...In the big evolutionary picture of where the red pigment came from in the beginning, we are left to conjectural hypotheses. The seeds of the evolutionary ancestor were no doubt bird and mammal dispersed, so perhaps the red fruit was more visible and hence conferred an adaptive advantage.
Here is the problem with this popular way of reasoning: almost all mammals have dichroic vision, so they do not see a red apple as red, while the birds that do have color vision are not interested in fleshy fruit, but only seeds. There seems to be no adaptive advantage for an apple to be red.
The color itself derives from anthocyanin dyes that are responsible for red coloration in falling leaves, which is another mystery
. From what little is known, the mechanism of coloration in apples is different from that in flowers. In the latter, the absorption of the anthocyanins is tuned by interaction with a flavonoid copigment. The apples tune their color by layering anthocyanin filled vacuoles with other pigmented organelles (such as plastids), so the approach is different from that in the flowers, it is more like in the leaves. Incidentally, one of the most popular theories about the leaves turning red in the fall is a warning signal (Hamilton's) hypothesis: the trees are warning aphids (which, like all other insects, have color vision) about their prowess to kill their eggs ("I am so healthy I can turn some of my sugars to pigment => I can also turn these sugars into poison for your progeny. Do not mess with me"). If apples are not red for mammals or birds, the logical conclusion is that either they must be red for humans (selectively breeding apples) or bugs. Since plenty of wild Malus fruit (such as crabapples) are red, humans are not the cause. It must be the bugs.
What can be the reason to attract insects? We do not enjoy maggots in our apples, but it is likely that mammals that fed on wild apples somewhere in the mountains of Central Asia not only didn't mind but, actually, valued the extra protein in their food. The plants can provide protein, of course, cereal grasses do, but protein synthesis takes energy and nitrogen, so the apples embarked on a better solution: providing cheap-to-make carbohydrates, attracting insects to infest the fruit, and then attracting their dispersing animals with a maggoty, protein-containing treat. Crabapples are the favorite food for many Asian moths http://en.wikipedia.org/wiki/List_of_Lepidoptera_that_feed_on_Malus
and crabapples would not be called crabapples for nothing: these are acidic, woody, and tart. The animals get interested in this kind of fallen fruit only when it begins to rot and the yamies get inside; most of these animals, like hedgehogs are omnivorous or preferentially insectivorous. I suspect that the apples are turning red to attract the insects infesting the ripe fruit, either before it falls or shortly thereafter.
There is certainly some connection between the redness and the insects, though its exact nature remains unknown. As recently as last week it was found that...62.2% of Central Asian wild apple trees had leaves that turn red in the autumn, compared with just 2.8% for cultivated British apple trees. To test the idea that red leaves spell trouble for insects, in the fall of 2007, Archetti placed nesting aphids in red-leaved and green-leaved apple trees. The following spring, 60% of aphids nesting in green trees had survived, compared with only 29% of those in the red trees. The reason behind this disparity is unclear, but Archetti's and other studies suggest that the red leaves either have toxic chemical defenses or hold fewer nutrients for young aphids. http://sciencenow.sciencemag.org/cgi/content/full/2009/415/1
Why are the apples red?