Interestingly enough a paper addressed this question without even looking at chickens. Raox and Robinson-Rechavi examined the level of genotypic constraint on certain genes involved in development in both zebrafish and mouse.
They were testing between two hypothesis. One, presented as an extension to an idea from an early embryologist , von Baer, was that constraint between species happened earlier in development with more species specific traits coming after. The second hypothesis is described as an hourglass where early and late stages of development have low constraint and a middle period, known as the phylotypic stage has a highly constrained genotype.
One problem with this type of question, is how do you measure constraint. Evolutionary rates like dN/dS had not worked in previous studies. And other methods (like number of gene duplications) had not been used in vertebrates. So the authors used two separate types of data, EST's and microarray. EST's (expressed sequence tags) are small bits of genes expressed at a given time in a certain tissue. Microarrays, at least here, measure the presence or absence of a gene. They then compared the presence of essential genes (lethal when removed from the animal before development) to other genes to measure the ralative level of tolerance each stage had. Both sets of data in both species shared a consistent result, the ratio of essential to normal decrease linearly over developmental time in both mouse and zebrafish.
This supports the early conservation model over the hourglass model and so the chicken most likely came after its genotypic pattern of development.
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