A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Wong GK, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, Huang X, Tong W, Chen J, Ye J, Chen C, Wei N, Li G, Dong L, Lan F, Sun Y, Zhang Z, Yang Z, Yu Y, Huang Y, He D, Xi Y, Wei D, Qi Q, Li W, Shi J, Wang M, Xie F, Wang J, Zhang X, Wang P, Zhao Y, Li N, Yang N, Dong W, Hu S, Zeng C, Zheng W, Hao B, Hillier LW, Yang SP, Warren WC, Wilson RK, Brandstrom M, Ellegren H, Crooijmans RP, van der Poel JJ, Bovenhuis H, Groenen MA, Ovcharenko I, Gordon L, Stubbs L, Lucas S, Glavina T, Aerts A, Kaiser P, Rothwell L, Young JR, Rogers S, Walker BA, van Hateren A, Kaufman J, Bumstead N, Lamont SJ, Zhou H, Hocking PM, Morrice D, de Koning DJ, Law A, Bartley N, Burt DW, Hunt H, Cheng HH, Gunnarsson U, Wahlberg P, Andersson L, Kindlund E, Tammi MT, Andersson B, Webber C, Ponting CP, Overton IM, Boardman PE, Tang H, Hubbard SJ, Wilson SA, Yu J, Wang J, Yang H; International Chicken Polymorphism Map Consortium.

Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China.

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.


While mtDNA has clearly shown that red jf are the matriarchal ancestors of most domestic fowl
www.cib.nig.ac.jp/gfr/research_pdf/Shamo.pdf
The Nuclear DNA told a different story of the male founders of some birds.

Ive provided references on nuclear DNA data- evidence of genetic contributions from two wild junglefowl species that split from the wild ancestor of the domestic fowl sometime during the end of the Miocene ( about five MILLION years ago) in COMMON JAPANESE AND CHINESE CHICKEN BREEDS.


[elibrary.unm.edu].

Applesauce continues to go on about fancy chickens as though I have not clearly stated that the birds in question are not genetically, phenotypically or behaviorally typical chickens.
I explained that hybrid founders in genetic isolation on oceanic islands often survived human settlement failures and typhoons when typical domestic chickens did not. Having lost secondary sexual traits, tails, vocalizations typical of chickens some of these island fowl were given species status by early explorers. They were even described as megapodes and scrubfowl in some instances. In other situations where successive generations of hybrids arrived with different waves of human migrants after periods of isolation a host of different traits emerged producing unique phenotypey classified as violaceous and temminick's junglefowl and shoal fowl.

The feathersite article was lifted from notes I provided to a student of mine some years ago from translated texts. It is a poor example of Yamashina's forty years of study on the subject to which I was a lowly curatorial intern and steward of living collections.
Few of you are truly interested in the veracity of the claims of the original paper on human lymphocyte antigens. I thought it was curious given the fact that Guns Germs and Steel was playing on the Discovery Channel while I typed in the first chicken notes. Don't people generally come into contact with the diseases of their domestic animals?
Dont isolated populations of humans generally fare poorly when new humans arrive with their own viruses?
This is certainly true for wild jf that come into contact with domestic chickens. The wild jf quickly die out anywhere domestic chickens come into contact with them.
This is particulary true for the green and ceylon jf ( varius and lafayetti) which is curious given the fact that the nuclear DNA of varius is present in Koeyoshi and Rapanui, Quechua and Sumatran domestic and feral fowl. The nuclear DNA of lafayetti is present in the
Belgium quail bantam, the rumpless bantam, marans chicken, colloncas and quetero fowl of South America. Many scientists including William Beebe, Jean Delacour and Yamashina attempted to hybridize the different wild jf species and discovered that while males are occasionally fertile in eggs hatched between varius males and lafayette males with domestic hens, Yamashina experimented with females of divergent rflp types. Each of the research groups discovered that fecundity was a major problem. Females never produce eggs that develop completly in f1, f2 or f3 hybrids.
Males often have abnormal sperm. It was determined by these experiments that these distantly related species could not have contributed to domestication unless as Yamashina's crew discovered females of a different RFLP type were used.
Simply put, the domestic fowl sharing the RFLP type with the Indonesian red jf versus the Burmese red jungleofowl produced a higher rate of male hybrids producing normal sperm.
Female hybrids continue to have the same fecundity issues.

So how can basically steril hybrids survive on isolated islands for thousands of years with typhoons, tropical storms, lack of food, not to mention human and any number of opportunistic predators? I don't know. Yamashina believed that the arrival of new migrations FROM THE SAME region as the pioneers or at least carrying the same rflp type fighting games the ayam kedu and ayam katai endemic to Indonesia south of Sumatra insured that males with normal sperm came into contact with domestic fighting game hens.
The sterile hens produced eggs for human and other nest predators and also set on eggs even when it was not in their interest. This is crucial for domestication by the way. Some of the sterile hybrid females were behaving abnormally even for a domestic chicken. CHickens were nowhere near as domesticated as they are today in those centuries. Fighting games at that time were little more than wild red jf.

Researchers discovered that (sterile) hybrid females lay eggs all year. They are abnormally shaped and never hatch. Other hybrid females incubate on anything remotely looking like an egg and do so long after a normal hen domestic or otherwise would have quit the nest.
Early inhabitants of the oceanic ( versus Pacific) islands between South America and New Caledonia had their own organic egg machines and incubators. Non hybridized hens which only laid seasonally like wild red jf and primitive fighting games were in Yamashina's theory conserved to produce more of the same. Their eggs were probably not eaten. Hybrid males with normal sperm were thus able to consistently fertilize the fighting games. The hybrid roosters were important for navigational reasons so it is believed that just about every new canoe from Indonesia had a hybrid male aboard as well as the normal semi domestic fighting games. The more isolated islands ended up generating what could almost be described as new species. A number of photos of skins collected in the 1500's ,1600's, and 1700's collected in Oceania and South America and live birds by Yamashina can be viewed here: [kickingthorn.com].

Im probably not articulating this in the genetic terminology that might be preferred to the best armed experts. Im not serving pedant machinations but would actually like people intimidated by some of the over the top attitude to have an opportunity to look at the evidence presented by the paper on Human Lymphocyte Antigens to learn about what they may have taken for granted. Kenuchelover writes as if there is but one chicken the kind that they serve at KFC the all white meat kind.
Im attempting badly to explain how Yamashina came to the conclusion that chickens arrived in South America before the European conquest.

If you continue to think about a chicken as an homologous man made creation than it will be impossible for you to take the important facts into consideration.

The fact is it required thousands of generations to fix the blue egg gene into the domestic
fowl because of genetic compatability issues between the Green JF and the domestic fowl.
It required females of an archaic Indonesian game that has all but diseappeared with the arrival of Thailand's more domesticated genes and diseases. That these RFLP types exist in Oceania and South America is fascinating.
How they got there is anyone's guess work. Yamashina believed that they drifted there ever so slowly on the ocean with a very few migrations of survivors.


www.urbanext.uiuc.edu/eggs/res10-breedhistory.html - 53k

The most serious evidence is the blue egg itself.
It did not exist in Asia nor Europe before Spaniards brought it back From South America.
The South American birds were nearly wiped out by the diseases of the chicken brought to South America. The only surviving stock of the South American breeds is genetically and phenotypically unique. The genetic distance between those tested birds and those collected on Ponape near Saipan and Rapanui suggests that the ancestral population of the hybrid founders must have been genetically isolated from one another for at least one thousand years probably more.



Contact: Michael C. Purdy
(314) 286-0122
purdym@wustl.edu



Printable Version


First Analysis of Chicken Genome Offers Many New Insights


Embargoed until 1 p.m. ET on Wednesday, Dec. 8

(Editor’s Note: A phone press conference, led by Richard K. Wilson, will take place under embargo at 10 a.m. EST on December 8. Participants dial in and give the conference ID# to the operator: Conference ID # 2536965
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St. Louis, Dec. 8, 2004 — The first detailed analysis of the chicken genome has identified a chicken counterpart to an important human immune system protein, revised scientists’ assessment of the chicken’s sense of smell, and suggested that the chicken, long used to study gene activity in the earliest stages of life, may provide a good model for studying changes in DNA linked to aging and death.

Other findings from the analysis, reported in the Dec. 9 issue of Nature by the International Chicken Genome Sequencing Consortium, include the identification of genes that affirm the chicken’s value as a model for study of developmental disorders like cleft palate and diseases like muscular dystrophy.

Researchers completed and made available the genetic sequence of the red jungle fowl — a wild ancestor of the domestic chicken whose scientific name is Gallus gallus — in March 2004. The genome provides several firsts: it is the first bird, the first agricultural animal, and the first descendant of the dinosaurs to have its genome sequenced.