Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph
Melissa Hubisz, Amy Williams & Adam Siepel
PLoS ONE, August 2020
The sequencing of Neanderthal and Denisovan genomes has yielded many new insights about interbreeding events between extinct hominins and the ancestors of modern humans. While much attention has been paid to the relatively recent gene flow from Neanderthals and Denisovans into modern humans, other instances of introgression leave more subtle genomic evidence and have received less attention. Here, we present a major extension of the ARGweaver algorithm, called ARGweaver-D, which can infer local genetic relationships under a user-defined demographic model that includes population splits and migration events. This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topologies and branch lengths along the genome, but also indicate migrant lineages. The sampled ARGs can therefore be parsed to produce probabilities of introgression along the genome. We show that this method is well powered to detect the archaic migration into modern humans, even with only a few samples. We then show that the method can also detect introgressed regions stemming from older migration events, or from unsampled populations. We apply it to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. Finally, we predict that 1% of the Denisovan genome was introgressed from an unsequenced, but highly diverged, archaic hominin ancestor. About 15% of these “super-archaic” regions — comprising at least about 4Mb — were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.
Fire and grass-bedding construction 200 thousand years ago at Border Cave, South Africa
Lyn Wadley et al.
Science, 14 August 2020, Pages 863-866
Early plant use is seldom described in the archaeological record because of poor preservation. We report the discovery of grass bedding used to create comfortable areas for sleeping and working by people who lived in Border Cave at least 200,000 years ago. Sheaves of grass belonging to the broad-leafed Panicoideae subfamily were placed near the back of the cave on ash layers that were often remnants of bedding burned for site maintenance. This strategy is one forerunner of more-complex behavior that is archaeologically discernible from ~100,000 years ago.
Fluted-point technology in Neolithic Arabia: An independent invention far from the Americas
Rémy Crassard et al.
PLoS ONE, August 2020
New World archaeologists have amply demonstrated that fluted point technology is specific to Terminal Pleistocene American cultures. Base-fluted, and rarer tip-fluted, projectile points from the Americas have been well-documented by archaeologists for nearly a century. Fluting is an iconic stone tool manufacturing method and a specific action that involves the extraction of a channel flake along the longitudinal axis of a bifacial piece. Here we report and synthesize information from Neolithic sites in southern Arabia, demonstrating the presence of fluting on a variety of stone tool types including projectile points. Fluted projectile points are known from both surface sites and stratified contexts in southern Arabia. Fluting technology has been clearly identified at the Manayzah site (Yemen) dating to 8000–7700 cal. BP. Examination of fluted points and channel flakes from southern Arabia enable a reconstruction of stone tool manufacturing techniques and reduction sequences (chaines opératoires). To illustrate the technological similarities and contrasts of fluting methods in Arabia and the Americas, comparative studies and experiments were conducted. Similarities in manufacturing approaches were observed on the fluting scars of bifacial pieces, whereas technological differences are apparent in the nature and localization of the flute and, most probably, the functional objective of fluting in economic, social and cultural contexts. Arabian and American fluted point technologies provide an excellent example of convergence of highly specialized stone tool production methods. Our description of Arabian and American fluting technology demonstrates that similar innovations and inventions were developed under different circumstances, and that highly-skilled and convergent production methods can have different anthropological implications.
Emergence of corpse cremation during the Pre-Pottery Neolithic of the Southern Levant: A multidisciplinary study of a pyre-pit burial
Fanny Bocquentin et al.
PLoS ONE, August 2020
Renewed excavations at the Neolithic site of Beisamoun (Upper Jordan Valley, Israel) has resulted in the discovery of the earliest occurrence of an intentional cremation in the Near East directly dated to 7031–6700 cal BC (Pre-Pottery Neolithic C, also known as Final PPNB, which spans ca. 7100–6400 cal BC). The funerary treatment involved in situ cremation within a pyre-pit of a young adult individual who previously survived from a flint projectile injury. In this study we have used a multidisciplinary approach that integrates archaeothanatology, spatial analysis, bioanthropology, zooarchaeology, soil micromorphological analysis, and phytolith identification in order to reconstruct the different stages and techniques involved in this ritual: cremation pit construction, selection of fuel, possible initial position of the corpse, potential associated items and funerary containers, fire management, post-cremation gesture and structure abandonment. The origins and development of cremation practices in the region are explored as well as their significance in terms of Northern-Southern Levantine connections during the transition between the 8th and 7th millennia BC.
The exceptional finding of Locus 2 at Dehesilla Cave and the Middle Neolithic ritual funerary practices of the Iberian Peninsula
Daniel García-Rivero et al.
PLoS ONE, August 2020
There is a significant number of funerary contexts for the Early Neolithic in the Iberian Peninsula, and the body of information is much larger for the Late Neolithic. In contrast, the archaeological information available for the period in between (ca. 4800-4400/4200 cal BC) is scarce. This period, generally called Middle Neolithic, is the least well-known of the peninsular Neolithic sequence, and at present there is no specific synthesis on this topic at the peninsular scale. In 2017, an exceptional funerary context was discovered at Dehesilla Cave (Sierra de Cádiz, Southern Iberian Peninsula), providing radiocarbon dates which place it at the beginning of this little-known Middle Neolithic period, specifically between ca. 4800–4550 cal BC. Locus 2 is a deposition constituted by two adult human skulls and the skeleton of a very young sheep/goat, associated with stone structures and a hearth, and a number of pots, stone and bone tools and charred plant remains. The objectives of this paper are, firstly, to present the new archaeological context documented at Dehesilla Cave, supported by a wide range of data provided by interdisciplinary methods. The dataset is diverse in nature: stratigraphic, osteological, isotopic, zoological, artifactual, botanical and radiocarbon results are presented together. Secondly, to place this finding within the general context of the contemporaneous sites known in the Iberian Peninsula through a systematic review of the available evidence. This enables not only the formulation of explanations of the singular new context, but also to infer the possible ritual funerary behaviours and practices in the 5th millennium cal BC in the Iberian Peninsula.