Were the Denisovans the first humans in Southern California 130,000BP?

Since the Holen (2017) paper describing human modified bone and stone tools from Southern California dated to 130,000BP, I have been fascinated by the possibility that some form of human was most likely well established in the Americas by this date.

But which one?

Previously I have detailed the Holen et al. (2017) evidence here and here and reviewed the possibility that the hominid could have been Homo erectus here.

Now I will consider whether the Denisovans were the species of humans in the Americas 130,000BP. A little background first.

Who were the Denisovans?

The Denisovans are named after the cave in which the first evidence for them, was found. That was in the form of four tiny fossils, from which DNA was extracted showing that they were a different kind of human, namely a sister group to Neanderthals.

Denisova cave, is located in the Altai region of southern Russia as shown on the map below:

The cave itself, is named after its 18^th century inhabitant, a hermit, called Saint Dionisij (Denis). It, is located in, Altai Krai, on the borders of the southern Altai Republic, Kazakhstan and Mongolia, near the village of Chorny Anui (Чёрный Ануй), and about 150 km south of the city of Barnaul.

Situated 28m above the right bank of the Anuy River, it is a karst cave. The floor area is ca. 270 spread over three galleries. The central chamber, known as the Main Gallery, has a floor of 9m x 11m. From here two galleries, the East Gallery and the South Gallery branch off.

Hominin remains, belonging to Denisovans have been found in all three, galleries. However, despite an extensive search I have been unable to discover any depth of detail about the history of excavations or the cave stratigraphy.

The best sources that I could find were firstly, Brown et al. (2016) who says: “Denisova Cave is a key site for our understanding of the north Asian Palaeolithic record.. Excavations undertaken by the Russian Academy of Sciences have been ongoing for more than three decades, revealing a 4.5 metre stratigraphic sequence that is key to archaeological, geological, faunal, palynological and chronological reconstructions of the Altai during the Pleistocene. While this sequence has been pivotal in our understanding of Pleistocene environments, it is the hominin fossil record of the site that has become the focus of much attention.”

Secondly Slon et al. (2017) who included in their paper a useful floor plan of the East Gallery:

Slon et al. (2017). Original caption reads:

Fig. 3. Hominin mtDNAs along the stratigraphy of the East Gallery in Denisova Cave. Layer numbers are noted in grey. The layers of origin for sediment samples and skeletal remains yielding Neandertal (orange) and Denisovan (green) mtDNA genomes are denoted.

According to Hirst (2017) the dates of the various layers are as follows:

• Stratum 9, Upper Palaeolithic (UP), Mousterian and Levallois, ~46,000 (OIS-2)

• Stratum 11, Initial Upper Palaeolithic, Altai Mousterian, ~29,200-48,650 BP (OIS-3)
• Strata 20-12, Later Middle Palaeolithic Levallois, ~69,000-155,000 BP
• Strata 21 and 22, Initial Middle Palaeolithic Levallois, Mousterian, ~171,000-182,000 BP (OIS-5)

The four fossils discovered are:

Table adapted from Wikipedia (2017)

The site is an extremely rich one, in terms of its bone assemblage. For instance, according to Brown et al. (2016) “Within the East Gallery of Denisova Cave alone, excavations between 2005 and 2013 yielded approximately 135,600 bones; however 128,591 could not be identified.”

Herein lies the problem. Whereas many soviet scientists suspected that some of the bone samples were of hominin origin, on morphological grounds, they could not be identified. Of particular, interest, to the scientists, of course was whether any of the bones were those of Neanderthals or early humans on their out of Africa migration.

This interest stemmed from the Krause et al. (2007) paper, which had examined bones from the partial skeleton of an 8–10-year-old child discovered in the late 1930s in Teshik-Tash Cave, Uzbekistan and three partial long bones from Okladnikov Cave in the Altai. Their results had established, via mtDNA analysis, that Neanderthals both sites.

Hence this new technique, it was hoped, would be able to establish the identity of the hominin remains from Denisova cave.

Therefore, in 2010, a team headed by David Reich set about obtaining mtDNA from two samples from Denisova cave: a finger phalanx (Denisova 3) and an upper 2^nd or 3^rd molar (Denisova 4). What they found astounded them. Neither bone was from either a Neanderthal or a modern human. No, what they had found was DNA from an up to this point undiscovered hominin group, which they dubbed the “Denisovans”. The rest, as they say, is history.

The fossils in detail

Denisova 2

Source: Slon et al. (2017).

“A worn deciduous molar was discovered in 1984 in layer 22.1 of the Main Gallery of Denisova Cave and was initially described as a right lower first deciduous molar (dm1) However, Shpakova and Derevianko believed that the tooth was more likely a lower second deciduous molar (dm2), and we concur with their opinion on the basis of the lack of a tuberculum molare and the large size. The crown of the tooth is almost completely worn away, and only a thin rim of enamel is preserved buccally, mesially, and lingually. The only feature of crown morphology preserved is a small remnant of the buccal groove. The roots are mostly resorbed, with only short stumps remaining mesiobuccally and mesiolingually. The exposed pulp cavity shows five diverticles entering the crown. The resorption of the roots and the fact that the specimen exfoliated naturally indicate an age equivalent to about 10 to 12 years in modern humans. The strong wear makes most morphological comparisons impossible. However, the cervical mesiodistal and buccolingual diameters are very large, falling outside of the range of variation seen in modern humans and in the range of Neanderthals.”

Denisova 2.

Source: Siberian Times (2015)

Original Caption reads:

It was here in the Denisova Cave in 2008 that Siberian scientists discovered a finger bone fragment of 'X woman', a juvenile female. Picture: Max Planck Institute

The attribution of the fossil as originating from a Denisovan individual was certain due to the frequency of derived alleles found by the Slon et al. (2017) team: “Of fragments that overlap positions where only the Denisovan genome is derived, 49% (2051 of 4160) carry the Denisovan-like allele, whereas the corresponding values for the sharing of Neandertal- and modern human–specific alleles are 6% (252 of 4231) and 5% (307 of 5924), respectively. We thus conclude that the Denisova 2 specimen originated from a Denisovan individual.”

Denisova 3

Source: Reich el al. (2010)

“In 2008, the distal manual phalanx [little finger bone] of a juvenile hominin was excavated at Denisova Cave. The phalanx was found in layer 11.2 of the East Gallery, which has been dated to 50,000 to 30,000 years ago.

This layer contains microblades and body ornaments of polished stone typical of the ‘Upper Palaeolithic industry’ generally thought to be associated with modern humans, but also stone tools that are more characteristic of the earlier Middle Palaeolithic, such as sidescrapers and Levallois blanks.

.., we used a DNA capture approach10 in combination with high-throughput sequencing to determine a complete mtDNA genome from the Denisova phalanx. Surprisingly, this mtDNA diverged from the common lineage leading to modern human and Neanderthal mtDNAs about one million years ago.”

Further on in the paper, after having shown that the mtDNA from the cave was not that of a modern human, the team looked closely at its affinity to Neanderthals and concluded: “Thus, we conclude that late Neanderthals across a broad geographical range have a population history distinct from that of the Denisova individual.. We call the group to which this individual belonged Denisovans in analogy to Neanderthals, as Denisovans are described for the first time based on molecular data from Denisova Cave just as Neanderthals were first described based on skeletal remains retrieved in the Neander Valley in Germany.”

Denisova 3 adapted from Hawks (2015), original caption reads: A modern human juvenile distal fifth phalanx (left) compared to the Denisova fragment (right).

Denisova 4

Source: Reich et al. (2010)

“In 2000, a hominin tooth was discovered in layer 11.1 of the south gallery of Denisova Cave. The tooth is from a young adult and therefore from another individual than the phalanx which stems from a juvenile. To elucidate the relationship of the tooth to the individual from which the phalanx is derived, we extracted DNA from 50 mg of dentin from the root of the tooth and prepared a sequencing library. About 0.17% of random DNA sequences determined from this library aligned to the human genome, whereas the rest is likely to represent microbial contamination common in ancient bones.

We therefore used a novel DNA capture approach to isolate mtDNA sequences from the sequencing library. A total of 15,094 sequences were identified which allowed the complete mtDNA genome to be assembled at an average coverage of 58-fold. This sequence differs at two positions from the mtDNA of the phalanx whereas it differs at about 380 positions from both Neanderthal and present-day humans.

The time since the most recent common ancestor of the two mtDNAs from Denisova Cave is estimated to be 7,500 years, with a 95% upper bound of 16,000 years. We

conclude that the tooth and the phalanx derive from two different individuals that are probably from the same hominin population.

Denisova 4 from Reich et al. (2010). Original caption reads: Figure 4. Morphology of the Denisova molar. a, b, Occlusal (a) and mesial (b) views.

Denisova 4, also believed to be from Reich, but attribution uncertain.

Denisova 8

Source: Sawyer et al. (2015)

Discovered in 2010, another molar (Denisova 8) was found in Denisova Cave.

The molar, designated Denisova 8 was found at the interface between layers 11.4 and 12 in the East gallery of Denisova Cave. Excavated from slightly below the Neanderthal toe phalanx (Denisova 5, layer 11.4) and the Denisovan finger (Denisova 3, layer 11.2). Radiocarbon dates for layer 11.2, as well as for the underlying 11.3 layer, yield ages more than ∼50,000 y (OxA-V-2359-16 and OxA-V-2359-14)

(2). Denisova 8 is thus older than Denisova 3, which is at least 50,000 years old. It was reassembled from four fragments that fit well together, although a piece of enamel and most of the root is missing.

Denisova 8.

Source: Zubova, et al. (2017)

Original caption reads: Fig. 5. Denisova 8 molar before the restoration.

Denisova 8.

Source: Yirka, Phys Org (2015)

Original caption reads: Denisova 8 molar, top view. Credit: Bence Viola.

Introgression of Denisova DNA into modern humans

As part of the process of assigning the Denisovan sequences to a hominid group, Reich et al. (2010) looked at the data to answer this question: “A fundamental question is whether the Denisova individual is an outgroup to Neanderthals and modern humans, as the mtDNA suggests, whether it is a sister group to Neanderthals or to modern humans, or whether it falls within the range of variation of either of these two

groups.”

The results were surprising:

•        Their estimated time of divergence between Denisovans and Neanderthals was 640ka
•    The estimated time of divergence between Denisovans/Neanderthals and modern Africans   is 804ka
•    They propose that the divergence of the Denisova mtDNA results either from the persistence of a lineage purged from the other branches of humanity through genetic drift or else an introgression from an older hominin lineage, such as Homo erectus.
•      That 4-6% of the DNA of Melanesians (Papuans and Bougainville Islanders) originates from an Denisovan Introgression, possibly as long ago as 50k
•    No Denisovan DNA was found to have introgressed into the ancestors of modern Europeans

Further work, by other researchers, has since established that:

•     The complete mitochondrial genome of an Denisovan individual was determined by Krause et al. (2010). This paper also provided the first estimate of the split times of modern humans, Neanderthals and Denisovans
•     Australian Aborigines, have received some Denisovan DNA via introgression at lower level than Melanesians (Rasmussen; et al. (2011))
•    From Reich et al (2011): Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a “Negrito” group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbour Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.
• 
  

Reich et al. (2011). Fig 1. Original caption reads:

Denisovan Genetic Material as a Fraction of that in New Guineans

Populations are only shown as having Denisova ancestry if the estimates are more than two standard errors from zero (we combine estimates for populations in this study with analogous estimates from CEPH-Human Genome Diversity Panel populations reported previously). No population has an estimate of Denisova ancestry that is significantly more than that in New Guineans, and hence we at most plot 100%. The sampling location of the AU2 population is unknown and hence the position of this population is not precise.

• Meyer et al. (2012) used a new technique to produce a high coverage Denisovan genome from the Denisova 3 fossil and re-dated it, based on the DNA mutation rate as ca. 78,000 years old. Secondly, discovered that, the Denisovan individual carried alleles that in present-day humans are associated with dark skin, brown hair and brown eyes. Estimated the time interval that Denisovans inhabited the Altai region for at least 110,000 years based on DNA divergence. Lastly discussed the geographical range of the Denisovans, placing the Melanesian interbreeding event in southeast Asia as opposed to just “Asia” as stated by Reich et al. (2011) 
• Prüfer, et al. (2013) sequenced a hominin finger phalanx from the east gallery of Denisova Cave in the Altai Mountains. From this bone, they generated the full genome sequence of a Neanderthal female to 52-fold coverage. The team compared this genome to that of a number of, other Neanderthals, the Denisova genome and 24 genomes of modern day humans. They then constructed a neighbour-joining tree based on transversion mutations, to show the relationships between the hominid groups and their time of separation. They found a minimum of 5 gene flow events between hominin groups, Denisovans to modern humans in both Oceania and into mainland Asians and Native Americans (around 0.2%), Altai Neanderthals into Denisovans, Neanderthals most closely related to the Mezmaiskaya specimen into the ancestors of both Eurpoeans and Asians and lastly the introgression into the Denisovan genome of DNA from an even more ancient hominin group, most likely Homo erectus.  This paper also indicates that some gene from Denisovans occurred in mainland Asia, perhaps at an earlier date than the gene flow into those populations beyond Wallace Line.

Prüfer, et al. (2013) Fig. 8 Pleistocene gene flow events. Original caption reads: Figure 8. A possible model of gene flow events in the late Pleistocene

The direction and estimated magnitude of inferred gene flow events are shown. Branch lengths and ages gene flows are not drawn to scale. The dashed line indicates that it is uncertain if Denisovan gene flow into modern humans occurred once or more times. D.I. denotes the introgressing Denisovan, N.I. the introgressing Neanderthal. Note that the age of the archaic genomes precludes detection of gene-flow from modern humans into the archaic hominins.

• Furthermore, Cooper and Stringer (2013) suggested that this area may have been the Denisovan’s last refugium. 
• A paper from Huerta-Sanchez et al. (2014), found that the EPAS1 gene that assists with adaptation to low oxygen levels at high altitude found in Tibetans is also found in the Denisovan genome. This implies that there was gene flow into the ancestors of modern Tibetans from the Denisovans.
• Meyer et al. (2014) studied the skeletal remains from Sima de los Huesos, in northern Spain. Morphologically these specimens are close to Homo heidelbergensis but also display distinct Neanderthal traits. They determined an almost complete mitochondrial genome sequence and showed that it is closely related to the lineage leading to mitochondrial genomes of Denisovans. This was a big surprise. Hence their discussion considers a range of evidence and explores several scenarios to account for it. “The fact that the Sima de los Huesos mtDNA shares a common ancestor with Denisovan rather than Neanderthal mtDNAs is unexpected in light of the fact that the Sima de los Huesos fossils carry Neanderthal-derived features for example, in their dental, mandibular, midfacial, supraorbital and occipital morphology” “although almost no morphological information is available for Denisovans, a molar that carries Denisovan DNA is of exceptionally large size and does not exhibit the cusp reduction seen in the Sima de los Huesos hominins. After a number of options are considered the authors comment “..the Sima de los Huesos hominins may be related to the population ancestral to both Neanderthals and Denisovans. Considering the age of the Sima de los Huesos remains and their incipient Neanderthal-like morphology, this scenario seems plausible to us”
• Meyer et al. (2015) managed to extract nuclear DNA from the Sima de los Huesos hominin remains, they confirmed their suppositions of the previous year: “In contrast to the mitochondrial DNA, the nuclear genomes from the three specimens are significantly more, similar to, Neanderthals than to Denisovans. Our results thus place the Sima de los Huesos hominins on the Neanderthal evolutionary lineage, in congruence with previous morphological analyses. This shows that the Neanderthal/Denisovan population split predates 430 kyr, the geological age of the Sima remains.
• More Denisovan introgression into the Melanesian genome was found by Vernot et al. (2016) who studied a previously unsampled population from the Bismarck Archipelago: Furthermore, our Melanesian samples show genetic similarities to both Neanderthals and Denisovans, whereas all other non-African populations only exhibit affinity toward Neanderthals. Using an f4 statistic, we find significant evidence of Denisovan  ancestry (Z > 4) in our Melanesian samples, with admixture proportions varying between 1.9 and 3.4%.

Adapted from Vernot et al. (2016). Locations of Melanesian DNA samples. Original caption reads: Fig. 1. A. Melanesian genomic variation in a global context. (A) Locations of the 159 geographically diverse populations studied. Information about the Melanesian individuals sequenced (blue triangles) is shown in the inset.

Adapted from Vernot et al. (2016). Percentages of Melanesian DNA found in samples from the Bismarck Archipelago and other related samples. Original caption reads: Fig. 1. (D) Estimates of Denisovan ancestry in Oceanic populations estimated from an f4 statistic (14).The 11 Melanesian populations are highlighted by the light blue box.

• Finally, a paper on extracting DNA from soil samples recovered from Denisova Cave, by Slon et al. (2017) found that Neanderthal mtDNA was present in samples taken from layer 15 from the Main Gallery. This is important because this is a layer associated with Palaeolithic artifacts, but from which no Neanderthal fossil has ever been found. More importantly, the researchers also identified Neanderthal and Denisovan mtDNA taken from layers 14 and 15, respectively, from the East Gallery, at layers lower than any previous fossil finds, layers where no hominin fossil has ever been found. This last finding therefore extends the time of occupation of the cave by both Neanderthals and Denisovans and shows unequivocally that they co-existed in this area of the Altai for some time, perhaps 100’s of years, thus proving the result of the Prüfer et al. (2013) paper.

The populations of hominins, their migrations and dates of split over time can be seen reasonably well in a map by Croft (2014):

I have summarised the distribution of Denisovan fossil and DNA finds in a google My Maps map:

And here is my zoomable and clickable version from My Maps. Each site has a short bio.

Conclusions

I will now try to unpick this mass of evidence and give an assessment as to whether it is possible that the Denisovans were the group of humans that left modified bones and stone tools in southern California 130,000BP.

To decide whether the Denisovans could be the group that left evidence of the occupation of the Americas 130,000 years ago we need to consider two questions:

Firstly, what is there geographical distribution?

As explored above the Denisovans certainly reached the Siberian Altai by ca. 200,000BP as evidenced by their fossil remains. Their DNA is found in near and far Oceania, Australia and to a lesser degree in mainland Asia and South America.  Some authors have postulated, that this shows they had migrated and settled beyond the Wallace line. Other enigmatic hominin settlement/evidence has been found as far as apart as Happisburgh in the UK (see here) and Diring Yuriakh in Russia (see here). The first site shows that humans other than Homo erectus were widely distributed as long ago as 0.8Mya. The second in the far eastern Sakha Republic of Russia, is located only 450km south of the Arctic Circle and only a short distance from Bering Land bridge, the presumed point of entry of humans into America.

Other specimens unattributed to any hominin group, which could be Denisovans include those from Sel-Unger, Hetao, Salkhit, Dali, Maba, Jinnisshan and Dokchon.

Consequently, I can only conclude that Denisovans were widely distributed enough to be a candidate for the humans who were in southern California 130,000BP.

Did Denisovans or their ancestors migrate outside Africa at a suitable time?

Genetic studies on modern day Africans and Europeans show no Denisovan admixture. Hence by the time the two groups made contact the Denisovans were distributed outside these two regions, almost certainly across large swathes of Asia. According, to Meyer et al. (2015), the common group of hominins from which, the Denisovans and the Neanderthals evolved was Homo heidelbergensis. Evidence from Sima des Huesos shows that the descendants of the common ancestors of Neanderthals and Denisovans were definitively outside Africa by 430,000BP

The population ancestral to both Denisovans and Neanderthals separated from the genetic line leading to modern humans approximately 1 million years ago [0.7 to 1.3 Mya] according, to, Krause et al. (2010), whereas Reich et al. (2010) put the split time as 800Kya and Prüfer et al. (2013) 550-725kya

The split time between Neanderthals and Denisovans has been estimated by Reich et al. (2010) as 640Kya and by Prüfer et al. (2013) 381-473Kya

The oldest unequivocally, Denisovan fossil, from the Altai may be 227,000 years old.

These facts, taken together, show that the Denisovans were temporally and spatially in the ‘the right place at the right time’. Given the length of time the Denisovans or their ancestors were outside Africa, and given the known adaptations to altitude and a variety of environments that hominins of this period, including Denisovans, had they seem a good candidate for the hominin group that left the modified bones and stone tools in southern California 130,000 years ago.  

References

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