Neanderthals, Denisovans and everything else

A recent analysis of the nuclear DNA of a Neanderthal toe from Altai has caused widespread interest.

Kay Prüffer et al., The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 2013. Pay per view → LINK [doi:10.1038/nature12886]

The story of a finger and a toe

Both the Denisovan and Neanderthal DNA sequences discussed in this paper come from small bones found at the same location: Denisova cave, Altai Republic. The Denisovan sequence that revolutionized human paleogenetics a few years ago corresponds to a finger phalanx bone of some 50,000 years ago. The less notorious Neanderthal sequence discussed in this study corresponds to a toe imal phalanx, which was found in a lower layer in the same gallery of the same cave, and hence should be older.

This is very interesting to underscore because it seems to imply that Neanderthals were in Altai and specifically in Denisova cave very early, at dates similar to those we find in West Asia (Tabun excepted) and they may even be older than Denisovans in the very cave that gave them their name.

The toe sequence was found in a previous study to have Neanderthal mtDNA, closely related to the lineages of European Neanderthals of various dates and sites. Instead the finger mtDNA (Denisovan) was derived from a more ancient branch of humankind than the very point of split between Neanderthals and modern humans (H. sapiens) and has been recently shown to be related to European H. heidelbergensis from Atapuerca. 

Notes in red are mine.

This study focuses on the autosomal DNA of both Neanderthals and Denisovans. Unlike mtDNA, whose phylogenetic position is simple and quite straightforward, autosomal or nuclear DNA (nDNA) is extremely much more complex to understand because of its recombining nature, requiring of statistical approaches, which may get extremely complex and potentially subject to premise biases. When comparing two individuals this gets largely simplified but it is a lot more complex when doing the same with larger samples.

And that is precisely what this study does: comparing one Denisovan, several Neanderthals and also several modern humans. Therefore it is a very complex paper and the authors necessarily assume some evaluation risks, which nevertheless are discussed in depth in the supplemental material, a methodology of the Pääbo team that we can’t but greatly appreciate.

Age estimates

The study makes two age estimates, one based on a very conservative and truly unbelievable Pan-Homo split date of 6.5 Ma BP and the other based on observed per generation mutation rates, which happens to be perfectly coincident with a Pan-Homo split of 13 Ma BP, the oldest extreme of Langergraber’s estimate. This coincidence alone is of enough relevance for all molecular clock approaches, because it effectively demands the doubling of all age estimates based on the ridiculously short 6.5 Ma Pan-Homo split supposition. 

Red outlines are mine. Click to enlarge.

It also produces a semi-reasonable San-West African age estimate of c. 86-130 Ka, although I would think it a bit older in fact or at the very least at the top end. This highlights the severe difficulties of such molecular clock estimates, because a 4 Ma divergence between the alleged introgressing mystery archaic in the Denisovan genome, seems out of the question according on the archaeological and paleontological record, which only documents Homo species since c. 2 Ma ago, half that time (within the estimate but clearly very far from the top end).

Altai Neanderthal inbreeding

An important finding of this study is that the studied individual was extremely inbred, with parents in effective relationship comparable to that of grandparent and grandchild or half siblings. This inbreeding tendency, even if extreme, is not so strange in populations that have experienced founder effect bottlenecks and small population sizes. The Denisovan and the modern human Karitiana people are not so extreme but range in the lower end of double first cousins level of genetic relationship between the parents. Other Native Americans like the Mixe are close to that range, while the other compared populations, Papuans and Sardinians, show much lower levels of inbreeding.

Whatever we may think of Altai Neanderthal inbreeding, their drift parameter is still very low when compared with European Neanderthals. This is not discussed in the paper but such extreme drift also seems to imply extreme inbreeding issues in European Neanderthals, even if these may have other causes such as an extremely strong founder effect or whatever.

Bonobo-specific segments were removed, so the bonobo position is not realistic.

Inferred population history

Both populations leading to the Altai Neanderthal and Denisovans, but not modern humans, appear to have gone through a strong decline in population size since hundreds of millennia ago. The Denisovan decline seems to begin c. 800 Ka ago while the Neanderthal one may have begun c. 500 Ka ago. While this is coincident with a general expansion of the H. sapiens branch (still undifferentiated in Africa), peaking around c. 250 Ka ago before differentiation and relative decline. In their words:

All genomes analysed show evidence of a reduction in population size that occurred sometime before 1.0 million years ago. Subsequently, the population ancestral to present-day humans increased in size,whereas the Altai and Denisovan ancestral populations decreased further in size. It is thus clear that the demographic histories of both archaic populations differ substantially from that of present-day humans.

Neanderthal and Denisovan admixture in modern humans

The new tests confirm in essence the previous findings: there is significant Neanderthal introgression in modern humans descending from the migrants out of Africa and there is also significant Denisovan one among Australasian populations.

Additionally and with some caution, the authors think that much lesser Denisovan introgression (of around 0.2%) is found among East Asians and that these, as well as Native Americans, show slightly more Neanderthal admixture than West Eurasians. In my understanding this may be caused by minor African flow to West Eurasia after the admixture event (and/or residual “First Arabian” persistence) and I would think that measuring South Asians would help to clarify this issue (because African admixture is negligible in the subcontinent but they are also distinct from East Asians).

These measurements are so weak that the authors agree to all kind of cautions about them in any case.

In addition to all this, the supplemental material (section 13) also detects tiny, almost homeopathic, amounts of Neanderthal gene flow to Yorubas (~0.02%), obviously mediated by H. sapiens backflow from Asia and Europe into parts of Africa, which eventually influenced other African populations. An even more diluted amount may also be present among the Mbuti Pygmies.

Altai Neanderthal admixture in Denisovans

This issue is not really explained in the paper as such, and we have to reach out to the Supplemental Information chapter 15 in order to grasp it.

It is clear that the Altai Neanderthals are closer to Denisovans than other Neanderthals are by approx. the following fractions (directly deduced from the raw affinities listed in fig. S6a.2):

• 2% more than Mezhmaiskaya
• 7% more than Vindija (avg.)
• 9% more than El Sidrón

Feldhofer appears closer instead but this sequence was not used by the authors in most tests because it has too dubious quality.

In section 15 of the supplementary material, using complex methodology and lamenting the lack of a second Denisovan sample which would be most useful, they estimate a minimal 0.5% (Altai) Neanderthal introgression in Denisovans, with strong warnings that this could well be quite higher. I don’t know why they are not even considering a more direct approach, but I would dare to guesstimate the introgression to be close to 8% from the above raw data, assuming that there are no further complexities at play, such as other Heidelbergensis introgression in European Neanderthals, etc. The drift parameter (see above) does not seem to be one such complexity because Mezhmaiskaya is almost as drifted as Vindija yet it is consistently much closer, as it seems to correspond to its specific relatedness to Altai Neanderthals in mtDNA (and possibly also in nDNA if it is admixture what causes their pseudo-tree positioning closer to the root, what would be typical).

Note in blue is mine.

Mystery archaic genetic flow into Denisovans

The authors find that some 0.5-8% of the Denisovan genome appears to come from another hominin, which split from the human trunk even earlier.

We caution that these analyses make several simplifying assumptions. Despite these limitations, we show that the Denisova genome harbors a component that derives from a population that lived before the separation of Neanderthals, Denisovans and modern humans. This component may be present due to gene flow, or to a more complex population history such as ancient population structure maintaining a larger proportion of ancestral alleles in the ancestors of Denisovans over hundreds of thousands of years.

Later in the discussion section they ponder further the implications of this finding:

The evidence suggestive of gene flow into Denisovans from an unknown hominin is interesting. The estimated age of 0.9 to 4 million years for the population split of this unknown hominin from the modern human lineage is compatible with a model where this unknown hominin contributed its mtDNA to Denisovans since the Denisovan mtDNA diverged from the mtDNA of the other hominins about 0.7–1.3 million years ago⁴¹. The estimated population split time is also compatible with the possibility that this unknown hominin was what is known from the fossil record as Homo erectus. This group started to spread out of Africa around 1.8 million years ago⁴², but Asian and African H. erectus populations may have become finally separated only about one million years ago⁴³. However, further work is necessary to establish if and how this gene flow event occurred.

Going to the detail of the matter (i.e. supplemental material sections 16a and 16b), one of the key details is that present-day Africans share more derived alleles with Neanderthals than with Denisovans. This can only be explained because Denisovans have other archaic ancestry prior to their apparent divergence from Neanderthals or (what is about the same) because Denisovans diverged themselves prior to the Neanderthal-Sapiens split, what is what the mtDNA (unlike the nDNA) suggests. However the difference, even if consistent across comparisons, is too small (a few percentage points) to be attributed to the later scenario.

This means that Denisovans appear to be at nDNA level some sort of an independent branch of proto-Neanderthals with some other but minor archaic admixture. Instead at mtDNA level they appear to be unrelated to Neanderthals and related instead to H. heidelbergensis (a detail not discussed in this paper because it is a too recent independent discovery).

There are still many details to explore but, in principle, it would seem that the Denisovan branch appears to be a divergent proto-Neanderthal one (maybe related to the Hathnora hominin, which looks very much Neanderthal) with lesser other archaic (H. heidelbergensis?) admixture, which nevertheless remained prominent in their mtDNA for whatever accidental reason.

Whether the H. heidelbergensis population of Atapuerca responds to this same profile (i.e. they were Denisovans too) or belongs instead to the “other archaic” population which introgressed in the Denisovan genome remains to be solved. So far we only know the mitochondrial lineage and this one may be misleading, as seems to be the case with the Denisova hominin.

Note in red is mine

Modern human genetic evolution

Benefiting from the high quality of the archaic genomes of Altai, the authors cataloged a long list of simple mutations exclusive to our species: 31,389 single nucleotide substitutions and 4,113 short insertions and deletions (indels). Additionally they found other 105,757 substitutions and 3,900 indels shared by 90% of their modern human sample of 1094 individuals.

They suggest some lines for future research in this regard, maybe focusing on genes known to influence brain development or regions that could show signs of positive selection. These preliminary lines of research are explored in SI-20, noticing potential selection in genes that affect the ventricular zone of the brain and cell proliferation in fetal brain development.

 

Echoes from the past (May 17 2013)

Some interesting news I cannot dedicate much effort to:

Human intelligence not really linked to frontal lobe.

New research highlights that the human frontal lobe is not oversized in comparison with other animals. Instead the human intelligence seems to be distributed through all the brain, being the network what really matters → Science Daily. 

Ref. Robert A. Barton and
Chris Venditti. Human frontal lobes are not relatively large. PNAS, May 13, 2013 DOI: 10.1073/pnas.1215723110
 

Early hominin ear bones found together in South Africa.

The three bones, dated to c. 1.9 Ma show intermediate features between modern humans and apes → PhysOrg.

New hominin site in Hunan (China).

The sediments of Fuyan cave, in which five human teeth (Homo erectus?) were found, along with plenty of animal ones, are dated to 141,700 (±12,100) years ago. → IVPP – Chinese Academy of Sciences.

The five human teeth

Neanderthal workshop found in Poland.

In Pietrowice Wielkie (Silesia), which is at the end of a major natural corridor from the Danubian basin → PAP.

Ancient Eastern Europeans ritually killed their pets to become warriors.

In the Bronze Age site of Krasnosamarkskoe (Volga region, Russia) more than 50 ritually pieced skulls of dogs have puzzled archaeologists, who have reached the conclusion, after researching Indoeuropean accounts from India, that the animals may have been killed in adulthood rituals: the boys who were to become warriors had to kill their most beloved pet in order to be accepted as such, and did so in a precise and macabre ritual → National Geographic.

Ancient log boat found in Ireland.

In the Boyne river, which was in the past a major artery of the island. Not yet dated: it could be from prehistoric times or the 18th century. → Irish Times.

 

An infant’s milk tooth from Orce is the earliest known human remain in West Europe

The discovery was made in 2002 but is only to be published in a formal paper now, at the Journal of Human Evolution (not yet published, it seems). The molar from a young child of, possibly, Homo erectus, habilis or, if you wish, georgicus was found in the Cave of Orce (Granada province, Andalusia) and dated to c. 1.4 million years ago, being therefore the most ancient human inhabitant known in Western Europe. 

This finding correspond to Oldowan findings by Catalan archaeologist Josep Gibert, which he dated to c. 1.5-1.8 Ma ago but that other scholars prefer to date somewhat more recently (1.2 Ma ago?) The Gibert dates in any case correlate well with the recent discovery of H. georgicus and the general estimate for the first migrations out of Africa by H. habilis/erectus, dated also to c. 1.8 Ma ago. 

“Orce Man” scapula

It would also add some support to the claim by Gibert of a bone found in that same cave in 1983 being part of the skull of an archaic human, the so-called Orce Man, which he dated to 1.3 Ma. Back in the day the finding was strongly contested and even claimed to be an equid’s scapula, however the debate has not yet settled and it seems that these days only creationists are heavily opposed to Orce Man being real, while the scientific establishment remains divided. 

Whatever the case, if Orce Man was real, this kid could well have been his direct ancestor.

Sources[es/cat]: Pileta (incl. videos); Catalan Institute of Human Paleontology (IPHES) → blog (many photos), press release; 20 Minutos.

Update:

The son of Josep Gibert, Luis, laments in interview by press agency EFE (published today at Diario Vasco, for example) that some people (in direct reference to IPHES’ director) still discredit his father’s work but he feels happy about the tooth finding.

He argues that it cannot be the scapula of a ruminant among other reasons because these animals have a much thicker skull than us humans.

He also feels personally affected because he had hoped that his team could have obtained a license to work in the Orce area but the Andalusian authorities have only produced one single license for one single team.

(Via Pileta again).

Update (Mar 23): Gibert controversy delays publication

Publication of the relevant paper has been delayed after Luis Gibert asked the Journal of Human Evolution why a tooth fragment, dated to 1.25 Ma., published by his father Josep in Human Evolution 1999 (now extinct), is not even mentioned. Other works by Josep Gibert on Olduwayan tools found in the very same site of Barranco de León with dates as old as 1.5 Ma. are also ignored in the study’s text and bibliography. For these reasons Elsevier has decided to provisionally pull back the publication until these works are cited.

Paul Palmqvist, one of the members of the team currently digging at Orce, laments the decision on the grounds that the tooth fragment found by Gibert is not at all conclusively human.

It is a fragment of tooth enamel that in my opinion belonged to a hippopotamus, he said.

Luis Gibert claims that the humanity of the tooth was confirmed to his father in a telephone conversation by reputed archaeologist José María Bermúdez de Castro, however this one denies such thing ever happening and the humanity of the Gibert molar fragment. He also attacked the defunct publication Human Evolution as a third tier magazine, a parochial flier in which everything was allowed.

Source: Paleorama en Red[es].

Update (Mar 25):

Ama Ata dedicates today an entry to a documentary (in Spanish, 1hr long, split in four videos) titled Orce Man, homage to Josep Gibert. It is interesting to realize that many scientists are supportive of the position of Gibert, very notably Yves Coppens, discoverer of famous australopitecine Lucy, who says that Josep died too young (in 2007) because otherwise he might have lived to see the triumph of his theories.

The real issue seems to be that in the early 80s, there was a widespread belief in the Academic establishment on Europe had not being inhabited by any kind of humans until some 500,000 years ago. This finding did not only more than double those dates (something now widely accepted) but Gibert was even suggesting that they might have arrived by crossing the Strait of Gibraltar, something that even today some find hard to believe for Homo erectus.

However the skull fragment was widely accepted initially as real. But then a small “occipital crest” was found in it, what led Lumbley to argue that it was a horse instead. Gibert lamented that instead of communicating this to him or otherwise debating cleanly, the French leaked this to the press surreptitiously and pulled strings within the circles of power of the Academia, a similar method of pseudoscientific disqualification by established “armchair scientists” to calumniate the findings of Iruña-Veleia.

 

Million years old human remains from Eritrea

Fragments of a human skull dated to some one million years ago have been found at Muhuli Amo, Eritrea. They are probably correlated with a previous finding of hundreds of Acheulean tools. 

The skull fragments found

Sources: The Archaeology Network, Pileta, Noticias de Prehistoria[es].

 

Technological revolution in African Acheulean some 800,000 years ago

Well, maybe the title is a bit of a hype but something like that seems to be the most relevant finding on the Acheulean of Konso (SNPP region, Ethiopia): that the technique stood the same for a million years and then, some 800,000 years ago, became more refined in which was apparently one of the first technological leaps of archaic Humankind. Specifically it is the edges of the handaxes (the archetypal Acheulean finding, which may have been more a knife of sorts than a true axe) which became more refined and apt for its cutting purpose.

Yoyas Beyene et al., The characteristics and chronology of the earliest Acheulean at Konso, Ethiopia. PNAS 2013. Open access → LINK [doi:10.1073/pnas.1221285110]

Abstract

The Acheulean technological tradition, characterized by a large (>10 cm) flake-based component, represents a significant technological advance over the Oldowan. Although stone tool assemblages attributed to the Acheulean have been reported from as early as circa 1.6–1.75 Ma, the characteristics of these earliest occurrences and comparisons with later assemblages have not been reported in detail. Here, we provide a newly established chronometric calibration for the Acheulean assemblages of the Konso Formation, southern Ethiopia, which span the time period ∼1.75 to <1.0 Ma. The earliest Konso Acheulean is chronologically indistinguishable from the assemblage recently published as the world’s earliest with an age of ∼1.75 Ma at Kokiselei, west of Lake Turkana, Kenya. This Konso assemblage is characterized by a combination of large picks and crude bifaces/unifaces made predominantly on large flake blanks. An increase in the number of flake scars was observed within the Konso Formation handaxe assemblages through time, but this was less so with picks. The Konso evidence suggests that both picks and handaxes were essential components of the Acheulean from its initial stages and that the two probably differed in function. The temporal refinement seen, especially in the handaxe forms at Konso, implies enhanced function through time, perhaps in processing carcasses with long and stable cutting edges. The documentation of the earliest Acheulean at ∼1.75 Ma in both northern Kenya and southern Ethiopia suggests that behavioral novelties were being established in a regional scale at that time, paralleling the emergence of Homo erectus-like hominid morphology.

Fig. 4. Handaxe refinement through time. Upper, dorsal; Lower, ventral. From left to right, two each are shown from KGA6-A1 (∼1.75 Ma), KGA4-A2 (∼1.6 Ma), KGA12-A1 (∼1.25 Ma), and KGA20 (∼0.85 Ma). In each pair of handaxes from the respective sites, near-unifacial (left) and more extensively bifacial (right) examples are shown (except with the KGA20 handaxes, which are both well worked bifacially).

I am a bit intrigued by the all-covering work style of the last handaxes, which remind somewhat to the later MSA technology, which belongs already to Homo sapiens. Our species may have also evolved in that very area of the Nile Basin, with the oldest specimen known being from nearby Omo River.

Of course that there are hundreds of thousands of years in between and of course that the peculiar orography of the Rift Valley is susceptible of offering archaeological findings from old much more easily than other areas but still…

Other sources: Pileta, NBC News.

Update: much more than just the edges but a whole technological paradigm change:

I was not really appreciating the whole extent of the technological revolution implicit in these changes. I just took note (reading too fast, too many things to do) of the edge refinement but Va_Highlander has correctly called my attention on that it was a much more ample and complex change in the whole technology of stone flaking and not just the edges, maybe even a whole jump in our mental capacities:

In contradistinction to the >1.2-Ma assemblages, the younger ∼0.85-Ma Konso Acheulean is characterized by considerably refined handaxes. Some of these handaxes are refined to the extent that they would qualify as approaching “three-dimensional symmetry” (i.e., symmetric not only in plan view but also in cross-section form) (Fig. 4 and Fig. S2). Some suggest that manufacturing 3D symmetric tools is possible only with advanced mental imaging capacities and that such tools might have emerged in association with advanced spatial and navigational cognition, perhaps related to an enhanced mode of hunting adaptation. It has been pointed out that purposeful thinning of large bifacial tools is technologically difficult, even in modern human ethnographic settings. In modern humans, acquisition and transmission of such skills occur within a complex social context that enables sustained motivation during long-term (>5 y) practice and learning.
 
In light of the above information, it is of interest that our metric analysis shows that there may be a fundamental difference between the handaxe technologies of >1.2 and ∼0.85 Ma. Whereas refinement of handaxe shape did occur from ∼1.6 to ∼1.2 Ma, this refinement did not result in tool thinning and advanced 3D symmetry.

 

Asian Homo erectus may have used fire and clothes

That is what a media news is claiming on this New Year’s night: that Peking man, an early member of a long diverged branch of Humankind (understood as the genus Homo in full) may have already used artificial fire and leather clothing.

While this may seem quite necessary for any kind of people living as far North as Beijing (roughly the latitude of Philadelphia) the possibility that our cousin’s adaption to cold was biological, by means of retaining ancestral fur instead of our techno-cultural way, was open.

Now some researchers from the Chinese Academic of Science’s Institute of Palaeoanthropology and the University of Toronto think that they have some evidence that could support the use of fire and clothing.

As far as I can tell no study has been published yet, so I’m telling from the media alone.

Sources: Live Science, MSBCN – h/t Unreported Heritage News.

PS – Happy 2013 to all. 

 

The Paleolithic of the Three Gorges region of China

The controversial construction of the Three Gorges Dam served at least to make some extensive and intensive archaeological research in the area, evidencing human presence in much of the last million years. 

Pei Shuwen et al., Middle to Late Pleistocene hominin occupation in the Three Gorges region, South China. Quaternary International (2012). Pre-publication free access → LINK (PDF) [doi:10.1016/j.quaint.2012.04.016]

Abstract


The contributions of the Chinese Paleolithic record to broader ranging paleoanthropological debates have long been difficult to decipher. The primary problem that hinders many contributions that include or focus on the Chinese record is that relatively few regions outside of the main flagship sites/basins (e.g., Zhoukoudian, Nihewan Basin, Bose Basin) have been intensively researched. Fortunately, systematic archaeological survey and excavations in the Three Gorges region, South China over the past two decades has led to the discovery of a number of important hominin fossils and Paleolithic stone artifact assemblages that have contributed to rethinking of ideas about hominin adaptations in Pleistocene China. This paper provides a detailed review of the results of recent paleoanthropological, particularly Paleolithic archaeological, research from this region.

The Three Gorges region is located in the transitional zone between the upper and middle reaches of the Yangtze River (Changjiang River). Vertebrate paleontological studies indicate that the faunas from this region belong primarily to the AiluropodaeStegodon faunal complex, a group of taxa representative of a subtropical forest environment. Systematic field surveys identified sixteen Paleolithic sites in caves and along the fluvial terraces of the Yangtze River. Based on geomorphology, biostratigraphy, and geochronology studies, these sites were formed during the Middle to Late Pleistocene. Follow up excavations at these sites led to the discovery of a large number of Paleolithic stone artifacts, Pleistocene mammal fossils, as well as some hominin fossils. Analysis of these materials has provided the opportunity to reconstruct hominin technological and mobility patterning in a restricted spatial point. The Paleolithic technology from the Three Gorges region is essentially an Oldowan-like industry (i.e., Mode 1 core and flake technologies) comprised of casual cores, whole flakes, fragments, and chunks as well as a low percentage of retouched pieces. The utilized stone raw material is primarily high sphericity cobbles and limestone, which were locally available along the ancient river bed and surrounding terraces. Most of the artifacts are fairly large in size. All flaking is by direct hard hammer in a single direction without core preparation. Unifacial choppers are the predominant core category, with fewer bifacial choppers, sporadic discoids, polyhedrons, and bifaces. The flake types demonstrate that the first stage of core reduction is represented by a low percentage of Type III and VI flakes. Some flakes are retouched unifacially by direct hard hammer percussion on the dorsal surface of the blanks. Archaic Homo sapiens and modern H. sapiens identified from some of the cave deposits are likely the hominins responsible for the production of the stone artifacts. Implications for Oldowan-like technological patterning in South China are discussed.

There is rather high detail in this paper in spite of the stone tools of East Asia tending almost invariably to simple flake forms hard to classify, arguably caused by the lack of good quality materials. But I guess that the most relevant of all is this chronology:

Of great interest are no doubt the human (or hominin) fossils found in these and previous digs. If my recollection is correct these are:

• Xinlong cave (Wushan Co., c. 118-154 Ka): Four hominin permanent teeth were recovered during the 2001 excavation field season (Fig. 2). These hominin fossils have been tentatively assigned to archaic H. sapiens, though more detailed morphometric analysis is warranted.
• Leiping cave (Wushan Co., middle or late Pleistocene): Hominin fossils including one occipital, some fragments of skull, and a frontal bone of one juvenile, and one upper incisor were collected from the sediments and tentatively assigned to archaic H. sapiens…
• Migong cave (Wushan Co., c. 13,100 BP): The hominin fossils are two fragments of parietal bones which belong to one individual (Fig. 2) and can be assigned to modern H. sapiens.
• An archaic jaw bone was also found in the 1950s without context.

It is not clear if by archaic Homo sapiens the authors mean Homo sapiens with debatable archaic features or, using obsolete terminology, other species of Homo such as Homo erectus. I’m guessing that the latter but no idea.

 

Folic acid deficiency detected in Olduway c. 1.5 Ma ago

The headlines and even contents in commercial media and blogs alike are all about meat eating (much of which must be blamed on the lead researcher himself, who seems to have a bias) but it does not need to be the reason at all and rather reflects an ideological bias. 

All that paleoanthroplogists have detected is a folate deficiency in a fragment of a skull of what is probably an Homo erectus/ergaster young child (est. 2 y.o. or less) from East Africa. There is no dietary isotope research that can confirm or deny the meat hypothesis.

Manuel Domínguez-Rodrigo et al., Earliest Porotic Hyperostosis on a 1.5-Million-Year-Old Hominin, Olduvai Gorge, Tanzania. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0046414]

The authors found exactly this:

Figure 3. Ectocranial (top right) and endocranial (top left) close-up views of the OH 81 fossil, accompanied by magnifications of the porotic hyperostosis paleopathology as observed ectocranially (lower left) and edge-on at the diploic-table junction (lower right). Scale = 1 mm.

They conclude that this porosity of the bone, known as porotic hyperostosis, should indicate folate deficiency (in which vitamins B9 and B12 are involved) caused by malnutrition. They also argue that weaning may have been a cause because, at least in other contexts, it is a key period for nutritional illnesses, often implying B12 deficiency. 

The archaeo-environmental context (persistent drought) may have contributed to this illness and death as well.

Still the emphasis in meat eating, even if possibly correct, strikes me as very ideological:

The presence of anemia-induced porotic hypertostosis on the 1.5 Ma OH 81 hominin parietal, indicates indirectly that by at least the early Pleistocene meat had become so essential to proper hominin functioning that its paucity or lack led to deleterious pathological conditions. 

Were do we get that from, Dr. Domínguez? Some sort of nutritional lack seems obvious but there are many reasons why folate deficiency can develop; for example excess of solar radiation (it has been proposed that the ancestral dark skin of humans serves to prevent folate loss, rather than cancer, which only develops in the long term). Was this child an albino maybe? 

Or had it celiac disease (another possible cause of malabsorption)?

And (update), as the Subersive Archaeologist discusses rather emotionally, the maybe simplest explanation: that malaria could be the cause is dismissed in the paper without satisfactory explanation.

Sure thing that lack of sufficient animal protein intake is a plausible cause but by no means demonstrated. An isotopic analysis could support or reject this hypothesis, although I am uncertain if it is possible to perform on this particular bone.

See also labels Paleolithic food, human evolution and pigmentation in this blog.  

 

Evolving bigger brains everywhere?

Peking Man (CC by Mutt)

New craniometric research on the NE Asian Homo erectus (also known as Peking Man or Homo erectus pekinensis) seems to confirm that the population grew bigger brains with limited external input. If correct, this may mean that the pressure towards bigger brains has been a generalized tendency in all Homo sp. populations. 

Late H. erectus pekinensis had cranial capacities above 1000 cc., in some cases bordering our own averages and certainly within our range. 

This research highlights that there is no apparent evolution in the shape of the head while the size did grow along time. However craniometry is a very inexact science.

Source: Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences.

 

Denisovan and Neanderthal proviral DNA

A provirus is a strand of autosomal DNA that was inserted by a virus once upon a time and got lost in our genome as junk DNA, not being anymore active (would it remain active it’d be a retrovirus). Such insertions are thought to be unique phylogenetic events. 

New research has identified a provirus* (HERV-K-Ne1 = HERV-K-De6, inserted in Chromosome 5) shared by Neanderthals and Denisovans but not Homo sapiens. This is consistent with the previous data that placed their autosomal DNA closer to each other than to Homo sapiens.

Lorenzo Agoni et al., Neandertal and Denisovan retroviruses. Current Biology, 2012. Freely accessible (letter with supplementary material) at the time of writing this.

It must be noted however the mitochondrial DNA, inherited by pure matrilineage, is much closer among our species and Neanderthals than either one with Denisovans, what to me suggest that Denisovans are no new species but a hybrid of Neanderthal and Homo erectus. A theory not yet fully testable for lack of DNA from Asian Homo erectus.

Interestingly Denisovans have also several proviruses not found in Neanderthals, what could well support my theory of hybridization. The detected provirus could hence have migrated from Neanderthals to Denisovans in the hybridization episode (along with lots of other autosomal DNA), while the rest could have been retained from the H. erectus ancestors by the maternal line. 

However as the article is both very technical and succinct, I can’t be sure right now of how strongly or weakly can this info support the hybridization model (founded opinions welcome). 

In total the researchers detected three Neanderthal proviruses and 12 Denisovan ones, one of which is shared between both nominal species. It is convenient to remind that while the Denisovan genome was very well preserved and sequenced almost completely, the Neanderthal genome is only known in fragmentary form, amounting to about 60% of the actual genome.