Multiple Deeply Divergent Denisovan Ancestries in Papuans

Genome sequences are known for two archaic hominins—Neanderthals and Denisovans—which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time

Genetic insights into the social organization of Neanderthals

Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans1–8, but the social organization of Neanderthal communities remains poorly understood. Here we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave9,10 and 2 from Okladnikov Cave11—making this one of the largest genetic studies of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father–daughter pair and a pair of second-degree relatives, indicating that at least some of the individuals lived at the same time. Up to one-third of these individuals’ genomes had long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range

Ancient genomes show social and reproductive behavior of early Upper Palaeolithic foragers

Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. Here, we investigate whether the contemporary HG strategy was already present in the Upper Paleolithic (UP), using complete genome sequences from Sunghir, a site dated to ~34 thousand years BP (kya) containing multiple anatomically modern human (AMH) individuals. Wedemonstrate that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that UP social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network

The use of a range of ultrasound frequencies to reduce colouration caused by dyes

The formation of hydrogen peroxide and the degree of decolourisation of six different dyes as a result of sonication over several ultrasonic frequencies (20, 40, 380, 512, 850, 1,000 and 1,176 kHz) was investigated and correlated. It was found that the highest levels of hydrogen peroxide and also the greatest amount of decolourisation occurred at 850 kHz. 380 and 512 kHz also resulted in some decolourisation, however higher and lower ultrasonic frequencies were not effective.</jats:p

Single amino acid radiocarbon dating of two Neanderthals found at Šal’a (Slovakia)

Human remains from the (late) Middle Paleolithic remain rare. Improving our understanding of their spatio-temporal distribution is essential for obtaining insights into human evolution and the dynamics between Neanderthals and early Anatomically Modern Humans (AMHs). We present the single-amino-acid radiocarbon dating and ancient DNA results from the only Neanderthal skeletal remains known in Slovakia (Šal’a I and Šal’a II). As they were found without archaeological context and in secondary deposition, recontextualization is important. By employing the hydroxyproline radiocarbon dating method, we were able to successfully counteract contamination issues and circumvent problems caused by highly degraded collagen. By contrast, DNA analysis did not detect any endogenous DNA at the limits of our resolution. We conclude that the radiocarbon ages of >44,800 BP (OxA-X-2731-16) and >45,100 (OxA-X-2731-15) firmly place the two individuals in the Middle Paleolithic, and before the arrival of AMHs to the region. Furthermore, indirect evidence based on morphology and possibly related faunal remains suggest ages younger than 100 ka. This time frame coincides with a period in which Neanderthal populations were highly dispersed in Europe, yet in decline

Increasing accuracy for the radiocarbon dating of sites occupied by the first Americans

Genetic analysis of Paleoamerican human remains suggests that people first entered the Americas sometime between ∼14,000 and ∼16,000 years ago. Evaluation of these data requires unequivocal archaeological evidence in a solid geological context that is well dated. Accurately determining the age of late Pleistocene sites is thus crucial in explaining when and how humans colonized the Americas. There are, however, significant challenges to dating reliability, especially when vertebrate fossils (i.e. bones, teeth and ivory) are often the only datable materials preserved at sites. We re-dated vertebrate fossils associated with the North American butchering sites of Wally's Beach (Canada), La Prele [also known as Fetterman (Wyoming)], Lindsay (Montana), and Dent (Colorado). Our work illustrates the crucial importance of sample chemical preparation in completely removing contaminants derived from sediments or museum curation. Specifically, our work demonstrates that chromatographic methods, e.g. preparative High Performance Liquid Chromatography and column chromatography using XAD resins, are currently the only efficient methods for removing environmental and museum-derived contaminants. These advanced techniques yield demonstrably more accurate AMS 14C measurements that refine the ages of these four sites and thereby contribute to advancing our understanding of human dispersals across North America during the late Pleistocene

Reassessing the chronology of the archaeological site of Anzick

Found in 1968, the archaeological site of Anzick, Montana, contains the only known Clovis burial. Here, the partial remains of a male infant, Anzick-1, were found in association with a Clovis assemblage of over 100 lithic and osseous artifacts—all red-stained with ochre. The incomplete, unstained cranium of an unassociated, geologically younger individual, Anzick-2, was also recovered. Previous chronometric work has shown an age difference between Anzick-1 and the Clovis assemblage (represented by dates from two antler rod samples). This discrepancy has led to much speculation, with some discounting Anzick-1 as Clovis. To resolve this issue, we present the results of a comprehensive radiocarbon dating program that utilized different pretreatment methods on osseous material from the site. Through this comparative approach, we obtained a robust chronometric dataset that suggests that Anzick-1 is temporally coeval with the dated antler rods. This implies that the individual is indeed temporally associated with the Clovis assemblage

Compound-specific radiocarbon dating and mitochondrial DNA analysis of the Pleistocene hominin from Salkhit Mongolia

A skullcap found in the Salkhit Valley northeast Mongolia is, to our knowledge, the only Pleistocene hominin fossil found in the country. It was initially described as an individual with possible archaic affinities, but its ancestry has been debated since the discovery. Here, we determine the age of the Salkhit skull by compound-specific radiocarbon dating of hydroxyproline to 34,950 – 33,900 Cal. BP (at 95% probability), placing the Salkhit individual in the Early Upper Paleolithic period. We reconstruct the complete mitochondrial genome (mtDNA) of the specimen. It falls within a group of modern human mtDNAs (haplogroup N) that is widespread in Eurasia today. The results now place the specimen into its proper chronometric and biological context and allow us to begin integrating it with other evidence for the human occupation of this region during the Paleolithic, as well as wider Pleistocene sequences across Eurasia