Complex adaptation in Zea

Complex adaptation in Zea
Jeffrey Ross-Ibarra
@jrossibarra • www.rilab.org
Dept. Plant Sciences • Center for Population Biology • Genome Center
University of California Davis

acknowledgements
Tanja Pyhäjärvi
(U. Oulu)
Shohei Takuno
(Sokendai)
John Doebley
(U Wisconsin)
Michelle Stitzer Paul Bilinski
Sofiane Mezmouk Vince Buffalo
Anne Lorant
(KWS)
Nathan Springer
(U Minnesota)

Matthew Hufford
(Iowa State)
Pyhäjärvi T, Hufford MB, Mezmouk S, Ross-Ibarra J§ (2013) Complex patterns of local
adaptation in teosinte. Genome Biology and Evolution 5: 1594-1609.†
Hufford MB, Lubinsky P, Pyhäjärvi T, Devengenzo MT‡, Ellstrand NC, Ross-Ibarra J§
(2013) The genomic signature of crop-wild introgression in maize. PLoS Genetics 9(5):
e1003477.
Hufford MB∗, Xun X∗, van Heerwaarden J∗, Pyhäjärvi T∗, Chia J-M, Cartwright RA,
Elshire RJ, Glaubitz JC, Guill KE, Kaeppler S, Lai J, Morrell PL, Shannon LM, Song C,
Spinger NM, Swanson- Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen
MD, Ware D, Buckler ES§, Yang S§, Ross-Ibarra J§ (2012) Comparative population
genomics of maize domestication and improvement. Nature Genetics 44:808-811†
van Heerwaarden J§, Hufford MB, Ross-Ibarra J§ (2012) Historical genomics of North
American maize. PNAS 109: 12420-12425
Kanizay LB, Pyhäjärvi T, Lowry E, Hufford MB, Peterson DG, Ross-Ibarra J, Dawe RK
(2013) Diver- sity and abundance of the Abnormal chromosome 10 meiotic drive complex
in Zea mays. Heredity 110: 570-577.
Hufford MB§, Gepts P, Ross-Ibarra J (2011) Influence of cryptic population structure on
observed mating patterns in the wild progenitor of maize (Zea mays ssp. parviglumis).
Molecular Ecology 20: 46-55
Chia J-M∗, Song C∗, Bradbury P, Costich D, de Leon N, Doebley JC, Elshire RJ, Gaut BS,
Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu
Y, McCombie R, Nel- son R, Poland J, Prasanna BM, Pyhäjärvi T, Rong T, Sekhon RS,
Sun Q, Tenaillon M, Tian F, Wang J, Xu X, Zhang Z, Kaeppler S, Ross-Ibarra J,
McMullen M, Buckler ES, Zhang G, Xu Y, Ware, D (2012) Maize HapMap2 identifies
extant variation from a genome in flux. Nature Genetics 44:803-807†
Hufford MB, Bilinski P, Pyhäjärvi T, Ross-Ibarra J§ (2012) Teosinte as a model system
for population and ecological genomics. Trends in Genetics 12:606-615†
Swanson-Wagner R, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL,
Tiffin P, Springer NM. Reshaping of the maize transcriptome by domestication. (2012)
PNAS 109: 11878-11883
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J§ (2011) Genome size and TE content
as determined by high-throughput sequencing in maize and Zea luxurians. Genome
Biology and Evolu- tion 3: 219-229

how do plants adapt?
Clausen, Keck, and Hiesey 1940
Jane Shelby Richardson

what evolutionary processes are involved?
hard sweep
Diversity

hard sweep multiple
mutations
Diversity

hard sweep multiple
mutations
Diversity
standing
variation

hard sweep multiple
mutations polygenic adaptation
Diversity
standing
variation

what is the genetic basis of adaptation?
Lowry & Willis 2010 PLoS Biology

Zea: teosinte & maize
Tripsacum dactyloides
Zea diploperennis
Hufford et al. 2012 Trends in Genetics
Zea mays ssp. mexicana
Zea mays ssp. parviglumis
Zea mays ssp. mays
Zea nicaraguensis
Zea luxurians
Zea mays ssp. huehuetenangensis
Zea perennis

Zea as an evolutionary model
Arabidopsis Purugganan and Fuller 2010 Evolution
Most of the studies that document rapid evolution Brandon Gaut
M. D. PURUGGANAN AND D. Q. FULLER
Figure 4. Comparison of evolutionary rate estimates. Box plots of the rates of evolution in (A) log (darwins) and (B) log domestication (DOM) as well as plants (PLAN) (from Bones and Farres 2001) and anthropogenic (AN) and natural (NAT) conditions animal species (Hendry et al. 2008). The asterisk indicates domestication rates under the assumption of the shortened 2000-for legume species. The vertical lines give the estimate ranges, whereas the boxes span the minimum and maximum quartile horizontal line within the box gives the median rate.
while for grain/seed increase is 0.68 ± 0.15 × 10−3 haldanes.
maize
Kew C-Value Database
Hufford et al. 2012 Trends in Genetics

grassytillers: evolution of plant architecture
Wills et al. 2013 PLoS Genetics

prolificacy mapped to upstream of gt1
Figure 3. Fine-mapping of prol1.1 on chromosome 1S. At the top, there is a map of the prol1.1 chromosomal region with genetic markers and
their APG v2 positions. The upper set of 25 horizontal bars represents the 23 recombinant chromosome lines and the maize and teosinte control
lines. White segments indicate maize genotype, black segments teosinte genotype, and gray segments unknown or regions where maize and
teosinte are identical. Prolificacy trait values and standard errors for each recombinant and control line are shown by the blue column graphs on the
right. The lower set of 25 bars is a close-up view of the region near gt1 to which prol1.1 localized. At the bottom, a fine-scale map showing the
Genetics of Prolificacy during Maize Domestication

prolificacy mapped to upstream of gt1

gt1 controls lateral bud formation
Wills et al. 2013 PLoS Genetics Whipple et al. 2011 PNAS

gt1 controls lateral bud formation
Genetics of Prolificacy during Maize Domestication
Figure 5. Longitudinal sections of ear-forming primary lateral branches hybridized with antisense gt1 RNA probe. (A) M:M and (B) M:T
genotypes, showing gt1 expressed at low levels in the nodes. (C) T:M and (D) T:T genotypes in which there is no viable gt1 expression in the nodes.
Weak gt1 expression is seen in the leaves surround the branch in all sections.
doi:10.1371/journal.pgen.1003604.g005
Wills et al. 2013 PLoS Genetics greater efficiency of harvest is achieved by having all seed mature Whipple et al. 2011 PNAS
synchronously. Similarly, harvesting a single large inflorescence or
fruit from a plant is easier than harvesting dozens of smaller ones
[18]. Thus, diverse crops have been selected to produce smaller
Balsas teosinte by a US inbred line (W22), seven prolificacy QTL
were detected [21]. All seven QTL had small effects, but the one
that explained the greatest portion of the variance (4.5% averaged
over two environments) was on the short arm of chromosome 1. As

partial sweep upstream of gt1
density.default(x = teopi - lrpi, from = -0.02, to = 0.02, breaks = 100)
-0.02 -0.01 0.00 0.01 0.02
0 50 100 150
πteo − πmz

density.default(x = teopi - lrpi, from = -0.02, to = 0.02, breaks = 100)
-0.02 -0.01 0.00 0.01 0.02
0 50 100 150
πteo − πmz
MAIZE
TEO
genome-wide
gt1 upstream

convergent evolution at gt1
A B
A B
T/T
M/T
M/M
T/T
M/T
M/M
T/T
M/T
M/M
T/T
M/T
M/M
3’ UTR
5’ control region

convergent evolution at gt1
Multiple
Mutations
Standing
Variation

maize colonization of highlands
6,000 BP Mexico highland
• Maecenas aliquam maecenas ligula nostra,
accumsan Mexico taciti. lowland
Sociis mauris in integer
9,000 BP
• El eu libero cras interdum at eget habitasse
elementum est, ipsum purus pede
• Aliquet sed. Lorem ipsum dolor sit amet, ligula
suspendisse nulla pretium, rhoncus
Matsuoka et al. 2002; Piperno 2006
Perry et al. 2006; van Heerwaarden et al. 2011 PNAS Piperno et al. 2009
Title Text Title Text

• Maecenas aliquam maecenas 6,000 BP
ligula S. America
nostra,
lowland
9,000 BP

• Maecenas aliquam maecenas 6,000 BP
ligula S. America
nostra,
lowland
9,000 BP
S. America
Highland
4,000 BP

PC 1 and 3, suggesting that the similarity of highland maize to
parviglumis may reflect admixture with mexicana.
Admixture Analysis. Simulation of gene flow of mexicana into the
Meso-American Lowland maize group suggests that 13% cu-mulative
differences between lowland and highland maize in terms of
heterozygosity and differentiation from parviglumis (Fig. S3).
Structure analysis (21) of all Mexican accessions lends support
for this magnitude of introgression (Fig. 2). The three subspecies
form clearly separated clusters, but evidence of admixture is
Mexico Monthon Wachirasettakul Andes
Matt Hufford
historical introgression is sufficient to explain observed
with this ancestor is sensitive to introgression from these It therefore is not surprising that estimates of F between
individual maize populations and the common ancestor of three taxa identify the Mexican Highland group as being similar (Fig. 3A). This pattern is maintained in an analysis mexicana, in which Mexican Highland maize is tied the West Mexico group as the most ancestral population (Fig. To mitigate the impact of introgression, we used a slightly
modified approach that excludes both parviglumis and mexicana
and calculates genetic drift with respect to ancestral frequencies
inferred from domesticated maize alone. Because the genetic
Fig. 1. (A) Map of sampled maize accessions colored by genetic group. (B) First three genetic PCs of all sampled accessions.
van Heerwaarden et al. PNAS | January 18, 2011 | vol. 108 | no. 3 | van Heerwaarden et al. 2011 PNAS

independent genetic origins
• 96 samples from four highland/lowland
populations
• 100K SNPs: GBS, Maize SNP50
Takuno et al. 2014 10.5281/zenodo.11692

Density
10–1
10–2
10–3
–4
0
10Observation Mexico
Title Text
Table 2 Inference of demographic parameters
demography explains most
Mexico Model I Model II
differentiation
Likelihood 5592.80 Likelihood 4654.79
↵ 0.92 ↵ 1.5
0.38 0.76
# 1 # 1
of demographic parameters
South America Model I Model III
Model I Model II
5592.80 Likelihood 4654.79
0.92 ↵ 1.5
0.38 0.76
↵ 0.52 ↵ 1.0
0.97 1 0.64
# 88 2 0.95
1 # 1
Model I Model III
Mexico
Lowland
Mexico
Highland
NA
NB
NC
N1 N2
N2P
tD
tE
tF
NA
NB
NC
N1 N2
N2P
tmex
tD
tE
tF
Nmex
Mexico
NA
NB
NC
N1 N2
tD
tE
tF
# 54
N3 N4
NC ĮNA
N1 ȕNC
N2 ȕ

NC
N2P ȖN2
NC ĮNA
N1 ȕNC
N2 ȕ

NC
N2P ȖN2
NC ĮNA
N1 ȕ1NC
N2 ȕ1

N2
N4P ȖN4
tG
N4P
Lowland Highland mexicana Mexico
Lowland
SA
Lowland
SA
Highland
Model IA Model IB Model II
3855.28 Likelihood 8044.71
0.52 ↵ 1.0
0.97 1 0.64
Population structure
We performed a STRUCTURE analysis (Pritchard et al. 2000;
Falush et al. 2003) of our landrace sample, varying the number
of groups from K = 2 to 6 (Figure 1, Figure S3). Most lan-draces
88 2 0.95
# 54
10–1
10–2
10–3
–4
0
Figure 2 Demographic models of maize low- and high-land
populations. Parameters in bold were estimated in
this study. See text for details.
likelihood is a bit better in my original Model IB: We expand Model by incorporating admixture from highland Mexican maize population. ”Mexican” (and thus ”South American”) ”consistent probably OK either way. vote The time of differentiation between occurs at tmex generations ago. is assumed to be constant at Nmex. the Mexican highland population between the Mexican lowland from the teosinte mexicana .
Model II: The final model is American lowland and highland was used for simulating SNPs below). At time tF , the Mexican Takuno et al. 2014 10.5281/zenodo.11692
populations are differentiated, after splitting are determined A
Lowlands
Highlands
Observation Expectation Residual
Model IA
Model IB
Density
10were assigned to groups consistent with a priori popu-lation
definitions, but admixture between highland and lowland
A
B
Lowlands
Highlands
Observation Mexico
South America
Highlands
Lowland
Mexico
Highland
NA
NB
NC
N1 N2
N2P
Nmex
NA
NB
NC
N1 N2
tD
tE
tF
N3 N4
NC ĮNA
N1 ȕNC
N2 ȕ

N2
N4P ȖN4
tG
N4P
mexicana Mexico
Lowland
SA
Lowland
SA
Highland
Model IB Model II
Demographic models of maize low- and high-land
Parameters in bold were estimated in
text for details.
likelihood is a bit better in my original model.
Model IB: We expand Model IA for the Mexican populations
by incorporating admixture from the teosinte mexicana to the
highland Mexican maize population. do we say ”Mexico population” or
”Mexican” (and thus ”South American”) ”population” throughout? as long as we’re
consistent probably OK either way. vote to Mexican population second
The time of differentiation between parviglumis and mexicana
occurs at tmex generations ago. The mexicana population size
is assumed to be constant at Nmex. At tF generations ago,
the Mexican highland population is derived from admixture
between the Mexican lowland lowlands
population and a portion Pmex
from the teosinte mexicana .
Model II: The final model is for the Mexican lowland, S.
American lowland and highland populations. This model
was used for simulating SNPs with ascertainment bias (see
below). At time tF , the Mexican and S. American lowland
populations are differentiated, and the sizes of populations
after splitting are determined by #1. At time tG, S. Amer-ican
highlands
density
Mexico
observed expected

little evidence for convergent sweeps
Density
of altitude include transport S3). Overall, fell under to hypoxia” than the The strongest endothelial 1 (EPAS1) EPAS1 was branch relative 2). In order PBS simulations model. None the PBS remained for the number Bonferroni although after correcting enrichment also contribute EPAS1 factor 2a factors lowlands
10–1
10–2
–3
101
10–1
10–2
10–3
–4
0
10Fig. 1. Two-dimensional unfolded site frequency spectrum for SNPs in Tibetan (x axis) and Han (y axis)
population samples. The number of SNPs detected is color-coded according to the logarithmic scale
plotted on the right. Arrows indicate a pair of intronic SNPs from the EPAS1 gene that show strongly
elevated derived allele frequencies in the Tibetan sample compared with the Han sample.
Yi et al. 2010 Science
REPORTS
Likelihood 4654.79
Maize Han Chinese
Tibetan
Model II
↵ 1.5
0.76
# 1
-log(p) S. America
Model III
PS
Likelihood 8044.71
↵ 1.0
PM
1 0.64
2 0.95
# 54
19 SNPs
668 SNPs
390 SNPs
90,702 SNPs
-log(p) Mexico
Figure 5 Scatter plot of log1 0P-values of observed FST
values based on simulation from estimated demographic
models. P-values are shown for each SNP in both Mex-ico
(Model IB; PM on x-axis) and South America (Model
II; PS on y-axis). Red, blue, orange and gray dots rep-resents
SNPs showing significance in both Mexico and
South America, only in Mexico, only in South America,
respectively (see text for details). The number of SNPs in
Lowlands
Highlands
Observation Expectation Model Model Density
–4
10highlands
0
1
0.38 0.76
# 1 # 1
South America Model I Model III
↵ 0.52 ↵ 1.0
0.97 1 0.64
# 88 2 0.95
# 54
Population structure
We performed a STRUCTURE analysis (Pritchard et al. 2000;
Falush et al. 2003) of our landrace sample, varying the number
of groups from K = 2 to 6 (Figure 1, Figure S3). Most lan-draces
were assigned to groups consistent with a priori popu-lation
definitions, but admixture between highland and lowland
populations was evident at intermediate elevations (⇠ 1700m).
Consistent with previously described scenarios for maize dif-fusion
(Piperno 2006), we find evidence of shared ancestry
between lowland Mexican maize and both Mexican highland
and S. American lowland populations. Pairwise FST among
B
Lowlands
Highlands
South America
Lowlands
Highlands
Observation Density
10–1

theory predicts little convergence
0.000 0.002 0.004 0.006
truth
2*s/var
cline location
ACTGCTG
• Build on models of parallel adaptation
−1000 −500 0 500 1000
distance (km)
ACTCCTG
•Model new mutation vs. gene flow
prob of survival
Peter Ralph
(USC)

0.000 0.002 0.004 0.006
truth
2*s/var
cline location
ACTGCTG
−1000 −500 0 500 1000
distance (km)
ACTGCCTG
prob of survival
Peter Ralph
(USC)
Tmut = 1/mut = 2μ⇢Asb
⇠2 ⇡ 104 gens

0.000 0.002 0.004 0.006
truth
2*s/var
cline location
ACTGCTG
−1000 −500 0 500 1000
distance (km)
ACTGCCTG
prob of survival
Peter Ralph
(USC)
Tmut = 1/mut = 2μ⇢Asb
⇠2 ⇡ 104 gens
Tmig = (2/N) exp(Rp2sm/) ⇡ 5 ⇥ 1034 gens

polygenic adaptation
standing
variation

no change in frequency for growth SNPs
Biomass (Hot-Cold)
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GWAS
−1.0 −0.5 0.0 0.5 1.0
indHei−Mex_10−3
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0.05 0.15 0.25 0.35 0.45 0.55 0.65 0.75 0.85 0.95
Mexico
lowland allele freq.
Highland - Lowland freq. difference
Sofiane Mezmouk, unpublished

in progress: mapping pops
M Hufford (ISU), R. Sawers (Langebio)
Summer 2013
S. Flint-Garcia (MU)
Winter 2012
MX x MX
F2
SA x SA
F2
Highland Landrace (PT) x
B73 BC2 NILs
Highland x Lowland Landrace
F2 populations

the genome’s a mess
A2. Divergence, repeats, or PAVs?
166100000
165900000
165700000
0e+00 1e+05 2e+05 3e+05 4e+05
Query Position
Subject Position
chromosome
1
2
3
4
5
6
7
8
Subject position
Brunner Mo17 contig position et al. 2005 Plant Cell
B73 genome position

…and that mess is important
all SNPs GWAS hits
Wallace et al. unpublished

Kolmogorov–Smirnov test). FST outliers …and that mess is important
SNPs associated with the architecture in a diverse maize panel (Flint-all SNPs GWAS hits
fold-Wallace et al. unpublished
maximum rank distribution of these lists.
further control for nonindependence of SNPs within
putative inversions, we conducted an additional BAYENV
fold nongenic enrichment
enrichment
Pyhäjärvi et al. 2013 GBE

transposable elements: 85% of maize
McClintock 1984 Science
Baucom et al. 2009 PLoS Genetics
Damon Lisch

TEs impact morphology, flowering time
Studer et al. 2011 Nature Genetics
Ducrocq et al. 2008 Genetics
Yang et al. 2013 PNAS
tb1
ZmCCT
lines that were identical at both mite and CGindel587,
which is consistent with no QTL of major effect being
detected at Vgt1. Finally, no QTL has been reported in
bin 8.05 in three distinct mapping populations involv-ing
F2 and MBS847 (Mechin et al. 2001; Poupard et al.
2001; Bouchez et al. 2002). These inbred lines differ at
mite but share the same allele at CGindel587.
Relationship between allele frequencies and
geographical origin: Data obtained in the inbred line
frequencies varying from 0.3 in the late tropical to 0.87 in the European and Northern Flint with an intermediate frequency of 0.45 in Stiff Corn Belt Dent groups. For ease of genotyping considering its high LD with CGindel587 when genetic diversity is addressed, we used mite as CGindel587 and analyzed its frequency in a collection (Figure 2). This collection exhibits cline for flowering time (supplemental Figure 2.—distribution (A)for256European
and American and (B) for 77 landraces America and considering and elevation. analysis was focused on its strong association flowering time level of LD with Moreover it could genotyped by on a standard Genotyping was on a bulk of population as by Dubreuil (2006). Additional is given in Materials and vgt1

Control Cold Length of 4th
-3 0 3
B O M B M O B O M B M O
Heat Salt Chill UV
Log2(Stress/Control)
Length of the
longest root
dagaf
flip
Zm02117
stress response associated with TEs
Cold Heat Salt UV
B
4% 4%
Control
Cold
Zm03238
ipiki
jeli
gyma
naiba
joemon
pebi
3% 4%
Length of the
Stress activated – near TEs Stress up-regulated – near TEs
longest root
cm
A
B
C
Control Cold Length of 4th
leaf
Hierarchical Clustering
Downloaded from http://Makarevitch B O M B M O B O M B M O
Heat Salt Chill UV
Log2(Stress/Control)
et al. 2014 bioRxiv
C
leaf
Hierarchical Clustering
-3 0 3
control
cold
Cold Heat Salt UV
odoj
Zm05382
nihep
riiryl
uwum
ubel
alaw
etug
Cold Heat Salt UV
0 1.5 2.5 6 9
10
5
0
-5
-10
ipiki etug
Cold
Heat
Salt
UV
Log2(stress/control)
E
41% 52%
17% 3%
Cold
(3624 genes)
Heat
(2454 genes)
High salt
(4267 genes)
3% 2%
UV
(3450 genes)
45%
35%
45%
47%
40%
55%
Stress activated – not near TEs Stress up-regulated – not near TEs

enrichment of specific TEs near genes
Heat Salt UV
Heat Salt UV
Downloaded from http://biorxiv.org/ on September 9, 2014
raider
dagaf
flip
Zm02117
Zm03238
odoj
ipiki
Zm05382
jeli
nihep
riiryl
uwum
ubel
alaw
gyma
naiba
joemon
pebi
etug
Cold Heat Salt UV
Zm00346
0 1.5 2.5 6 9
C
15
10
5
0
-5
-10
ipiki etug Log2(stress/control)
Cold
Heat
Salt
UV
D
41% 52%
3% 4%
Cold
genes)
4% 4%
Heat
(2454 genes)
High salt
(4267 genes)
3% 2%
UV
(3450 genes)
45%
3%
45%
47%
40%
55%
Makarevitch et al. 2014 bioRxiv

enrichment of specific TEs near genes
Heat Salt UV
Heat Salt UV
A
raider
dagaf
flip
Zm02117
Zm03238
odoj
ipiki
Zm05382
jeli
nihep
riiryl
uwum
ubel
alaw
gyma
naiba
joemon
pebi
etug
Cold Heat Salt UV
Zm00346
0 1.5 2.5 6 9
C
15
10
5
0
-5
-10
ipiki etug Log2(stress/control)
-100
-500
-2000
-10000
Cold
Heat
Salt
UV
D
41% 52%
3% 4%
Cold
genes)
4% 4%
Heat
(2454 genes)
High salt
(4267 genes)
1.4
1.2
1
0.8
0.6
0.4
0.2
B
3% 2%
UV
0
Proportion with CBF
(3450 genes)
45%
3%
45%
47%
binding site
40%
55%
Zm05382
jeli
odoj
nihep
raider
uwum
Zm03228
dagaf
Zm02117
alaw
ubel
0 .15 .40 flip
riiryl
Zm00346
ipiki
pebi
gyma
naiba
joemon
etug
TSS
Zm05382
nihep
raider
uwum
Zm03228
dagaf
Zm02117
Zm00346
pebi
gyma
naiba
joemon
Cold
Heat
Salt
UV
Random TEs
Random genomic regions
1.4
1.2
1
0.8
0.6
0.4
Cold
Heat
Salt
UV
Random TEs
alaw
ubel
A
10000
B
-100
100
500
2000
10000
-500
-2000
-10000
0 .15 .40 1
100
TSS
jeli
odoj
flip
riiryl
ipiki
etug
500
2000
Average # CBF binding
sites per element
Figure S1. Properties of TE insertions that condition stress-responsive expression. (A) In our initial
screening we only analyzed TE insertions located within 1kb of the TSS. Here we assessed the
proportion of genes that exhibit stress-responsive expression for TE insertions located at different
distances from the TSS (for the stress condition most associated with each TE family). Some of the TE
families appear to only affect genes if they are inserted quite near the TSS while others can have
influences at distances. (B) The CBF/DREB transcription factors have been associated with stress-responsive

new insertions activate expression
Downloaded from http://biorxiv.3.5
3.0
2.5
2.0
1.5
1.0
0.5
-0.5
A
100%
80%
60%
40%
20%
GRMZM2G108149
GRMZM2G071206
Lines with the
TE insertion
Lines without the
TE insertion
14
Log2(stress/control) control)
12
10
0 2 4
6 8
12
10
0 2 4 6 8
-2
Lines with the
TE insertion
Lines without the
TE insertion
12
10
0 2 4
6 8
-2
GRMZM2G400718
C
D 2.0
1.5
1.0
GRMZM2G102447
-2
Lines with the
TE insertion
Lines without the
TE insertion
A
B
0.0
Heat
Cold
Salt
UV
B73
Mo17
Oh43
1 2 3 4 5 6 7 8 9 10
- - + - - + - + - - ++ - - + - - + - - + - - + - - + - - +
Gene
TE
presence
0%
alaw
dagaf
etug
flip
gyma
ipiki
jeli
joemon
naiba
nihep
odoj
pebi
raider
riiryl
ubel
uwum
Zm00346
Zm02117
Zm03238
Zm05382
B
Percent of conserved
genes
*
**
* * *
*
*
* * *

evolutionary patterns differ among TEs
Michelle Stitzer, unpublished

fitness cost of inversions
Griffiths et al. 2010 10th Ed.

limited underdominance in maize
1072 20% M. P. MAGUIRE 34%
Maguire 1966 Genetics
46%
34%
nonhomologous none loop

of Z. mays with a genome-wide set of 941 SNPs from 2782
samples. Using computationally phased genotypic data, we
searched for pairs of markers in high LD (r2 . 0.6) and
separated by .1 Mb. Our scan identified two such regions,
an !50-Mb region on chromosome 1 and an !15-Mb span
of chromosome 8. Because the region on chromosome 8 is
near a likely assembly error in the reference genome (J.
Glaubitz, unpublished data), we focused our analysis on
chromosome 1. The region of high LD on chromosome 1
in our data corresponds closely to the 65- to 115-Mb region
on the physical map of the reference mays genome (B73
RefGen v2, release 5a.59, 2010–2011) recently reported
by Hufford et al. (2012) as a putative inversion. Our data
reveal high LD (mean r2 = 0.24) among the 17 SNPs from
Mb 65.09 to 106.16 (Figure 1), compared to a genome-wide
average of 0.004. Gametic disequilibrium, as estimated from
unphased SNP genotyping data, also demonstrates this ex-cess
Inv1n common and old
bridges and acentric fragments at anaphase I (Dawe and
Cande 1996).
Results
We examined the level of LD in each of the three subspecies
of Z. mays with a genome-wide set of 941 SNPs from 2782
samples. Using computationally phased genotypic data, we
searched for pairs of markers in high LD (r2 . 0.6) and
separated by .1 Mb. Our scan identified two such regions,
an !50-Mb region on chromosome 1 and an !15-Mb span
of chromosome 8. Because the region on chromosome 8 is
near a likely assembly error in the reference genome (J.
Glaubitz, unpublished data), we focused our analysis on
chromosome 1. The region of high LD on chromosome 1
in our data corresponds closely to the 65- to 115-Mb region
on the physical map of the reference mays genome (B73
RefGen v2, release 5a.59, 2010–2011) recently reported
by Hufford et al. (2012) as a putative inversion. Our data
reveal high LD (mean r2 = 0.24) among the 17 SNPs from
Mb 65.09 to 106.16 (Figure 1), compared to a genome-wide
average of 0.004. Gametic disequilibrium, as estimated from
unphased SNP genotyping data, also demonstrates this ex-cess
also evident in genotypic data from a panel of 13 individuals
of parviglumis genotyped using the 55,000 SNPs on the
MaizeSNP50 Illumina Infinium Assay (Hufford et al.
2012), suggesting that the LD observed is not an artifact
of the genotyping platform used.
The extended region of high LD on chromosome 1
is a putative inversion
Because mays and the teosintes are outcrossing taxa with
large effective population sizes, LD in the genome gener-ally
bp in domesticated mays) (Remington et al. 2001). The
region of high LD is distinct from both the centromere
(Wolfgruber et al. 2009) and known heterochromatic
knobs (Buckler et al. 1999) and exhibits relatively low re-combination
unexpected, and while parviglumis and mexicana show
evidence of high LD in this chromosomal region, levels
of LD in our large sample of domesticated mays are similar
to genome-wide averages (Figure 1). Other wild taxa also
do not show an excess of LD on the short arm of chromo-some
ascertainment bias. Finally, a recent genetic map from
a BC2S3 population derived from a cross between a mays
line and a parviglumis line with the putatively inverted
arrangement shows no crossovers inside the !50-Mb span
in the 881 progeny genotyped, consistent with the puta-tive
Fang et al. 2012 Genetics
of LD (data not shown). Finally, high levels of LD are
declines rapidly with distance (r2 , 0.1 within 1500
(Figure 1). An !50-Mb span of high LD is
of LD (data not shown). Finally, high levels of LD are
also evident in genotypic data from a panel of 13 individuals
of parviglumis genotyped using the 55,000 SNPs on the
MaizeSNP50 Illumina Infinium Assay (Hufford et al.
2012), suggesting that the LD observed is not an artifact
of the genotyping platform used.
The extended region of high LD on chromosome 1
is a putative inversion
Because mays and the teosintes are outcrossing taxa with
large effective population sizes, LD in the genome gener-ally
1, although our power to measure LD in these sam-ples
is likely hampered by smaller sample size and SNP
declines rapidly with distance (r2 , 0.1 within 1500
Figure 1 Population genetic evidence for the Inv1n inversion. Top, cu-mulative
genetic distance by physical position along chromosome 1. The
dashed curve is based on the teosinte–maize backcross map of Briggs
et al. (2007) and the solid curve is from the maize nested association-mapping
(NAM) population (Yu et al. 2008). Bottom, haplotype number
(blue curve) and FST between the inverted and standard arrangements
(red curve). The number of haplotypes present across chromosome 1 was
#
#
Figure'S3###Geographic#distribution#of#the#33#parviglumis#populations.#The#size#of#the#circle#is#proportional#to#the#
Inv1n#frequency,#and#color#represents#elevation.#The#study#area#in#Mexico#is#shown#in#the#inset.##
#########################

Neighbor-joining tree for all SNPs outside Inv1n, using 15 parviglumis inbred lines. (B) Neighbor-joining tree for all SNPs inside Inv1n, using
inbred lines. (C) Neighbor-joining tree for all unique haplotypes in each taxon, using all SNPs inside Inv1n. The haplotypes in the gray
multiple approaches to estimate the age of
the resequencing data. Using the MCMC ap-proach
Becquet and Przeworski (2007), which estimates
divergence time from patterns of shared polymorphism un-der
an isolation model, divergence was estimated to be
!296,000 generations, with a 95% confidence interval
the Inv1n-I arrangement.
Inv1n common and old

Inv1n: selection and associations
homozygous for alternate arrangements (Mano et al. 2012),
we view these multiple lines of evidence as a strong case that
recombination is suppressed due to an inversion in this re-gion,
henceforth identified as Inv1n.
To test for evidence of pairing and recombination within
the large Inv1n region, we examined male meiocytes from
six F1 plants derived from two crosses between mays and an
inbred parviglumis line containing Inv1n. Both hybrids
revealed a low frequency of dicentric bridge formation at
!4% (7/167), but no acentric fragments were observed
(Table S5). Although such bridges were rare, an anaphase
I bridge in a plant heterozygous for Inv1n was observed
(Figure S1). In addition, we observed no obvious reduction
in pollen viability or seed set in a total of five F1 plants (data
not shown).
Haplotype variation and divergence time
STRUCTURE (Pritchard et al. 2000; Falush et al. 2003) anal-ysis
of SNPs on all 1936 parviglumis chromosomes inside
Inv1n shows the highest likelihood for K = 2 clusters, a pat-tern
not seen from the full set of genome-wide SNPs (data
not shown). These groups are hereafter referred to as Inv1n-I
and Inv1n-S for the inverted and standard arrangements,
respectively (Figure 2). Recombination among loci within a
chromosomal arrangement should be unaffected, and levels
of LD within Inv1n-I (mean r2 = 0.11) and Inv1n-S arrange-ments
(mean r2 = 0.07) are indeed low and similar to back-ground
levels (Figure S2). Average FST between chromosomes
with alternate arrangements is notably higher inside the Inv1n
region (0.54) than across the rest of the genome (0.01) (Fig-ure
1). Genetic distance among accessions for SNPs along
chromosome 1 outside the Inv1n region shows little evidence
of haplotype structure (Figure 3A), while genetic distance for
SNPs inside Inv1n divides parviglumis into two clear haplo-typic
groups representing Inv1n-I and Inv1n-S (Figure 3B).
The Inv1n-S cluster includes all taxa of Zea and Tripsacum in-vestigated,
and it is parsimonious to assume that the Inv1n-I
cluster, present only in parviglumis and mexicana, represents
the derived inverted arrangement (Figure 3C). Despite strong
differentiation, the two arrangements share polymorphic SNPs
(Figure 2), even in homozygous individuals unaffected by hap-lotype
phasing (data not shown). Among the 968 parviglumis
samples, 345 (35.6%) are heterozygous at Inv1n, while 369
(38.1%) and 254 (26.3%) are homozygous for the Inv1n-I
Figure 2 Diagram of haplotype diversity in parviglumis based on the 17
SNPs within Inv1n. Haplotypes are divided into the two clusters identified

Nielsen 2004; Nielsen et al. 2005; McVean 2007). However,
the largest sweep identified in maize to date is only 1.1 Mb
(Tian et al. 2009), and both the age of the inversion and
common tests for departures from neutrality do not provide
evidence of strong selection. Another alternative explana-tion
would be the presence of strong negative interactions
between distantly linked loci, potentially due to synthetic
lethality (Boone et al. 2007). Such interactions should not
Figure 5 (A) Bayes factors for correlation between allele
frequencies and altitude in 33 natural parviglumis popula-tions.
Inv1n is indicated by red vertical lines. The 99th
percentile of the distribution of Bayes factors is indicated
by a horizontal dashed line. Chromosomes 1–10 are plot-ted
in order and in different colors. (B) Association be-tween
all SNPs and culm diameter. SNPs significant at
5% FDR are above the dashed line.
region (Burnham 1962; Maguire and Riess 1994; Lamb et al.
2007). When gene density is low, such as in pericentromeric
regions, or there is a lack of continuous homology, chromo-somes
will often synapse in a nonhomologous manner with-out
recombination (McClintock 1933). In maize, for example,
an inversion on the long arm of chromosome 1 similar in size
to Inv1n (19 cM) was seen to undergo homologous pairing in
only about one-third of cases (Maguire 1966). Since Inv1n is
Temperature
Culm diameter

r2=0.34 Temperature
Nielsen 2004; Nielsen et al. 2005; McVean 2007). However,
the largest sweep identified in maize to date is only 1.1 Mb
(Tian et al. 2009), and both the age of the inversion and
common tests for departures from neutrality do not provide
evidence of strong selection. Another alternative explana-tion
would be the presence of strong negative interactions
between distantly linked loci, potentially due to synthetic
lethality (Boone et al. 2007). Such interactions should not
0.0 0.2 0.4 0.6 0.8 1.0
Inversion Frequency
Figure 5 (A) Bayes factors for correlation between allele
frequencies and altitude in 33 natural parviglumis popula-tions.
Inv1n is indicated by red vertical lines. The 99th
percentile of the distribution of Bayes factors is indicated
by a horizontal dashed line. Chromosomes 1–10 are plot-ted
in order and in different colors. (B) Association be-tween
all SNPs and culm diameter. SNPs significant at
5% FDR are above the dashed line.
600 800 1000 1200 1400 1600
Altitude (m)
region (Burnham 1962; Maguire and Riess 1994; Lamb et al.
2007). When gene density is low, such as in pericentromeric
regions, or there is a lack of continuous homology, chromo-somes
will often synapse in a nonhomologous manner with-out
recombination (McClintock 1933). In maize, for example,
an inversion on the long arm of chromosome 1 similar in size
to Inv1n (19 cM) was seen to undergo homologous pairing in
only about one-third of cases (Maguire 1966). Since Inv1n is
Culm diameter

large inversions common, clinal
Inv9d.
haplotype group is in the y-axis. Colors indicate populations. A) nIv1n, B) Inv4m and C)
they differ) of each haplotype from the most distal haplotype in the main low diversity
and haplotype distance within each inversion. Distance (as a number of SNPs for which
Figure S8 Altitudinal clines of three inversions presented as a relationship between altitude
Inv9d

!

Inversion Frequency

Altitude

!$

Figure S8 Altitudinal clines of three inversions presented as a relationship between altitude
and haplotype distance within each inversion. Distance (as a number of SNPs for which
they differ) of each haplotype from the most distal haplotype in the main low diversity
haplotype group is in the y-axis. Colors indicate populations. A) nIv1n, B) Inv4m and C)
Inv9d.

Complex adaptation in Zea

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Complex adaptation in Zea