A new reconstruction of the Yunxian 2 skull, and its implications for the relationship between the 'Archaic Homo sapiens' of China and Modern Humans.

The Middle Pleistocene, or Chibanian (roughly 774 100 to 129 000 years ago), has produced a range of Hominin fossils, with a surprising range of morphological diversity. Recent finds from Callao Cave on Luzon Island in 2007 and Rising Star Chamber in South Africa in 2013, have led to the description of two new Human species, Homo luzonensis and Homo naledi respectively, from this age. 

China has produced a diverse assemblage of Chibanian and older Hominin fossils, often labelled as 'Archaic Homo sapiens', although their relationship to Modern Humans has been the subject of debate for a long time. The Yunxian 1 & 2 crania were discovered on on a terrace of the Hanjiang River in the Yunyang District (formerly Yunxian) of Shiyan City, in Hubei Province, China, in 1989 and 1990. These skulls have been dated to between 1.1 million and 940 000 years ago, and are considered important for the understanding of the genus Homo in China, and to a certain extent the world, although both are heavily distorted, hampering attempts to reconstruct their original morphology and therefore phylogenetic relationships. 

The Yunxian 2 skull. Although the least distorted of the two crania from Yunxian, it is still partially crushed, and therefore difficult to interpret. Garry Todd/Hubei Provincial Museum/Wikimedia Commons.

In a paper published in the journal Science on 25 September 2025, a team of scientists led by Xiaobo Feng of the School of History and Culture at Shanxi University, Hubei Polytechnic University, and the Institute of Yunxian Man Site and School of History, Culture and Tourism, at Hanjiang Normal University, Qiyu Yin of the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences, and the College of Earth and Planetary Sciences of the University of the Chinese Academy of Sciences, Feng Gao of the Yunnan Institute of Cultural Relics and Archaeology, and Dan Lu, also of the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences, and the College of Earth and Planetary Sciences of the University of the Chinese Academy of Sciences, present a new reconstruction of the Yunxian 2 skull, and discuss the implications of that reconstruction for the relationship between the 'Archaic Homo sapiens' of China and Modern Humans.

Our understanding of the relationship between Modern Humans and our extinct Hominin relatives is based almost entirely on the reconstruction of the anatomy of extinct species from fossil specimens, many of which are quite distorted. Of the three fossil crania discovered at Yunxian, one (Yunxian 3) is still under preparation, having been found in 2022. Both of the previously discovered specimens are distorted, with Yunxian 1 being quite badly crushed as well. Computed tomography scans of Yunxian 2 have suggested that most of the deformation is due to the fragmentation and displacement of parts of the skull, rather than actual warping of the material. Feng et al. built a digital reconstruction of this fossil, using software to move parts back into their original position, and filling in some gaps with data from Yunxian 1. 

The reconstructed cranium is large and long, with a braincase which appears flattened in lateral view. It is smaller than the Harbin Xuchang crania, approximately the same size as the as Kabwe, Petralona, Bodo, Jinniushan, and Sangiran 17 crania, and larger than the Jebel Irhoud 1, Dali, and Maba crania. The reconstruction still lacks small parts of the zygomatic arches and the central incisors, but is otherwise intact. It contains a number of traits associated with earlier members of the genus Homo, including a thick supraorbital torus, a broad basicranium and palate, a long and low vault in lateral view, a receding frontal con￾tour, and a rather flat parietal contour, and a high, anteriorly projecting face. However, it lacks other traits associated with early members of the genus, such as a strongly angulated occipital with a prominent transverse torus. The specimen lacks the occipital bun, forward projecting midface, and general rounded 'en bombe' shape of Neanderthal skulls, and the upper parietal expansion of Modern Humans. The zygomaxillary region is transversely flat and faces anteriorly, similar to the Harbin, Dali, Jinniushan, and Hualongdong crania from Asia, as well as specimens assigned to Homo antecessor from Europe, as wellas Modern Humans. Its cheek￾bones are large and high.

Reconstruction of the Yunxian 2 cranium in standard views. (A) to (F) Anterior, posterior, inferior, superior, left, and right views, respectively. Brown colour indicates the fossil bone. The zygomatic bone and the tip of the left maxilla, as indicated with dark brown, were grafted and reconstructed by incorporating elements of Yunxian 1. White colour indicates the reconstructed parts inferred from the fracture edge and Yunxian 1. Neutral grey indicates the bones crushed and covered by other bones and matrix. Scale bar is 5 cm. Feng et al. (2025).

The matrix filling the skull is dense, and does not produce a good contrast with the bone material in computed tomography scans, preventing analysis of the features of the interior of the skull. However, Feng et al. were able to calculate an endocranial capacity of 1143 cm². However, the frontal lobe appears low and narrow, little expanded from the situation in early Homo, and unlike the expanded frontal lobes of Neanderthals and Modern Humans. 

Reconstruction of the endocranial cast of Yunxian 2. (A to F) Anterior, posterior, inferior, superior, left, and right views, respectively. Scale bar is 5 cm. Feng et al. (2025).

The traits which can be measured suggest that morphologically, Yunxian 2 appears to be intermediate between early Homo species and specimens such as Home erectus, Homo ergaster, and the Kabwe and Petralona crania, and later Asian skulls such as Harbin, Dali, and Jinniushan. 

A phylogenetic analysis based upon the new reconstruction of Yunxian 2, found it grouped with a group of Asian specimens including Dali, Jinniushan, Xujiayao, and Hualongdong and the Xiahe and Penghu mandibles, which have together been referred to as the Homo longi clade, based upon the suggestion that the Xujiayao, Xuchang, Xiahe, and Penghu specimens, as well as the Denisovans should be grouped together as a new species, Homo longi (although Feng et al. did not recover the Xuchang specimens as part of this group). Feng et al.'s reconstruction found this clade to be the sister to Homo antecessor, with the Homo longi clade plus Homo antecessor being the sister clade to Homo sapiens. Yunxian 2 is the oldest member of the Homo longi clade as recovered by Feng et al., but not the earliest branching. 

Phylogeny and divergence time of 57 selected fossil operational taxonomic units from the genus Homo. The topology of the tree was the majority consensus of the most parsimonious trees from the parsimony analysis in TNT. The divergence time was inferred from the Bayesian tip-dating analysis in MrBayes 3.2. Branch lengths are proportional to the division age in thousands of years (Ka). Numbers at the internal nodes are the median ages, and the blue bars indicate the 95% highest posterior density interval of the node ages. The red half-brackets on the right indicate the ranges of the Neanderthal, Homo longi, and Homo sapiens clades. The numbers in red highlight the ages of division of the three clades. Yunxian is also highlighted in red. Feng et al (2025).

The term 'Denisovan' was coined for a group of highly fragmentary fossils from the Denisova Cave in the Altai Mountains of Russia. Because of the fragmentary nature of these fossils, it has been possible to determine little about their original morphology, but DNA has been recovered from the specimens, revealing a great deal of genetic information. Studies of mitochondrial DNA from these specimens has suggested that this group branched off from the lineage that led to modern Humans before the Neanderthal line. However, studies based upon nuclear DNA have suggested that Denisovans and Neanderthals were sister groups, with a common ancestor more recent than their last common ancestor with Modern Humans. While the limited amount of data available makes this hard to resolve, Feng et al. suggest that the Denisovans were probably members of the Homo longi clade, with those morphological traits known all consistent with membership of this group. 

The divergence between the ancestors of Neanderthals and those of Modern Humans was for a long time considered to have happened between 700 000 and 500 000 years ago. However, more recent studies incorporating DNA recovered from Neanderthal specimens have suggested a much earlier split. Feng et al.'s analysis suggests that the Homo longi clade emerged as a distinct lineage about 1.2 million years ago, with Homo sapiens first appearing about 1.02 million years ago, around the time when Yunxian 2 was alive. The Homo longi and Homo sapiens clades are recovered as having diverged about 1.32 million years ago, while the Neanderthal clade diverged from the ancestors of these two groups about 1.38 million years ago.

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Evidence for two separate dispersals of Neanderthals into southern Siberia

The period of existence of Neanderthals, their geographical range, and the timing of their dispersal and extinction are key issues in the study of human evolution and migration. Most Neanderthal remains and associated artifacts have been reported from Europe and western Asia, where they range in age from about 430 000 to 40 000 years ago. Further east, the unequivocal presence of Neanderthals prior to the last interglacial (which began around 130 000) until about 50 000 is based on Hominin remains and DNA analyses of skeletal remains and sediments at three caves (Okladnikov, Denisova, and Chagyrskaya) in the Altai Mountains of southern Siberia. Additional evidence is required to support suggestions that Neanderthals had reached eastern and northern China by 125 000 to 105 000 and 45 000, respectively. Two genetically distinct Neanderthal populations inhabited the Altai region sometime during the Late Pleistocene, but the geographical origin of these populations and the timing of their migrations into the region remain unclear. On current evidence, Neanderthals were present at Denisova Cave between about 200 000 and 100 000 years ago.

In a paper published in the Proceedings of the National Academy of Sciences of the United States of  America on 27 January 2020, a team of scientists led by Kseniya Kolobova of the Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, and Richard Roberts of the Centre for Archaeological Science at the University of Wollongong, and the Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, present the results of a study which sought to identify the most probable ancestral source region for the Neanderthals of Chagyrskaya Cave in the Altai foothills of southern Siberia.

Chagyrskaya Cave s situated 19 m above the Charysh River in the western piedmont of the Altai Mountains, approximately 100 km west of Denisova Cave. The cave consists of two chambers, with a stratigraphic sequence up to 3.5 m thick. The dense basal deposit (layer 7) is archaeologically sterile and composed mainly of gravel and fine-grained sediments. An erosional contact (unconformity) separates it from overlying layers 6 and 5, which consist of poorly sorted sediments that contain approximately 90 000 Middle Palaeolithic artifacts (including numerous bone tools), 74 Neanderthal specimens, about 250 000 Animal fossils, and a range of Plant remains. The sequence is capped by Bronze Age deposits, with no evidence of Upper Palaeolithic occupation.

Chagyrskaya Cave. (A) Site location in the Altai region of southern Siberia. (B) View of the cave entrance, which faces north. (C) Plan of the cave interior showing the excavated area (in blue). (D) and (E) Stratigraphic profiles along the two transects (A)–(A′) and (B)–(B′), respectively) shown in (C). Kolobova et al. (2020).

Optical ages for 23 sediment samples indicate that layer 7 was deposited 329 000 ± 16 000 years ago (weighted mean age of four samples) and that layers 6 and 5 accumulated sometime between 63 000 ± 4 000 and 48 000 years ago (weighted mean age of 54 000 ± 2500 years ago). The latter are consistent with the mostly infinite radiocarbon ages obtained for 20 Bison, Bison priscus, remains. but are younger than the DNA-based age estimate of 87 000 to 71 000 years for the 'Chagyrskaya Neanderthal' (Chagyrskaya 8), a distal manual phalanx retrieved from the sieved sediments of subunit 6b. This discrepancy may reflect a higher mutation rate in Neanderthals than in modern Humans that has not been taken into account and/or the omission of other uncertainties in the genetic age estimates, such as population size and generation interval. Chagyrskaya 8 and Denisova 3 (the youngest Denisovan fossil) share similar proportions of 'missing' genetic mutations compared to present-day Humans, which suggests that they are similar in age. Denisova 3 has been dated to between 76 200 and 51 600 years ago, an age range compatible with the optical ages for layers 6 and 5 at Chagyrskaya Cave.

 

(A) Location map of Chagyrskaya Cave, Okladnikov Cave, Denisova Cave, Ust’-Karakol-1 and Kara-Bom in the Altai Mountains. (B) View upstream (i.e., to the southeast) along the Charysh River valley, with the location of Chagyrskaya Cave indicated by the arrow. Kolobova et al. (2020).

The subunits of layer 6 have statistically indistinguishable ages, which indicate that these Neanderthal-associated Middle Palaeolithic deposits accumulated over a few millennia or less, during the final phase of Marine Isotope Stage 4 and/or the start of Marine Isotope Stage 3. This was a period of cold climate (but warmer than during Marine Isotope Stage 4), as indicated by pollen and Mammal and Bird remains from layer 6 compatible with a dry steppe environment and a rarity or lack of tundra species. Layer 5 was deposited during a period of relatively warm and humid climate, characterised by steppe and forest-steppe vegetation. The main Hominin occupation of Chagyrskaya Cave occurred during accumulation of subunit 6c, which represents the primary depositional context of the Middle Palaeolithic assemblage; subunits 6b and 6a and layer 5 include redeposited Middle Palaeolithic artifacts, bones, and sediments. Sedimentology and micromorphology analyses support these interpretations of cave use, site formation, and environmental conditions. Neanderthal hunting activity was focused on bison (juveniles and females in particular) and may have been connected to the seasonal migration of Bison herds to and from the mountain foothills. Other prey hunted to a lesser extent included Horse, Reindeer, Siberian Ibex, and Argali.

 

(A) Plan map of Chagyrskaya Cave showing excavation squares, locations of optical dating samples collected in 2012, 2014 and 2017 (CHAG12-1 to -10, CHAG14-2 to -12 and CHAG17-3 to -9, shown in orange) and locations of micromorphology samples collected in 2014 (MM2–4, shown in green) and 2017 (2969, 2970, 2984, 2985, 2987–2989, shown in blue). The area shaded in yellow was excavated in 2016 and 2017. (B) Stratigraphic profile along the purple line in panel (A). (C) Stratigraphic profile along the red line in panel (A). Both vertical scales are in cm below reference datum, the horizontal scale is in bottom right-hand corner, and the layer, subunit and sublayer numbers are circled. Kolobova et al. (2020).

A total of 89 539 artifacts have been recovered from layer 6. Detailed lithic analysis of 4249 artifacts from subunits 6a to 6c indicates that the assemblage represents a single technocomplex, with no marked differences between subunits. Subunit 6c consists of two sublayers (6c/2 and 6c/1) with indistinguishable ages. Sublayer 6c/1 contains more artifacts than does sublayer 6c/2, which is preserved in only a few, spatially restricted, parts of the site. Accordingly, we focus here on the technological and typological characteristics of the 3021 artifacts from sublayer 6c/1 and on the morphological variability of plano-convex bifacial tools (commonly retouched using bone) and convergent scrapers in particular.

 

Stone artifacts from Chagyrskaya Cave, sublayer 6c/1. (A)–(C) Photographs, line drawings, and cross-sectional profiles of three plano-convex bifacial tools diagnostic of Micoquian Bocksteinmesser and Klausennischemesser types. Scale bar is 5 cm. Kolobova et al. (2020).

The lithic assemblage consists of 25 raw materials, including high-quality jaspers, chalcedonites, and porphyrites, which were sourced as pebbles from the nearby riverbed. The assemblage is dominated by debris and chips, with the remaining artifacts characterised by a high proportion of tools and a few cores. Most of the flakes have asymmetrical trapezoidal and rectangular shapes and were manufactured on site using bifacial plano-convex, radial (Levallois centripetal), and orthogonal core-reduction flaking methods; blades occur in low numbers as occasional byproducts. Scrapers dominate the toolkit, with a preference for trapezoidal and leaf shapes.

 

Photo montage of micromorphology samples collected by Maciej Krajcarz. in 2017. panels (A)–(D), and by Mike Morley in 2014, panels (E)–(G). Kolobova et al. (2020).

The Chagyrskaya toolkit had been previously been grouped with the small artifact assemblage from Okladnikov Cave and named the Sibiryachikha variant, Only the remains of Neanderthals have been found in association with this variant, whereas the assemblages found at Denisova Cave and at the open-air sites of Kara-Bom and Ust’-Karakol-1 cannot be related unambiguously to a specific Hominin species. Both Neanderthals and Denisovans (a genetically related group of archaic Hominins) were present at Denisova Cave during the Middle Palaeolithic, while Kara-Bom and Ust’-Karakol-1 have not yielded any Hominin remains. These assemblages reflect the local development of Levallois-based industries with Mousterian features, and they differ markedly from the Sibiryachikha variant, which is dominated by bifacial plano-convex, radial, and orthogonal flaking methods; bifacial tools; convergent scrapers and points; and the absence of Levallois preferential and Levallois convergent core reductions.

 

Overview of the Human remains from Chagyrskaya Cave. The teeth and postcranial remains are not to scale. (A) Remains from the northern cluster, squares К6, К7 and Л6. (B) Remains from the southern cluster, squares Н10 and Н11. (C) Remains from outside the two clusters. Kolobova et al. (2020).

Similarities between Middle Palaeolithic artifacts and associated Hominin remains in the Altai, central Asia, and eastern Europe have been proposed, but limitations in the archaeological and fossil records have precluded firm conclusions. Kolobova et al. used a set of statistical methods (including hierarchical cluster analysis, nonmetric multidimensional scaling, and principal component analysis) to compare the technological and typological attributes of the Chagyrskaya artifacts with Levallois-Mousterian Middle Palaeolithic and Upper Palaeolithic assemblages in central Asia, and with Micoquian assemblages in central and eastern Europe. The analysis clearly distinguishes the Chagyrskaya assemblage from the central Asian Levallois-Mousterian Middle Palaeolithic and Upper Palaeolithic assemblages. Analysis of debitage that has been examined using a technological approach yields the same outcome. This suggests that the Chagyrskaya assemblage and that from Okladnikov Cave, the age of which is uncertain but is likely also younger than that of the Denisova Neanderthals, constitute a separate and unique regional Middle Palaeolithic variant, technologically and typologically distinct from the Altai Levallois-Mousterian technocomplex.

 

Location of sites with Levallois-Mousterian and Micoquian assemblages used for statistical comparison with Chagyrskaya Cave artifacts. Kolobova et al. (2020).

There are strong similarities between the Chagyrskaya assemblage and the Micoquian/Keilmessergruppen technocomplex, which is based on non-Levallois corereduction flaking methods and bifacial tool production using plano-convex methods. Micoquian/Keilmessergruppen sites dating to between approximately 130 000 and 30 000 years ago have been found across central and eastern Europe. Statistical analysis of the Micoquian/Keilmessergruppen and Chagyrskaya assemblages (using the same methods as above) demonstrates a uniformity of the European assemblages grouped by 26 variables, the most significant of which are related to the plano-convex technological and typological characteristics. All assemblages from Chagyrskaya and central/eastern Europe contain bifacial tools diagnostic of the Micoquian, such as the Bocksteinmesser and Klausennischemesser types. The Chagyrskaya assemblage fits most closely with the eastern European Micoquian complexes.

 

Selected isolated teeth from Chagyrskaya Cave. (A), (B) Chagyrskaya 13 I1 in occlusal and labial view. Note the pronounced shoveling and large basal tubercle. (C), (D) Chagyrskaya 12 P3 in occlusal and mesial view. (E), (F) Chagyrskaya 14 P4 in occlusal and distal view. (G), (H) Chagyrskaya 41 P3 in occlusal and distal view. (I), (J) Chagyrskaya 50 P3 in occlusal and mesial view. Kolobova et al. (2020).

The pronounced similarity of European Micoquian and Chagyrskaya bifacial tools is also supported by a geometric morphometric shape analysis of bifaces, including Bocksteinmesser and Klausennischemesser types, from the key Micoquian/Keilmessergruppen site of Sesselfelsgrotte (Germany) and Chagyrskaya Cave. This result suggests the existence of a common design in the technological concept of bifacial production of Micoquian/Keilmessergruppen complexes.

 

Chagyrskaya 6 mandible fragment preserving right C–M2. (A) Buccal view; note the relatively posterior position of the mental foramen. (B) Lingual view and (C) occlusal view. Kolobova et al. (2020).

Chagyrskaya 8 genetically resembles Neanderthals from northern Croatia and the northern Caucasus, Vindija 33.19 (radiocarbon age approximately 48 000 years before present), and Mezmaiskaya 1 (electron spin resonance ages around 70 000 to 55 000 years). The associated Middle Palaeolithic assemblage at Vindija Cave is in questionable stratigraphic context, but the Micoquian assemblage at Mezmaiskaya Cave is characterized by numerous plano-convex bifacial tools, including Bocksteinmesser bifaces, numerous convergent scrapers, retouched/Mousterian points, and angled scrapers. Kolobova et al. compared the Chagyrskaya assemblage with the combined European Micoquian (including Mezmaiskaya) and Altai/Central Asian Middle Palaeolithic and Upper Palaeolithic datasets using a more limited number of technological and typological variables common to these technocomplexes. The Chagyrskaya and European Micoquian assemblages cluster together, and the Altai/Central Asian assemblages form a separate cluster.

 

Core, core preparation blanks and tools from Chagyrskaya Cave (subunit 6a): straight ventral scraper with natural back (1), overpassed bifacial thinning flake (2), bifacial thinning flake (3), semi-crescent dorsal scraper (4), sub-trapezoidal alternate scraper (5), semi-leaf dorsal, thinned base point (6), bifacial scraper straight, thinned base, naturally back (7), unidentifiable bifacial fragment (8), radial core (9), semi-leaf dorsal, thinned back scraper (10). Kolobova et al. (2020).

The Chagyrskaya assemblage and the European Micoquian technocomplex overlap chronologically between about 59 000 and 49 000 years ago and have strong technological and morphological similarities. The Chagyrskaya assemblage can therefore be viewed as a southern Siberian variant of the European Micoquian, and the Sibiryachikha variant seen more broadly as an expression of Micoquian variability across Eurasia. Micoquian populations are commonly considered specialised Horse and Bison hunters, adapted to steppe and piedmont environments. Kolobova et al. attribute their presence in the Altai to the eastward migration of Neanderthals from eastern Europe along the Eurasian steppe belt during the cold and arid conditions of Marine Isotope Stage 4. 

 

Core and tools from Chagyrskaya Cave (subunit 6b): semi-leaf alternate point (1), unidentifiable convergent bifacial scraper (2), semi-crescent dorsal thinned base scraper (3), sub-trapezoidal alternate scraper (4), semi-trapezoidal point (5), semi-triangular dorsal thinned base point (6), semi-triangular dorsal point (7), sub-trapezoidal alternate scraper (8, 11), sub-trapezoidal dorsal thinned base scraper (9), orthogonal core (10). Kolobova et al. (2020).

DNA recovered from Human remains and sediments indicates that Neanderthals first appeared in the Altai before or during Marine Isotope Stage 5. These early populations are not associated with Micoquian artifacts, which appear at Chagyrskaya only toward the end of Marine Isotope Stage 4 or the start of Marine Isotope Stage 3. It is not possible to distinguish Neanderthal from Denisovan technocomplexes in the cultural sequence at Denisova Cave due to the homogeneous technological and typological characteristics of the lithic assemblages. However, the absence of Micoquian-like artifacts at Denisova Cave in deposits dated to between 59 000 and 49 000 years ago indicates that Denisova and Chagyrskaya Caves were occupied by two distinct Neanderthal populations, most likely at different times given current evidence that Neanderthals were present at Denisova Cave much earlier than at Chagyrskaya Cave. Genetic data from Denisova Cave have also revealed several episodes of gene flow between Neanderthals and Modern Humans  and two different Neanderthal components in Denisova 11, the Neanderthal-Denisovan offspring. 

 

Cores from Chagyrskaya Cave (sublayer 6c/1): radial core (1), orthogonal cores (2), (3). Kolobova et al. (2020).

Kolobova et al. therefore propose that Neanderthals entered southern Siberia on at least two separate occasions, with the most recent incursion originating in eastern Europe and the northern Caucasus, which lie 3000 to 4000 kilometers to the west of Chagyrskaya Cave. The identification of Micoquian assemblages in all three regions is consistent with the genetic similarities between Neanderthal remains at Chagyrskaya, Vindija, and Mezmaiskaya Caves. Kolobova et al.'s archaeological data supports a rarely observed case of long-distance demic dispersal in the Palaeolithic and illustrate that artifacts are culturally informative markers of ancient population movements.

 

Core preparation blanks from Chagyrskaya Cave (sublayer 6c/1): crested débordant flake (1), débordant flake from radial core (2), bifacial thinning flakes (3, 4), cortical débordant flake (5), technical flake (6), lateral débordant flake (7), débordant flake from radial core/pseudo-Levallois point (8). Kolobova et al. (2020).

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Deciphering the imput of Neanderthal and Denisovan genetic material into modern, non-African, Human populations.

Early Modern Humans migrating from Africa are known to have encountered and interbred with two Archaic Human populations, Neanderthals and Denisovans, with almost all non-African Humans carrying some DNA from these groups and most Africans carrying little if any. Previous studies have suggested that modern Eurasians have inherited about 2% of their DNA from Neanderthal ancestors, while Melanesians have about 5% Denisovan DNA.

In a paper published in the journal Cell on 22 March 2018, Sharon Browning of the Department of Biostatistics at the University of Washington, Brian Browning of the Division of Medical Genetics at the University of Washington, Ying Zhou, also of the Department of Biostatistics at the University of Washington, Serena Tucci of the Department of Ecology and Evolutionary Biology at Princeton University, and Joshua Akey of the Department of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics at Princeton University, publish the results of a new study in which genomes from non-African populations from the 1000 Genomes Project were compared to the genomes of two Archaic Humans from the Altai Mountains of southern Siberia, one Denisovan and one Neanderthal, in order to better understand the genetic contribution of these two groups to non-African Modern Human groups.

All Humans, including Archaic populations such as Neanderthals and Denisovans, share almost all of their DNA. In this context 'Neanderthal DNA' or 'Devisovan DNA' refers to variable alleles found in the ancient population, but not in modern African populations not thought to share any genetic heritage since the ancestors of these groups left Africa in the Middle Pleistocene.  An allele is one of two or more different genes that can occur at a gene locus, for example different alleles for blue or brown eyes may be found at the gene locus for eye colour in Humans

Reconstruction of a Neanderthal Woman. Morten Jacobsen.

In line with previous studies, Browning et al. found that East Asian populations had a higher proportion of Neanderthal DNA than European populations, while the proportion of Neanderthal DNA in South Asians and Europeans was roughly similar, while the Papuan population had a significant proportion of Denisovan DNA. Modern Europeans were also shown to have a significantly higher proportion of Neanderthal DNA than modern West Africans (who have almost no Neanderthal DNA), while Americans have lower levels of Neanderthal DNA than Europeans (though this may be due to recent mixing with other population groups. Denisovan DNA was found at a higher level in East and South Asians than Europeans, with some European groups, such as Finns, having a higher proportion of Denisovan DNA than others. Native American populations also had some Denisovan DNA, though less than in South and East Asians.

Curiously modern East Asian populations seemed to carry Denisovan DNA from two sources, one closely related to the Altai Denisovan, and one more distantly related, whereas all Denisovan DNA in other populations, including Papuans, appeared to carry only DNA from the distantly related population. This suggests that East Asians went through an additional phase of interbreeding with Denisovans after their split from Papuans and South Asians, while Papuans may have had a second phase of interbreeding with the distantly related Denisovan population after their split from East and South Asians, or simply have derived from a subsection of that early population that had interbred with Denisovans more extensively.

Reconstruction of a Denisovan Man. John Baravo.

East Asians were shown to have an average of 30% more Neanderthal DNA than Europeans, though there was no suggestion that this came from more than one source. Browning et al. suggest that the most likely explanation for this is interbreeding between the ancestors of modern Europeans and other Modern Human populations with no admixture of Neanderthal DNA after their split from East Asians.

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Identifying Archaic Human DNA in gene sequences from modern Melanesians.

Modern DNA recovery techniques have allowed scientists to recover genetic sequences from a number of Neanderthal individuals (members of a fairly well known Archaic Human population found in Europe and West Asia before about 40 000 years ago) as well as some Denisovans (members of a poorly understood Archaic Human population found in Central Asia before about 50 000 years ago). This has led to the discovery of genetic material derived from these ancient populations within many modern Human groups, and, more recently, attempts to determine what genes preserved from Archaic Human groups might contribute to modern Humans. Such studies have found evidence of Neanderthal DNA in all non-African modern populations, while Denisovan DNA has been found only in Melanesian populations.

In a paper published in the journal Science on 17 March 2016, a team of scientists led by Benjamin Vernot of the Department of Genome Sciences at the University of Washington present the results of a study of the genomes of 1523 modern Humans from around the globe, including 35 Melanesians from Papua New Guinea and the Bismarck Archipelago, and attempt to analyse the preserved DNA sequences in these individuals.

Melanesian genomic variation in a global context. (A) Locations of the 159 geographically diverse populations studied. Information on the Melanesian individuals sequenced (blue triangles) is shown in the inset. Vernot et al. (2016).

All Humans, including Archaic populations such as Neanderthals and Denisovans, share almost all of their DNA. In this context 'Neanderthal DNA' or 'Devisovan DNA' refers to variable alleles found in the ancient population, but not in modern African populations not thought to share any genetic heritage since the ancestors of these groups left Africa in the Middle Pleistocene.  An allele is one of two or more different genes that can occur at a gene locus, for example different alleles for blue or brown eyes may be found at the gene locus for eye colour in Humans

The highest proportion of Neanderthal DNA was found in modern East Asians, with Europeans having a slightly lower level and South Asians a slightly lower level still. The proportion of Neanderthal found in Melanesians was much lower (roughly half) than that found in any of these groups, but still much larger than the highest found in any African group (people from the Western Division of The Gambia).

Only Melanesians were found to have significant levels of Denisovan DNA (trace amounts were found in samples from East and South Asians), who had slightly higher levels of Denisovan DNA than they did Neanderthal DNA - though the combined level of Denisovan and Neanderthal DNA found in Melanesians was slightly higher than that found in East Asians.

The areas of DNA from Archaic populations were not random, but rather similar sections of Archaic DNA appear to have been retained in different populations. This suggests that some Archaic DNA alleles were strongly selected against in the ancestors of modern humans, while others appear to have been more useful. In particular Vernot et al. note that a section of Archaic DNA alleles in an area of chromosome 7 associated with language skills has been lost in all modern Humans. Conversely a number of Archaic alleles associated with the metabolism have been retained in different modern Human populations, including genes associated with glucose metabolism and lipid processing. A number of genes associated with the immune system have also been conserved.

See also...

Genetic data from two new Denisovan individuals.                                                                 The Denisonvans were an ancient people who are known from only a single archaeological site, a cave...

Neanderthal DNA from a 37 000-42 000 modern Human jaw from Romania.     Neanderthals first appeared in Europe around 300 000 years ago and were replaced by anatomically modern Humans between 45 000 and 35 000 years ago. Genetic studies if modern Human populations show that almost all non-Africans have traces of Neanderthal...

Human remains from the Middle Pleistocene of Normandy.                                                                Early and Middle Pleistocene Human remains are extremely rare in northern Europe, having to date...

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Genetic data from two new Denisovan individuals.

The Denisonvans were an ancient people who are known from only a single archaeological site, a cave in the Altai Mountains of southern Siberia. The group were identified as being genetically distinct after scientists studied genetic data from the fingerbone of a child found in 2008 and thought to have lived at least 50 000 years ago.  Mitochondrial DNA from this individual suggests that the most recent female direct ancestor that this individual shared with Neanderthals and Modern Humans that lived about a million years ago. This was possible because mitochondrial DNA is found in the mitochondria, organelles outside the cell nucleus, it is passed directly from mother to child without being sexually recombined each generation, enabling precise estimations of when individuals shared common ancestors, at least through the female line (it is also possible to trace direct ancestry through the male line, using DNA from the Y chromosome, which is passed directly from father to son without sexual recombination). However analysis of the main nuclear DNA of the individual (DNA which is found in the nucleus of the cell and which is recombined with each generation), suggests that he or she shared a more recent common ancestor with Neanderthals (though clearly from a genetically distinct and separate population), and came from a population that had supplied about 5% of the DNA found in modern Melanesian populations and about 0.2% of the DNA found in modern East Asian and Native American populations.

In 2010 a foot bone was recovered from the same site, thought to be from an individual that lived in the area at approximately the same time (i.e. to within a few thousand years). However genetic material recovered from this specimen revealed it to be of Neanderthal rather than Denisovan origin.

In a paper published in the Proceedings of the National Academy of Sciences of the United States of America on 16 November 2015, a team of scientists led by Susanna Sawyer and Gabriel Renaud of the Department of Evolutionary Genetics at the Max Planck Institute for Evolutionary Anthropology describe the results of a study of two molars found in the Denisova Cave in 2000 and 2010.

The molars are distinctly larger and flatter than anything seen in Modern Humans or Neanderthals, more similar to those seen in Pliocene Hominids. Only two comparable teeth have been found at Late Pleistocene sites elsewhere, one from Romania and one from Uzbekistan. Both are heavily worn, and were most likely third molars.

Occlusal surfaces of the Denisova 4 and Denisova 8 molars and third molars of a Neandertal and a present-day European. Sawyer & Renaud (2015).

Radiocarbon dating of the layers from which the teeth were recovered suggests that they were deposited more than 50 000 years ago and about 48 600 years ago. A molecular clock approach (which measures the rate of mutation on non-sequencing DNA), suggests that the oldest individual may have lived as long as 60 000 years before the youngest. This suggests that Denisovans were in the area and using the cave for a considerable period of time, possibly intermittently with the cave being inhabited by Neanderthals at other times.

Genetic comparison placed the teeth in a group along with the fingerbone, suggesting that the Denisovans do form a separate population, distinct from either Neanderthals or Modern Humans. However the study showed more genetic diversity among the three Denisovan individuals (who were all buried in the same cave) than among all known Neanderthals sequenced (who come from a large area of Europe and West Asia), though this diversity was still considerably lower than found in modern Europeans.

The study again found the Denisovans shared more genetic material with Neanderthals than Modern Humans, but that this was probably the result of interbreeding, with the ancestors of the Denisovans having diverged from the common ancestor of Neanderthals and Modern Humans long before these two groups split, and all Modern Humans having shared a common ancestor more recently than the split with Neanderthals.

See also...

Neanderthal DNA from a 37 000-42 000 modern Human jaw from Romania.     Neanderthals first appeared in Europe around 300 000 years ago and were replaced by anatomically modern Humans between 45 000 and 35 000 years ago. Genetic studies if modern Human populations show that almost all non-Africans have traces of Neanderthal...

Rainforest resources in the diet of Late Pleistocene Humans from Sri Lanka.              Early modern Humans expanded from Africa around the globe in the Late Pleistocene, from about 125 000 years ago onwards. In doing so they adapted to a wide variety of environments, though some habitats...

Hominin teeth from the Middle Pleistocene of Anhui Province, China.                                     In the 1970s and 1980s a collection of Hominin bones and teeth were unearthed in the Longtan Cave at Hexian in Anhui Province in eastern China. The bones of these remains have been extensively studied, and assigned to the species Homo erectus, though...

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