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.

The Toba supereruption in Sumatra, ∼74 thousand years (ka) ago, was the largest terrestrial volcanic event of the Quaternary. Ash and sulfate aerosols were deposited in both hemispheres, forming a time-marker horizon that can be used to synchronize late Quaternary records globally. A precise numerical age for this event has proved elusive, with dating uncertainties larger than the millennial-scale climate cycles that characterized this period. We report an astronomically calibrated 40 Ar/ 39 Ar age of 73.88 ± 0.32 ka (1σ, full external errors) for sanidine crystals extracted from Toba deposits in the Lenggong Valley, Malaysia, 350 km from the eruption source and 6 km from an archaeological site with stone artifacts buried by ash. If these artifacts were made by Homo sapiens, as has been suggested, then our age indicates that modern humans had reached Southeast Asia by ∼74 ka ago. Our Ar age is an order-of-magnitude more precise than previous estimates, resolving the timing of the eruption to the middle of the cold interval between Dansgaard-Oeschger events 20 and 19, when a peak in sulfate concentration occurred as registered by Greenland ice cores. This peak is followed by a ∼10°C drop in the Greenland surface temperature over ∼150 y, revealing the possible climatic impact of the eruption. Our Ar age also provides a high-precision calibration point for other ice, marine, and terrestrial archives containing Toba sulfates and ash, facilitating their global synchronization at unprecedented resolution for a critical period in Earth and human history beyond the range of 14 C dating.geochronology | ice core timescale | paleoclimate | volcanic ash | human dispersal

There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the “out-of-Taiwan” mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20 % of mtDNA lineages in the modern ISEA pool result from the “out-of-Taiwan” dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6–7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.Electronic supplementary materialThe online version of this article (doi:10.1007/s00439-016-1640-3) contains supplementary material, which is available to authorized users.

Two fundamental issues for tephrostratigraphic work are the differentiation of primary from reworked tephra and the characterization of reworking mechanisms. We study the depositional processes of four deposits of Youngest Toba Tuff in the Lenggong valley, Malaysia. We focus on site stratigraphy, particle-size distributions, magnetic susceptibility and mineralogical associations. Reworked tephra display variable sedimentological characteristics including polymodal and unimodal, very fine to coarse-grained distributions, and variable concentrations of ash. Particle-size distributions from this study are similar to published analyses for primary deposits, demonstrating that particle size alone cannot distinguish primary from secondary tephra. The tephra sequences are associated with fluvial and colluvial deposition. Three facies are identified: flood flow, mudflow and slumping. The ash accumulated rapidly, over a period of a few days to months. In this valley the ideal site for paleoenvironmental reconstructions is Kampung Luat 3, where ash accumulated at least in two distinct phases. Despite the rapid accumulation, the Lenggong sites are not well-suited for paleoenvironmental studies of the YTT impact. The time lag between the primary deposition and the floods is unknown and the records could have been modified by site-specific characteristics. Such variables should be considered when proposing paleo-environmental reconstructions based on reworked tephra.

Evidence of Early Palaeozoic volcanism inPeninsular Malaysia is largely represented by felsic Gerik-Dinding meta-volcanic rocks; however, reliable absolute ages for the meta-volcanic rocks are still lacking. This restricts correlation of these meta-volcanic rocks with other Early Palaeozoic East Gondwana Proto-Tethys margin tectonic elements identified in the evolution of Southeast Asia. Here, we report petrographic data and zircon U-Pb age of the Gerik-Dinding metavolcanic rocks. Zircons from three Gerik-Dinding meta-volcanic rock samples yield Early to Middle Ordovician weighted mean 206 Pb/ 238 U ages between 480 and 460 Ma. The formation age of the meta-volcanic rocks coincides with the post-collision stage from the final amalgamation of Asian micro-continental fragments with the East Gondwana Proto-Tethys margin. Tectonic processes such as lithospheric delamination during the post-collision period could have induced the hot asthenosphere to underplate the continental crust and trigger crustal anatexis. With these findings, the Early Palaeozoic tectonic history of Peninsular Malaysia needs careful review.