Table 1.

Predictions about associations between genomic and ecological traits and the evolution of protein atomic content

Trait(s)	Expected or potential associations with protein stoichiometry
Genome size (130 – 364 Mb); Intron percent (19.6–24.0%) [17]	Larger proteomes (as indicated by larger genomes) require more intensive translation activity, and so should contain proportionally less of a limiting element (C, N or S), owing to selection for efficiency of element usage. This may be confined to the proteins involved in translation, which are overexpressed when intensive translation is required. Similarly, higher percentages of protein–coding DNA (i.e. lower intron percent) should select for higher efficiency of usage owing to a proportionally greater effect on the phenotype.
Male and female body size (thorax width; males, 0.64–1.78 mm; females, 0.80–1.89 mm); Sexual dimorphism (female thorax – male thorax; 0.00–0.18 mm); Development time (10–27d); Male and female specific growth rate (development time/thorax width) [16]	Contrasting predictions arise from the growth rate hypothesis [21]. First, smaller organisms have faster specific growth rates than larger organisms and therefore require proportionally more transcription activity. Thus they should require more nutrient conservation in proteins, particularly the proteins of transcription and translation that are overexpressed when increased protein synthesis is required. Conversely, owing to higher rates of protein synthesis, smaller organisms have a lower protein:nucleic acid ratio, the N:P ratio of their tissues is accordingly lower, and they are predicted to be more easily P limited rather than N limited. This predicts that smaller organisms should be under weaker selection to conserve nitrogen in their protein sequences.
Ovariole number (16–43) [16]	With limited nutritional choices, organisms often prioritize allocation to fertility over lifespan [22]; this may impose selection for nutrient conservation in key proteins. Therefore evolutionary increases in ovariole number should result in nutrient depletion across proteomes, or differentially in the proteins of oogenesis.
Diet breadth (general, oligo, specialist) [16], [25], [34]	It is advantageous to maintain a stoichiometric balance close to that of one’s food (reviewed in [23]). Generalist flies are more likely to be able to adjust the nutritional balance of ingested food to their own nutrient demands [24], whereas specialist flies are more likely to evolve a body stoichiometry that corresponds with that of their resources [25]. Therefore the evolution of feeding specialization may involve evolution of distinctive protein stoichiometry, across proteomes or in the proteins of nutrient assimilation and digestion.

Ranges of trait values are given in parentheses where appropriate.