattaaag
ctagagctaa
gaaccaacgc
ttggccgacg
cctaccgtgg
gaaacggcta
ggaggtagtg
aatttaaacc
attccagctc
ctgttgagga
taaagaacgt
attagagtgt
acctcagttc
ggcattcgta
gaaagcattt
atcagatacc
ctatacgact
ggtcgcaagg
ggcttaattt
attgatagct
tgatttgtct
aacctcggtt
gaggcaataa
tgcgctcaac
gtgatgggga
gtcatcagct
gattgagtga
tggaaagttt
ggtgaacctg
aagccatgca
cagttataat
tacatgcacc
aggctccgcc
atgcatcttt
caatgacggg
ccacatctaa
acaagaaata
cctttatgag
caatagcgta
tgaccggtcc
atctgcactt
ttcaagcaag
tattttgttg
tttaactgtc
gccaaggatg
gtcctagtct
ccttcagcac
ctgaaactta
gactcaacac
ctttcttgat
ggttaattcc
acatgggcaa
caggtctgtg
gagtttgcaa
tagatcattg
cgtgctgatt
tccggtgaat
catgaacctt
cggaaggatc
tgtctcagta
ttatttgatg
aaaacccaac
tggttgtggt
caagtttctg
taacggagaa
ggaaggcagc
acaatacagg
tatcaattgg
tattaaagtt
gccttctggg
cattgtgtgg
cgattgcctt
gtttctagag
agaggtgaaa
ttttcattga
taaccataaa
cttatgagaa
aaggaattga
ggggaaactt
tctatgggtg
gttaacgaac
cttcttagag
atgcccttag
tcttgcctga
caattattga
acgtccctgc
tattcggact
atcacttaga
>patrick
1
61
121
181
241
301
361
421
481
541
601
661
721
781
841
901
961
1021
1081
1141
1201
1261
1321
1381
1441
1501
1561
1621
ctgcggatcg
ctgtggtaat
ttattaggaa
gccgatcgca
cgatggtacg
ccggagaggg
acccactccg
cggtaattgg
ggtgccagca
aaagctcgta
ggccttcctc
actttgaaaa
aatggaatag
gggactgacg
acgaccgact
ggttcgaagg
ccggcgttac
ggggaagtat
tggagcctgc
ggattgacag
gttggtggag
agtcgcgccg
gcgagattga
cactgaaggg
cccttcgtgc
gcgcaagtca
actaccgatt
cctcgctcgt
gctcattaaa
tctagagcta
caagaccaac
cggtctctgc
ttatgcgcct
agcttgagaa
acacggggag
aatgagtaca
gccgcggtaa
gttggatctt
tcggtctccg
aattggagtg
gacctcggtt
ggggcattcg
gcgaaagcat
cgatcagata
tccaatgacg
ggttgcaaag
ggcttaattt
attgagagct
cgatttgtct
gccgccgagc
gcaataacag
atcagcgggt
ttgggatagg
tcagctcgcg
gaatggttta
gcgcccggaa
tcagttatgg
atacatgcaa
ccgggtcgcc
accggcgacg
accatggtcg
acggctacca
gtagtgacga
ctttaaatcc
ttccagctcc
gggcgcagcg
cccggttctc
ttcaaagcag
ctattgcgtt
tattgcggtg
ttgccaagaa
ccgccctagt
cggcgggcag
ctgaaactta
gactcaacac
ctttcttgat
ggttaattcc
cgccgctgac
gtctgtgatg
gatcgtcctt
gacttgcaat
ttgattacgt
gtgagatcct
gaccatcgaa
ttccttggag
tcaagcgccg
cggctccgtt
gatccttcga
taacgggtaa
catccaagga
aaaatagcaa
tttaacgagg
aatagcgtat
tggcggtccg
ttgactgagt
gccgtgagcc
ggttttcgga
tgagaggtga
tgttttcatt
tctaaccata
tctgcgggaa
aaggaattga
ggggaaactc
tctgtgggtg
gataacgaac
ttcttagagg
cccttagatg
gtctggaagg
tgtctccctt
ccctgccctt
cggacgggcc
ctt
cgcatccctt
accttacggg
ggtgaactct
atgtctgccc
cggagaatca
aggcagcagg
tacaggactc
atctattgga
attaaaattg
caaggccgca
gccgggcgcg
tggacagcag
actcgaggta
aattcttgga
aatcaagaac
aacgatgccg
accaaagtct
cggaagggca
acccggcccg
gtggtgcatg
gagactctgg
gacaagtgcg
ttcggggcgc
cctgggcaat
aaacgaggaa
tgtacacacc
gcggcggggc
aaaagtgaaa
acatggataa
aggcgtgctc
ggataacctg
tatcaacttt
gggttcgatt
cgcgcaaatt
tttcgaggcc
gggcaagtct
ctgcagttaa
ctgcccgcct
cgaaacgttt
agcatggaat
atgattaaga
tcgccgcaag
gaaagttaga
actcggatcg
ttgggttccg
ccaccaggag
gacacagtga
gccgttctta
cttgctaaat
gttcagccac
acgcgcgcta
ccgctgaacc
ttcccagtaa
gcccgtcgct
gcctctggcg
>MrKrabs
1
61
121
181
241
301
361
421
481
541
601
661
721
781
841
901
961
1021
1081
1141
1201
1261
1321
1381
1441
1501
1561
1621
1681
1741
tacctggttg
aagtacgagc
tagatcttcg
tagcctcgac
cccgtccaat
ctctttcaaa
cgggtaacgg
ccaaggaagg
taacaatacg
acgaggatcc
gtatattaaa
ttcacctcac
cactgggtgc
gcgaatcgtt
tcggtactcg
gtgaaattct
cattaatcaa
ttaagcgatg
gggaaaccaa
ttgacggaag
tcaccaggcc
tggtggtgca
acgagactct
gacaaaggct
tctgggcaca
aacccgtcca
gaattcccgg
accgcccgtc
ggctttcggg
aaagtcgtaa
atcctgccag
cgaaataaat
gtatcctact
cttgcggaag
tggtgagtct
tgtctgcctt
agaatcaggg
cagcaggcac
ggactcatcc
attggagggc
gttgctgcgg
ggtgctacta
ttcgggagac
acattcgtgc
aggtaatggt
tagatcgtcg
gaacgaaagt
ccaactggcg
agtttttggg
ggcaccacca
cagacactag
tggccgttct
ggcctactaa
cgaagctgcg
cgcgctacac
atcaccttcg
taagtgcaag
gctactaccg
ctgcgtcggt
caaggtttcc
tagtcatatg
gtgagaccgc
tggataaccc
agcgtttttg
gaacaacctt
atcaacttga
ttcgtagccg
gcaaattacc
gaggccccgt
aagtctggtg
ttaaaaagct
cctggaccgg
cagagcgtct
atgagtaatg
tgaagggaca
caagacggac
cagaggtcga
atccgtcggg
ttcgggggaa
ggagtgagca
aaggattgac
tagttggtgg
atagacggcg
tgaaacgggg
tgaaggtgac
tgctggggat
tcatagcgtc
cattgaatga
attcccggaa
gtaggtgaac
cttgtctcaa
gaatggctca
tggaaattct
ttagaccaaa
gacggatcgc
tggtaggtta
gagagggagc
cactcccggc
aattggaatg
ccagcagccg
cgtagttgga
acctattgct
gctttgaaaa
aaaatggcct
gacgggggca
tactgcgaaa
aggcgatcag
ggtatttcca
gtatggttgc
gtgcgttaat
agattgagag
agtgatttgt
gatcattgcg
caataacagg
aacgtgttcg
tgaggttcgc
gcgctgacta
tttagtgagg
agatgtcaaa
ctgcggaagg
agattaagcc
ttacatcagt
agagctaata
accaatcggg
acggtcttgt
tgtgcctacc
ctgagaaacg
acggaggtag
agtacacttc
gtaattccag
tctcagttac
ggttcctccg
aattggagtg
cggtgctatt
ttcgtattgc
gcatttgcca
ataccgccct
tgacctgacg
aaagctggaa
ctgactcaac
ctctttcttg
ctggttaatt
tccgttatgt
tctgtgatgc
tctggctcga
aattgtcctt
cgtccctgcc
cttcggactg
ctgtatcatt
atcatta
atgcaggtct
tatggttcct
catgcaaatg
gagcttgcga
actggcgaaa
atggtgataa
gctaccacat
tgacgaaaaa
aaatccttta
ctccaatagc
gggcaggtgg
aggtgccctt
ctcaaagcag
ttgttggttc
gacgttagag
agaatgtttt
agttctgacc
ggcagcttcc
cttaaaggaa
acgggaaacc
atttggtggg
ccgataacga
cttcttagag
ccttagatgt
aagggtgggt
catgaacgag
ctttgtacac
ggaccgatgc
tagagaagta
>Squidburt
1 tatctggttg
61 aagttcacgc
121 cctcgggacc
181 tacatgtgac
241 gtgggcaccc
301 gcgtatttcc
361 gggttgctat
421 accggctttc
481 cggttaagtg
541 gggagcatgc
601 ccggcacggg
661 cggaatgagt
721 gcagccgcgg
781 gtagtccgaa
841 gtcgttgact
901 gtacatccgc
961 cgttcggggc
1021 ggccttctcg
1081 gtcgtcgccc
1141 ccaagggtgc
1201 agtgctcaga
1261 ctcgtctacg
1321 gccactcgta
1381 gatggcgtgt
1441 atcagatacc
1501 cttccatgac
1561 ttgcaaagct
1621 cttaatttga
1681 cgatagctct
1741 atccgtctgg
1801 tgtgtgcgtt
1861 ttgtgcgttc
1921 cgtcgtttcc
1981 gcgtgcggta
2041 gagggacggg
2101 agatgtccgg
2161 cgagagggct
2221 ccccgtgaac
2281 gccctttgta
2341 tctggccgac
2401 tccgccgctt
2461 tagaggaagt
atcctgccag
cacgcattag
gtaatcctcc
accagccgcg
gcgtcgatcg
gtcctcccgt
gggcggcgcg
atgcctggcg
cctaccgtgg
gaaacggctc
gaggtagtga
acacttcaaa
taattccagc
ctcgggttcg
ttggtcgtcc
ctcgcggtcc
ggcccagggc
ctcccctcca
gtgcaatgtt
tcttaaccga
gcgggctgtt
tctgtcggtc
ttgcgacgtt
ggcaagcacg
gtcgtagttc
ccggcgggta
gaaacttaaa
ctcaacacgg
ttctcgattc
ttgattccga
ttttgctacg
gcgttcgttt
cgcattcgtc
gtgcgtgcgg
tggcagaaag
ggccgcacgc
gggaaacctc
gaggaattcc
cacaccgccc
gacgccgccg
gtgccgcctc
aaaagtcgta
tagtcatatg
aacgggcgaa
tcttggaggc
atcggtcggc
ttccgggtcg
tcgttgcgcc
ctccgctttg
acgggtctct
ttactacggg
cacatccaag
cgaaaaataa
tccgttaacg
tccggtagcg
tggtcgctcg
gttcgcattc
tgccggcgaa
gttcgatcgg
tcacccgccg
tcgtcgcgcg
gtgtccgcgg
caagcttgca
tccgtctacg
agaggtgaaa
ttttcctcga
cgaccgtaaa
gcctgcggga
ggaattgacg
gaaaactcac
ggtgggtggt
taacgaacga
gcgggctcgg
cgttctcgtg
ccggcgtcgg
tttccgccgg
ccacacgagg
gcgctacact
tcaaccacct
cggtaggcgc
gtcgctacta
ggctgcctgg
ggcgttcgac
acaaggtttc
cttgtctcaa
accgcgaatg
gttggataac
gcgcagccgt
cggcgctaca
tcgctgctcc
gtgactctgg
cgagggtccg
taacggggaa
gaaggcagca
cgacgcggga
aggaccaacc
tatattaaag
cgcggccccg
ccggcccttt
aatcttttgc
gcggggggaa
ttcgccctcg
cgcgtgtttg
cggccggtac
tacgataagc
gcgaggcaat
ttcttggatc
tcaagagcga
cgatgccgac
aaccagagtt
gaagggcacc
ccggtccgga
ggtgcatggc
gactccggcc
gccgtgcgtg
cgtcggtcgg
gggcggcggg
gtccgggtcg
cggagcgata
ggaggtatca
cccgtgatag
gggtcaacag
ccgatcgaac
tgggtctggg
gcctggagaa
cgtaggtgaa
agcttaagcc
gctcaggaac
tgtggcaatt
cgccttcgcc
tattagactg
ggcggcgttg
ataactcact
ccctatcaac
tcggggttcg
ggcgcgcaaa
ctctgtcgag
ggagggcaag
ttgttgcggt
gggcggcggc
ccgccggtgt
gcggatggcg
ccagggtggg
tcccgtcttc
cggtccgggc
gttcactttg
atggaatgat
gatcgaaggg
gtcgcaagac
aagtcggagg
cggcgatccg
cggttccggg
accaggagtg
caccggtagg
cgttcttagt
tgctaactag
ttcgtcgcgc
gtgtgggggc
cgtgggcgtc
gttttctcac
acaggtctgt
gcggggactt
ggatcggggc
cccgcgtcga
ggtccggtga
gagggggttc
gacgaccgaa
cctgcggaag
atgcaagtgt
cggacctaat
ctagagctaa
tttactgcgc
agaccgatgc
cgcggcggcg
ggtcgatcgc
tgtcgacggt
attccggaga
ttacccactc
gccccgcgac
tctggtgcca
taaaaagctc
gccatcgtcc
cgactgccat
tccggtgcgg
tcggtcttcg
gtctcccgtc
ggtttctcct
aaaaaattag
ggaagagggc
agcggtcggg
gaactgcagc
ttcgaagacg
ccggcgttcg
gggagtatgg
gagcctgcgg
attgacagat
tggtggagcg
tgcgccgatg
gtcgcttcgg
ggcggttcgc
gtcgatggtg
gcacttctta
gatgcccctt
cgccccggcc
ctgtaaccaa
tcacgtccct
ggtcctcgga
gcctccttcg
cccgatcgtt
gatcatta
http://nsdl.org
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A Tree
of Life
placozoa
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True or False:
There are 5 major kingdoms of life
Stamp your answer
True
http://nsdl.org
False
3 Super-domains
YES
Eukaryota
Bacteria
Archaea
6 Kingdoms
Bacteria
Archaea
Fungi
http://nsdl.org
YES… well maybe
Plants
Animals
PROTISTA (darn)
Fungi are
closer to
us beyond
just being
between
our toes
placozoa
http://nsdl.org
http://nsdl.org
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99.9%
98.7%
3 MY
6-7 MY
8 MY
11 MY
http://nsdl.org
When a genetic testing
company tells you that you are
Yugoslavian, are you?
http://nsdl.org
Polly
?
Rob
Rob’s
mom
?
= son
= daughter
?
Tito
?
= son
= daughter
http://nsdl.org
Rob’s
dad
Rob
Tito
http://nsdl.org
Polly
mtDNA
Y-DNA
X-DNA
http://nsdl.org
Dr. Rob DeSalle
[email protected]
THANK
YOU!
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