The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the "two-layer" hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.

Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testing.

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' (Movius 1960: 355). The passage of time is equally vital for a proper understanding of the prehistoric sequence in Southeast Asia. While the cultural sequence is agreed by most scholars, its timing is not. The ancestors of the first rice farmers in Southeast Asia probably lived in the Yangtze Valley to the north (Liu et al. 2007), and spread south, via the coast and the major rivers, to enter the broad riverine plains of Southeast Asia. They brought their Austro-Asiatic languages, and a way of life that centred on settled village communities incorporating widespread exchange in exotica, a sophisticated ceramic industry, weaving, and a mortuary tradition that involved both extended inhumation and interment in lidded jars. This Neolithic settlement phase was followed by the adoption of copper-base metallurgy, in which copper and tin were alloyed from the earliest known contexts. The transition into the Iron Age has not been precisely dated, but it is known that early states were forming by the fourth to fifth centuries AD. The timing and the degree to which Iron Age communities developed social and technological sophistication prior to the rise of early states is poorly documented: Noen U-Loke is the only extensively-excavated Iron Age site in Thailand to be published ). A new chronological framework for prehistoric Southeast Asia, based on a Bayesian model from Ban Non WatWe do not know when the first farmers reached Southeast Asia and there remains a basic uncertainty over the date for the inception of copper-base metallurgy in Southeast Asia. This has generated a lack of understanding of the social changes that occurred with the early Bronze Age. As Muhly (1988: 16) In retrospect, the causes of controversies over chronology are readily understood (Solheim 1968;1970;Bayard 1972 Bayard , 1979Gorman & Charoenwongsa 1976;Bayard & Charoenwongsa 1983;Higham 1983;Loofs-Wissowa 1983). Radiocarbon determinations have virtually all been derived from charcoal, with its problems of 'old wood'. Only very rarely has the species of tree been specified, a practice that needs to be addressed in future dating programmes. No recognition was given to the unreliability of mixed samples (Ashmore 1999). In many cases, the relationship between a charcoal sample and the event being dated was unreliable. Major cultural changes, such as the beginning of copper-base metallurgy, have been dated on the basis of only a handful of determinations. When a sample of dates was available, the construction of the site's chronology followed procedures now shown to be importantly wrong (Bayliss et al. 2007: 9).Resolving this situation first requires a prehistoric site with a cultural sequence spanning the early Neolithic to the end of the Iron Age. Such sites are very rare in Southeast Asia. Phases within such a site would need to be ordered in terms of a relative chronology, and we would then require a sufficient number of radiocarbon determinations, preferably generated on the basis of samples with no inbuilt age, to provide dates for the su...