A.P. Derevianko

Neanderthals in central Asia and Siberia

Morphological traits typical of Neanderthals began to appear in European hominids at least 400,000 years ago and about 150,000 years ago in western Asia. After their initial appearance, such traits increased in frequency and the extent to which they are expressed until they disappeared shortly after 30,000 years ago. However, because most fossil hominid remains are fragmentary, it can be difficult or impossible to determine unambiguously whether a fossil is of Neanderthal origin. This limits the ability to determine when and where Neanderthals lived. To determine how far to the east Neanderthals ranged, we determined mitochondrial DNA (mtDNA) sequences from hominid remains found in Uzbekistan and in the Altai region of southern Siberia. Here we show that the DNA sequences from these fossils fall within the European Neanderthal mtDNA variation. Thus, the geographic range of Neanderthals is likely to have extended at least 2,000 km further to the east than commonly assumed.

A complete mtDNA genome of an early modern human from Kostenki, Russia

The recovery of DNA sequences from early modern humans (EMHs) could shed light on their interactions with archaic groups such as Neandertals and their relationships to current human populations. However, such experiments are highly problematic because present-day human DNA frequently contaminates bones [1, 2]. For example, in a recent study of mitochondrial (mt) DNA from Neolithic European skeletons, sequence variants were only taken as authentic if they were absent or rare in the present population, whereas others had to be discounted as possible contamination [3, 4]. This limits analysis to EMH individuals carrying rare sequences and thus yields a biased view of the ancient gene pool. Other approaches of identifying contaminating DNA, such as genotyping all individuals who have come into contact with a sample, restrict analyses to specimens where this is possible [5, 6] and do not exclude all possible sources of contamination. By studying mtDNA in Neandertal remains, where contamination and endogenous DNA can be distinguished by sequence, we show that fragmentation patterns and nucleotide misincorporations can be used to gauge authenticity of ancient DNA sequences. We use these features to determine a complete mtDNA sequence from a approximately 30,000-year-old EMH from the Kostenki 14 site in Russia.

The genetic history of Ice Age Europe

Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. We analyze genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas the earliest modern humans in Europe did not contribute substantially to present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. A ~35,000 year old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe during the Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a new genetic component related to present-day Near Easterners appears in Europe. These results document how population turnover and migration have been recurring themes of European pre-history.

Nuclear and mitochondrial DNA sequences from two Denisovan individuals

Significance Denisovans are a sister group of Neandertals that were identified on the basis of a nuclear genome sequence from a bone from Denisova Cave (Siberia). The only other Denisovan specimen described to date is a molar from the same site. We present here nuclear DNA sequences from this molar and a morphological description, as well as mitochondrial and nuclear DNA sequences from another molar from Denisova Cave, thus extending the number of Denisovan individuals known to three. The nuclear DNA sequence diversity among the Denisovans is higher than among Neandertals, but lower than among present-day humans. The mtDNA of one molar has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over several millennia. Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.

Identification of ancient remains through genomic sequencing.

Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In these studies, we developed and applied a genomewide adapter-mediated emulsion PCR amplification protocol for ancient mammalian samples estimated to be between 45,000 and 69,000 yr old. Using 454 Life Sciences (Roche) and Illumina sequencing (formerly Solexa sequencing) technologies, we examined over 100 megabases of DNA from amplified extracts, revealing unbiased sequence coverage with substantial amounts of nonredundant nuclear sequences from the sample sources and negligible levels of human contamination. We consistently recorded over 500-fold increases, such that nanogram quantities of starting material could be amplified to microgram quantities. Application of our protocol to a 50,000-yr-old uncharacterized bone sample that was unsuccessful in mitochondrial PCR provided sufficient nuclear sequences for comparison with extant mammals and subsequent phylogenetic classification of the remains. The combined use of emulsion PCR amplification and high-throughput sequencing allows for the generation of large quantities of DNA sequence data from ancient remains. Using such techniques, even small amounts of ancient remains with low levels of endogenous DNA preservation may yield substantial quantities of nuclear DNA, enabling novel applications of ancient DNA genomics to the investigation of extinct phyla.

New hominin remains from Uzbekistan

Although the Paleolithic occupations of Uzbekistan and the neighboring foothill regions of Tajikistan and Kazakhstan are well-documented, almost no hominin fossil material has been discovered in the area since Teshik-Tash 1 in 1938. Here we describe and offer a preliminary comparative framework for hominin remains that were recovered in 2003 from two Middle Paleolithic sites in Uzbekistan, Obi-Rakhmat Grotto and Anghilak Cave. The description of Teshik-Tash as a Neandertal and the preponderance of lithic assemblages identified as Mousterian in character has supported the interpretation of the region as the eastern-most extent of the Neandertal range. The material from Obi-Rakhmat (OR-1), a subadult represented by part of a permanent maxillary dentition and a fragmentary cranium, expresses a relatively Neandertal-like dentition coupled with more ambiguous cranial anatomy. The remains from Anghilak Cave include a non-diagnostic, diminutive right fifth metatarsal (AH-1). These findings are important additions to the Central Asia hominin fossil record.

Neandertal and Denisovan DNA from Pleistocene sediments

Tracing our ancestors in cave sediments Analysis of DNA from archaic hominids has illuminated human evolution. However, sites where thousand-year-old bones and other remains can be found are relatively rare. Slon et al. wanted to exploit any trace remains that our ancestors left behind. They looked for ancient DNA of hominids and other mammals in cave sediments, even those lacking skeletal remains. They identified mitochondrial DNA from Neandertal and Denisovan individuals in cave sediments at multiple sites. Science, this issue p. 605 DNA from archaic humans can be retrieved from Pleistocene sediments, even in the absence of their skeletal remains. Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA, we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples, we detected Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave, we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility of detecting the presence of hominin groups at sites and in areas where no skeletal remains are found.

Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis

DNA sequencing has revolutionised our understanding of archaic humans during the Middle and Upper Palaeolithic. Unfortunately, while many Palaeolithic sites contain large numbers of bones, the majority of these lack the diagnostic features necessary for traditional morphological identification. As a result the recovery of Pleistocene-age human remains is extremely rare. To circumvent this problem we have applied a method of collagen fingerprinting to more than 2000 fragmented bones from the site of Denisova Cave, Russia, in order to facilitate the discovery of human remains. As a result of our analysis a single hominin bone (Denisova 11) was identified, supported through in-depth peptide sequencing analysis, and found to carry mitochondrial DNA of the Neandertal type. Subsequent radiocarbon dating revealed the bone to be >50,000 years old. Here we demonstrate the huge potential collagen fingerprinting has for identifying hominin remains in highly fragmentary archaeological assemblages, improving the resources available for wider studies into human evolution.

The Aurignacian in Altai

Research in the Altai region of central Asia is attempting to establish the development and expansion of the Aurignacian to Europe and the Caucasus. New sites and early dates provide important new data on this key question about the emergence of modern humans in Eurasia.

Suggested guidelines for invasive sampling of hominid remains

The last few years have witnessed remarkable technical developments in paleoanthropology. On the one hand, accurate imaging techniques have limited the need to access actual specimens. On the other hand, direct dating, isotopic studies, and the study of ancient DNA, proteins, and microstructures have experienced great technical improvements but still require a degree of invasive sampling. The power of these invasive approaches for answering important questions in evolutionary anthropology brings forward the question of how to balance preservation of fossil hominid remains for the future against the application of current scientific analyses. In order to address these issues, a workshop was hosted by the Max-Planck Institute for Evolutionary Anthropology in Leipzig on April 26– 27, 2007 where the issues that emanate from the need for sampling of hominid remains versus the need for preservation of specimens for the future were discussed. At the end of the meeting, the participants produced a set of recommendations that might be useful to museums and other institutions as well as scientists that have to make decisions on requests for invasive sampling of hominid remains.