Reconstructing the genetic history of late Neanderthals.

Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA. Here we use hypochlorite treatment of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.

Genomic analysis of a novel Neanderthal from Mezmaiskaya Cave provides insights into the genetic relationships of Middle Palaeolithic populations.

The Mezmaiskaya cave is located on the North Caucasus near the border that divides Europe and Asia. Previously, fossil remains for two Neanderthals were reported from Mezmaiskaya Cave. A tooth from the third archaic hominin specimen (Mezmaiskaya 3) was retrieved from layer 3 in Mezmaiskaya Cave. We performed genome sequencing of Mezmaiskaya 3. Analysis of partial nuclear genome sequence revealed that it belongs to a Homo sapiens neanderthalensis female. Based on a high-coverage mitochondrial genome sequence, we demonstrated that the relationships of Mezmaiskaya 3 to Mezmaiskaya 1 and Stajnia S5000 individuals were closer than those to other Neanderthals. Our data demonstrate the close genetic connections between the early Middle Palaeolithic Neanderthals that were replaced by genetically distant later group in the same geographic areas. Based on mitochondrial DNA (mtDNA) data, we suggest that Mezmaiskaya 3 was the latest Neanderthal individual from the early Neanderthal's branches. We proposed a hierarchical nomenclature for the mtDNA haplogroups of Neanderthals. In addition, we retrieved ancestral mtDNA mutations in presumably functional sites fixed in the Neanderthal clades, and also provided the first data showing mtDNA heteroplasmy in Neanderthal specimen.

Sedimentary Dosimetry for the Saradj-Chuko Grotto: A Cave in a Lava Tube in the North-Central Caucasus, Russia.

Karst caves host most European Paleolithic sites. Near the Eurasian-Arabian Plate convergence in the Caucasus' Lower Chegem Formation, Saradj-Chuko Grotto (SCG), a lava tube, contains 16 geoarchaeologically distinct horizons yielding modern to laminar obsidian-rich Middle Paleolithic (MP) assemblages. Since electron spin resonance (ESR) can date MP teeth with 2-5% uncertainty, 40 sediment samples were analyzed by neutron activation analysis to measure volumetrically averaged sedimentary dose rates. SCG's rhyolitic ignimbrite walls produce very acidic clay-rich conglomeratic silts that retain 16-24 wt% water today. In Layers 6A-6B, the most prolific MP layers, strongly decalcified bones hinder species identification, but large ungulates inhabited deciduous interglacial forests. Unlike in karst caves, most SCG's layers had sedimentary U concentrations > 4 ppm and Th, > 12 ppm, but Layer 6B2 exceeded 20.8 ppm U, and Layer 7, > 5 ppm Th. Such high concentrations emit dose rates averaging ~ 1.9-3.7 mGy/y, but locally up to 4.1-5.0 mGy/y. Within Layer 6, dose rate variations reflect bone occurrence, necessitating that several samples must be geochemically analyzed around each tooth to ensure age accuracy. Coupled with dentinal dose rates up to 3.7-4.5 mGy/y, SCG's maximum datable ages likely averages ~ 500-800 ka.

ESR at Treugol'naya Cave, Northern Caucasus Mt., Russia: dating Russia's oldest archaeological site and paleoclimatic change in Oxygen Isotope Stage 11.

At 1510 m asl, Treugol'naya Cave, Russia, is the highest cave showing evidence for human occupation in eastern Europe. Layers 4-7 in the 4.5-m-thick sequence yielded many artifacts representing Lower Paleolithic pebble and flake tool industries. Abundant faunal remains include extinct Middle Pleistocene species. Palynological, paleomagnetic, and microsedimentological analyses indicate that several climatic changes of different magnitudes occurred in the sequence. To determine absolute ages for Treugol'naya, 32 independent subsamples from nine ungulate teeth collected from the Lower Paleolithic layers were dated by standard and isochron electron spin resonance (ESR) analyses. Isochron analyses indicate that the teeth experienced no significant U leaching or secondary uptake, and that linear uptake (LU) provides accurate ages. Layers 4b through 5b dated to 365+/-12-406+/-15 ka. Therefore, hominids visited the site periodically throughout Oxygen Isotope Stage (OIS) 11, indicating that they utilized resources at elevations >1000 m at least seasonally by 400 ka. ESR, paleomagnetic, palynological and paleontological analyses all indicate that the Lower Paleolithic Layers 4-5 correlate with OIS 11. The thickness of Layers 4-5 (more than 1.5 m) makes this one of the thickest OIS 11 terrestrial deposits known.