Metabolic consequences of various fruit-based diets in a generalist insect species
- UMR CBGP (INRAE-IRD-CIRAD, Montpellier SupAgro), Campus International de Baillarguet, France
- Department of Agricultural Biology, Colorado State University, United States
- Université de Strasbourg, INRAE, France
Figures
Figure 1 with 4 supplements
Schematic overview of experimental design, host use analyses, and expectations according to the ‘metabolic generalism’ and ‘multi-host metabolic specialism’ hypotheses.
In order to investigate whether different food sources were treated similarly or differently by a generalist species, we followed a simple experimental procedure (A), where eggs of a single founder …
Figure 1—figure supplement 1
Principal component analysis (PCA) of fruits’ metabolomes.
(A) Dimension 1 vs. dimension 2, and (B) dimension 2 vs. dimension 3. Different fruit samples are represented by colored dots. Eigenvalues of the PCA of fruit metabolomes showed that only three …
Figure 1—figure supplement 2
Upset plot of the number of shared ions between all fruits (ten largest intersections).
Figure 1—figure supplement 3
Comparison between the taxonomy of investigated plant species and the biochemical proximity of their fruits.
(A) Phylogenetic dendrogram of investigated plant species, (B) Hierarchical clustering of fruit samples using the fruit dataset.
Figure 1—figure supplement 4
Relation between ion quantity in fruit vs. in flies that developed on the same fruit.
(A) Blackcurrant, (B) Cherry, (C) Cranberry, (D) Strawberry. Linear regression coefficients, R-square, and Kendall’s τ are indicated for each fruit-fly pair.
Figure 2
Overall trends of shared ions between all fruits and all flies.
(A) The ten largest intersections between all metabolomes comprise many high-degree intersections, including ions shared between all fruit and all flies’ samples (#1), ions, shared between all flies …
Figure 3 with 1 supplement
Relationships between ions respectively found in fruits and flies, according to their degree of intersection.
Ions that are shared within fruits or within flies show a higher degree of intersection. Most ions found in flies are found in all flies, but not necessarily in all fruits. It is also noteworthy …
Figure 3—figure supplement 1
Fruits and flies’ metabolomes cluster separately and do not form pairs.
Fruit and fly samples in this overall principal component analysis (PCA) are represented by dots and triangles, respectively. Colors represent different fruits or diets in the case of flies. All …
Figure 4 with 7 supplements
Flies’ metabolomes differ according to diet.
Flies’ samples only were included in this principal component analysis (PCA). Differently oriented triangles indicate biological replicates (fly generations). (A) Dimensions 1 and 2; (B) Dimensions …
Figure 4—figure supplement 1
Plots of all individual ions of the principal component analysis of fruit metabolomes.
(A) Dimension 1 vs. dimension 2, and (B) dimension 2 vs. dimension 3. Fruit-specific ions are indicated in color, all other ions are indicated in gray.
Figure 4—figure supplement 2
Classification of fruit and fly samples following selection of diet-specific ions through GLM with Elastic Net regularization.
Heatmap scale colors indicate the relative quantity of each ion (row) of the ‘large’ list of diet-specific ions (specificity indicated by discrete colors; see main text for details).
Figure 4—figure supplement 3
Quantitative levels of diet-specific fly ions in flies and fruits.
(A) Blackcurrant, (B) Cherry, (C) Cranberry, (D) Strawberry. Medians and their confidence intervals are represented by black bars.
Figure 4—figure supplement 4
Relationships between the quantities of diet-specific fly ions in fruit and flies of the following fruit-fly pairs.
(A) Blackcurrant, (B) Cherry, (C) Cranberry, (D) Strawberry.
Figure 4—figure supplement 5
Intersection sizes (in fruits and flies) and relationships of fly ions specific to the following diets.
(A) Blackcurrant, (B) Cherry, (C) Cranberry, (D) Strawberry. Ions that are shared within fruits or within flies show a higher degree of intersection.
Figure 4—figure supplement 6
Number and degree of intersection of major fruit ions relative to their presence in the consumer flies.
(A) Blackcurrant, (B) Cherry, (C) Cranberry, (D) Strawberry.
Figure 4—figure supplement 7
Classification performance of qualitative vs quantitative fly datasets to infer diet.
(A) Percentage of correct classification, and (B) Adjusted mutual information.
Figure 5 with 1 supplement
Heatmap of the relative quantity of identified metabolites in each fruit and fly sample.
Heatmap scale colors indicate the relative quantity of each metabolite (row). Additional columns represent diet specificity in flies, major presence (top 50) in fruits, presence in literature in …
Figure 5—figure supplement 1
Quantities of identified metabolites in the following fruit-fly pairs.
(A) Blackcurrant, (B) Cherry, (C) Cranberry, (D) Strawberry. Most metabolites are present ten to a hundred times less in flies than in their respective diet.
Appendix 1—figure 1
Relation between ion quantity in fruit vs in flies that developed on the same fruit.
(A) Blackcurrant, (B) Cherry, (C) Cranberry, (D) Strawberry. Linear regression coefficients, R-square and Kendall’s τ are indicated for each fruit-fly pair.
Appendix 1—figure 2
Overall trends of shared ions between all fruits and all flies.
(A) The ten largest intersections between all metabolomes comprise many high degree intersections, including ions shared between all fruit and all flies’ samples (#1), ions, shared between all flies …
Appendix 1—figure 3
Relationships between ions respectively found in fruits and flies, according to their degree of intersection.
Ions that are shared within fruits or within flies show a higher degree of intersection. Most ions found in flies are found in all flies, but not necessarily in all fruits. It is also noteworthy …
Appendix 1—figure 4
Fruits and flies’ metabolomes cluster separately and do not form pairs.
Fruit and fly samples in this overall principal component analysis (PCA) are represented by dots and triangles, respectively. Colors represent different fruits or diets in the case of flies. All …
Appendix 1—figure 5
Flies’ metabolomes differ according to diet.
Flies’ samples only were included in this principal component analysis (PCA). Differently oriented triangles indicate biological replicates (fly generations). (A) Dimensions 1 and 2; (B) Dimensions …
Appendix 1—figure 6
Plots of all individual ions of the principal component analysis of fruit metabolomes.
(A) Dimension 1 vs. dimension 2, and (B) dimension 2 vs. dimension 3. Fruit-specific ions are indicated in color, all other ions are indicated in gray.
Appendix 1—figure 7
Classification of fruit and fly samples following selection of diet-specific ions through GLM with Elastic Net regularization using the raw fly dataset.
Heatmap scale colors indicate the relative quantity of each ion (row) of the ‘large’ list of diet-specific ions (specificity indicated by discrete colors; see main text for details).
Appendix 1—figure 8
Quantitative levels of diet-specific fly ions in flies and fruits.
(A) Blackcurrant, (B) Cherry, (C) Cranberry, (D) Strawberry. Medians and their confidence intervals are represented by black bars.
Appendix 1—figure 9
Relationships between the quantities of diet-specific fly ions in fruit and flies of the following fruit-fly pairs.
(A) Blackcurrant, (B) Cherry, (C) Cranberry, (D) Strawberry.
Appendix 1—figure 10
Intersection sizes (in fruits and flies) and relationships of fly ions specific to the following diets.
(A) Blackcurrant, (B) Cherry, (C) Cranberry, (D) Strawberry. Ions that are shared within fruits or within flies show a higher degree of intersection.
Appendix 1—figure 11
Number and degree of intersection of major fruit ions relative to their presence in the consumer flies.
(A) Blackcurrant, (B) Cherry, (C) Cranberry, (D) Strawberry.
Appendix 1—figure 12
Classification performance of qualitative vs. quantitative fly datasets to infer diet.
(A) Percentage of correct classification, and (B) Adjusted mutual information.
Author response image 1
Left = negative ions; right = positive ions.
Author response image 2
Left = negative ions; right = positive ions.
Author response image 3
Above = negative ions; below = positive ions.
Tables
Appendix 1—table 1
Figure names for each analysis performed on raw and controlled fly dataset.
| Analysis | Raw fly dataset | Controlled fly dataset |
|---|---|---|
| Relation between ion quantity in fruit vs. in flies that developed on the same fruit | Appendix 1—figure 1 | Figure 1—figure supplement 4 |
| Overall trends of shared ions between all fruits and all flies | Appendix 1—figure 2 | Figure 2 |
| Relationships between ions respectively found in fruits and flies, according to their degree of intersection | Appendix 1—figure 3 | Figure 3 |
| Fruits and flies’ metabolomes Principal Component Analysis | Appendix 1—figure 4 | Figure 3—figure supplement 1 |
| Flies’ metabolomes Principal Component Analysis | Appendix 1—figure 5 | Figure 4 |
| All individual ions of the Principal Component Analysis of fruit metabolomes | Appendix 1—figure 6 | Figure 4—figure supplement 1 |
| Classification of fruit and fly samples following selection of diet-specific ions through GLM with Elastic Net regularization | Appendix 1—figure 7 | Figure 4—figure supplement 2 |
| Quantitative levels of diet-specific fly ions in flies and fruits | Appendix 1—figure 8 | Figure 4—figure supplement 3 |
| Relationships between the quantities of diet-specific fly ions in fruit and flies of the following fruit-fly pairs | Appendix 1—figure 9 | Figure 4—figure supplement 4 |
| Intersection sizes (in fruits and flies) and relationships of fly ions specific to the following diets | Appendix 1—figure 10 | Figure 4—figure supplement 5 |
| Number and degree of intersection of major fruit ions relative to their presence in the consumer flies | Appendix 1—figure 11 | Figure 4—figure supplement 6 |
| Classification performance of qualitative vs. quantitative fly datasets to infer diet | Appendix 1—figure 12 | Figure 4—figure supplement 7 |
Additional files
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MDAR checklist
- https://cdn.elifesciences.org/articles/84370/elife-84370-mdarchecklist1-v1.pdf
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Supplementary file 1
Table of all identified metabolites, their physicial properties, presence in fruits and flies (this study), and previous identifications in fruits.
- https://cdn.elifesciences.org/articles/84370/elife-84370-supp1-v1.xlsx
