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Demography and
deleterious alleles in maize
Jeffrey Ross-Ibarra
@jrossibarra • www.rilab.org
Dept. Plant Sciences • Center for Population Biology • Genome Center
University of California Davis
photo by lady_lbrty
Burkhard Schulz
Arif Mümtaz
IAMDGC 2015
population genetics of deleterious alleles
Ne effective population size
s selection coefficient
selection effective when 2Nes > 1
Lawrie and Petrov 2014
2Nes=0
2Nes=5
2Nes=100
population genetics of deleterious alleles
Ne effective population size
s selection coefficient
selection effective when 2Nes > 1
genetic load: difference between fitness of
optimal and averaged genotype
Lawrie and Petrov 2014
2Nes=0
2Nes=5
2Nes=100
population genetics of deleterious alleles
Ne effective population size
s selection coefficient
selection effective when 2Nes > 1
increased load due to out-of-Africa bottleneck
heterozygousperindividual
homozygousderivedper
individual
Lohmueller et al 2008
relativediversity(B)
distance (cM)
mutation
distribution of
selective effects
distance from sitesum over all
selected sites
⇡e
⇡0
⇡ e
P
x
R 1
0
uxfx(t)dt
t(1+(1 t)rx/t)2
Nordborg 1996
Genome-wide diversity
reduced by linked selection
purifying selection reduces diversity at linked sites
relativediversity(B)
distance (cM)
mutation
distribution of
selective effects
distance from sitesum over all
selected sites
⇡e
⇡0
⇡ e
P
x
R 1
0
uxfx(t)dt
t(1+(1 t)rx/t)2
Nordborg 1996
How does demography affect the impact of selection
on linked sites?
Genome-wide diversity
reduced by linked selection
purifying selection reduces diversity at linked sites
Suketoshi Taba
high nucleotide diversity in maize
VS = 1.5-2%
high nucleotide diversity in maize
VS
Photo: Peter Yang
VS=
considerable segregating genetic load
Jones 1924
Darwin 1876
maizeteosinte
Photos: Matt Hufford, Brandon Gaut, John Doebley
how has the demography of
domestication changed the impacts of
selection against deleterious alleles?
13 teosinte
23 landrace maize
Chia et al. 2012
Maize HapMap2
teosinte
landrace
Tim Beissinger
USDA-ARS (U. Missouri)
beissingerlab.org ANGSD: Korneliussen et al 2014
•3-5X sequencing depth
•allele frequencies, diversity from genotype-likelihoods
genic nongenic genic nongenic
pairwisenucleotidediversity maize teosinte
diversity suggests selection and demography
Tim Beissinger
USDA-ARS (U. Missouri)
beissingerlab.org ANGSD: Korneliussen et al 2014
•3-5X sequencing depth
•allele frequencies, diversity from genotype-likelihoods
genic nongenic genic nongenic
pairwisenucleotidediversity
Tajima’s D Tajima’s D
density maize teosinte
diversity suggests selection and demography
nucleotidediversity
distance to nearest substitution (cM)
classic hard sweeps rare in maize
classic hard sweeps rare in maize
Sattah et al. 2011
maize
classic hard sweeps rare in maize
maize
classic hard sweeps rare in maize
teosinte
purifying selection removing diversity in genes
purifying selection removing diversity in genes
teosinte
maize
DATA
teosinte
maize
MODEL
domestication: bottleneck and expansion
dadi: Gutenkunst 2009
teosinte
maize
DATA
teosinte
maize
MODEL
domestication: bottleneck and expansion
dadi: Gutenkunst 2009
0.05Na
Na
Na 3Na
teosinte maize
pairwise diversity reflects long-term Ne
pairwise diversity reflects long-term Ne
⇡ =
X
ij
xixj⇡ij
⇡1 > ⇡2
Ne ~ 150,000 Ne ~ 50,000
pairwise diversity reflects long-term Ne
teosinte maize
0.05Na
Na
Na 3Na
dadi diffusion:
Ne ~ 450,000
model underestimates expansion
0.05Na
Na
Na 3Na
dadi diffusion:
Ne ~ 450,000
SeeDs singletons:
Ne ~ 1,000,000
model underestimates expansion
0.05Na
Na
Na 3Na
dadi diffusion:
Ne ~ 450,000
SeeDs singletons:
Ne ~ 1,000,000
1e+05
1e+07
1e+09
1e+03 1e+042e+04 1e+05
years(u=3e−8, generation=1)
effectivepopulationsize
pop
BKN_4Hap
BKN_6Hap
TIL_4Hap_Jalisco
TIL_6Hap
MSMC coalescent:
Ne ~ 1,000,000,000
model underestimates expansion
0.05Na
Na
Na 3Na
dadi diffusion:
Ne ~ 450,000
SeeDs singletons:
Ne ~ 1,000,000
1e+05
1e+07
1e+09
1e+03 1e+042e+04 1e+05
years(u=3e−8, generation=1)
effectivepopulationsize
pop
BKN_4Hap
BKN_6Hap
TIL_4Hap_Jalisco
TIL_6Hap
MSMC coalescent:
Ne ~ 1,000,000,000
49M hectares:
Ne ~ 5,000,000,000
model underestimates expansion
rapid growth changes linked selection
nucleotidediversity
distance to gene (cM)
rapid growth changes linked selection
singletondiversity
distance to gene (cM)
simulations find effect for s (1/2Nteo)
singletons
pairwise diversity
simulations find effect for s (1/2Nteo)
bottleneck reduced
neutral diversity
singletons
pairwise diversity
simulations find effect for s (1/2Nteo)
no change
2Ns 1
singletons
pairwise diversity
simulations find effect for s (1/2Nteo)
singletons show
reduced diversity
2Ns 10
singletons
pairwise diversity
simulations find effect for s (1/2Nteo)
2Ns >>1
in both
singletons
pairwise diversity
simulations find effect for s (1/2Nteo)
2Ns >>1
in both
singletons
pairwise diversity
patterns of linked selection affected by both
long-term and recent demographic change
Mexico lowland
9,000 BP
Matsuoka et al. 2002; Piperno 2006
Perry et al. 2006; Piperno et al. 2009
geographic spread post-domestication
Mexico highland6,000 BP
Mexico lowland
9,000 BP
Matsuoka et al. 2002; Piperno 2006
Perry et al. 2006; Piperno et al. 2009
geographic spread post-domestication
Mexico highland6,000 BP
S. America
lowland
6,000 BP
Mexico lowland
9,000 BP
Matsuoka et al. 2002; Piperno 2006
Perry et al. 2006; Piperno et al. 2009
geographic spread post-domestication
Mexico highland6,000 BP
S. America
lowland
6,000 BP
S. America
Highland
4,000 BP
Mexico lowland
9,000 BP
Matsuoka et al. 2002; Piperno 2006
Perry et al. 2006; Piperno et al. 2009
geographic spread post-domestication
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize
Demography and deleterious alleles in maize

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Demography and deleterious alleles in maize