Table S1. Statistics for the de novo transcriptome assembly.
Total Trinity
components
After Trinity
assembly
66582
Total
Trinity
transcripts
92312
DE analysis
12003
23184
Percent
GC
Average
contig
44.03
Median
contig
length
479
1079.68
Total
Contig
assembled N50
bases
99667695 2274
46.84
1764
2250.70
52180211
2967
Table S2. Fold change for detoxification genes that were differentially regulated in comparisons within and between populations. For
within population comparisons, only genes that were induced on a population’s native host are listed. Fold changes for population
differences represent values for the population in which expression was higher. CPP= coastal prickly pear; LF= laboratory food;
class= EI, environmentally independent or ED, environmentally dependent; population: S= Sonora, C= Santa Catalina Island.
Trinity Gene id
Gene family
D. moj.
BLAST hit
D. mel. ortholog
CPP vs
LF/Santa
Catalina
Island
Saguaro
Population
vs
differences
LF/Sonora (class/population)
comp39362_c1
carboxylesterase
GI13369
neurotactin
3.2
2.7
comp38113_c1
carboxylesterase
GI22473
GI22474
GI22476
esterase P
esterase 6
6.4
comp38113_c0
carboxylesterase
GI22473
GI22474
GI22476
esterase P
esterase 6
comp37771_c0
carboxylesterase
GI22473
GI22474
GI22476
esterase P
esterase 6
18.3
comp38965_c0
carboxylesterase
GI24124
α-esterase-2
11.1
comp38650_c0
carboxylesterase
GI24125
neuroligin 1
3.47
comp36288_c0
carboxylesterase
GI23477
α-esterase-6
comp33391_c2
carboxylesterase
GI10706
CG10175
EI/C: 2.3
comp23912_c0
carboxylesterase
GI13386
CG5665
EI/C: 2.9
EI/S: 27.7
EI/S: 2.3
31.4
ED/S: 4.1
4.9
comp36026_c0
carboxylesterase
GI23292
CG6296
EI/C: 1.8
comp36514_c2
carboxylesterase
GI15322
CG5966
3.0
6.3
comp36514_c3
carboxylesterase
GI15322
CG5966
3.0
5.9
comp35387_c0
carboxylesterase
GI22497
CG7367
14.4
comp38157_c0
carboxylesterase
GI22654
sex-specific
enzyme 2
3.0
comp34213_c0
carboxylesterase
GI23290
CG6283
10.9
comp34213_c1
carboxylesterase
GI23920
CG6283
11.0
comp35867_c0
carboxylesterase
GI16995
CG34447
4.1
comp33195_c1
carboxylesterase
GI23291
CG6295
2.4
comp36036_c0
carboxylesterase
GI24275
CG8526
3.7
comp39760_c4
carboxylesterase
GI23315
lipase 4
2.9
comp38330_c0
cytochrome P450
GI17433
cyp6t1
22.3
84.5
comp36625_c0
cytochrome P450
GI18694
cyp4e1
cyp4e2
cyp4e3
9.3
53.3
comp32867_c0
cytochrome P450
GI23968
GI10480
spook
spookier
5.9
2.3
comp24403_c0
cytochrome P450
GI24740
cyp6d5
EI/S: 5.7
comp64131_c0
cytochrome P450
GI24740
cyp6d5
EI/S: 6.7
comp39297_c4
cytochrome P450
GI24740
cyp6d5
comp38651_c0
cytochrome P450
GI22266
cyp313a4
comp38854_c0
cytochrome P450
GI23350
GI23351
cyp304a1
comp38469_c0
cytochrome P450
GI20372
GI18650
comp31344_c0
cytochrome P450
GI17558
cyp4p3
cyp4p1
cyp4p2
cyp28a5
2.9
comp38253_c0
cytochrome P450
GI11726
cyp312a1
2.4
comp30434_c0
cytochrome P450
GI13888
Disembodied
3.9
comp38308_c1
cytochrome P450
GI11185
Phantom
3.5
comp34136_c0
glutathione S-transferase
GI11974
sepia
comp32794_c0
UDP-glycosyltransferase
GI17522
GI17523
CG5999
CG5724
comp33150_c0
UDP-glycosyltransferase
GI22630
ugt86Dd
EI/S: 3.8
comp37376_c0
UDP-glycosyltransferase
GI22630
ugt86Dd
EI/C: 3.8
comp30485_c0
UDP-glycosyltransferase
GI22630
ugt86Dd
EI/S: 4.1
3.53
ED/S: 2.9
EI/S: 3.1
5.58
EI/C: 2.2
EI/C: 1.8
EI/S: 11.2
2.8
comp33973_c0
UDP-glycosyltransferase
GI17058
ugt36Bb
comp36246_c0
UDP-glycosyltransferase
GI20954
CG17323
comp26928_c0
UDP-glucosyltransferase
GI13887
CG18869
EI/C: 3.3
3.6
ED/C: 2.0
EI/C: 4.6
Figure legends
Figure S1. Functional enrichment analysis for the 1,095 genes that were differentially expressed in the Santa Catalina Island
population on coastal prickly pear relative to laboratory food. A false discovery rate cut-off of 0.1 was used to identify enriched terms.
Node size indicates degree of significance, and larger font indicates the most significant term in cluster. Edges indicate degree of
connectivity between biological terms.
Figure S2. Functional enrichment analysis for the 1,541 genes that were differentially expressed in the Sonoran population on saguaro
relative to laboratory food. A false discovery rate cut-off of 0.1 was used to identify enriched terms. Node size indicates degree of
significance, and larger font indicates the most significant term in cluster. Edges indicate degree of connectivity between biological
terms.
Figure S3. Functional enrichment analysis for the 211 genes that were differentially expressed in the Santa Catalina Island population
relative to the Sonoran population across all three food types (environment-independent genes). A false discovery rate cut-off of 0.1
was used to identify enriched terms. Node size indicates degree of significance, and larger font indicates the most significant term in
cluster. Edges indicate degree of connectivity between biological terms.
Figure S4. Functional enrichment analysis for the 32 genes that had a significant population x food interaction and were differentially
expressed in the Santa Catalina Island population relative to the Sonoran population specifically on coastal prickly pear. A false
discovery rate cut-off of 0.1 was used to identify enriched terms. Node size indicates degree of significance, and larger font indicates
the most significant term in cluster. Edges indicate degree of connectivity between biological terms.
Figure S5. Functional enrichment analysis for the 86 genes that that had a significant population x food interaction and were
differentially expressed in the Sonoran population relative to the Santa Catalina Island population specifically on saguaro. A false
discovery rate cut-off of 0.1 was used to identify enriched terms. Node size indicates degree of significance, and larger font indicates
the most significant term in cluster. Edges indicate degree of connectivity between biological terms.
Figure S6. Functional enrichment analysis for the 5,803 genes that were plastic and had overlapping reaction norms between the
populations. A false discovery rate cut-off of 0.1 was used to identify enriched terms. Node size indicates degree of significance, and
larger font indicates the most significant term in cluster. Edges indicate degree of connectivity between biological terms.
Figure S7. Functional enrichment analysis for the 122 genes that diverged in expression between populations, but were not plastic in
the Sonoran population. A false discovery rate cut-off of 0.1 was used to identify enriched terms. Node size indicates degree of
significance, and larger font indicates the most significant term in cluster. Edges indicate degree of connectivity between biological
terms.
Figure S8. Functional enrichment analysis for the 4 genes that had reaction norms consistent with genetic assimilation. A false
discovery rate cut-off of 0.1 was used to identify enriched terms. Node size indicates degree of significance, and larger font indicates
the most significant term in cluster. Edges indicate degree of connectivity between biological terms.
Figure S9. Functional enrichment analysis for the 65 genes that that had reaction norms consistent with the Baldwin effect. A false
discovery rate cut-off of 0.1 was used to identify enriched terms. Node size indicates degree of significance, and larger font indicates
the most significant term in cluster. Edges indicate degree of connectivity between biological terms.
Figure S1
up-regulated
down-regulated
Figure S2
up-regulated
down-regulated
Figure S3
Figure S4
Figure S5
Figure S6
Figure S7
Figure S8
Figure S9