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Aphid's Color Comes From a Fungus Gene
Iron Nose writes with an account from Byte Size Biology of horizontal gene transfer from a fungus to an insect. The author suspects that we will see lots more of this as we sequence more genomes. "The pea aphid is known for having two different colors, green and red, but until now it was not clear how the aphids got their color. Aphids feed on sap, and sap does not contain carotenoids, a common pigment synthesized by plants, fungi, and microbes, but not by animals. Carotenoids in the diet gives many animals, from insects to flamingos, their exterior color after they ingest it, but aphids do not seem to eat carotenoid-containing food. Nancy Moran and Tyler Jarvik from the University of Arizona looked at the recently sequenced genome of the pea aphid. They were surprised to find genes for synthesizing carotenoids; this is the first time carotenoid synthesizing genes have been found in animals. When the researchers looked for the most similar genes to the aphid carotenoid synthesizing genes, they found that they came from fungi, which means they somehow jumped between fungi and aphids, in a process known as horizontal gene transfer."
Well fuck me sideways.
Most knowledge about evolutionary biology is based on evidence like this, and there are lots of ways to be pretty confident about such conclusions, even if there's no way to 100% rule out chance. If this gene and/or others like it are widespread in fungi, that's a hint that it developed in fungi--and under some conditions you might be able to show that the gene evolved in fungi before aphids even existed. Conversely, if no other aphids or related species have anything like this gene, it's a good bet that it came from outside. If the gene evolved suddenly in one lineage of aphids and transferred to a fungus, you would expect only a limited range of fungi, and only those that evolved after aphids did, to have the gene.
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The transfer definitely did not go in the other direction, as the genes for the carotenoids would have had to travel back up the phylogenetic tree and down its other branches to all the other organisms containing carotenoids. The argument that the aphids evolved genes to express carotenoids in parallel to the part of the phylogenetic tree containing them does not fit into the current model for evolution, as a gene only evolves once, and any other organism containing that gene is descended from the organism that originally mutated to express that gene (this uses statistics and probabilities too!).
Anyway, in almost every science nothing is solidly proven, there are merely theories. Everyone objecting to the validity of this article has been doing too much statistics and not enough biology. You can rest assured the article went under much more intense scrutiny than comparison to a webcomic to get published in Science (no matter how awesome that webcomic is).