How to analyze a hybrid.....

So, let's consider the problem we face. If the chicken is a two-species hybrid as I've stated, how do you prove it? What is the evidence?

Firstly, the differences between the Asiatic Game and the Red Jungle Fowl are obvious, but to analyze these two forms against each other directly is virtually impossible. Even though comparison can be a useful form of measurement, it is too complex a problem to solve by comparing the whole birds. Good men have tried and fallen short.

                     This is a genuine Red Jungle Fowl hen in my possession.

This is the head of another bird also in my possession, half Saipan, a breed closely allied to the Japanese Shamo, the mother being one of my small sized project birds.

One individual, Dr. Frederick B. Hutt, one of the most respected men in the Poultry Science of his day and with whom I have an indirect connection through his student and lifelong colleague, my Poultry Genetics and Anatomy teacher at Cornell, Dr. Randy K. Cole, did manage to frame the origin problem in a reasonable and systematic way. There is either a monophyletic origin or a polyphyletic origin to the fowl. If one is inclined to support the polyphyletic theory, he or she "may choose between two possibilities. Either (1) all fowls are descended from two or more of the four existing wild species of Gallus; or (2) the Mediterranean breeds may have had such an origin, but some other ancestor now extinct gave rise to the Asiatic breeds." pg. 10 Bingo!

His book, Genetics of the Fowl (1949), was known as "The Breeder's Bible" and for good reason. His writing style was relaxed and informal, very readable, not unlike the science writers of today, belying the wealth of information he provided. It is still available through Norton Creek Press.
http://www.nortoncreekpress.com/genetics_of_the_fowl.html

Alright then, so how do you solve a complex problem? You first break it down into it's most elemental components, solve these simpler parts, "disassemble and solve" as the engineers say, then reassemble and see what you've got.

An easy problem, right? No, not really. If it were an easy problem, someone would have figured it out since Darwin first tackled it nearly 150 years ago. No one need feel embarrassed for missing it.

However, and this is an edit (2019), what has been missed is the fact that the single alleles, genes, which follow and that were first studied more then 120 years ago are now understood to be far more complex then formerly realized. They are not simple point mutations. These are evolved genes differing by many base pairs from the accepted wild-type alleles. As such they could not possibly have come about in the relatively short time (8000 + years) since domestication of the fowl. This and this alone is the smoking gun. Complex genes/alleles that are not found in the Red Jungle Fowl had to come from somewhere else, i.e. another species, long before the chicken was ever domesticated.

The phenotypic traits reviewed by Dr. Hutt provided the basic pieces I needed. Many are all or nothing characters determined by single alleles. I liken them to pieces of a jigsaw puzzle. Here we have many pieces from two separate and distinct pictures all jumbled together needing to be sorted out. Luckily, we have one more or less complete picture in the Red Jungle Fowl. I say more or less because over the last ten thousand years or so there has certainly been considerable introgression of the domestic fowl back into the wild. Being as nature is an unforgiving taskmaster, the observed changes in the wild form would tend to be rather slight.

Phenotypic traits can be sorted in one of three ways. They can belong to the Red Jungle Fowl, wild-type alleles, easy to identify. The remaining characters can then be considered as either disadvantageous point mutations (most likely) under domestication, or as more complex alleles, possible candidates for a second wild-type belonging to the Malayoid genome.

Like any puzzle, the first pieces are going to be the hardest to recognize. I had to look at traits and decide whether there was the slightest possibility that one trait or another could belong to the ancestral Malayoid, sort of a "pin the tail on the donkey". This was in no way a proof to be sure, only a possibility. I had to muster all the evidence I could find no matter how seemingly trivial, search for the slightest relevant connection. In fact I used to call it my trivia collection, anything to perfect my Malayoid model, but as you can imagine it has grown into a fair store of information over time.

Examples. One very good candidate gene has already been discovered, Dr. Laden, you know this one; the yellow skin gene. Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken
 http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000010

It is reasonable because it inhibits the breakdown of carotinoid pigments in the skin, shank and beak, but not in the liver where the breakdown is necessary for Vitamin A metabolism. It could very well belong to the flightless Jungle Fowl.

For another example, two actually, look at the comb of "Brow" in the above picture. It is not a comb at all, only a flat cushion. The Red Jungle Fowl hen has an upright single comb. It is much better developed in the cock bird.

The cushion comb differs from the single comb at two distinct loci. One manifests as the so-called pea comb, the other as the rose comb. The flat comb is reasonable, more so than either the pea or rose alone.

This bird has the cushion comb, yellow skin, and two more; crest and 'beard and muff'. On a loose feathered more Red Jungle Fowl type of chicken, these can appear monstrous, especially the crest which is often associated with a noticeable knob, a cerebral hernia. On this hen, half Cornish bantam in breeding and close feathered as are all Asiatic Games, the crest and beard look quite natural.

Am I making sense so far? Please question me if it is not clear. I will gladly answer any and all, and thanks for reading this. Take care.