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Supporting Information | Turcotte et al.
New Phytologist Supporting Information The impact of domestication on resistance to two generalist herbivores across 29
independent domestication events Martin M. Turcotte, Nash E. Turley and Marc. T. J. Johnson
The following Supporting Information is available for this article: Methods S1–S3, Fig. S1, Tables
S1–S4
Methods S1 Methodological details of the characterization of plant traits
To understand how domestication affects the expression of putative defensive traits we measured
10 plant traits. From each plant we measured average leaf toughness from two fully expanded
leaves as the grams of force required to penetrate a leaf surface using a force gauge penetrometer
(Type 516; Chatillon, USA). We measured leaf wet weight to 10-6 g from a single leaf disc (7.91
mm2) collected from a fully expanded leaf using an ultra micro balance (XP2U, Mettler Toledo,
USA). Leaf discs were removed adjacent to the main veins. We calculated trichome density by
averaging counts on each side of the discs. We dried leaf discs for three weeks at room
temperature and measured their dry mass to 10-6 g. Specific leaf area (SLA) was calculated as area
of the hydrated leaf disc surface (mm2) divided by dry mass (mg). We calculated leaf dry matter
content (LDMC) as dry weight (mg) divided by its wet weight (g).
Phloem sugars were quantified by first collecting phloem samples using an EDTA
extraction procedure from each plant (Wilkinson & Douglas, 2003). Given the variety of growth
forms we inserted either a large leaf with its petiole or a portion of the stem with its attached
shoots into 300 µL of 5 mM Na2EDTA solution at pH 7.0 for 45 minutes. The extraction was
carried out in a cooler at room temperature that contained beakers filled with saturated KH2PO4
solution to maintain high humidity. Extracts were filtered using 4 mm nylon filters (0.45 µm, Cat#
02542903, Perkin Elmer, USA). Analyses of plant traits treated plant species as the unit of
replication, and so we combined 10 µL of each replicate plant extract and measured phloem
sucrose concentration for each species using methods similar to Wilkinson and Douglas (2003).
We first converted sucrose to glucose by adding 10 µL of extract to 10 µL of 40 U / mL invertase
(Cat. # 9458402; Ward’s Science, USA). We then assayed glucose concentration by combining
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Supporting Information | Turcotte et al.
this solution with 155 µL of assay reagent and incubated at 37°C using the GAGO20-KIT (Sigma-
Aldrich; USA). The reaction was stopped after 30 minutes with 150 µL of 12N H2SO4 and the
absorbance of samples were measured at 450 nm at room temperature on a microplate
spectrophotometer (Multiskan GO, Thermo Scientific, USA). Concentrations were calculated by
comparison to glucose standards.
To measure phenolic, carbon, and nitrogen concentration, we harvested all aboveground
plant tissue, flash froze it in liquid nitrogen, and homogenized the tissue using a spatula. This
approach estimates whole plant-level concentrations of metabolites. We placed approximately 60
mg of tissue into 2 mL tubes with several 2.3 mm zirconium beads and further homogenized using
a Powergen High Throughput Homogenizer (Fisher Scientific, USA) until samples were a fine
powder. We combined equal parts powder by weight from each replicate (10 mg) to get one
sample per species. Percent carbon and nitrogen were measured at the Ecosystem Analysis
Laboratory at University of Nebraska-Lincoln using an HCN elemental combustion analyzer (ECS
4010 CHNSO Analyzer, Costech Analytical Technologies, Valencia, USA). We extracted
phenolics by adding 10 mg of powdered tissue to 600 µL of 70% acetone for 45 minutes with
vortexing every 15 minutes. We centrifuged samples at 19000 RCF for 10 minutes, removed 500
µL of the supernatant and added 500 µl of fresh 70% acetone. These steps were repeated four
times resulting in 2 mL of extract from each sample. Acetone was then evaporated off in a vacuum
centrifuge and remaining extract was freeze-dried. Each sample was re-diluted with 200 µL of
distilled water.
Total phenolics and phenolic oxidative capacity were measured following the methods of
Salminen & Karonen (2011). We used a colorimetric assay that first combined 10 µl of our
phenolic extracts with 140 µl of a solution of pH 10 carbonate solution and 0.6% formic acid
solution mixed with a ratio of 9/5 (v/v) respectively in a 96 well plate. Then 50 µl of this solution
was combined with 50 µL 1 N Folin-Ciocalteau and 100 µL 20% sodium carbonate solution. After
60 min of intermittent shaking at 25ºC, absorbance was measured at 730 nm with the microplate
spectrophotometer. Oxidative capacity was measured by first standardizing phenolic
concentration of samples to an absorbance of 1 and oxidizing them by combining 10 µL of
normalized extract with 90 µL of pH 10 carbonate solution. We stopped the oxidization after 90
minutes by adding 50 µL 0.6% formic acid solution. Then, we measured total phenolics on the
oxidized solution as described above. The difference in total phenolics before and after oxidization
was used as a measure of oxidative capacity (Salminen & Karonen, 2011).
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Supporting Information | Turcotte et al.
S3
Supporting Information | Turcotte et al.
Methods S2 Summary of focal R script for statistical analysesThe statistical significance of model terms were tested by creating nested models and comparing
them using likelihood ratio tests with the function anova (model1, model2). We here illustrate the
full models:
1) Herbivore performance: Analyses performed at the level of the plant.
Survival:
glmer( cbind(Live caterpillars, Dead caterpillars) ~ 1 + DOMESTICATION + (1|
PAIR:SPECIES)+ (DOMESTICATION|PAIR), data=data, na.action=na.omit,
family=binomial)
Caterpillar growth or aphid number:
lmer( log(aphids +1) ~ 1 + DOMESTICATION + (1|PAIR:SPECIES)+ (DOMESTICATION|
PAIR), data=data, na.action=na.omit, REML=F)
2) Effect of date of domestication or cultivation and the tissue under selection: Given that a
single value was required for each crop-wild pair we calculated a proportional change in herbivore
performance.
Difference in performance = (Crop mean value – Wild mean value) / mean (Wild mean value,
Crop mean value)
Date of cultivation or domestication:
lmer( Difference in performance ~ Date + (1|FAMILY), data=data, na.action=na.omit,
REML=F)
Tissue under selection:
lmer( Difference in performance ~ Tissue + (1|FAMILY), data=data, na.action=na.omit,
REML=F)
3) Plant traits under domestication: Traits were log-transformed and standardized before
analysis.
lmer( trait ~ 1 + DOMESTICATION + (DOMESTICATION|PAIR), data=SPP,
na.action=na.omit, REML = F)
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Supporting Information | Turcotte et al.
4) Multiple regression analyses of plant traits driving resistance:
Traits were log-transformed and standardized before analysis.
Survival:
dredge( glmer(cbind(Live caterpillars, Dead caterpillars) ~ DOMESTICATION*RGR +
DOMESTICATION*Toughness + DOMESTICATION*Trichomes +
DOMESTICATION*SLA + DOMESTICATION* LDMC + DOMESTICATION*Total
Phenolics + DOMESTICATION*Phloem Sugar+ DOMESTICATION*P.Carb +
DOMESTICATION*P.Nit+ (1|FAMILY/PAIR), data=s.ldata, family=binomial),
beta = F, evaluate = T, rank = AIC, trace = T)
Caterpillar growth and aphids number:
dredge( lmer( log(Aphids +1) ~ DOMESTICATION*RGR + DOMESTICATION*Toughness +
DOMESTICATION*Trichomes + DOMESTICATION*SLA + DOMESTICATION* LDMC +
DOMESTICATION*Total Phenolics + DOMESTICATION*Phloem Sugar+
DOMESTICATION*P.Carb + DOMESTICATION*P.Nit+ (1|FAMILY/PAIR), data=a.ldata,
REML= F), beta = F, evaluate = T, rank = AIC, trace = T)
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Supporting Information | Turcotte et al.
Methods S3 Phylogenetic inference and explicit analyses of resistance
traitsWe inferred the phylogeny of the wild relatives using the Phylomatic v.3 online tool
(http://phylodiversity.net/phylomatic/) based on the R20120829 megatree (Webb & Donoghue,
2005). The tree was dated using fossil dates from Wikstrom et al. (2001) and the “bladj” function
in Phylocom (http://phylodiversity.net/phylocom/ ; Webb et al., 2008). We increased the
resolution of the Poaceae and Solonaceae families using family specific phylogenies (Bouchenak-
Khelladi et al., 2010; Särkinen et al., 2013). Finally, we added the crop species next to their
corresponding wild relative species. Node depths were based on the estimated dates of
domestication (Table S1).
We conducted three different PGLS analyses (Grafen, 1989). These PGLS analyses
account for correlations between species trait values due to shared phylogenetic history given a
specific evolutionary model of trait evolution. The first PGLS assumed a star phylogeny where
there is no phylogenetic structure and all species were equally related. The second utilized our
phylogenetic tree (Fig. 1) and correlations were based on a Brownian Motion model of trait
evolution extracted using the corBrownian function in the “ape” package of R (Paradis, 2005). The
third PGLS utilized the same tree but modeled evolution as an ‘Ornstein-Uhlenbeck’ model of
stabilizing selection, performed using the corMartins function in ape. The PGLS analyses were
conducted using the “nlme” (Pinheiro et al., 2011) package in R (R Core Team, 2013). We could
not conduct a PGLS on survival data using a binomial error distribution and instead we used
arcsine square root transformed of mean percent survivorship. We compared the fit of these PGLS
models to that of the LME models for each herbivore performance trait using AIC values. All
models were fit using REML.
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Supporting Information | Turcotte et al.
Fig. S1 Domestication increased relative growth rate but it did not consistently influence other
plant traits. Values represent the mean difference between log-transformed trait values for crops
and wild relatives. Error bars represent 95% confidence intervals. Positive values imply that
domestication increases trait values. Statistical results of LME analyses (Table S3) are illustrated
above the bars; (*) represents P < 0.05 and (.) represents P < 0.10. “RGR” represents relative
growth rate, “SLA” is specific leaf area, and “LDMC” is leaf dry matter content. Morphological
traits are green whereas chemical traits are in orange. Numbers below bars represent the number of
independent domestication events tested.
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Supporting Information | Turcotte et al.
Table S1 Summary of crop species and their closely related wild relatives. For each crop - wild relative pair we provided the common
name of the crop and its hypothesized relationship with the wild relative. Although crops are selected for multiple tissues throughout
their cultivation history we identified the main tissue subject to direct artificial selection (Target). Years since first cultivation (Cult.)
and domestication (Dom.) are estimated from the literature (see Reference column). Seed sources included: GRIN (USDA Germplasm
Resource Information Network, www.ars-grin.gov), prseeds (Prairie Garden Seeds, Saskatchewan, Canada, http://prseeds.ca/), OSC
(OSC Seeds, Ontario, Canada, www.oscseeds.com), PRGC (Plant Gene Resources of Canada, Agriculture and Agri-Food Canada,
http://pgrc3.agr.gc.ca/index_e.html), Hendrick (Hendrick Seeds, Ontario, Canada, www.hendrickseeds.com), Richters (Richters Herbs,
Ontario, Canada, www.richters.com), Dianeseeds (Dianeseeds, Utah, U.S.A., www.dianeseeds.com), and TGRC (C.M. Rick Tomato
Genetics Resource Center, California, U.S.A., http://tgrc.ucdavis.edu)
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Supporting Information | Turcotte et al.
Table S1
Pair Crop and Relation to
Wild Relative
Species Target Target (simple)
*
Cult. (ybp)
Dom. (ybp)
Seed Source Origin Accession or Variety
References
1 Amaranth Amaranthus cruentus
seed; leaf
repro; veg
7000 6000 GRIN Guatemala PI 658727 (Chan & Sun, 1997;
Meyer et al., 2012)
Progenitor Amaranthus hybridus
GRIN Ohio, U.S.A.
PI 603886
2 Quinoa Chenopodium quinoa
seed repro 7000 5000 prseeds Chile Dave #407 (Rana et al., 2010; Meyer et al., 2012)Closely related
wild congenerChenopodium
albumGRIN India PI 658737;
PI 6587383 Beet Beta vulgaris
vulgarisleaf; root
veg 12000 2400 prseeds Canada Detroit Dark Red
(1892)
(Panella & Lewellen,
2007; Meyer et al., 2012)Progenitor Beta vulgaris
maritimaGRIN France PI 540598;
PI 5406014 Onion Allium cepa
ceparoot veg 7000 5200 OSC NA White
Sweet Spanish
(Gurushidze et al., 2007; Meyer et al.,
2012)Progenitor Allium vavilovii GRIN Former Soviet Union
PI 281727
5 Carrot Daucus carota sativa
root veg 4450 1050 OSC Canada Imperator (Bradeen et al., 2002;
Meyer et al., 2012)
Wild conspecific progenitor
Daucus carota carota
GRIN Switzerland Catalogne race delta PI
4788786 Chicory Cichorium
intybusroot; leaf
veg 2000 450 GRIN France PI 651937 (Van Cutsem et al., 2003; Meyer et al.,
2012)Wild
conspecific progenitor
Cichorium intybus
Peter Kotanen, Univ. of Toronto
Ontario, Canada
Wild collected
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Supporting Information | Turcotte et al.
Pair Crop and Relation to
Wild Relative
Species Target Target (simple)
*
Cult. (ybp)
Dom. (ybp)
Seed Source Origin Accession or Variety
References
7 Lettuce Lactuca sativa leaf veg 7500 4500 OSC Canada Iceburg (de Vries, 1997; Meyer et al., 2012)
Progenitor Lactuca serriola GRIN Israel PI 667819
8 Safflower Carthamus tinctorius inermis
seed repro 4500 3960 Inder Sheoran, Univ. of Toronto
NA WT-5 2006 (Sehgal et al., 2008;
Meyer et al., 2012)Progenitor Carthamus
palaestinusGRIN Israel PI 235663
9 Canola Brassica napus seed repro 7000 3000 OSC Canada NA (Meyer et al., 2012)Wild congener Brassica
tournefortiiGRIN Pakistan PI 426414
10 Radish Raphanus sativus
root veg 5000 4000 OSC Canada Sparkler White Tip
(Yamane et al., 2009;
Meyer et al., 2012)
Progenitor Raphanus raphanistrum
L. Campbell, Ryerson U
USA NA
11 Sweet Potato Ipomoea batatas root veg 10000 4500 GRIN Peru PI 531122 'Jewel'
(Srisuwan et al., 2006;
Meyer et al., 2012)
Progenitor Ipomoea trifida GRIN Mexico PI 618966
12 Cucumber Cucumis sativus fruit repro 10000 3500 OSC Canada Market-more
(Sebastian et al., 2010;
Meyer et al., 2012)
Progenitor Cucumis sativus hardwickii
GRIN and Z. van Herwijner,
R. Zwaan Breeding B.V.
India PI 504564
13 Chickpea Cicer arietinum seed repro 9100 8000 PGRC Canada CN 114662 'CDC Anna'
(Talebi et al., 2009; Meyer et al., 2012)Progenitor Cicer
reticulatumGRIN Turkey PI 593709;
PI 510656; PI 599072
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Supporting Information | Turcotte et al.
Pair Crop and Relation to
Wild Relative
Species Target Target (simple)
*
Cult. (ybp)
Dom. (ybp)
Seed Source Origin Accession or Variety
References
14 Common Bean
Phaseolus vulgaris
seed repro 8000 8000 OSC Canada Stringless green
(Hancock, 2004; Meyer et al., 2012)Progenitor Phaeolus
vulgaris aborigineus
GRIN Mexico, Peru
PI 535411; PI 535422; PI 535416
15 Pea Pisum sativum seed repro 9000 5000 OSC Canada Green Arrow
(Nasiri et al., 2009; Meyer et al., 2012)Progenitor Pisum sativum
elatiusGRIN Sudan,
Turkey, Israel, Latvia
W6 15044; W6 15010; W6 15008; PI 505059; PI 639959
16 Soybean Glycine max seed repro 5000 4000 OSC Canada Grand Forks
(Li et al., 2010; Meyer et al., 2012)Progenitor Glycine soja Hendrick Russia Identity:
009317 Flax Linum
usitatissimum usitatissimum
seed repro 11200 7500 Richters USA S2700G (Meyer et al., 2012; Zohary et al., 2012)
Progenitor Linum bienne GRIN Portugal PI 650308
19 Barley Hordeum vulgare vulgare
seed repro 12000 10000 prseeds Canada Bere (Badr et al., 2000; Meyer et al., 2012)
Progenitor Hordeum vulgare
spontaneum
GRIN Israel PI 296873 to PI
29688321 Corn Zea mays mays seed repro 10000 9000 OSC Canada Sunnyvee (Matsuoka et
al., 2002; Meyer et al.,
2012)Progenitor Zea mays
parviglumisGRIN Mexico Ames
21798
22 Einkorn Triticum seed repro 12700 10000 GRIN Turkey PI 428155 (Heun et al.,
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Supporting Information | Turcotte et al.
Pair Crop and Relation to
Wild Relative
Species Target Target (simple)
*
Cult. (ybp)
Dom. (ybp)
Seed Source Origin Accession or Variety
References
Wheat monococcum monococcum
to PI 428164
1997; Zohary et al., 2012)
Progenitor Triticum monococcum aegilopoides
GRIN Turkey PI 654312 to PI
65432623 Foxtail Millet Setaria italica
italicaseed repro 7500 5900 prseeds Canada NA
(Benabdelmouna et al.,
2001; Meyer et al., 2012)
Progenitor Setaria italica viridis
GRIN Russia Ames 21520
25 Oat Avena sativa seed repro 10000 3000 OSC Canada NA (Meyer et al., 2012; Zohary et al., 2012)Progenitor Avena sterilis PGRC NA CN 3653
'Australian 2651'
28 Pearl Millet Pennisetum glaucum glaucum
seed repro 5000 4000 PGRC NA CN 84424 'IDC 423 '
(Oumar et al., 2008;
Meyer et al., 2012)Progenitor Pennisetum
violaceumPGRC NA CN 87824
'S-88-197'
29 Pepper Capsicum annuum annuum
fruit repro 8000 6000 prseeds Canada Yankee Bell (Aguilar-Melendez et
al., 2009; Meyer et al.,
2012)
Progenitor Capsicum annuum
glabriusculum
GRIN Mexico PI 593491
30 Potato Solanum tuberosum
root veg 10000 8000 PGRC Canada Female Norvalley,
Male Atlantic
(Spooner et al., 2005;
Meyer et al., 2012)
Progenitor Solanum candolleanum
GRIN Bolivia PI 498226; PI 498227
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Supporting Information | Turcotte et al.
Pair Crop and Relation to
Wild Relative
Species Target Target (simple)
*
Cult. (ybp)
Dom. (ybp)
Seed Source Origin Accession or Variety
References
31 Tobacco Nicotiana tabacum
leaf veg 3000 1000 Inder Sheoran, U Toronto
NA Xanthi (Yukawa et al., 2006;
Tushingham et al., 2013)
Progenitor Nicotiana sylvestris
Dianeseeds NA Only the lonely
32 Tomato Solanum lycopersicum
fruit repro NA 1000 OSC Canada Brandywine (Ranc et al., 2008; Meyer et al., 2012)Progenitor Solanum
pimpinellifoliumTGRC LA2533
34 Okra Abelmoschus esculentus
fruit repro NA 3150 GRIN Cote D'Ivore
PI 489794; PI 489854
(Bisht et al., 1997; Meyer et al., 2012)Progenitor Abelmoschus
tuberculatusGRIN India PI 639677;
PI 63967835 Japanese
Barnyard Millet
Echinochloa esculenta
seed repro NA 5000 GRIN China PI 647850 (Hancock, 2004;
Yamaguchi et al., 2005)Progenitor Echinochloa
crus-galliGRIN Afghanista
nPI 211025
36 Indian Barnyard
Millet
Echinochloa frumentacea
seed repro NA 5000 GRIN India PI 183332 (Hancock, 2004;
Yamaguchi et al., 2005)Progenitor Echinochloa
colonaGRIN India PI 647849
NA Information not available
* Simplified groupings for the tissue subject to direct artificial selection “Target (simple)” include: “veg” for vegetative and “repro” for
reproductive tissue.
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Supporting Information | Turcotte et al.
Table S2 Comparison of the fit of four analytical approaches to test how plant traits impact
herbivore performance. Values represent AIC scores for the full multiple regression models fit
using restricted maximum likelihood. Models include nine plant traits, domestication status, and
the interactions between traits and domestication. Each row compares the fit of a LME, with pair
nested within family as random effects, to those of PGLS models. The first PGLS model was
conducted on a star phylogeny. The other two where conducted on the inferred phylogeny (Fig. 1)
and fit with a Brownian motion model or an Ornstein-Uhlenbeck model of evolution. For
caterpillar survival, we could not conduct PGLS analyses using generalized linear binomial
regression, and instead present results from arcsine square-root transformed mean percent survival.
Lower AIC values suggest better fits of the models to the data.
Herbivore
Response
Mixed
Model
Star
Phylogeny
Species
Phylogeny –
Brownian
Motion
Species
Phylogeny –
Ornstein-
Uhlenbeck
Caterpillar
survival
(GLMER)
123.3 NA NA NA
Caterpillar
survival
(% survival)
85.5 130.3 289.0 128.7
Caterpillar
weight168.6 215.9 383.5 217.7
Number of
aphids218.1 281.4 420.3 266.9
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Supporting Information | Turcotte et al.
Table S3 Results of LME analyses testing whether domestication consistently drives changes in
morphological and chemical plant traits. Values represent untransformed fixed effects (means and
± 1 standard error in parentheses). Percent change represents the impact of domestication on trait
value (crop – wild) / wild *100%. “Dom” represents the impact of domestication in the analyses
and “Pair” is the random effect of crop-wild groups.
TraitWild
RelativesCrops %
ChangeP-Values
Dom Pair Dom*PairRGR
(log dry g / day)6.86
(6.75 , 6.97)7.1
(6.98 , 7.22) 3.6 0.03 <0.001 0.288
Toughness(g)
99.9(92.4 , 108)
105.1(95.2 , 115.9) 5.1 0.51 <0.001 0.952
Trichomes(per mm2)
1.41(1.12 , 1.73)
1.03(0.67 , 1.45) -27.0 0.17 <0.001 0.701
SLA(mm2 / mg dry)
36.2(34 , 38.5)
37.1(35.3 , 39.1) 2.7 0.67 0.006 0.143
LDMC(mg dry / g wet)
171.5(162.8 , 180.7)
156.8(147.8 , 166.4) -8.6 0.09 <0.001 0.985
Caterpillar tolerance (Proportion of dry
weight lost)
-0.07(-0.10, -0.04)
-0.04(-0.05 , -0.03) -44.5 0.24 0.242 <0.001
Aphid tolerance(Proportion of dry
weight lost)
-0.02(-0.04 , -0.01)
-0.01(-0.02 , 0) -44.7 0.51 0.770 0.056
Total phenolics(mg gallic acid / g dry
tissue)
10.3(9.6 , 10.9)
11.0(9.9 , 12.2) 6.9 0.27 <0.001 0.052
Phenolic oxidation(mg gallic acid / g dry
tissue)
3.02(2.67 , 3.39)
3.16(2.57 , 3.85) 4.9 0.68 <0.001 0.331
% Nitrogen 3.6(3.47 , 3.72)
3.42(3.24 , 3.6) -4.9 0.15 <0.001 0.784
% Carbon 40.4(40.2 , 40.5)
40.3(40 , 40.5) -0.2 0.70 <0.001 0.705
C:N 11.3(11 , 11.7)
11.9(11.3 , 12.5) 5.3 0.12 <0.001 0.623
Phloem sugar(µg/mL)
0.85(0.71 , 1)
1.02(0.84 , 1.22) 19.8 0.26 <0.001 0.636
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Supporting Information | Turcotte et al.
Table S4 Best fitting multivariate models, Δ AIC <2, explaining variation in three herbivore
performance traits. “AIC weight” represents the relative likelihood of each model compared to all
others (Burnham & Anderson, 2002). “R2m” and “R2
c” represent the marginal and conditional
coefficients of determination, respectively. Plant trait codes include “A” Domestication, “B”
Phloem sugar, “C” % Carbon, “D” % Nitrogen, “E” RGR, “F” Total Phenolics, “G” LDMC, “H”
SLA, “I” Toughness, “J” Trichomes, and the interactions with domestication status including “K”
Dom * Phloem Sugar, “L” Dom * Percent Carbon, “M” Dom * Percent Nitrogen, “N” Dom *
RGR, “O” Dom * Total Phenolics, “P” Dom * SLA, “Q” Dom * Trichomes, and “R” Dom *
LDMC.
Plant traits included Parameters Δ AICAIC
weightR2
m R2c
Caterpillar survival
A+C+E+F+N+O 9 0 0.04 0.39 0.74
A+D+F+G+J+O+Q 10 0.32 0.03 0.43 0.74
A+D+E+F+G+N+O 10 0.39 0.03 0.42 0.75
A+C+D+E+F+N+O 10 0.44 0.03 0.38 0.73
A+D+E+F+N+O 9 0.53 0.03 0.35 0.75
A+D+F+J+O+Q 9 0.64 0.03 0.36 0.72
A+D+F+G+I+J+O+Q 11 0.74 0.03 0.48 0.77
A+D+F+G+M+O 9 0.87 0.02 0.50 0.73
A+D+F+G+J+M+O+Q 11 0.88 0.02 0.46 0.74
A+D+F+J+M+O+Q 10 0.99 0.02 0.40 0.73
A+C+D+F+M+O 9 1.07 0.02 0.46 0.72
A+C+D+I+J+L+Q 10 1.07 0.02 0.55 0.77
A+D+E+F+J+N+O 10 1.16 0.02 0.38 0.75
A+D+F+G+H+J+O+Q 11 1.19 0.02 0.43 0.72
A+D+F+M+O 8 1.2 0.02 0.43 0.72
A+C+E+F+L+N+O 10 1.29 0.02 0.43 0.75
A+D+E+F+G+J+N+O+Q 12 1.4 0.02 0.45 0.76
A+D+F+I+J+O+Q 10 1.41 0.02 0.41 0.74
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Supporting Information | Turcotte et al.
Plant traits included Parameters Δ AICAIC
weightR2
m R2c
A+D+E+F+G+M+N+O 11 1.43 0.02 0.45 0.75
A+C+D+E+F+M+N+O 11 1.43 0.02 0.41 0.73
A+D+F+G+I+J+M+O+Q 12 1.45 0.02 0.51 0.76
A+D+E+F+G+H+N+O 11 1.47 0.02 0.42 0.74
A+C+E+F+I+N+O 10 1.47 0.02 0.39 0.73
A+C+D+E+F+G+N+O 11 1.47 0.02 0.42 0.74
A+D+E+F+J+N+O+Q 11 1.52 0.02 0.38 0.75
A+B+D+G+H+J+K+P+Q 12 1.54 0.02 0.52 0.82
A+C+D+J+L+Q 9 1.55 0.02 0.50 0.74
A+D+E+F+G+J+O+Q 11 1.57 0.02 0.44 0.76
A+C+I+J+L+Q 9 1.57 0.02 0.51 0.78
A+D+E+F+M+N+O 10 1.6 0.02 0.39 0.75
A+D+F+G+H+M+O 10 1.62 0.02 0.49 0.72
A+C+D+E+F+L+N+O 11 1.64 0.02 0.43 0.74
A+D+E+F+G+I+N+O 11 1.64 0.02 0.45 0.75
A+C+D+F+J+O+Q 10 1.65 0.02 0.38 0.70
A+C+D+F+J+M+O+Q 11 1.66 0.02 0.41 0.71
A+D+F+I+J+M+O+Q 11 1.67 0.02 0.46 0.75
A+C+D+E+I+J+L+Q 11 1.69 0.02 0.56 0.80
A+D+F+J+M+O 9 1.71 0.02 0.47 0.74
A+C+F+I+J+L+Q 10 1.72 0.02 0.55 0.77
A+C+D+E+F+J+N+O 11 1.74 0.02 0.40 0.74
A+C+E+F+J+N+O 10 1.81 0.02 0.39 0.74
A+D+E+F+G+J+N+O 11 1.85 0.02 0.42 0.74
A+D+F+G+I+M+O 10 1.86 0.02 0.54 0.75
A+C+E+F+H+N+O 10 1.87 0.02 0.41 0.74
A+B+D+F+J+M+O+Q 11 1.89 0.01 0.43 0.73
A+B+C+E+F+N+O 10 1.91 0.01 0.39 0.74
A+D+E+F+J+O+Q 10 1.95 0.01 0.37 0.74
S17
Supporting Information | Turcotte et al.
Plant traits included Parameters Δ AICAIC
weightR2
m R2c
A+D+E+F+G+I+J+O+Q 12 1.97 0.01 0.49 0.79
A+D+E+F+G+M+O 10 1.98 0.01 0.53 0.76
A+D+E+F+M+O 9 1.99 0.01 0.48 0.76
A+C+E+F+G+N+O 10 1.99 0.01 0.39 0.74
Caterpillar growth
A+D+G+J+Q 9 0.00 0.10 0.27 0.54
A+D+F+G+J+Q 10 0.00 0.10 0.31 0.53
A+D+J+Q 8 0.36 0.08 0.22 0.54
A+D+F+J+Q 9 0.85 0.06 0.25 0.55
A+D+F+G+J+M+Q 11 1.38 0.05 0.33 0.53
A+D+G+J 8 1.44 0.05 0.23 0.51
A+D+G+J+M+Q 10 1.54 0.04 0.28 0.54
A+D+J 7 1.65 0.04 0.19 0.50
A+D+F+G+J+O+Q 11 1.75 0.04 0.31 0.54
A+D+F+G+H+J+Q 11 1.82 0.04 0.31 0.54
A+D+E+G+J+Q 10 1.86 0.04 0.27 0.53
A+D+G+H+J+Q 10 1.87 0.04 0.26 0.54
A+D+E+F+G+J+Q 11 1.87 0.04 0.31 0.53
A+B+D+F+G+J+Q 11 1.90 0.04 0.32 0.54
A+D+F+G+I+J+Q 11 1.90 0.04 0.31 0.55
A+C+D+G+J+Q 10 1.91 0.04 0.28 0.54
A+B+D+G+J+Q 10 1.92 0.04 0.27 0.54
A+D+G+J+P+Q 10 1.92 0.04 0.27 0.54
A+D+J+M+Q 9 1.95 0.04 0.22 0.54
A+D+G+I+J+Q 10 2.00 0.04 0.27 0.54
A+C+D+F+G+J+Q 11 2.00 0.04 0.31 0.53
Aphids
F+J 6 0.00 0.03 0.17 0.89
S18
Supporting Information | Turcotte et al.
Plant traits included Parameters Δ AICAIC
weightR2
m R2c
A+C+G+H+J+L+P+Q+R 13 0.27 0.03 0.15 0.95
F+H+J 7 0.33 0.03 0.20 0.89
A+C+F+G+H+J+L+P+Q+R 14 0.33 0.03 0.20 0.94
C+F+J 7 0.54 0.02 0.17 0.91
A+C+G+H+J+L+P+R 12 0.57 0.02 0.15 0.94
A+C+E+G+H+J+L+P+Q+R 14 0.60 0.02 0.16 0.94
A+C+E+G+H+J+L+P+R 13 0.69 0.02 0.16 0.94
D+F+H+J 8 0.69 0.02 0.21 0.90
A+C+E+F+G+H+J+L+P+Q+R 15 0.85 0.02 0.21 0.94
A+C+F+G+H+J+L+P+R 13 0.85 0.02 0.20 0.94
A+C+E+G+H+J+L+N+P+R 14 0.95 0.02 0.17 0.95
C+F+H+J 8 0.96 0.02 0.19 0.91
A+C+G+H+J+P+R 11 0.99 0.02 0.14 0.94
F+G+H+J 8 0.99 0.02 0.20 0.90
A+C+E+G+H+J+L+N+P+Q+R 15 1.05 0.02 0.17 0.95
C+J 6 1.10 0.02 0.11 0.91
A+C+E+F+G+H+J+L+P+R 14 1.15 0.02 0.21 0.93
D+F+J 7 1.15 0.02 0.18 0.89
A+C+E+F+G+H+J+L+N+P+Q+R 16 1.29 0.02 0.22 0.95
A+C+G+H+I+J+L+P+Q+R 14 1.30 0.02 0.16 0.95
F+H+I+J 8 1.32 0.02 0.22 0.90
C+F+G+H+J 9 1.35 0.02 0.18 0.91
A+C+D+G+H+J+L+P+Q+R 14 1.36 0.02 0.15 0.95
A+C+G+H+J+R 10 1.36 0.02 0.15 0.93
A+C+E+G+H+J+P+R 12 1.37 0.02 0.15 0.93
A+C+G+H+I+J+P+R 12 1.38 0.02 0.16 0.94
A+C+E+F+G+H+J+L+N+P+R 15 1.38 0.02 0.21 0.95
A+C+F+G+H+J+P+R 12 1.43 0.02 0.19 0.93
A+B+C+G+H+J+K+L+P+Q+R 15 1.43 0.02 0.16 0.95
S19
Supporting Information | Turcotte et al.
Plant traits included Parameters Δ AICAIC
weightR2
m R2c
A+C+E+G+H+J+N+P+R 13 1.43 0.02 0.16 0.95
E+F+J 7 1.53 0.01 0.18 0.89
A+B+C+F+G+H+J+L+P+Q+R 15 1.59 0.01 0.20 0.94
B+F+J 7 1.64 0.01 0.17 0.90
A+C+D+G+H+I+J+L+P+Q+R 15 1.68 0.01 0.16 0.95
A+C+F+G+H+J+R 11 1.70 0.01 0.21 0.93
A+B+C+G+H+J+L+P+Q+R 14 1.70 0.01 0.15 0.95
A+C+G+H+I+J+R 11 1.73 0.01 0.17 0.94
D+E+F+H+J 9 1.73 0.01 0.22 0.89
A+C+D+G+H+J+L+P+R 13 1.74 0.01 0.15 0.95
A+B+C+F+G+H+J+K+L+P+Q+R 16 1.74 0.01 0.20 0.95
E+F+H+J 8 1.77 0.01 0.20 0.89
F+G+H+I+J 9 1.80 0.01 0.22 0.91
A+F+J 7 1.83 0.01 0.18 0.89
C+F+H+I+J 9 1.85 0.01 0.20 0.92
A+B+C+G+H+J+K+P+R 13 1.86 0.01 0.16 0.94
A+C+G+H+I+J+P+Q+R 13 1.89 0.01 0.17 0.94
A+C+D+E+G+H+J+L+N+P+R 15 1.90 0.01 0.17 0.96
A+C+E+G+H+I+J+L+P+Q+R 15 1.91 0.01 0.17 0.95
A+C+F+G+H+I+J+L+P+Q+R 15 1.91 0.01 0.21 0.94
A+C+G+H+I+J+L+P+R 13 1.92 0.01 0.16 0.94
B+F+H+J 8 1.93 0.01 0.19 0.90
A+C+D+E+G+H+J+L+N+P+Q+R 16 1.93 0.01 0.17 0.96
A+C+E+F+G+H+J+P+R 13 1.94 0.01 0.20 0.93
A+C+F+G+H+J+L+O+P+R 14 1.95 0.01 0.22 0.94
A+B+C+G+H+J+K+R 12 1.95 0.01 0.17 0.94
C+H+J 7 1.96 0.01 0.11 0.91
F+I+J 7 1.98 0.01 0.17 0.89
A+C+E+F+G+H+J+N+P+R 14 1.98 0.01 0.21 0.94
S20
Supporting Information | Turcotte et al.
Plant traits included Parameters Δ AICAIC
weightR2
m R2c
A+C+D+F+G+H+J+L+P+Q+R 15 1.99 0.01 0.19 0.94
F+G+J 7 2.00 0.01 0.17 0.89
References for Supporting InformationAguilar-Melendez A, Morrell PL, Roose ML, Kim S-C. 2009. Genetic diversity and structure in
semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico. American
Journal of Botany 96(6): 1190-1202.
Badr A, Muller K, Schafer-Pregl R, El Rabey H, Effgen S, Ibrahim HH, Pozzi C, Rohde W,
Salamini F. 2000. On the origin and domestication history of barley (Hordeum vulgare).
Molecular Biology and Evolution 17(4): 499-510.
Benabdelmouna A, Abirached-Darmency M, Darmency H. 2001. Phylogenetic and genomic
relationships in Setaria italica and its close relatives based on the molecular diversity and
chromosomal organization of 5S and 18S-5.8S-25S rDNA genes. Theoretical and Applied
Genetics 103(5): 668-677.
Bisht IS, Patel DP, Mahajan RK. 1997. Classification of genetic diversity in Abelmoschus
tuberculatus germplasm collection using morphometric data. Annals of Applied Biology 130(2):
325-335.
Bouchenak-Khelladi Y, Verboom GA, Savolainen V, Hodkinson TR. 2010. Biogeography of
the grasses (Poaceae): a phylogenetic approach to reveal evolutionary history in geographical
space and geological time. Botanical Journal of the Linnean Society 162(4): 543-557.
Bradeen JM, Bach IC, Briard M, Le Clerc V, Grzebelus D, Senalik DA, Simon PW. 2002.
Molecular diversity analysis of cultivated carrot (Daucus carota L.) and wild Daucus populations
reveals a genetically nonstructured composition. Journal of the American Society for Horticultural
Science 127(3): 383-391.
Burnham KP, Anderson DR. 2002. Model selection and multimodel inference: a practical
information-theoretic approach. New York: Springer-Verlag.
S21
Supporting Information | Turcotte et al.
Chan KF, Sun M. 1997. Genetic diversity and relationships detected by isozyme and RAPD
analysis of crop and wild species of Amaranthus. Theoretical and Applied Genetics 95(5-6): 865-
873.
de Vries IM. 1997. Origin and domestication of Lactuca sativa L. Genetic Resources and Crop
Evolution 44(2): 165-174.
Grafen A. 1989. The phylogenetic regression. Philosophical Transactions of the Royal Society of
London Series B-Biological Sciences 326(1233): 119-157.
Gurushidze M, Mashayekhi S, Blattner FR, Friesen N, Fritsch RM. 2007. Phylogenetic
relationships of wild and cultivated species of Allium section Cepa inferred by nuclear rDNA ITS
sequence analysis. Plant Systematics and Evolution 269(3-4): 259-269.
Hancock JF. 2004. Plant Evolution and the Origin of Crop Species. Oxford: Oxford University
Press.
Heun M, Schaferpregl R, Klawan D, Castagna R, Accerbi M, Borghi B, Salamini F. 1997.
Site of einkorn wheat domestication identified by DNA fingerprinting. Science 278(5341): 1312-
1314.
Li Y-H, Li W, Zhang C, Yang L, Chang R-Z, Gaut BS, Qiu L-J. 2010. Genetic diversity in
domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence
repeat and single-nucleotide polymorphism loci. New Phytologist 188(1): 242-253.
Matsuoka Y, Vigouroux Y, Goodman MM, G.J. S, Buckler E, Doebley J. 2002. A single
domestication for maize shown by multilocus microsatellite genotyping. Proceedings of the
National Academy of Sciences of the United States of America 99(9): 6080-6084.
Meyer RS, DuVal AE, Jensen HR. 2012. Patterns and processes in crop domestication: an
historical review and quantitative analysis of 203 global food crops. New Phytologist 196(1): 29-
48.
Nasiri J, Haghnazari A, Saba J. 2009. Genetic diversity among varieties and wild species
accessions of pea (Pisum sativum L.) based on SSR markers. African Journal of Biotechnology
8(15): 3405-3417.
Oumar I, Mariac C, Pham J-L, Vigouroux Y. 2008. Phylogeny and origin of pearl millet
(Pennisetum glaucum [L.] R. Br) as revealed by microsatellite loci. Theoretical and Applied
Genetics 117(4): 489-497.
Panella L, Lewellen RT. 2007. Broadening the genetic base of sugar beet: introgression from
wild relatives. Euphytica 154(3): 383-400.
S22
Supporting Information | Turcotte et al.
Paradis E. 2005. Statistical analysis of diversification with species traits. Evolution 59(1): 1-12.
Pinheiro JC, Bates DM, DebRoy S, Sarkar D, R Development Core Team 2011. nlme: Linear
and nonlinear mixed effects models.
R Core Team 2013. R: a language and environment for statistical computing. Vienna, Austria: R
Foundation for Statistical Computing.
Rana TS, Narzary D, Ohri D. 2010. Genetic diversity and relationships among some wild and
cultivated species of Chenopodium L. (Amaranthaceae) using RAPD and DAMD methods.
Current Science 98(6): 840-846.
Ranc N, Muños S, Santoni S, Causse M. 2008. A clarified position for Solanum lycopersicum
var. cerasiforme in the evolutionary history of tomatoes (solanaceae). BMC Plant Biology 8: 130.
Salminen J-P, Karonen M. 2011. Chemical ecology of tannins and other phenolics: we need a
change in approach. Functional Ecology 25(2): 325-338.
Särkinen T, Bohs L, Olmstead RG, Knapp S. 2013. A phylogenetic framework for evolutionary
study of the nightshades (Solanaceae): a dated 1000-tip tree. BMC Evolutionary Biology 13(1):
214.
Sebastian P, Schaefer H, Telford IRH, Renner SS. 2010. Cucumber (Cucumis sativus) and
melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of
melon is from Australia. Proceedings of the National Academy of Sciences of the United States of
America 107(32): 14269-14273.
Sehgal D, Rajpal VR, Raina SN. 2008. Chloroplast DNA diversity reveals the contribution of
two wild species to the origin and evolution of diploid safflower (Carthamus tinctorius L.).
Genome 51(8): 638-643.
Spooner DM, McLean K, Ramsay G, Waugh R, Bryan GJ. 2005. A single domestication for
potato based on multilocus amplified fragment length polymorphism genotyping. Proceedings of
the National Academy of Sciences of the United States of America 102(41): 14694-14699.
Srisuwan S, Sihachakr D, Siljak-Yakovlev S. 2006. The origin and evolution of sweet potato
(Ipomoea batatas Lam.) and its wild relatives through the cytogenetic approaches. Plant Science
171(3): 424-433.
Talebi R, Jelodar N-AB, Mardi M, Fayaz F, Furman BJ, Bagheri N-A. 2009. Phylogenetic
diversity and relationship among annual Cicer species using random amplified polymorphic DNA
markers. General and Applied Plant Physiology 35(1-2): 03-12.
S23
Supporting Information | Turcotte et al.
Tushingham S, Ardura D, Eerkens JW, Palazoglu M, Shahbaz S, Fiehn O. 2013. Hunter-
gatherer tobacco smoking: earliest evidence from the Pacific Northwest Coast of North America.
Journal of Archaeological Science 40(2): 1397-1407.
Van Cutsem P, Du Jardin P, Boutte C, Beauwens T, Jacqmin S, Vekemans X. 2003.
Distinction between cultivated and wild chicory gene pools using AFLP markers. Theoretical and
Applied Genetics 107(4): 713-718.
Webb CO, Ackerly DD, Kembel SW. 2008. Phylocom: software for the analysis of phylogenetic
community structure and trait evolution. Bioinformatics 24(18): 2098-2100.
Webb CO, Donoghue MJ. 2005. Phylomatic: tree assembly for applied phylogenetics. Molecular
Ecology Notes 5: 181-183.
Wikstrom N, Savolainen V, Chase MW. 2001. Evolution of the angiosperms: calibrating the
family tree. Proceedings of the Royal Society B 268(1482): 2211-2220.
Wilkinson TL, Douglas AE. 2003. Phloem amino acids and the host plant range of the
polyphagous aphid, Aphis fabae. Entomologia Experimentalis et Applicata 106(2): 103-113.
Yamaguchi H, Utano A, Yasuda K, Yano A, Soejima A. 2005. A molecular phylogeny of wild
and cultivated Echinochloa in East Asia inferred from non-coding region sequences of trnT-L-F.
Weed Biology and Management 5(4): 210-218.
Yamane K, Lue N, Ohnishi O. 2009. Multiple origins and high genetic diversity of cultivated
radish inferred from polymorphism in chloroplast simple sequence repeats. Breeding Science
59(1): 55-65.
Yukawa M, Tsudzuki T, Sugiura M. 2006. The chloroplast genome of Nicotiana sylvestris and
Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor
is the maternal genome donor of Nicotiana tabacum. Molecular Genetics and Genomics 275(4):
367-373.
Zohary D, Hopf M, Weiss E. 2012. Domestication of Plants in the Old World. Oxford: Oxford
University Press.
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