Monday, September 16, 13 - Integrative...
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Monday, September 16, 13
Transcript of Monday, September 16, 13 - Integrative...
Monday, September 16, 13
Monday, September 16, 13
Holly Wichman Jim Bull
Monday, September 16, 13
Monday, September 16, 13
X174φ
A
A*
B
KC
D
E
F
G
H
J
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Phage Population Growth at 43° C
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Adaptation for cryptic coloration
Monday, September 16, 13
Mouse coat color genetics
Adamts20, Ectodysplasin-A (Eda), Endothelin 3
ligand (Edn3),Endothelin receptor B (Ednrb)
Epidermal growth factor receptor (Egfr),
Fibroblast growth factor receptor2 (Fgfr2),
Inhibitor of kappaB kinase gamma (Ikbkg), C-kit
receptor (kit), Ligand for c-kit receptor (kitl),
Keratin complex 2, gene 17 (Krt2-17), LIM
homeodomain protein 1 (Lmx1a), Mucolipin
3(Mcoln3), Pax-3 transcription factor (Pax3),
Sideroflexin (Sfxn1), Neural crest transcription
factor (Snai2), Sry-box containing gene 10
(Sox10), Sry-box containing gene 18 (Sox18), T-
box 15 (tbx15), Growth factor (Wnt1), Growth
factor (Wnt3a), Tyrosinase-related protein 2
(Tyrp2/Dct), Glycoprotein (Gpnmb), Membrane-
assoc. transporter protein (Matp), Member of RAS
oncogene family (Rab38), Silver protein
(Pmel17), Tyrosinase (Tyr), Tyrosinas-related
protein 1 (Tyrp1), Beta 3 subunit of adaptor
protein 3 (Ap3b1), Delta subunit of adaptor
protein 2 (Ap3d), Vacuoloar protein sorting 33a
(Vps33a), Cno, Hermansky-Pudlak syndrome
gene 1 (Hps1), Hermansky-Pudlak gene 3 (Hps3),
Hermansky-Pudlak gene 4 (Hps4), Hermansky-
Pudlak gene 5 (Hps5), Hermansky-Pudlak gene 6
(Hps6), Lysosomal trafficking regulator (Lyst),
Ocular albinism type 1 (Oa1), Pallidin (Pldn), Rab
geranylgeranyl transferase (Rabgtta),
Melanophilin (Mlph), Myosin type Va (Myo5a),
Myosin type 7a (Myo7a), RAS associated protein
(Rab27a), Agouti signaling protein (Asip),
Attractin (atrn), Gamma gluyltranspeptidase 1
(Ggt1), Melanocortin-1 receptor (Mc1r), E3
ubiquitin ligase (Mgrn1), Proopiomelanocortin
(Pomc1), ATPase (Atp7a), ATPase (Atp7b),
Excision repair deficiancy (Ercc)
Genes Phenotypes
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Endothelin receptor B (piebald) mutation
Mouse Human
neutral mutation
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Tyrosinase (albino) mutation
HumanMouse
deleterious mutation
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O’Neill Hills Pinacate Lava2 miles
mou
sehab
itat
Adaptive color polymorphism in rock pocket mice
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Distribution of lava in the SouthWest
Age (yrs) 1,700,000 530,000 760,000 1,000
Area (km2) 3500 142 435 329
Pinacates Kenzin Armendaris Carrizozo
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Phenotypic variation in coat color
Pinacates Kenzin Armendaris Carrizozo
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Approach: Association studies
phenotype
t = 1
t = 2
t = 3
Coding Region
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Dark
Agouti
MSH Mc1r
cAMP
Light
Phaeomelanosome
Eumelanosome
pulse of
agouti
expression
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Mc1r polymorphisms in light and dark C. intermedius from the Pinacates
Phenotype ID
0
5
2
1
2
6
2
0
5
2
4
3
2
9
8
3
1
3
3
2
4
3
2
5
4
7
8
4
8
1
4
9
5
6
3
3
6
5
1
6
9
9
7
2
0
7
8
7
8
1
9
9
1
5
9
2
7
C T C T G G C C C G C T T A T C C C C
R R R R R R R R
Dark 1371 T
T
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T
T
T
T
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C
C
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C
C
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Dark 1373 T
T
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T
T
T
T
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C
C
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C
C
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Dark 1374 T
T
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T
T
T
T
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C
C
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C
C
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Dark 1375 T
T
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T
T
T
T
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C
C
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C
C
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Dark 1376 T
T
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T
T
T
T
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C
C
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C
C
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Dark 1377 T
T
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T
T
T
T
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C
C
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C
C
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Dark 1378 T
T
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T
T
T
T
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C
C
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C
C
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Dark 1381 T
T
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T
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T
T
T
T
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C
C
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C
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Dark 1383 T
T
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T
T
T
T
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C
C
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C
C
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Dark 1385 T
T
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T
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T
T
T
T
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C
C
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C
C
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Dark 1386 T
T
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T
T
T
T
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C
C
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C
C
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Dark 1372 T
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T
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T
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C
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C
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Dark 1379 T
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T
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T
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T
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C
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C
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Dark 1382 T
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T
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T
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C
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C
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Dark 1384 T
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T
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T
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T
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C
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C
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Dark 1412 T
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T
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T
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T
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C
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C
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Dark 1416 T
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T
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T
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T
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T
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T
C
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C
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1387 .
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G
G
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T
T
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1402 .
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T
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A
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T
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G
T
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T
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1403 .
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1404 .
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C
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A
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G
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T
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T
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1405 .
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A
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T
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G
G
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T
T
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1406 .
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C
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C
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A
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G
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T
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T
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1407 .
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G
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T
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1408 .
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T
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A
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C
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1409 .
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A
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T
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G
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T
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1410 .
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A
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T
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G
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T
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T
1411 .
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A
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T
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G
G
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T
T
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1414 .
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G
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mela
nic
indiv
idua
ls
* Complete
association
holds for 102
melanic and 73
light individuals
Mc1r is responsible for melanic color
Mc1r DD
Mc1r dd
Mc1r Dd
Monday, September 16, 13
Perfect association between genotype and phenotype
Genotype: Mc1r locus Phenotype: coat color
Dark
Light
Dark
N = 202 individuals (404 alleles)
Monday, September 16, 13
Amino acid mutations in the Mc1r receptorin rock pocket mice
transmembrane
intracellular
extracellular
Monday, September 16, 13
Monday, September 16, 13
Dice 1947: Studied owl predation in deermice
Amok Time
Monday, September 16, 13
Distribution of Mc1r alleles in the Pinacates
Substrate color:
Sample size: 6 85 7 5 45 77 = 225
Xmas Tule West Mid East O'Neill
Coat color:
F.E.T.
P < 10-6
Xmas
O'NeillEast
Mid
5kmArizona, USA
lava
Sonora, Mexico
Tule
West
Arizona
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0
0.5
1
frequ
enc
y of
Mc1
r D
d m
ice
am
ong
dar
k m
ice
frequ
enc
y of
mtD
NA
hap
loty
pes
0
0.5
1
Sampling localesX
mas
Tul
e
West
Mid
Eas
t
O’ N
eill
Different allele frequency clines in Mc1r and mtDNA
0
0
0
.5
1
0
.5
1fr
equ
enc
y of
mela
nic
pheno
type
frequ
enc
y of
Mc1
r D
allele
Xm
as
Tul
e
West
Mid
Eas
t
O’ N
eill
Sampling locales
selected neutral
Monday, September 16, 13
Monday, September 16, 13
