And, Apparently, The Stolen Bone is Only One Problem...

The journal Nature is reporting on a scandal of sizable proportions involving a site of early human occupation in Europe.  Ewen Callaway reports:

Serious concerns have surfaced about three research papers claiming evidence for one of the earliest human occupations of Europe.

In an extraordinary letter posted to the bioRxiv.org preprint server on 31 October1, archaeologists allege that the papers, published in 2013, 2016 and 2017, included material of questionable provenance, and that results reported in the 2016 paper were based on at least one stolen bone. Editors at the journals concerned are publishing expressions of concern about the papers.

The bioRxiv paper is available from the site and, since it is a preprint server, is accessible to anyone wishing to read the story. Here is the bombshell from the paper:

A series of recent papers on the Early Pleistocene palaeontological site of Untermassfeld (Germany) makes claims that are of great interest for studies of earliest Europe and are at odds with the described pattern: the papers suggest that Untermassfeld has yielded stone tools and humanly modified faunal remains, evidence for a one million years old hominin presence in European continental mid-latitudes, and additional evidence that hominins were well-established in Europe already around that time period. Here we evaluate these claims and demonstrate that these studies are severely flawed in terms of data on provenance of the materials studied and in the interpretation of faunal remains and lithics as testifying to a hominin presence at the site. In actual fact any reference to the Untermassfeld site as an archaeological one is unwarranted.

The site is said to have been occupied beginning around a million years ago, which was an astounding claim when it was made.  Critical, however, is that, despite the wealth of archaeological, taphonomic, faunal and floral evidence from the site, there have never been any hominin remains found. 

The article is lengthy but is a fascinating account of a palaeontological mystery and sleuthing.  If the accusations are true, it is blow for the study of early human European occupation and puts a stain on the whole proceedings. 

H. floresiensis Not As Young or As Unique As We Thought

In other words, so much for the pathology argument.  Many news outlets, National Geographic being one of them, are reporting on new fossils that closely match those of Homo floresiensis that were found at Liang Bua Cave on the island of Flores in the late 1990s.  Adam Hoffman writes:

The 700,000-year-old human remains are the first found outside Liang Bua cave, the site on Flores that yielded the original hobbit fossils. The much older samples show intriguing similarities to H. floresiensis, including their small size, and so provide the best evidence yet of a potential hobbit ancestor.

“Since the hobbit was found, there have been two major hypotheses concerning its ancestry,” says Gerritt van den Bergh, an archaeologist at the University of Wollongong in Australia and a contributor to the work.

According to one theory, H. floresiensis is a dwarfed form of Homo erectus, an ancient human relative that lived in East Asia and parts of Africa until about 143,000 years ago. But other researchers think the hobbits evolved from even earlier, smaller-bodied hominins such as Homo habilis or Australopithecus.

“These new findings suggest that Homo floresiensis is indeed a dwarfed form of Homo erectus from Java, a small group of which must have gotten marooned on Flores and evolved in isolation,” van den Bergh says.

The article goes on to note that the competing argument, that the fossils of Liang Bua represent some kind of pathological condition, and that they maintained this condition for some 700 ky, is now untenable. Clearly this is a side-branch of human evolution.The other key finding is that they also had stone tools, specifically a “straightforward core and flake” technology. Further, the tools show a striking similarity to those found at Liang Bua, suggesting that there was remarkable cognitive "stability" in this population. 

The more we think we know about human evolution, the less, it turns out, that we do.  For now, the entire article is available from Nature for free here. 

More Evidence of Hybrization Between Archaics and Moderns in Africa

Nature's Research Highlights points to a paper written for the journal Genome Research, in which the authors, using whole genome analyses, argue that, for the first time, conclusive evidence of admixture between archaic Homo sapiens and early modern Homo sapiens occurred in Africa.  From the Nature blurb:

Michael Hammer at the University of Arizona in Tucson and his team analysed the entire genomes of seven individuals from two contemporary Western African Pygmy groups. The researchers identified 265 regions of the Pygmy genomes that may have been acquired through ancient interbreeding with other species, events that could have happened as recently as 9,000 years ago.

The article, itself, points out the nature of introgression in hominin evolution, thus:

Introgression, the transfer of genetic material between closely related species through hybridization, is an important and ubiquitous evolutionary force in both plants and animals (Mallet 2007). Although hybrids are often nonviable or infertile, hybridization can be an important driving force for the origin of novel traits and new species (Mallet 2007; Zinner et al. 2011). Within our genus, Homo, there is strong evidence for multiple introgression events between our own species, H. sapiens, and now extinct sister taxa outside Africa (Pääbo 2014). Neanderthal whole-genome sequencing (Green et al. 2010; Prüfer et al. 2014) revealed that Neanderthals contributed an average of ∼2% of the genetic variation of present-day humans living outside of sub-Saharan Africa. This gene flow likely took place 37–86 thousand yr ago (kya), after early modern humans emigrated from Africa and before archaic forms went extinct in Eurasia (Sankararaman et al. 2012), and it may have occurred multiple times (Vernot and Akey 2014, 2015; Kim and Lohmueller 2015).

It has been found, for example, that aspects of our immune system owe themselves to Neandertal introgression. This is an often overlooked aspect of how evolution proceeds.  There is continual debate about whether or not Neandertals represent a separate species from modern humans but the evidence that they interbred and exchanged genes is pretty good at this point.  The authors suggest that introgression of archaic genes occurred continually from the period of one million years down to less than 5 thousand years ago. That says something about the depth of the hybridization as well as the persistence of archaic genes in the modern human genome. 

Nuclear DNA From the Simo de los Huesos Fossil Material

Nature has a paper that focuses on DNA that has been extracted from the Sima de los Huesos fossil material from the site of Atapuerca, in northern Spain.  The letter does not appear to be behind the pay wall, at the moment.  In 2014, researchers completed a mitochondrial genome sequence for a hominin and the results were interesting, to say the least.  Here is the abstract from the 2014 paper:

Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene¹. One of these sites, the ‘Sima de los Huesos’ (‘pit of bones’), has yielded the world’s largest assemblage of Middle Pleistocene hominin fossils^{2, 3}, consisting of at least 28 individuals⁴ dated to over 300,000 years ago⁵. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits^{6, 7, 8}. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans^{9, 10}, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.

The authors argued at the time that Denisovans and the population from Sima de los Huesos shared a common ancestor, with a split of about 700 kya, and that both are more closely related to each other than either is to Neandertals.  This strongly suggests that Neandertals are a later derivation from a common crown group that represented the progenitors of all three groups.  The authors suggest that these findings are unexpected because of the incipient Neandertal traits found in the Sima collection, including occipital bunning in the back of the head and some mid-facial prognathism (it looks like the maxilla is puffed out).  Arsuaga and others have stated previously that they thought all of the Sima de los Huesos material belonged to the Neandertal lineage. That, apparently, is not the case.  As these authors point out, there may have been more than one evolutionary lineage roaming the valleys and forests of Europe.

Now the nuclear DNA has been  sequenced and these results strongly suggest that the people represented by the SH population were, in fact, early Neandertals.  From the paper by Meyer et al:

The nuclear DNA sequences of femur AT-5431 and the incisor show that they belonged to the Neanderthal evolutionary lineage, and the limited data available for the molar suggest that the same is true for this specimen. Thus, the results show that the SH hominins were early Neanderthals or closely related to the ancestors of Neanderthals after the divergence from a common ancestor shared with Denisovans. Although it is difficult to determine the age of Middle Pleistocene sites with certainty, geological dating methods¹, as well as the length of the branches in trees relating the mtDNAs from femur XIII and an SH cave bear to other mtDNAs^{2, 12}, suggest an age of around 400,000 years for the SH fossils. This age is compatible with the population split time of 381,000–473,000 years ago estimated for Neanderthals and Denisovans on the basis of their nuclear genome sequences and using the human mutation rate of 0.5 × 10⁻⁹ per base pair per year⁷

These authors now suggest that, in combination with the MtDNA results from last year, that the SH hominins are ancestral to Neandertals and that the MtDNA found in later Neandertals is derived relative to that in the SH hominins and that the SH hominins may have had several different MtDNA strands. 

It appears that the evidence supports a model in which the classic Neandertals from France and Germany, which are dated to between 50 and 70 kya, represent a more stabilized, homogenous genome relative to that of earlier hominins.  I have always been struck by the similarities between the Atapuerca 4 cranium and Petralona, from Greece, and this suggests that there may have been extensive migration between regions and considerable gene flow between groups (J. Lawrence Angel, again).  We know that the range of Neandertals extended from the lower Iberian peninsula to Teshik-Tash, north of the Taurus Mountains and Okladnikov, in Siberia.  It does not seem like a stretch that their precursors did the same thing. 

Hat tip to Todd Wood.

Science Timeline in Nature

Nature News has an interactive timeline of all of the major science stories of the year here. It is a good recap.


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