Learning how complex traits like eyes originate is fundamental for understanding evolution. In this review, we first sketch historical perspectives on trait origins and argue that new technologies afford key new insights. Next, we articulate four open questions about trait origins. To address them, we define a research program to break complex traits into component parts and to study the individual evolutionary histories of those parts. By doing so, we can learn when the parts came together and perhaps understand why they stayed together. We apply this approach to five structural innovations critical for complex eyes and review the history of the parts of each of those innovations. Eyes evolved within animals by tinkering: creating new functional associations between genes that usually originated far earlier. Multiple genes used in eyes today had ancestral roles in stress responses. We hypothesize that photo-oxidative stress had a role in eye origins by increasing the chance that those genes were expressed together in places on animals where light was abundant.


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