Since their domestication, chickens (Gallus gallus domesticus) have been venerated by diverse cultures across the world. Relative to other domestic animals including sheep, cattle and pigs, chickens are currently both the preferred source of animal protein and the most numerous domestic animal.1 Despite their popularity and ubiquity, both the geographic and temporal origins of domestic chickens remain controversial. The red jungle fowl (RJF, G. gallus; Supplementary information, Fig. S1) is believed to be the wild progenitor of domestic chickens, and chicken domestication is thought to have occurred during the Holocene.2,3,4 Which subspecies of extant RJF (G. g. gallus, G. g. spadiceus, G. g. jabouillei, G. g. murghi, and G. g. bankiva) was first domesticated and to what degree domestic chickens interbred with other (sub)species of jungle fowl remain unresolved questions.4,5,6,7,8

From an archaeological perspective, a significant challenge has been how to confidently identify chickens since no osteomorphological markers can readily distinguish the five RJF subspecies from each other, or discriminate between RJF and early domestic chickens.3,9,10 Additionally, attempts to characterize the spatiotemporal origins and subsequent dispersals of chickens have been hampered by a lack of direct radiocarbon dating of presumed early archaeological remains.9,11

Numerous genetic studies based on mitochondrial DNA (mtDNA) sequences raised the “multiple origins” hypothesis, which claimed that wild RJFs were incorporated into ancient food-producing cultures in multiple occasions.5,6 However, the general propensity of domestic animals to admix with their wild relatives, including those that were never independently domesticated, can lead to spurious claims of multiple and independent origins based on this single genetic marker.2,12 Additionally, as a maternally inherited non-recombining DNA, mtDNA has a limited power to reveal complex past demography.13 Conversely, the rapid development of whole-genome sequencing holds a great promise for inferring the evolutionary history of domestication processes.14,15,16,17,18,19