Genome of Kostenki-14, an Upper Paleolithic European (Seguin-Orlando, Korneliussen, Sikora, et al. 2014)

A new paper in Science reports on the genome of Kostenki-14 (K14), an Upper Paleolithic European from Russia. This is now the third oldest Homo sapiens for which we have genetic data, after Ust'-Ishim (Siberia, 45 thousand years), Tianyuan (China, 40 thousand years), and now Kostenki (European part of Russia, 37 thousand years). Of these three genomes, the Ust'-Ishim is both the highest coverage and earliest (Siberia is the gift that keeps on givin'), Tianyuan only has its chromosome 21 known, and K14, a complete 2.42x coverage sequence (and, apparently, good teeth, after all these years; left).

The publication of the Tianyuan genome showed that populations related to East Asians and Oceanians existed in the world 40 thousand years ago. So, models based on modern humans that put the split of East Asians from Europeans to a much more recent time period were basically wrong (more on this a little below). The Ust'-Ishim genome showed that populations basal to both East Asians and Europeans existed in the world 45 thousand years ago. So, either East Asians and Europeans hadn't gone along their different paths yet, or, if they had, Ust'-Ishim happened to be a side branch and not the major East Asian and European lineages.

K14 may not be the older Upper Paleolithic human, but as of this writing it is the only Upper Paleolithic European that has been published so far, the next ones being the Loschbour, Motala, and La Brana Mesolithic Europeans who who have about 1/5 of its age. The new paper shows that K14 was definitely European (or more correctly West Eurasian or Caucasoid), as it was more similar to modern Europeans than to East Asians or other non-West Eurasian populations. Thus, the morphological description of the sample as "Australoid" by some early anthropologists did not reflect its ancestral makeup. Also, this proves that Caucasoids existed 37,000 years ago, which most physical anthropologists would believe, but it is nice to have direct confirmation. This pushes the lower bound from 24,000 years ago (because MA-1 was West Eurasian according to the results of Raghavan et al.). It will be nice to push the lower bound further to the past as there are much older bones (and plenty of teeth) from earlier Upper Paleolithic Europeans.

But there is a slight kink in the story, as K14 also belonged to Y-haplogroup C which is predominantly East Asian/Ocenian/Native American today. So, maybe there is some distant link to these populations in its ancestry. But, there is definitely a link to much more recent Europeans: the tiny percentage of living Europeans who have preserved K14's Y-chromosomal type (some of which were doubtlessly told a few years back that they were descendants of Genghis Khan, before the phylogenetic structure of C was known), the La Brana hunter-gatherer from Mesolithic Spain, as well as Neolithic Europeans from Hungary.

The authors of the current paper also date the date of Neandertal admixture to 54 thousand years. This seems very compatible with the finding of between 50 and 60 thousand years by Fu et al. (2014) based on the Ust'-Ishim genome (which is both earlier and better, so the chunks of Neandertal ancestry in it are probably be longer and more well-defined).

The authors propose the following model for how various populations are related to each other:

This model is not formally tested, but at least it seems to derive Europeans as a 3-way mixture that is basically identical to that of Lazaridis et al., with some relabeling of populations (MHG=WHG and NEOL=EEF).

The model also includes Yeniseian Siberians as a mixture of MHG and East Asians (although it does not include actual East Asians). It's strange that Yeniseians apparently are given no ANE ancestry but only WHG/MHG. Both Raghavan et al. and Lazaridis et al. mentioned that ancestry related to MA-1 in living Siberians is diminished, but none at all?

The major new finding of this paper, however, is that K14 had Basal Eurasian ancestry, which was first proposed for EEF from Germany 7,000 years ago, so now it postulated for Russian hunter-gatherers 37,000 years ago. I don't think many archaeologists would derive European farmers from Russia (Russia is actually one of the last places in Europe that became agricultural). So, maybe the hunter-gatherers from Russia had Basal Eurasian ancestry and this wasn't limited to the ancestors of the EEF? If they did, it's strange that Loschbour, La Brana, MA-1, Ust'-Ishim, Swedish Mesolithic (and maybe KO1?) didn't have it. So, either Kostenki was very unique or there is an alternative explanation for its strangeness.


The evidence for the Basal Eurasian ancestry in K14 is summarized in the figure above in bullet point (b).

• The statistic D(Mbuti, East Asia; HG, K14) is less than 0. So, there's some link between HG and East Asians. Is this because of Basal Eurasian admixture in K14 or due to some admixture between Caucasoids and Mongoloids after the time of K14? (this might cause the lower dates of European-East Asian splits alluded to above).
• The statistic D(Mbuti, East Asia; NEOL, K14) is 0. So, East Asians don't "prefer" either Neolithic Europeans (NEOL) or K14. I guess the value of this statistic depends on how much Basal Eurasian the different populations have and what's the relationship between East Asians, K14, and the non-Basal Eurasian part in K14.
• Finally, "NEOL component for K14 in ADMIXTURE". I think they are referring to the "Middle East" component (right). This may be Basal Eurasian ancestry, or maybe because K14 is so old, it pre-dates the European/Middle Eastern divide and its ancestry isn't attracted to either Europe or the Middle East, so it gets ancestry from both (and many other colors besides).

It is fascinating how many new questions are both answered and raised each time a new genome gets published (and there has been a constant stream of these over the last couple of years).

Science DOI: 10.1126/science.aaa0114

Genomic structure in Europeans dating back at least 36,200 years

Andaine Seguin-Orlando1,*, Thorfinn S. Korneliussen1,*, Martin Sikora1, et al.

The origin of contemporary Europeans remains contentious. We obtain a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. We find that K14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a meta-population that at times stretched from Europe to central Asia.

Link

ESHE 2013 abstracts

219 pages worth of abstracts from the upcoming meeting of the European Society for the study of Human Evolution (pdf).

I will post some excerpts:

Evolutionary History And Biological Diversity Of Homo Sapiens In Southeast Asia: Contour Shape Analysis Of Modern Human Upper Molars:

The evolutionary history and the pattern of biological diversity of modern humans in Southeast Asia has long been regarded as resulting of two major migrations waves. In this hypothesis it is generally considered that a first wave of migration (generally referred as “Australo-Melanesians”) reached Australia around 60000 BP while the second wave (often referred as “Mongoloids”) is correlated to a demic diffusion of the Neolithic from a Southeast China homeland which started around mid-Holocene. ... Our results also bring very interesting perspectives concerning the detection of the signature of a possible Denisovan admixture in the phenotype of modern human populations. Indeed, past and recent modern human groups which are hypothetically sharing Denisovan ancestry have closer phenetic affinities with each other than with other populations.

Podium Presentation: Session 9, Sa (14:20) A fine scale survey of the worldwide similarity between humans and archaic hominids and its implication on the proposed admixture scenario 

Since the publications of Green et al. 2010 and Reich et al. 2010, several investigations have followed suit addressing the question regarding anatomically modern human and archaic hominin admixture. The genetic analyses of the Neanderthal draft genome and the Denisova genome concluded that these archaic hominins made a 1-4% contribution to non-African populations and 4-6% contribution to Melanesian populations, respectively. The argument of whether the observed genetic similarity is consistent with admixture or ancient substructure is still under debate. While observations have been consistent with an admixture scenario of Neanderthals and the ancestors of non-Africans coming into contact 50 – 80 kya in the Middle East, the lack of power in these experiments falter in providing reliable results. Here we look at the relationship between AMH and these archaic hominins on a fine-scale level by using several methods (including revised D-statistic) on the Neanderthal draft genome, Denisova high-coverage genome, and a collection of published and unpublished genotype and sequence data. We use our findings to clarify the proposed admixture scenario as well as discuss new findings in newly analyzed comparisons of African, South Asian and American populations with archaic hominins, Neanderthal and Denisova. Our results shed light on understanding the observed genetic similarity within and between humans (African and non-African) and archaic hominins, particularly in relevance to the admixture versus ancient substructure scenarios. 

How ‘modern’ are the earliest Homo sapiens? 

Previous research (reviewed in Trinkaus, 2005) has suggested that the African and western Asian contemporaries of Neandertals, generally considered to be the earliest Homo sapiens, are not particularly ‘modern’ looking in their cranial anatomy. Here we test whether the dental morphological ‘signal’ agrees with this assessment. We examined and recorded dental morphological variation in the earliest H. sapiens and asked: how ‘modern’ are they dentally? We used a Bayesian statistical approach to classifying individuals into two possible groups based on dental non-metric traits. e classification was based on dental trait frequencies and sample sizes for two ’known’ samples of 120 Neandertals and 106 Upper Paleolithic H. sapiens individuals. A cross- validation test of these individuals resulted in a correct classification rate of 95%, which is even better than the results of a previous study using the same method based on fewer individuals (Bailey et al 2009). Our early H. sapiens sample included 41 individuals from Southern Africa (Die Kelders, Klasies River Mouth and Equus Cave), Northern Africa (Temara, El Harhoura, Dar es Soltan) and the Levant (Qafzeh, Skhul). We treated our early H. sapiens individuals as ‘unknown’ and calculated the probability that each belonged to either the Upper Paleolithic or Neandertal sample. While understanding that technically these individuals did not belong to either group, we hypothesized that if the earliest H. sapiens were already dentally modern then, when forced into a group, they should fall into the Upper Paleolithic H. sapiens group. We also hypothesized that if there had been significant admixture in the Levant during the initial dispersal out of Africa - as has been sometimes proposed based on paleontological - and more recently on genetic - evidence (Green et al 2010) that these samples would have the largest proportion of individuals classified as Neandertal. Our results indicated that this was not the case. While a surprising number (27%) of early H. sapiens did classify as Neandertal, the smallest proportion of these came from the Levant (7% - one out of 14 individuals). The African sample was more of a ‘mixed bag’. None of the individuals from Die Kelders or Klaises River Mouth classified as Neandertal, while four out of five of the individuals from Equus Cave did. Moreover, 6 out of 13 (46%) of the Northern African individuals were classified as Neandertal. An inspection of the individual specimens that classified as Neandertals revealed that in most cases it is the predominance of primitive features, rather than derived Neandertal traits, that is driving the classification. We conclude (1) by the time the earliest H. sapiens dispersed from Africa they had already attained a more-or-less ‘modern’ dental pattern; (2) in the past, as is the case today, Late Pleistocene Africans were not a homogeneous group, some retained primitive dental traits in higher proportions than others. Furthermore, we acknowledge that while our method is an excellent tool for discriminating between Upper Paleolithic H. sapiens and Neandertals, it may not be appropriate for testing Neandertal – H. sapiens admixture because all traits (primitive and derived) are weighed equally. 

The potential for catastrophic impact of the Campanian Ignimbrite (CI) tephra on human evolution: new data from the Lower Danube loess steppe:

Here we investigate an unexpectedly thick CI tephra deposit at Urluia in the southeast Romanian loess steppe, 1200 km from the super-eruption vent in Italy. Existing models suggest that the CI tephra thickness might reach a maximum 5-10 cm in Eastern Europe; the Urluia ash deposit is up to 100 cm thick. Additional, recently discovered Lower Danube sites also reveal substantially thicker than modelled CI ash beds. 

Radiocarbon dating the extinction of European Neanderthals

The transitional industries and their makers:

The demonstration of modern settlements pre-dating the earliest Aurignacian in Europe has important implications (Hublin 2012). It is consistent with a patchy pattern of modern colonization, with some significant chronological overlap between Neandertals and modern humans on a continental scale. In this model innovations observed in the Neandertal world around or after 50 ka cal BP may have resulted from cultural diffusion triggered by these influxes of populations into western Eurasia.

The Upper Paleolithic of the Ikh Tulberin Gol (Northern Mongolia): new excavations at the Tolbor 16 open-air site:

Numerous questions remain regarding the timing and the context of Upper Paleolithic emergence in Northeast Asia. Available data allow the recognition of a form of Initial Upper Paleolithic (IUP) (Brantingham et al, 2001) documented in the Altai circa 45-40 ka uncal BP (Goebel et al., 1993, Derevianko et al, 2000, Zwyns et al., 2012), in the Cis- and Transbaikal around 40 ka uncal BP (Lbova, 2008) ...

New data on the radiocarbon chronology of the Stretleskayan at Kostenki (Voronezh, Central Russia) :

It concerns cultural layer III at Kostenki 12 and cultural layer V at Kostenki I, respectively previously dated 36,280±360 and 34,900 ±350 BP in Groningen (Damblon et al., 1996). ... Remaining material of the charcoal sample from cultural layer III at Kostenki 12, previously dated 36,280 ±250 BP, was also submitted for dating to Oxford with ABOx-SC pretreatment. the results show that the two Groningen dates and the three Oxford dates are in good agreement and fit within a time interval of 1 millennium, but provide ages several millennia older than the ages obtained previously. Taking into account this new chronology, the appearance of the Stretleskayan at Kostenki will be compared with the chronological background of the Early Aurignacian, Szeletian and Bohunician occurrences in the MiddleDanube sequence, also based on ABA and ABOx-SC cross-dating (Haesaerts et al., 2013). 

Two Waves of Paleolithic Settlers Migrations to North West Beringia in Pleistocene End (End of Karginsky Interstadial) :

Way of 1st wave is marked by sites Afontova Gora V, Ust-Kova on Angara, than along Lena river up to Central Ykut plain, turn Aldan (Ikhine I etc), than round Kolyma plain to Chukotka, where they left abt 30 Ka Orlovka II site in North of West and Kymyneykey site in North of East Chukotka. In Aldan basin migration slowly down. Its reason could be glaciation of Verkhoyansk and Chersky ranges. During this delay “technical re-equipment” happened of migrations. Orlovka II and Kymyney artefacts are clear Aldan. 2nd wave migration was abt 29-28 Ka during final karginsky (middle: würm, wisconsin) warming, when paleoclimate along all northern outskirts of Asia was like to recent or more warm (Drozdov and Laukhin, 2010). Migrants of 2nd wave went to Yana mouth and left here site. Artifacts of this site don’t have Aldanian traditions, but are very close to Yeniseisk. There were little of favorable niches to North of South Mountain Belt; and their demographic capacity were nor big. 

Modern human dispersal into Eurasia: Preliminary results of the multi-disciplinary project on the replacement of Neanderthals by modern humans (RNMH)

Both the chronometric dating and the geographic distribution of archaeological entities indicate that modern human populations equipped themselves with blade products based on the Levallois method, a technology that emerged in North Africa (Taramsan) around 60 ka and then dispersed into the Eastern Mediterranean Levant (Emiran) between 49 and 48 ka. Blade technology further expanded into Eastern and Central Europe (Bachokirian and Bohunician) between 48 and 45 ka and into Southern Siberia (Kara-Bom horizons 6 and 5) at around 47 ka. The rapid expansion of modern humans into Western and Eastern Eurasia followed by the demise of archaic populations in these regions may imply technological and cognitive advantages of modern humans.