Home > Denisova, DNA, Evolution, Hybridization, Neanderthal, Paleoanthropology > Denisova Cave and the Mystery of the mtDNA Phylogenetic Tree

Denisova Cave and the Mystery of the mtDNA Phylogenetic Tree

Nobody expected a great surprise. Genetic testing of the little finger of an early hominin child found in the Siberian Denisova Cave, Kostenki, in the middle of archeological remains pertaining to Upper Paleolithic culture, would almost for sure confirm DNA similar to ours. There was a slim change that the pinky belonged to a Neanderthal from the neighborhood that got lost, but everything pointed at a an unequivocal member of the advanced group of hominins responsible for introducing symbolic art all over the world, the so-called anatomically modern humans (AMH).

The collection of personal adornments and artifacts suggestive of symbolic behavior from the Early Upper Paleolithic deposits of Denisova Cave, Altai, is one of the earliest and the most representative of the Upper Paleolithic assemblages from Northern and Central Asia. Especially important is a fragment of a bracelet of dark-green chloritolite, found near the entrance to the eastern gallery of the cave in the upper part of stratum 11. The estimated age of the associated deposits is ca 30 thousand years. According to use-wear and technological analysis, techniques applied for manufacturing the specimen included grinding on various abrasives, polishing with skin, and technologies that are unique for the Paleolithic – high-speed drilling and rasping. The high technological level evidences developed manual skills and advanced practices of the Upper Paleolithic cave dwellers. (Derevianko et al., 2008)

Humans spend more time gathering around the campfire to celebrate their victory on Nature, only to challenge evolution in an entirely new way.

Neanderthal were readily dismissed as potential authors of local Upper Paleolithic art, due to what boils down to a deep distrust against anything that would deem them capable of such a feat, and they were the only other early hominins around that we knew of – at least culturally speaking, since we don’t have much more than a little pinky after all. And indeed, the first genetic results showed the world was right about one thing: the little finger did not belong to a Neanderthal child. But nobody could have guessed how wrong the usual lot of junk scientists were about almost anything else. This was not the child from the same flesh and blood of modern humans, but a member of a previously unknown ancestral human subgroup.

Dr. Johannes Krause, of the Max Planck Institute in Germany, sequenced the entire mitochondrial DNA (mtDNA) genome and showed almost two times as many differences to modern human mtDNA as does Neanderthal mtDNA. You can find the genome at GenBank or EMBL using record ID FN673705 and check it out by yourself: Even Neanderthal was a close relative to modern humans compared to this hominin!

A phylogenetic analysis similarly shows that the Denisova hominin mtDNA lineage branches off well before the modern human and Neanderthal lineages (Fig. 3). Assuming an average divergence of human and chimpanzee mtDNAs of 6 million years ago, the date of the most recent common mtDNA ancestor shared by the Denisova hominin, Neanderthals and modern humans is approximately one million years ago (mean = 1,040,900 years ago; 779,300–1,313,500 years ago, 95% highest posterior density (HPD)), or twice as deep as the most recent common mtDNA ancestor of modern humans and Neanderthals (Krause, 2010)

Established paleo-anthropology is now faced with the challenge to rewrite the book of human evolution. And of course first things first, the dates were adjusted to make a better fit with pre-AMH cultures:

We note that the stratigraphy and indirect dates indicate that this individual lived between 30,000 and 50,000 years ago. At a similar time individuals carrying Neanderthal mtDNA were present less than 100 km away from Denisova Cave in the Altai Mountains, whereas the presence of an Upper Palaeolithic industry at some sites, such as Kara-Bom and Denisova, has been taken as evidence for the appearance of anatomically modern humans in the Altai before 40,000 years ago. (Krause et al., 2010)

Nobody has ever heard of pre-AMH bracelets, so let’s conveniently forget for a while about that fragment of a polished bracelet with a drilled hole, that was found earlier in the same layer that yielded the bone. Is it possible that here we have evidence that points to a third species, next to Neanderthal and AMH? A species, that might have been as civilized as a AMH, or a beast our ancestors didn’t breed with, or anything else that didn’t involve “us” so we can understand? The publication of Krause carefully omitted this pressing question and the word went out that for sure Krause had already access to autosomal data that could explain why. That Denisova child might have been anything but a Yeti.

Sure, mtDNA doesn’t make a species, no matter how different it may be from modern humans. There was no need for Krause to mention this. But divergence of mtDNA lineages has been taken as an indication of divergent hominin developments before. Explicitly with respect to Neanderthal, whose attested and validated mtDNA lineage was deemed sufficiently homogeneous and different from ours to provoke a definite ordeal. However, now we have the Denisova mtDNA sample to teach us modesty. After all, there are lots of things about mtDNA that need better understanding before we can even attempt to solve the question of how the modern forms spread, and how they evolved.

All conspires against the notion that paleogenetic mtDNA of Neanderthal, and now even more so the mtDNA from Denisova Cave, might be the precursor of modern mtDNA. It couldn’t have evolved so rapidly to modern mtDNA. A study on 44,000-year-old remains of Adelie penguins in Antarctica even confirmed the potential overestimation of the mutational change that is used for dating mtDNA of paleogenetic samples. This stems from a bias that is caused by nonsynonymous mutations, involving notable coding changes that are potentially deleterious and most likely won’t persist very long due to natural selection. Accordingly, only a portion of the mutational changes can be observed over a longer period of time:

Rates of evolution of the mitochondrial genome are two to six times greater than those estimated from phylogenetic comparisons. Subramanian et al., 2009)

The investigation showed that only the effect of synonymous mutations (“silent mutations”) in the mtDNA genome, that involve coding synonyms for the same proteins, remain stable. To retrieve the phylogenetic dates only these “silent mutations” should be measured, ie. changes on coding genes that produce coding synonyms that won’t affect the function of the gene. Mutations that effectively change the functionality of a gene and thus are most likely to be (slightly) harmful, get lost over time, since such mutations would finally bring about the extinction of a lineage and thus shouldn’t count for calculating the age of surviving lineages. The mtDNA “molecular clock” thus should only involve properly identified “silent mutations”.
This results were also important for interpreting the paleogenetic mtDNA samples of hominins.

Mildly deleterious mutations initially contribute to the diversity of a population, but later they are selected against at high frequency and are eliminated eventually. Using over 1,500 complete human mitochondrial genomes along with those of Neanderthal and Chimpanzee, I provide empirical evidence for this prediction by tracing the footprints of natural selection over time. The results show a highly significant inverse relationship between the ratio of nonsynonymous-to-synonymous divergence (dN/dS) and the age of human haplogroups. Furthermore, this study suggests that slightly deleterious mutations constitute up to 80% of the mitochondrial amino acid replacement mutations detected in human populations and that over the last 500,000 years these mutations have been gradually removed. (Subramanian, 2009)

Interestingly, this dN/dS ratio among Neanderthal was initially reported strikingly high.

These results suggest that slightly deleterious amino acid variants segregate within populations, and that differences in the intensity of purifying selection may affect mtDNA dN/dS ratios. Previous estimates based on mean pairwise differences (MPD) within the mtDNA HVRI suggested that Neandertals (MPD = 5.5) had an effective population size similar to that of modern Europeans (MPD = 4.0) or Asians (MPD = 6.3), but lower than that of modern Africans (MPD = 8.1) (Krause et al., 2007b). Recent population genetic analyses have revealed a higher mtDNA amino acid substitution rate (Elson et al., 2004) and relatively more deleterious autosomal nuclear variants (Lohmueller et al., 2008) in Europeans than in Africans, presumably due to the smaller effective population size of Europeans. Thus, it seems plausible that Neandertals had a long-term effective population size smaller than that of modern humans. (Green et al., 2008)

However, the new information supplied by the Denisova hominin reveals this assumed feature of Neanderthal mtDNA was actually a mistake:

The 12 proteins encoded by the Denisova hominin mtDNA (excluding ND6, Supplementary Information) show low per-site rates of amino acid replacements (dN) when compared to the per-site rates of silent substitutions (dS), consistent with strong purifying selection influencing the evolution of the mitochondrial proteins (dN/dS=0.056). Notably, when the evolution of mitochondrial protein-coding genes in modern humans, Neanderthals, chimpanzees and bonobos is gauged in conjunction with the Denisova hominin mtDNA, a previously described reduction of silent substitutions causing an increased dN/dS in Neanderthals is not observed. This is probably due to a more accurate reconstruction of substitutional events when the long evolutionary lineage leading to modern humans and Neanderthals is subdivided by the Denisova hominin mtDNA (see Supplementary Information) (Krause et al., 2010)

The immediate result of this new finds is that an earlier proposed reduction in length of the Neanderthal mtDNA lineage “about three times as large as would be expected if it was entirely due to the age of the fossil” (Green, 2008), resulting in an earlier common ancestor to modern humans, is wrong. The shrunken phylogenetic tree was accordingly corrected for by Krause: the mean age of the most recent mtDNA ancestor of modern humans and Neanderthal went down from 660.000 t0 465,700 years ago.

(mean = 465,700 years ago; 321,200–618,000 years ago, 95% HPD) (Krause et al., 2010)

The feature that contemporary dN/dS values of modern humans are high, especially among Europeans, also corresponds to current assumptions that concern a younger age or (in the case of Europeans) of a smaller effective population size. May this be another lousy interpretation of results that are barely understood? This could be another example of a solution that supplies an easy way out of a complex issue.

There might be more. COX2 is a coding gene located on mtDNA. According to Green et al.(2008):

COX2 has experienced four amino acid substitutions on the human mtDNA lineage after its divergence from the Neandertal lineage [...]

Fixed mutations indeed tend to define both human lineages as mono-phyletic blocks. But the paper only mentions COX2 as a potential indication of divergent evolution, and due to the new information revealed by the Denisova hominin nothing remains of Green’s assertions that Neanderthal coding mtDNA is strikingly different from modern human mtDNA. The main argument why this would be irreconcilable with a continuous development can now be rejected:

The observation of four nonsynonymous substitutions on the modern human lineage, and no amino acid changes on the Neandertal lineage, stands in contrast to the overall trend of more nonsynonymous evolution in Neandertal protein-coding genes (Table 1), and deserves consideration. (Green, 2008)

There is NO overall trend among Neanderthal towards a more nonsynonymous evolution, hence the four new proteins that correspond to four nonsynonymous substitutions on the modern human lineage do not indicate a striking new tendency, since this kind of mutations happened all the time, also among Neanderthal.
The age calculations gain in reliability once the synonymous mutations involved are better identified and harbored on the phylogenetic tree, by comparing more hominins and branches. Quite considerable purifying selection has now been identified as applicable to both Denisova and Neanderthal mtDNA. However, the mtDNA of an old skeleton in Australia already showed us that neither of this leads us closer to the mtDNA of modern humans.

Whatever the nuance of details, that scream variety and continuity in human evolutionary development, we can’t deny a striking, almost exclusive unity of AMH mtDNA compared to the different forms that have been recovered from Neanderthal and – even more – Denisova:

The genealogies of mtDNA sequences in most human populations, including Aboriginal Australians, characteristically have very little hierarchical branching structure. This pattern of sequence variation is consistent with a population expansion following a population bottleneck and is generally taken as supporting the recent out of Africa model. Under this model, all contemporary sequences spread globally with an expanding population that replaced all other people and all other lineages. Africa has been postulated as the source of the expansion because some populations in Africa have more sequence diversity than populations anywhere else. (Adcock et al., 2001)

Almost, since the discovery of ancestral mtDNA of the gracile early human, found at Lake Mungo, Australia (code named LM3, age 62 kya), that is unmistakably an AMH, also attests the extinction of quite distinct outliers. There must have been a huge and progressive selective thrust towards modern mtDNA. The mtDNA of LM3 was kind of “modern” alright, but definitely the genetic distance fell outside the range of modern humans. The investigators observed this find poses a serious challenge to the “interpretation of contemporary human mtDNA variation as supporting the recent out of Africa model” (Adcock et al., 2001), effectively reducing Africa as a refuge for outgroups that have accumulated change and drifted apart rather than being a true indication of the source of all AMH related mtDNA. But even more so, the find strongly indicates that the current lack of hierarchical branching structure among humans can’t be understood as the direct result of a succession of AMH migrational waves alone. Some waves phased out and lost their origin from the record. Could it be possible that something about mtDNA triggered the worldwide substitution of extremely divergent older forms by the reduced array of current forms? Then how did this happen?

The mtDNA genome, modelled as a circle.

Let us regard the issue in a wider genetic perspective and forget about cheap scenarios of cannibal hominins exterminating each other, a view that conveniently ignores autosomal evidence of inter-hominin gene flow. One little segment of non-coding mtDNA can be found on the Displacement (D-) loop or control region, that is involved in repair activities. It has an analogy in the telomers of nuclear DNA, that are highly prone to insertion and deletion processes. This little region may be subject to the random change and stochastic speed-density that are necessary to infer a neutral “molecular clock”, but the location of this region on the mitochondria introduces a substantial bias in the basic assumption of overall neutrality. I will return at this issue.
Several studies have demonstrated the ongoing transfer and integration of mitochondrial DNA sequences into nuclear chromosomes. The evolutionary inclination of mtDNA genes to move from the D-loop control zone to the nuclear autosomal part of the DNA could be studied in more detail on the paleogenetic sample of an AMH fossil found near Lake Mungo, Australia, dated 40kya (Bowler et al.,2003):
“His mtDNA belonged to a lineage that only survives as a segment inserted into chromosome 11 of the nuclear genome, which is now widespread among human populations.” (Adcock et al., 2001)

This particular strand of early human (AMH) mtDNA vanished from the mitochondrial record ever since, all over the world, but the insertion in chromosome 11 flourished, especially outside Africa:

Overall, 39% of chromosomes tested carried the insertion. In four African populations, the frequency of chromosomes carrying the insertion ranges between 10 and 25%, whereas it varies between 38% and 78% in populations tested in Europe, Asia, Oceania, and South America.(Zischler et al., 1995)

Assuming a lower evolutionary rate in nuclear DNA, “these mitochondrial integrations might preserve the ancestral state of the mitochondrial sequence that existed at the time of transposition and could therefore be regarded as ‘‘molecular fossils.’’” (Zischler et al., 1998). Previous investigation on a similar, albeit much older Insert on chromosome 9 that “took place on the lineage leading to Hominoidea (gibbon, orangutan, gorilla, chimpanzee, and human) after the Old World monkey–Hominoidea split” (Zischler et al., 1998), that happened in the range of 17–30 MYA in a common ancestor of all hominoids, already established the value of nuclear insertions for reconstructing ancestral mitochondrial sequences of the Most Recent Common Ancestor (MRCA):

Thus, the MRCA sequence deduced from homologous integrations in different species will represent the ancestral mtDNA sequence more reliably and with less sequence ambiguities than an ancestral sequence deduced from the fast-evolving mtDNA sequences. (Zischler et al., 1998)

The remarkable affiliation of the autosomal Insert with both LM3 and hominoid mtDNA. The newly discovered, potentially ancestral affiliation with the Denosova hominin is not drawn.

The Insert on chromosome 11 definitely suggests fossil information of some early AMH individual, or at least of a hominin that interbred with early AMH. The closest match to the mtDNA of this particular individual was indeed an AMH, the gracile LM3 dated 40kya (Bowler et al., 2003) found in Australia at Lake Mungo. However, a simple comparison of the Insert to the current genome of modern human mtDNA reveals that this individual can’t possibly be the direct ancestor of modern human mtDNA. No close mtDNA matches of LM3 nor the Insert survived and the mtDNA of LM3 doesn’t indicate direct matrilinear inheritance of the original mtDNA source of this autosomal Insert either.

The LM3 Sequence Belongs to an Early Diverging mtDNA Lineage. The divergence of the LM3 sequence before the MRCA of contemporary human sequences is indicated by its grouping with the Insert sequence, which other reports have suggested diverged before the MRCA of sequences in living humans.
Although this analysis did not reliably establish an early divergence of the LM3/Insert lineage, it demonstrated that the lineage is unusually long. (Adcock et al., 2001)

This presentation of the Insert as a member of a single branch together with LM3 may be an oversimplification. The location of the Insert at the mtDNA phylogenetic tree of humans suggest an even more pronounced outlier:

Upon comparing 243 bp of a human-specific integration (Zischler et al. 1995) that corresponds to the conserved part of the mitochondrial D-loop of all available hominoid (n=14) and human (n=261) mtDNA sequences, only two insert-specific substitutions were traced, with both the ape mtDNA sequences and all human mtDNA sequences being identical at these positions. (Zischler et al. 1998)

Salient detail is that the two Insert specific substitutions (A on 16259 and C on 16288) are now covered by the mtDNA of the Denisova hominin. Even though the other differences with Denisova are big enough to exclude a close affiliation, this remarkable detail invites to the tentative proposal that the divergence of the Insert sequence could have happened long before the MRCA of human sequences that also include LM3.

Between 16,259-16,381 the mtDNA variation of the Insert nucleotides is covered by the corresponding nucleotides of apes, Lake Mungo 3, current aboriginal polymorphisms (not drawn) and the Denisova hominin.

This rare scope on a deep Eurasian affiliation, combined with extant aboriginal polymorphisms that echo the survival of Insert and LM3 features in the haplogroup N and M branches of modern mtDNA, suggest a much more complicated phylogenetic tree than the one currently in use. Aboriginal mtDNA polymorphisms drawn in the figure of Adcock et al., 2001 (above) are part of a mixture of the closely related haplogroups N (~P?) and M (Q?) that up to now define the earliest Out of Africa scenario. Together they could be closer to an extinct group of Eurasian outliers than African branches separately. Also typical East Asian loci of mtDNA show a remarkable similarity, making the case of African branches being ancestral to haplogroups N and M less straightforward. The establishment of any “reversed tree”, however, is hampered by the apparent extinction or extreme “pruning” of what might have been an enormous Eurasian mtDNA variability. Any scenario that reverses the tree should account for this low extant Eurasian variability in comparison with Africa.

Let’s return to the assumed “neutrality” of mitochondrial DNA inheritance. High variability of the control region might suggest otherwise. One of the prerequisites of fast evolution is a fast mechanism underneath genetic change, and the purpose of fast mtDNA mutations could be just that, to put the precondition of rapid evolutionary change. Anyhow, a similar observation was made concerning the massive STR of chimps on the Y-chromosome, that seem to be secondary to the incredible evolutionary changes on the Y-chromosome as observed in the recent study of Hughes et al. (2010) I already wrote about here.

A set of interesting differences of mtDNA between humans is located on the Hypervariable Region (HVR). Most strikingly, HVR is not highly variable per definition. For instance, investigations on the Ayu fish (Takeshima et al., 2005) revealed the Hypervariable region may also turn into a Hypovariable region, what suggests a special functionality of the property defining HVR (or general D-loop) variability. And a substantial susceptibility to damage.

The mitochondria continuously reproduce themselves at intervals averaging about 2 weeks, like bacteria by a process of binary fission. They generate most of the cell’s (chemical) energy supply and because mitochondria use oxygen as an electron acceptor, they produce harmful free radicals that may cause genetic damage, often deletion mutations. This free radical damage to mtDNA cannot be repaired, basically because the regular repair mechanisms of the cells can’t access the mitochondria and the mitochondrion has no repair mechanism of its own. Therefore, mitochondria accumulate damage at each mitochondrial generation, what gradually leads to malfunction and ultimately affects the health of the organism as a whole.

However, this dreary scenario must have some constraints, or else all life on earth would already have ended millions of years ago. Somehow the reproductory system must have been exempted from this process, or at certain circumstances, and also it seems the genetic damage to mitochondria can be slowed down by exercise, both physical and mental, but especially by consuming antioxidants like vitamin C or omega-3 fatty acids. These are abundant in fresh fruit, raw meat and fish, indispensable supplements to the species that lost the functionality of the L-gulonolactone oxidase (GULO) gene – amongst whom one of the two major primate suborders, the Anthropoidea (Haplorrhini), that happens to include human beings, together with tarsiers, monkeys and apes. Originally meant as a genetic “improvement” for getting rid of the old and weak when food shortages occurred, ie. those most badly in need of antioxidants to remain healthy, the loss of this gene also effectively confined this suborder of primates to subsistence in the tropics. Only humans succeeded in finding new habitats in colder climates. They left the hot places where fruits were available all year round and traditionally made up an important addition to the menu, because they could. Only humans evolved into great hunters, and developed the necessary skills to catch fish, in order to compensate for the irregular availability of fresh fruits. Notwithstanding unfavorable climates, they managed to keep their necessary supply of antioxidants at a save level. And they did, for hundreds of thousands of years. Until everything changed at the eve of Upper Paleolithic – when human cultural advance reached a critical level.

What went amiss when humans reached their first cultural highlights? Their success triggered important improvements in their living standards, that moved their prime focus away from the concerns of harsh survival, and towards the community around the fire. They spend more time preparing their meals, started to cook their meat and fish and thus destroyed their main antioxidant food supplies. Degenerative diseases made their introduction and invoked new selective pressures, that caused a steady gene flow from the south to rejuvenate the slowly degenerating mitochondrial lineages in the north. In the mean while females ceased to worry about the survival of the fittest and developed a preference for “feminine looking men over their more rugged counterparts” (DeBruine et al., 2010), triggering the most notorious changes in the human anatomy that resulted in Anatomically Modern Humans as a progressive tendency all over the world.

However, this does not fully explain the current low overall variability of mtDNA even in fruit-rich tropical territories in comparison to the attested mtDNA of early AMH such as Lake Mungo 3. Still, cultural level related natural selection might be a good trail to follow.

Booming AMH culture most probably also entailed a closer contact between different groups within a wider economical areas. For sure this new behavioral patterns would have initiated a catastrophic increase of contagious diseases as soon viruses and bacteria could circulate freely among newly interconnected communities. However, this also implies a strong relation between resistance against (new) infections and mtDNA, that vastly exceed the benign effects of Vitamin C. The relation between mtDNA, antioxidants and the development of new “genetic” cures may reach a lot further. At this point it is tempting to regress to the behaviour of mtDNA and its facility to travel to nuclear DNA, and evaluate the genetic potential of mtDNA as a genetic laboratory against new diseases. Indeed, the immune system is where human DNA might have evolved most and is where most human variability occur.

Despite the high homology between chimpanzee and human genes at the level of amino acid sequences, human genome contains 1418 genes that do not have direct orthologues in chimpanzee, many of which are related to immune defence.
A number of genome-wide scans for positive selection have recently been performed (Wagner, 2007). They confirm that many immune genes and their regulatory sequences have been the subjects of positive selection in humans.
Population genomics is still in its infancy and the specific predictions may vary among studies but this is where future discoveries are anticipated. (Danilova, 2008)

Then, survival of just one little branch of early human mtDNA must point directly to the main focus of Upper Paleolithic development. Of the early mtDNA strands only those that accumulated in Africa were safeguarded against the effects of progressive damage, due to the continuous availability antioxidants. But in the center of change the preconditions for rapid change were set, including the extinction of mtDNA that did not meet the new standards of natural selection against the inevitable pandemics of cultural cohabitation and coexistence. Relatively low population density prevented the accumulation of high haplotype diversity, and the surviving mtDNA haplogroups in Eurasia obliterated all traces of a long, rich and diverse hominin history. To the effect that the false positives of mtDNA lured the public opinion into thinking that a long list of pre-AMH hominins, that include famous names like Neanderthal, Peking Man, Rhodesian Man, Denisova hominin etc., became extinct.

We can’t solve the origin question with a narrow scope, since the only truth is that we still don’t know. However, the Denisova hominin shows us one important clue: the more we know, the more complicated the solution. And most probably, the more hominins involved.


  • Krause et al. – The complete mitochondrial DNA genome of an unknown hominin from southern Siberia, 2010, link (paysite): try here
  • Krause et al. – A complete mtDNA genome of an early modern human from Kostenki, Russia; 2010, link
  • Derevianko et al. – A Paleolithic Bracelet from Denisova Cave, 2008, link
  • Howell et al. – Molecular clock debate: Time dependency of molecular rate estimates for mtDNA: this is not the time for wishful thinking, 2008, link
  • Adcock et al. – Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins, 2001, link
  • Ovchinnikov et al. – Molecular analysis of Neanderthal DNA from the northern Caucasus, 2000, link
  • Orlando et al. – Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence, 2006, link
  • Green et al. – A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing, 2008, link (paysite): try here
  • Takeshima et al. – Unexpected Ceiling of Genetic Differentiation in the Control Region of the Mitochondrial DNA between Different Subspecies of the Ayu Plecoglossus altivelis, 2005, link
  • Sankar Subramanian – Temporal Trails of Natural Selection in Human Mitogenomes, 2009, link
  • Subramanian et al. – High mitogenomic evolutionary rates and time dependency, 2009, link
  • Zischler et al. – A nuclear ‘fossil’ of the mitochondrial D-loop and the origin of modern humans, 1995, link
  • Zischler et al. – A Hominoid-Specific Nuclear Insertion of the Mitochondrial D-Loop: Implications for Reconstructing Ancestral Mitochondrial Sequences, 1998, link
  • DeBruine et al. – The health of a nation predicts their mate preferences: cross-cultural variation in women’s preferences
    for masculinized male faces, 2010, link
  • Nadia Danilova – Evolution of the Human Immune System Evolution of the Human Immune System, 2008, link
  • Allard et al. – Control region sequences for East Asian individuals in the Scientific Working Group on DNA Analysis Methods forensic mtDNA data set, 2004, link (paysite), try here
  • Bowler et al. – New ages for human occupation and climatic change at Lake Mungo, Australia, 2003, link
  • PhyloTree.org – Global human mtDNA phylogenetic tree, 2010, main

Recommended reading:

  1. September 24, 2010 at 16:34 | #1

    “This rare scope on a deep Eurasian affiliation, combined with extant aboriginal polymorphisms that echo the survival of Insert and LM3 features in the haplogroup N and M branches of modern mtDNA, suggest a much more complicated phylogenetic tree than the one currently in use. Aboriginal mtDNA polymorphisms drawn in the figure of Adcock et al., 2001 (above) are part of a mixture of the closely related haplogroups N and M that up to now define the earliest Out of Africa scenario, appear to be closer to an extinct group of Eurasian outliers than African branches. Also typical East Asian loci of mtDNA show a remarkable similarity, what might point at a counter-indication of African branches being ancestral to haplogroups N and M. The reverse may be true.”

    First of all, thanks for the great blog. I’ve just come across it. And welcome to the ranks of scholars rejecting/questioning the out-of-Africa model of human dispersals. In my book “The genius of Kinship”, I used linguistic and kinship data, which plainly contradicts the out of Africa scenario, as a springboard for calling into question the paradigm generated by mtDNA and Y-DNA. Since then, I’ve been a regular contributor/commenter on various blogs including anthropology.net, razib’s discover and dienekes. And I do believe that the conventional phylogenies would benefit from some reversals to account for ancient DNA data such as Mungo man, the Insert, the Denisova cave and the Green et al. 2010 study. Interetsingly, precisely such a reversed tree (for autosomes) appears as a “Map of Interconnected World Regions” on the DNATribes website http://www.dnatribes.com/populations.html. Also if you look at the earliest mtDNA studies (Johnson et al. 1983; or Fig 4 in “Mitochondrial DNA Polymorphism among Five Asian Populations”, S. Harihara // Am. J. Hum. Genet. 43:134-143, 1988), you’ll also see a reversed tree.

    “The establishment of such a “reversed tree”, however, is hampered by the apparent extinction or extreme “pruning” of what might have been an enormous Eurasian mtDNA variability. Any scenario that reverses the tree should account for this low extant Eurasian variability in comparison with Africa.”

    From the perspective of an out of America theory, the modern distribution of genetic diversities reflects population growth and mutational acceleration outside of the Americas required for/associated with the colonization of the vast Old World expanses. Notably, the New World harbors the greatest intergroup genetic diversities, which is consistent with this region retaining low effective population size for a long time. It also maps nicely onto the 140 linguistic stocks characteristic of the New World (compare only 20 in Africa), which attests to the great antiquity of human presence in Western Hemisphere.

    • September 24, 2010 at 18:30 | #2

      Nice thought experiment, this Out of America alternative. I would call it a draw, since we are missing additional evidence proving extinct lineages that exceed worldwide variability: eg. more divergent than Y-DNA A and B haplogroups or insert-like mtDNA. Besides I have the faint feeling we just don’t know enough about American languages and culture-dependent interaction (eg. even in the Old World words for commercial counting must have been a very recent innovation). In general I would caution against taking reversal theories as the new null hypotheses, for this is already happening elsewhere, eg. in applying Wave of Advance scenarios even where the model is clearly inappropriate. Such growth patterns can only be assumed at (rare) gene- or culture triggered growth events – and would eventually backfire against any assumed eternal source region “where time stood still”.

  2. September 27, 2010 at 17:47 | #3

    Nice feedback, thanks. A truly integrated, cross-disciplinary, unbiased and world-historic theory of human origins and dispersals should work with a full range of interpretative options. If we were to build a scale of theoretical models explaining extant biological and cultural diversity, it would have the following components: 1) Single-Origin Out of America from a New World primate source with one single migration out (Alvah Hicks at http://www.humanoriginsolved.com, http://articles.latimes.com/1993-07-27/local/me-17316_1); 2) Single Origin Out of America with an East Eurasian hominin source with two migrations out of America and two migrations into Africa (my thinking); 3) Classic Multiregional; 4) Out of Africa with an African hominin source with Hominin Admixture in Eurasia; 5) Out of Africa with an African hominin source Complete Replacement. I like the fact that, in this metascientific approach, one can generate a fully symmetrical set of theories: in 1-2 expansion from an “eastern source” with admixture between geographically isolated sapiens populations; in 4-5 expansion from a “western source” with admixture into pre-existing hominin population(s).

    “Such growth patterns can only be assumed at (rare) gene- or culture triggered growth events – and would eventually backfire against any assumed eternal source region “where time stood still.”

    Interestingly, various diversities have marked peaks across our species’ whole geographic range: genetically, Africans are most diverse, linguistically Amerindians are most diverse. Africans are very uniform in terms of skin color, hair texture, musical styles [see Victor Grauer's work http://music000001.blogspot.com/2007/05/12-phylogenetic-tree.html%5D, myths [Yuri Berezkin's work], kinship structures, tone languages [see WALS http://wals.info/feature/13?tg_format=map%5D. Amerindians are very uniform in blood groups (mostly type O) and have limited mtDNA and Y-DNA genetic diversity. Scholars tend to assign to features exhibiting uniformity a high “stability index,” while touting diversity as a sign of age in its own right. So, we end up seeing confirmations for our own version of “truth” in diametrically opposite surface manifestations. For instance, African agriculturalists are more genetically diverse than African foragers and they are also darker, which suggests some selection driving one parameter toward variability and the other one toward uniformity. Could this selective factor be high rates of polygyny, per Manning and Frost?

    The goal is to unearth hidden variability in those features that exhibit outward stability and the other way around. See this done in Blood Group O Alleles in Native Americans: Implications in the Peopling of the Americas, by Benito Estrada-Mena et al., in which Amerindians were found to have all known versions of blood group O, namely O1, O1v, O1v542, O05, O32, O33.

    “eg. more divergent than Y-DNA A and B haplogroups or insert-like mtDNA.”

    Notably, the insert was found at highest frequencies in America (Zischler et al. 1995). This is consistent with the earliest studies of mtDNA.

    • September 27, 2010 at 20:25 | #4

      I don’t think the latest genetic results support any Single Origin hypothesis at all. Like I explained in my Magic Stick and Denisova Cave articles I rather think about accelerated integration of different hominins, closely associated to rapid cultural change – a kind of Socializing Revolution that ultimately involved all hominins. The real challenge will be in identifying the origin of each and every genetic component. As I conceive it, the main component of AMH had its roots in Homo Heidelbergensis. This would explain the distance of less than half a million year to Neanderthal – peanuts compared with the age of some other shared AMH genetic components up to 2.5 mya, whether or not orginating in Africa. South East Asia/Pacific may have been an important expansion node, and also this region may have been an intermediary for continuous geneflow to and from the Americas. The Rosenberg geneflow chart presents modern humans as a steady genetic increment between the oldest nodes of human population, ie. Africa and SE Asia, having the Americas as a remarkable extrapolation communicating on the Asian side. The new unresolved question: did the Americas owe their extreme position on the geneflow chart (and on other grounds as well, eg. your kinship input) to quite early isolation that exceeded their Pacific kin, or could this geographic region be considered an expansion node all by itself? I have to admit this latter view is entirely new to me. Like I said, insert-like (paleogenetic) mtDNA like LM3 would be required to supply some support for origin hypotheses since so far genetic evidence is poor to say the least. Moreover, I don’t think an age up to 40kya for American presence would change so very much: first we would have to find some fossile specimen to find out that old American phenotypes would converge more to modern phenotypes than anywhere else, since this is the presumption I taste in your view. Kennewick Man already indicates this is probably not the case, what would be in accordance to my view that modern phenotypes are the result of modern human cultural developments and the accelerated geneflow of world-wide integration rather than full-blown Single Origin-like migrations.

  3. September 28, 2010 at 02:51 | #5

    “The new unresolved question: did the Americas owe their extreme position on the geneflow chart (and on other grounds as well, eg. your kinship input) to quite early isolation that exceeded their Pacific kin, or could this geographic region be considered an expansion node all by itself? I have to admit this latter view is entirely new to me.”

    Some time ago I came across an interesting paper by Australian paleobiologist, Peter Brown. Brown, P. 1999. The first modern East Asians ?: another look at Upper Cave 101, Liujiang and Minatogawa 1. In K. Omoto (ed.) Interdisciplinary Perspectives on the Origins of the Japanese, pp. 105-130. International Research Center for Japanese Studies: Kyoto. On p. 120 he notes:
    “At present the earliest people with a generalised East Asian cranial morphology are probably found in the
    Americas. Is it a possibility that migration across the Bering Straits went in two directions and the first morphological Mongoloids evolved in the Americas?”
    He is not talking about Paleoindian skulls that have been shown to lack diagnostic “Mongoloid” features, but about Amerindian skulls that begin to pop up in the archaeological record from 8500 BC. Once I read Brown, I instantly recalled another paper authored by my former professor of physical anthropology, which attested to some odd survivals of American Indian morphology in South Siberia: Kozintsev AG, et al. Collateral relatives of American Indians among the Bronze Age populations of Siberia? // Am J Phys Anthropol. 1999 Feb;108(2):193-204.

    I hypothesize that some of the striking similarities between Amerindian and Siberian genes and cultures come from a recent back-migration/admixture from America. Franz Boas talked about it a century ago, limiting this idea to only Paleoasiatic peoples such as Chukchees, Itelmens, Koryaks, etc. If this perspective is essentially right, then the current genetic picture in East Asia is rather distorted away from the picture that existed 15,000 years ago, namely mtDNA C, D and A, Y-DNA C3 markers being entirely confined to the New World. Under this scenario, the “Mongoloid” craniological complex and the Sinodonty dental complex are not springboards for Amerindian variation but a rear-view mirror image thereof. This would leave the New World at 12,000 BP with the degree of divergence appropriate for a long-term isolate. The fact that the Clovis technological complex is largely of flake-biface type in contrast to the largely blade-microblade technologies of pre-12,000K Siberia implies Middle and not Upper Paleolithic roots.

    Kinship systems document sharp contrast between parts of Asia, Sahul and America, containing full survivals or basic derivations of prescriptive alliance systems (inbreeding between cross-cousins over many generations), and Sub-Saharan Africa and Europe, showing large expansive marital networks with no heritable prescription for cross-cousin marriage. Kinship theory has always thought of the latter as derived from the former through the relaxation of marital prescription in larger populations. And South America is considered to be the area with the greatest diversity and “purity” of these basic prescriptive systems. This is the cornerstone of the theory of kinship evolution, which has been in place for the past 100 years. It seems to jibe well with what you wrote in your other post: “the ingression back into Africa of a reduced set of “bottlenecked” non-African haplotypes would have a similar result on the diagram if regions of higher Neanderthal divergence were caused by higher mutation rates of these regions, and thus bottlenecked were to remain within the bandwith of African variability. However, the low world-wide frequency of this off-modal variability would also imply the reduction of high mutation speed variability among non-African populations, possibly due to some kind of post-Neanderthal event.”

    Kinship systems may indeed document the peculiar evolutionary process affecting human populations, which, if translated into a population genetic framework, implies mutational acceleration in Africa and Europe, associated with specific marital practices, family dynamics and generational spans (“effective population size” sensu lato) and selective constraints on mutation rate in parts of Asia, Sahul and especially America, again associated with a specific set of socio-cultural practices with direct links to demography. Humans, as it were, self-domesticated themselves as a species.

    “Like I said, insert-like (paleogenetic) mtDNA like LM3 would be required to supply some support for origin hypotheses since so far genetic evidence is poor to say the least. Moreover, I don’t think an age up to 40kya for American presence would change so very much: first we would have to find some fossile specimen to find out that old American phenotypes would converge more to modern phenotypes than anywhere else, since this is the presumption I taste in your view.”

    Those finds are of course necessary. But, as I argued on Razib’s blog about a month ago (http://blogs.discovermagazine.com/gnxp/2010/08/the-new-world-in-three-easy-steps/comment-page-1/), the rate of archaeological recovery is uneven, with a boundary again running between Africa/Europe and Asia/America. It took Dillehay 20 years to prove Monte Verde, which is only 2000 years older than Clovis. Historically, it has taken longer for places like Sahul and the New World to accumulate the signs of human antiquity, but the earliest archaeological finds are growing on all continents. What is important at the current moment is that some 150 years of searching for the origins of American Indians in East Asia and Alaska haven’t yielded any identifiable technological or paleobiological signatures of the peopling of the Americas.

  4. September 28, 2010 at 16:32 | #6

    I just posted a comment on Dienekes that I thought could be interesting to you, too.

    There’s a sharp discrepancy between mtDNA and Y-DNA phylogenies. In mtDNA phylogenies non-African lineages are nested within one single African clade L3, in Y-DNA phylogenies the majority of African lineages, namely E, are nested within a largely non-African clade CDEF. (note, however, that mtDNA L3 is closer to M and N than it is to L0 and L1, just like in the Y-DNA situation). mtDNA is more hierarchical in Africa, Y-DNA is more hierarchical outside of Africa. If we further look at such diploid systems as X chromosome, we’ll discover that the earliest branch will be exclusively non-African (with highest frequencies in America, as in the case of the B006 lineage in dystrophin gene http://books.google.com/books?id=X88O8C3ZHvMC&pg=PA76&lpg=PA76&dq=X+chromosome+B006&source=bl&ots=mjlR3EUv2d&sig=PKQLXov-E5YfIT1JqXoBrXXwMQg&hl=en&ei=TQOiTO6rLMGC8gboo925CQ&sa=X&oi=book_result&ct=result&resnum=6&ved=0CDgQ6AEwBQ#v=onepage&q=X%20chromosome%20B006&f=false).

    This means, as we progress from mtDNA through Y-DNA to X chromosome African genes become a subset of non-African genes, with Amerindians often harboring the first outlier lineage at high frequencies. Apparently, there’s a mistake in mtDNA phylogenies, whereby 1) some non-African genes (I suspect a few lineages subsumed under the macrohaplogroup M label such as M31, M32 in Andaman islands, M7, M8 in Japan, M9 in Japan, Tibet, SE Asia) are closer to the African L2’3’4’6 clade than other M and N lineages.

    This archaic component is often interpreted, as in the book above, as a sign of hominin introgression into modern humans. But then it’s highest frequencies are in America (just like the insert), which is not known to have any pre-sapiens hominin species. This may mean that an “archaic hominin introgression” is nothing else but a signal for the single origin from a New World source after a bottleneck that accompanied the formation of our species from an isolated group of (Eastern) hominins such as Eastern Neanderthals or Asian Homo erectus or a third species with H. heidelbergensis roots attested in the Denisova cave find.

    In Rosenberg 2002, this Amerindian component in clearly visible in K=2 (100% frequency in Surui, very low frequencies in Africa). Finally, another unrelated source, namely human lice DNA, also documents, under the moniker “archaic introgression from Asian Homo erectus,” an ancient lineage found at high frequencies in the Americas (see Reed et al. 2004, Fig. 2: http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020340).

  5. niccolo caldararo
    December 16, 2010 at 21:29 | #7

    You might find my analysis of the Denisova Cave mtDNA of interest: http://precedings.nature.com/users/be5a358d4d9c7b6409daefed375315a8

    • December 16, 2010 at 22:22 | #8

      Thanks! I will try to figure out what would be the consequences, especially for the Insert part – that at least is all well above the corrupted sequence up to site 16,193.

      Does the following imply a complete rejection of the methodology, or a new interpretation of the results: “This changes the appearance of the Denisova sequence and makes it appear to reflect a combination of Neandertal sequences and AMH sequences consistent with the recent analysis of the Neandertal genome by Green et al. (2010).” ?

  6. December 22, 2010 at 19:38 | #9
    • December 22, 2010 at 23:29 | #10

      “This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone.”

      This has the taste of an astounding confirmation rather than a rejection of the previous results and methods of Krause et al. Maybe Denisova even supplies a much closer relative to the Insert and LM3 than I already thought! – then defining AMH mtDNA as a development somewhere on the extinct continuum between Neanderthal and Denisova rather than a completely separated development.

  7. December 23, 2010 at 03:13 | #11

    “then defining AMH mtDNA as a development somewhere on the extinct continuum between Neanderthal and Denisova rather than a completely separated development.”

    I like this interpretation. How are we to explain the constant lineage pruning outside of Africa, from the Denisova-Nenaderthal times on, that has kept non-African diversity at bay, while allowing for African diversity to flourish? Could it be that mutation rate is not independent of effective population size, so that African lineages diversified under the beneficial conditions of expansion into a territory free from the population size constraints as experienced in hominids in Eurasia, Melanesia and America?

  8. December 23, 2010 at 09:44 | #12

    Variance depends on the effective population size and the expansion model, but expansion can’t be the only explanation for current geographic mtDNA differences: expansion was considerable anywhere. However, there are some indications that mtDNA isn’t entirely neutral as a marker. The changed conditions in AMS society that I described in this article might have accelerated the extinction of mtDNA lineages where effective population sizes remained low (especially at an early stage!). Subsequent evolutionary changes might have been substantially higher at locations where effective population sizes remained high.

  9. December 24, 2010 at 01:30 | #13

    Check out this paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015582. It seems to support your interpretation by showing how local extinctions reduce diversity in metapopulations (regional, continental, etc.).

  10. March 31, 2011 at 13:07 | #14

    “The establishment of such a “reversed tree”, however, is hampered by the apparent extinction or extreme “pruning” of what might have been an enormous Eurasian mtDNA variability. Any scenario that reverses the tree should account for this low extant Eurasian variability in comparison with Africa.”

    Hello again, I’d like to mention a new paper that seems to address this problem from a general evolutionary perspective. http://www.amjbot.org/cgi/content/abstract/98/3/404. It abstract says: “major shifts in diversification may not be directly associated with major named clades, but rather with clades that are nested not far within these groups. An alternative explanation is that there have been increased extinction rates in early-diverging lineages within these clades.” This means that there may have been a long non-African “fuse” leading to the diversification of African clades. While punctuated evolution if the model the authors favor, they also note, “it is difficult to disentangle the effects of shifts in speciation [read: mutation rate-G.D.] from shifts in extinction.”

  11. dziebelg
    March 27, 2012 at 04:12 | #15


    This is to give you a heads up that I launched a new weblog at http://www.anthropogenesis.kinshipstudies.org to discuss the origins of modern humans and the out-of-America theory of human dispersals. It’s a work-in-progress and the content on the static changes gets updated every now and then, but it’s fully readable.


    German Dziebel

  12. November 17, 2013 at 05:40 | #16

    It seems to me that a shift in childcare accompanied the tendency of females to mate with more feminine males and loss of traits such as the brow ridges. The most recent common ancestor of modern humans may be reconstructed as living in multi-male, multi-female societies with alloparenting practices and increased male parental involvement. Under such circumstances the male face would feminise by neoteny as it did in platyrrhines, but this would mean a less efficient system in ie. Neanderthals. Not to endorse any single origin model that discounts continuity, but this behavioural shift would give anatomical moderns the edge over archaic hominins.

  13. November 17, 2013 at 06:32 | #17

    Sure, worldwide neotenic tendencies can still be observed and this has everything to do with culture. Not just the male phenotype “feminises”, also the female phenotype does! Although to me “feminised women” often appear rather boyish. I am happy not to see the end of this in a million years.

  14. November 17, 2013 at 16:01 | #18

    Of course this fits well enough with Peter Frost’s theory of human denudation as a result of sexual selection. To many people it will be an odd thought that hominins such as neanderthals might at once have displayed behaviours we think of as making us ‘uniquely human’ and yet also have still had hairy backs – but this is only because of either-or thinking about humans and the species we call ‘beasts’. It makes sense given that certain behavioural shifts inferred from anatomy had not yet taken place in Europe.

    Near Beijing at Lishu a fossil hominin was discovered that I suspect may be a late surviving Denisovan due to its provenance although without a Denisovan phenotype for comparative purposes it would be impossible to confirm without the analysis of a DNA sample from Lishu. John Hawks pointed out that modern humans cannot have acquired Denisovan admixture in Siberia because they were replaced there by neanderthals. And Greg Cochran pointed out that if we assume some Denisovans had adapted to the Oriental rainforests in southeast Asia where they found a refugium, genes for disease resistance picked up from the Denisovans would give hybrids an advantage over ‘full’ modern humans and this would explain the Denisovan autosomes in the southwest Pacific without assuming the Denisovans entered Wallacea. Fivepercenter also mentioned on our forum that Australian Aboriginals possess adaptations to the cold that make no sense unless this trait was itself inherited from formerly cold climate ancestors – the Denisovan people.


  15. November 18, 2013 at 23:42 | #19

    Bones, do you think Lishu was very different from Tianyuan? Unless mtDNA of the latter was subject to severe contamination or misdated, I don’t expect Denisovans popping up here so easily. A more northern origin of Denisovan DNA is attractive for more than one reason, except for its apparent disappearence in the continental region. Difficult to confirm the hybrid trail I perceived elsewhere through Corea and the East Asian islands to Australia since maybe this is all relict DNA without “direction”.
    BTW, huge changes in diet and habit happened as a result of megafauna extinction, sexual selection may be rather secundary against this background.

  16. November 19, 2013 at 07:32 | #20

    I think Tianyuan was misdated based upon the available stratigraphic evidence. If so then the DNA evidence is naturally brought back into line. And either way Lishu is clearly outside the hypodigm of anatomical modernity.

    Speaking of China the origins of people with a Mongoloid phenotype is a mystery in itself. We were discussing this on our forum.

    As for the effect of the megafaunal extinctions upon human biocultural evolution, whilst I agree there would have been some effect its noticeable that Nordics are still long limbed like Upper Palaeolithic humans and their Fuegian analogs, both the Fuegians and the Late Pleistocene Europeans being specialised hunters of large game animals. It would seem to me that the ancestors of the Nordic race at least were not sufficiently affected by the megafaunal extinctions to lose adaptations for hunting even though they make it more difficult for us to conserve body heat.

    Most Pleistocene populations of modern humans were likely hand collectors rather than specialised large game hunters because this is the predominant means of subsistence for Late Pleistocene Appropriate societies in the modern period. It is just that the lithics required by such a hunting society preserve easily and so there is a preservation bias in the archaeological record. If so then the megafaunal extinctions would have passed most people by.

  17. November 20, 2013 at 21:35 | #21

    As a matter of fact, running BLAST on a range of mtDNA samples, I found Tianyuan too much diverged from the Neanderthal outgroup, even compared with derived mtDNA of a similar haplogroup, to understand its 40ky difference of age compared to living people. Hence my idea of contamination. A thorough comparative anatomical study with Lishu is still missing, though neither count as especially “modern”, so: Could Both Be Linked? Shang 2007: Tianyuan 1 exhibits several features that place it close to the late archaic humans (represented primarily by the Neandertals) or between them and EMHs. Indeed, the mystery of the Mongoloid origin and the apparent regional availability of also other archaic hominins hold me back to link Denisovans directly to the Eastern Asian phenotype.

    The megafaunal extintions may not have been important to humble collectors in warmer climates, though we still don’t have much evidence on their identity, DNA or their eventual evolutionary success. Call this preservation bias if you want, but modern human evolution was driven by change rather than traditional continuation. Just think what an abundance of fresh meat could mean for the daily supply of antioxydants, and the need for evolutionary change when this supply suddenly falls back. Wasn’t there another discussion on the Light Skin Allele of SLC24A5, eg. useful for compensating a “natural lack of vitamin D”, that happened way too recent to understand extended human continuity in the north? While even Denisovans show genetic evidence of a dark complexion.

  18. November 21, 2013 at 15:00 | #22

    What do you think of Upper Cave 101? Friedline et all found UC101 to be closest to Skhul 5 and Qafzeh 6 although all the Upper Cave people are fully modern using the standards of Schwartz and Tattersall. Although the archaeological evidence suggests that the Upper Cave people at Zhoukoudien lived relatively close in time, Wescott cited Cunningham and Jantz that the morphometric distance between crania 101 and 103 exceeds that expected between two randomly chosen members of a homogeneous population. If there were late surviving archaic hominins present in China and the archaeological evidence suggests the Upper Cave people lived close together in time, does UC101 demonstrate hybridisation at Zhoukoudien? Its quite a shame they’re lost now that aDNA can be sampled.

  19. November 24, 2013 at 00:23 | #23

    The orbits of the Old Man of Upper Cave 101 near Peking are relatively low and rectangular, not unlike the European Cro Magnon 1 skull that is about the age of Mal’ta boy. Instead, living East Asians and Native Americans have a facial skeleton characterised by great facial height and high orbits. Kamminga (1992) argued this specimen to be distinct from the “modern Mongoloid morphology” and to be relatively close to that of the Ainu. If so, this apparent ancient European signature of Ainu has by now been obfuscated by “more recent” expansions of East Asians – that IMO consisted of a new brand of hybrids. However, since we don’t know the genetic composition of the archaic source population (~ Ordos Man from the Inner Mongolian Salawusu site?), it remains impossible per definition to establish the admixture components of such hybrid East Asians in relation with modern human immigrants like Mal’ta boy. In other words, the apparent absence of an East Asian component in Mal’ta boy and vice versa won’t have any meaning if East Asians are truly hybrids.
    BTW, I don’t think such a hypothesized archaic Mongoloid component was closely related to Denisovans, but maybe some Mal’ta-like immigrants absorbed their genes and moved on to follow a coastal route to Oceania. At least the closer genetic affinity of Oceania with Europe compared to East Asians can be observed in Raghavan’s figure 1b.

  20. November 25, 2013 at 21:47 | #24

    If the apparent ancient European signature of Ainu has by now been obfuscated by later migrations, what about the Jomonese?

  21. November 25, 2013 at 23:57 | #25

    Please read Adachi et al. – Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American (2009) for a treatment of the hypothesized origin of Ainu through Hokkaido Jomonese of 22,000 BP to the Mal’ta culture, now revealed as directly linked with Europe. However, they also point out how the original mtDNA signature changed over time, e.g. Ainu lost the Amerindian mtDNA D1 still available in the Jomon and mixed heavily with Siberian mongolids as well as Japanese. Discontinuity of the female lineage seems to be a recurrent theme especially for migrating people related with Amerindians. It is a pity we still don’t have nuclear DNA samples of Jomon people, though conceivably they were already quite admixed and diverse.

  22. November 26, 2013 at 01:59 | #26

    “Ainu lost the Amerindian mtDNA D1.”

    This lineage was re-classified as D4h2. To date, no Amerindian D1 lineages have been found in the Old World.

  23. November 26, 2013 at 15:17 | #27

    Has anyone tried to sample atDNA from Minatogawa? Despite its Upper Paleolithic date, Minatogawa clusters with the Jomonese in a craniometric analysis. Knowledge of the atDNA of Minatogawa ought to be invaluable.

    The distribution of D4 suggests a match with the distribution of macro-Altaic, whether it is a genetic group or not – it is present among the Japonic, Korean, Mongolic and Tungusic speakers though it extends south into southeast Asia and the Americas. Quite likely the Jomonese phenotype extended more widely into Asia and perhaps preceded Mongoloid people into the New World as suggested by Birdsell. I read that D4 is well documented to be present among the indigenous Californians, who Birdsell interpreted as New World “Amurrian” descendants.

    I also remember Dienekes blogging about a study of Japanese atDNA that identified a component that was termed ‘Okinawan’ by the authors and represents the old Jomonese racial stock. The Okinawan component broadly matches the same Altaic region in mainland Asia ie. the component is present among the Koreans but not the Han Chinese. (Again, the old racial typologists identified a ‘Chosunid’ type paralelling somewhat that of the Japanese ‘Choshu race’, the latter being partly Jomonese as well as Neomongoloid.)

  24. November 26, 2013 at 19:34 | #28

    “I read that D4 is well documented to be present among the indigenous Californians”

    There’s one outlier mtDNA lineage coded as D4h3a. It’s found in ancient remains in British Columbia, among Californian Chumash and sporadically elsewhere in North America. It expands in South America and becomes more common from Colombia to Tierra del Fuego. It’s closest relative is a single D4h3b sequence found in a Chinese individual.

  25. November 26, 2013 at 23:13 | #29

    The main contention of Adachi (2009) was to show that Jomon ancestors were related to the people that moved on to become Amerindians. They were at least culturally related to Mal’ta, that is more than just an educated guess based on their purported shared Caucasian physique. His study also demonstrated that we can’t rely on mtDNA as a static attribute of ancient populations. For sure the timedepths involved exceed the dates of the various D4h subclades.

  26. November 27, 2013 at 14:06 | #30

    Thank you both.

    Has anyone compared either Fuegian or Pericu aDNA to populations with known Denisovan ancestry yet?

    Something I find particularly interesting is a higher than average percentage of Denisovan autosomes in northeastern South America, and I can’t help but wonder whether this might be the result of a Luzia-type substrate population that arrived from the western Pacific prior to their subsequent replacement by later South Americans.

    Pichardo interpreted the native Fuegians as closest to Neumann’s Otamid type (though not an exact match,) an observation that fits with the presence of fishtail points (that are of ultimate derivation from the Clovis tradition) in the extreme south of South America, and the fact that the Fuegians possessed the East Asian gene for Mongoloid skin and hair traits (which is clearly true from old photographs.)

    This would suggest that the Fuegians are not really that unique, something that can itself be realised intuitively by comparing their faces to those of Amazonian Indians.

    Nonetheless ancient populations from the cone of southern South America were cranially very diverse, a situation that most likely arises from genetic mixture, so that their Otamid ancestors became mixed with a pre-Clovis population that clung on at the peripheries after they arrived and had previously begun to acquired pre-Amerind genes as they migrated south. Hence my interest in the question of Denisovan admixture in the extreme South Americans.

    I think that the ‘Melazonia’ complex is worth bringing up here as potential evidence for a substrate in the New World that is particular to South America alone and arrived from elsewhere. Melanesians and Melazonians are both tropical food producers (horticulturalists without the plow,) and share a complex of cultural traits either by shared descent or by parallelism. To their south, some of these traits are present in both indigenous Australians and peoples from the south of South America who have a ‘Melazonian’ approach to gender, so that a common Fuegian-Australian heritage would reduce the absurd degree of parallelism that would otherwise required to explain the Melazonian complex emerging twice.

    The question is whether this substrate was common to the ancestors of the Clovis and the Australians or whether it reached South America by sea along with parasitic worms and bottle gourds that would have been unable to survive for generations as humans migrated through the cold for generations.

    But against this, Berezkin cites other Russian authors that the only male rituals of the Amazonian-Melanesian type ever discovered in the northern hemisphere, were described by early Russian sources regarding the natives of the Unalaska and Kodiak islands. If this is correct then it supports a Beringian origin for the South American rituals and a wider past distribution of a proto-Melazonian culture.

  1. October 1, 2011 at 21:48 | #1
  2. April 10, 2012 at 14:28 | #2

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