The Pattern Of Chicken Origin And Domestication Revealed By Ancient DNA Analyses

The modern domestic chicken is originated from ancient jungle fowls, yet the original locations, timings and dispersal have been remaining controversial for more than a century. The focal point of the dispute is that modern gallus are living in area of southern Asia while the oldest remains are discovered in the middle Yellow River region. The best way so far to calm down the controversy is to identify the species status of early bones, and further more, to figure out their genetic relationships with modern chickens.In the present study, we amplified target sequences from39ancient chicken bones using loop-mediated PCR assay. Chicken bones were collected from Nanzhuangtou site (-10,000BP), Cishan site (-7,500BP) and Wangyin site (-4,500BP) in the area of the Yellow River, representing the earliest sites for chicken bones, and one younger archaeological site (Jiuliandun Chu Tombs at-3,000BP) in the middle area of the Yangtze River. Chicken bones from Nanzhuangtou and Cishan were radiocarbon dated by accelerator mass spectrometry. Results showed that1) the samples from Nanzhuangtou site and Cishan site, respectively, yielded calibrated dates of10,400and-7,900y, confirming the Neolithic context of these samples.2) The159-bp COI sequences were obtained from13ancient specimens and analyzed with196homologous sequences from six Galiformes genera. All investigated bones, including the oldest bones from Nanzhuangtou site, were derived from the genus Gallus, rather than any other related genus, such as Phasianus.3) A subset of8samples yielded a326-bp fragment of the mitochondrial control region. By comparison with10published ancient chicken sequences and1,001extant published sequences from four Gallus species, ancient bones from northern China presented closely related with regard to their mitochondrial haplotypes of the major modern domestic chicken haplogroups, suggesting that the early domesticated chickens contributed to the gene pool of modern chicken populations, and northern China was a original region for early chicken domestication, dating as early as10,000year BP.4) Massive climatic and environmental changes were well documented for the North China Plain since early Holocene age. Abundant remains of tropical animal and plant species excavated at the Cishan and Nanzhuangtou sites testified that northern China represented a suitable habitat for jungle fowls at that time, and the earliest cultivation of foxtail millets as well as early pig and dog domestication in this area had revealed technological bases for early chicken domestication. The genetic diversities in the oldest samples suggested the early stage of domestication and the continuous improvement of transitional society (Nanzhuangtou) and agricultural society (Cishan) in nortern China.5) Particular haplotypes amongst southern Asian population supported the idea that multiple members of the genus Gallus, specifically Gallus gallus and Gallus sonneratii contributed to the gene pools of modern domestic chickens at multiple times in different parts of Asia alongside with other early agricultural evidences.Altogether, we established an efficient method for DNA analysis, by which for the first time obtained several ancient chicken DNA sequences early than4,500BP, including the oldest chicken DNA sequences so far. The combined phylogenetic analyses on modern and ancient DNA sequences from all over the world documented northern China as acenter for chicken domestication as early as10,000y BP during early Neolithic period.