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 18th 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 2nd or 3rd 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.
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