"Eight thousand years of natural selection in Europe" preprint - updated with Anatolian Neolithic and other data

Eight thousand years of natural selection in Europe

The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height. [. . .]

Our sample of 26 Anatolian Neolithic individuals represents the first genome-wide ancient DNA data from the eastern Mediterranean. Our success at analyzing such a large number of samples is likely due to the fact that at the Barcin site–the source of 21 of the working samples–we sampled from the cochlea of the petrous bone 9 , which has been shown to increase the amount of DNA obtained by up to two orders of magnitude relative to teeth (the next-most-promising tissue) 3 . Principal component (PCA) and ADMIXTURE 10 analysis, shows that the Anatolian Neolithic samples do not resemble any present-day Near Eastern populations but are shifted towards Europe, clustering with Neolithic European farmers (EEF) from Germany, Hungary, and Spain 7 (Fig. 1b, Extended Data Fig. 2). Further evidence that the Anatolian Neolithic and EEF were related comes from the high frequency (47%; n=15) of Y-chromosome haplogroup G2a typical of ancient EEF samples 7 (Supplementary Data Table 1), and the low F ST (0.005-0.016) between Neolithic Anatolians and EEF (Supplementary Data Table 2). These results support the hypothesis 7 of a common ancestral population of EEF prior to their dispersal along distinct inland/central European and coastal/Mediterranean routes. The EEF are slightly more shifted to Europe in the PCA than are the Anatolian Neolithic (Fig. 1b) and have significantly more admixture from Western hunter-gatherers (WHG), shown by f 4 -statistics (|Z|>6 standard errors from 0) and negative f 3 -statistics (|Z|>4) 11 (Extended Data Table 3). We estimate that the EEF have 7- 11% more WHG admixture than their Anatolian relatives (Extended Data Fig. 2, Supplementary Information section 2).

On the presence of the "East Asian" EDAR variant in Scandinavian hunter-gatherers:

We find a surprise in six Scandinavian hunter-gatherers (SHG) from the Motala site in southern Sweden. In three out of six samples, we observe the haplotype carrying the derived allele of rs3827760 in the EDAR gene (Extended Data Fig. 5), which affects tooth morphology and hair thickness and has been the subject of a selective sweep in East Asia 24 , and today is at high frequency in East Asians and Native Americans. The EDAR derived allele is largely absent in present-day Europe except in Scandinavia, plausibly due to Siberian movements into the region millennia after the date of the Motala samples. The SHG have no evidence of East Asian ancestry 4,7 , suggesting that the EDAR derived allele may not have originated not in East Asians as previously suggested 24 . A second surprise is that, unlike closely related western hunter-gatherers, the Motala samples have predominantly derived pigmentation alleles at SLC45A2 and SLC24A5.

Polygenic selection on height in Europe:

We also tested for selection on complex traits. The best-documented example of this process in humans is height, for which the differences between Northern and Southern Europe have driven by selection 25 . To test for this signal in our data, we used a statistic that tests whether trait-affecting alleles are both highly correlated and more differentiated, compared to randomly sampled alleles 26 . We predicted genetic heights for each population and applied the test to all populations together, as well as to pairs of populations (Fig. 4). Using 180 height-associated SNPs 27 (restricted to 169 where we successfully targeted at least two chromosomes in each population), we detect a significant signal of directional selection on height (p=0.002). Applying this to pairs of populations allows us to detect two independent signals. First, the Iberian Neolithic and Chalcolithic samples show selection for reduced height relative to both the Anatolian Neolithic (p=0.042) and the Central European Early and Middle Neolithic (p=0.003). Second, we detect a signal for increased height in the steppe populations (p=0.030 relative to the Central European Early and Middle Neolithic). These results suggest that the modern South-North gradient in height across Europe is due to both increased steppe ancestry in northern populations, and selection for decreased height in Early Neolithic migrants to southern Europe. We do not observe any other significant signals of polygenetic selection in five other complex traits we tested: body mass index 28 (p=0.20), waist-to-hip ratio 29 (p=0.51), type 2 diabetes 30 (p=0.37), inflammatory bowel disease 21 (p=0.17) and lipid levels 16 (p=0.50).

Linguistics, Archaeology & Genetics conference abstracts

This conference, aimed at "integrating new evidence for the origin and spread of the Indo-European languages", will take place next week. Some abstracts (pdf):

Close genetic relationship of Neolithic Anatolians to early European farmers

Iosif Lazaridis 1,2 , Songül Alpaslan 3 , Daniel Fernandes 4 , Mario Nowak 4 , Kendra Sirak 4 , Nadin Rohland 1,2 , Swapan Mallick 1,2,5 , Kristin Stewardson 1,5 , Fokke Gerritsen 6 , Nick Patterson 2 , Ron Pinhasi 4, *, David Reich 1,2,5, *

We study 1.2 million genome-wide single nucleotide polymorphisms on a sample of 26 Neolithic individuals (~6,300 years BCE) from northwestern Anatolia. Our analysis reveals a homogeneous population that was genetically similar to early farmers from Europe (F ST =0.004±0.0003 and frequency of 60% of Y-chromosome haplogroup G2a). We model Early Neolithic farmers from central Europe and Iberia as a genetic mixture of ~90% Anatolians and ~10% European hunter-gatherers, suggesting little influence by Mesolithic Europeans prior to the dispersal of European farmers into the interior of the continent. Neolithic Anatolians differ from all present-day populations of western Asia, suggesting genetic changes have occurred in parts of this region since the Neolithic period. We suggest that the language spoken by the homogeneous Anatolian-European Neolithic farmers is unlikely to have been the same as that spoken by the Yamnaya steppe pastoralists whose ancestry was derived from eastern Europe and a different population from the Caucasus/Near East [Haak et al. 2015], and discuss implications for alternative models of Indo-European dispersals.

The Genetic History and Structure of Britain

Nick Patterson, Broad Institute, Boston and David Reich, Harvard Medical School and Broad Institute, Boston

The recently published paper on the genetic structure of Britain (Leslie et al. Nature 2015) has shown subtle genetic variation correlating with geography. Here we reexamine the evidence in the light of our understanding of the genetics of Ancient Europe and comment on some implications for how Indo-Europeans spread into Europe.

In search for initial Indo-European gene pool from genome-wide data on IE popula- tions as compared with their non-IE neighbors

Oleg Balanovsky, Vavilow Institue of General Genetics, Russian Academy of Sci- ences, Moscow

From Yamnaya to Bell Beakers: Mechanisms of Transmission in an Interconnected Europe, 3500–2000 BC

Volker Heyd, Universtiy Bristol, Bistol and University of Helsinki, Helsinki

Yamnaya Peoples in the East and Bell Beakers Users in the West are rightly seen as the apogees in a long-term process of individualisation, gender differentiation, warrior display and internationalisation/unification that fundamentally change the face of the European Continent from the mid fourth and throughout the third millennium BC. We can only approach the reasons why prehistoric peoples and cultures from regions across Europe, which were no more than marginally in touch before, join in the same emblematic pottery, new drinking habits, similar burial customs, anthropomorphic stelae, ostentatious display of weapons and other paraphernalia, and thus common values. However rather than seeing this development as an internal European progress I want to point to the importance of the Pontic-Caspian steppes, and a 2000 years lasting interaction scenario of infiltrating Suvorovo-Novodanilovka, Nizhnemikhailovka-Kvityana and Yamnaya peoples and populations with their more sedentary contemporaries in southeast Europe, the Carpathian basin and northeast of the Carpathian bow. A crucial part of this interaction –besides migrations and the exchange of genes and goods as recently highlighted in several publications not only in Nature and Science– is the forwarding of innovations in the sphere of subsistence economy. We see this archaeologically in a further importance of animal husbandry, with larger herds, specialised breeding and new forms of herding management in particular for cattle. This obviously sets in motion a substantial shift in general mobility patterns and of communication networks.

It is easily conceivable that this interaction must also have had a profound impact on the whole settlement organisation and people’s way-of-life, in consequence probably fundamentally affecting the basics of societies and thus challenging the whole system of ideas, imaginations, morale, symbols and terms – a new world-view and ultimately the base for a new language.

Pre-Indo-European speech carrying a Neolithic signature emanating from the Aegean

Guus Kroonen, Institute for Nordic Studies and Linguistics, Copenhagen University, Copenhagen

When different Indo-European speaking groups settled Europe, they did not arrive in terra nullius. Both from the perspective of the Anatolian hypothesis 1,2,3 and the Steppe hypothesis, 4,5,6 the carriers of Indo-European speech likely encountered existing populations that spoke dissimilar, unrelated languages. Relatively little is known about the Pre-Indo-European linguistic landscape of Europe, as the Indo-Europeanization of the continent caused a largely unrecorded, massive linguistic extinction event. However, when the different Indo-European groups entered Europe, they incorporated lexical material from Europe’s original languages into their own vocabularies. 7 By integrating these “natural samples” of Pre-Indo-European speech, the original European linguistic and cultural landscape can partly be reconstructed and matched against the Anatolia and the Steppe hypotheses. My results reveal that Pre-Indo-European speech contains a clear Neolithic signature emanating from the Aegean, 8 and thus patterns with the prehistoric migration of Europe’s first farming populations. 9,10,11 These results also imply that Indo-European speech came to Europe following a later migration wave, and therefore favor the Steppe Hypothesis as a likely scenario for the spread of the Proto-Indo-Europeans. 12

Collective violence in Early Neolithic Central Europe

The massacre mass grave of Schöneck-Kilianstädten reveals new insights into collective violence in Early Neolithic Central Europe

With the recently examined LBK mass grave site of Schöneck-Kilianstädten, Germany, we present new conclusive and indisputable evidence for another massacre, adding new data to the discussion of LBK violence patterns. At least 26 individuals were violently killed by blunt force and arrow injuries before being deposited in a commingled mass grave. Although the absence and possible abduction of younger females has been suggested for other sites previously, a new violence-related pattern was identified here: the intentional and systematic breaking of lower limbs. The abundance of the identified perimortem fractures clearly indicates torture and/or mutilation of the victims. The new evidence presented here for unequivocal lethal violence on a large scale is put into perspective for the Early Neolithic of Central Europe and, in conjunction with previous results, indicates that massacres of entire communities were not isolated occurrences but rather were frequent features of the last phases of the LBK.

Ancient mass grave reveals evidence of brutal massacre among Europe's prehistoric farmers

Archaeologists who painstakingly examined the bones of some 26 men, women and children buried in the Stone Age grave site at Schoeneck-Kilianstaedten, near Frankfurt, say they found blunt force marks to the head, arrow wounds and deliberate efforts to smash at least half of the victims' shins — either to stop them from running away or as a grim message to survivors. [. . .]

"What is particularly interesting is the level of violence. Not just the suppression of a rival community — if that is what it was — but the egregious and systematic breaking of the lower legs," said Scarre. "It suggests the use of terror tactics as part of this inter-community violence." [. . .]

"The LBK population had expanded considerably, and this increases the potential for conflict," said Meyer. "Also, the LBK were farmers, they settled. So unlike hunter gatherers, who could move away to avoid conflict, these people couldn't just escape. Add to this the fact that there may have been a period of drought that constrained resources, causing conflicts to erupt."

Meyer said the theory of conflict between different groups within the LBK is supported by the existence of an apparent ancient border near the Schoeneck-Kilianstaedten site. Archaeologists have found that flint was traded on either side of the divide but not necessarily across it — suggesting the two groups did not see each other as kin, he said.

The attackers, however, spared some members of the group, with victims skewed toward young children, adult men and older women.

"It's likely that the young women, who are missing in the grave, were kidnapped by the attackers," said Meyer.

Related:

• "Ancestral men probably competed for mates mainly by excluding competitors by force or threat"
• Sewall Wright on race differences, group selection, and cultural selection among humans (1978)
• More from Hamilton on kin recognition and intergroup hostility

  With pleasure in cruelty as the motivation to punishment,62 and with cruelty to create terror, an individualistic argument sounds less plausible; but considering inclusive fitness, or group selection (which may be a really appropriate term for many human situations), there is no theoretical difficulty. For example, a priori, terror seems as good a weapon as false promises in bringing about the early submission or removal of a threatened tribe.

The ancestry and affiliations of Kennewick Man

Kennewick Man ancient DNA. The paper is openly accessible. Results pretty much as I expected.

We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide.

The paper is marred by strained, politically-motivated attempts to tie Kennewick Man specifically to "the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man". So those interested in aboriginal American population structure are probably better off ignoring much of the authors's narrative and looking directly at the data.

Out of Eurasia

From Chris Stringer's most recent book ("The Origin of Our Species"):

And the evidence from Dmanisi is now being added to this rethink, since the lack of very ancient fossil human evidence from Asia, apart from Dmanisi, is considered by archaeologists like Robin Dennell and Wil Roebroeks to reflect a lack of preservation and discovery, rather than a real absence. Combining the primitiveness of the Dmanisi specimens and tools with a similar view of the Liang Bua finds, it is argued that there was a widespread phase of human evolution in Eurasia about 2 million years ago, which is now only represented by the isolated Dmanisi and "Hobbit" fossils. This alternative scenario has a small-brained and small-bodied pre-erectus species, perhaps comparable to Homo habilis or even a late australopithecine, dispersing from Africa with primitive tools over 2 million years ago, reaching the Far East and, eventually, Flores. In Asia, this ancestral species then gave rise to the Dmanisi people and Homo erectus, while Dmanisi-like people reentered Africa about 1.8 million years ago, and evolved into later populations there -- including, eventually, Homo sapiens. So the orthodoxy of Out of Africa 1 is being challenged because of new evidence, and new interpretations of old evidence.

Ötzi's Y-DNA haplogroup: G2a4

A few days ago a commenter at Dienekes' posted that this information had been revealed by "Dr. Eduard Egarter-Vigl, Head of Conservation and Assistant to research projects of the Archaeological Museum in Bozen [. . .] in a documentary [Ötzi, ein Archäologie-Krimi] broadcast by 3sat on 10th august 2011." Now someone has uploaded the relevant clip:

Subtitles: "Since six months, the full decoding of the genome of the Iceman is done. [. . .] Certain genes that are relevant to the origin, Y-chromosome, for example, can be examined well. [. . .] And the haplogroup to which the Iceman belonged is the haplogroup G2a4. [. . .] And this group is known, that it is now very rare in Europe. Interestingly, it is still in Sardinia. Sardinia is as an island a so-called micro-isolate where the poulation has hardly changed and so has developed genetically fairly constant. But there is this haplogroup in Eurasian regions, ie those from which we know that Europe was actually populated."

Sample size equals one, but the presence of G2a and absence of R1b is consistent with previous ancient DNA findings for Neolithic western and central Europe.

Neolithic Y DNA from Southwestern France

A post by Dienekes brings to my attention a paper in PNAS, "Ancient DNA reveals male diffusion through the Neolithic Mediterranean route":

The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition.

Note: contra the authors' assertion, lactase persistence was probably not carried by Neolithic central Europeans; the most common European LP-associated allele has been absent in all central European Neolithic samples tested to date.

Dienekes writes:

R-M269 which, because of its apparent young Y-STR age has been tied by some to either the Mediterranean or Central European Neolithic is conspicuous absently from both at the moment. It may yet surface in a Neolithic context, but its absence this late from a region where, today, it is abundant only adds to its mystery.

In fact, the amateur estimates using actual mutation rates put the spread of R1b into Western Europe clearly post-Neolithic.

R1b and LP in Western Europe are in all likelihood associated with the dispersal of Indo-European languages.

These findings add to ancient DNA evidence indicating large-scale post-Neolithic population replacement in Europe. Coon and other traditional physical anthropologists, it turns out, probably had a better handle on European prehistory 70 years ago than population geneticists did five years ago.

Craniometric data support a mosaic model of demic and cultural Neolithic diffusion to outlying regions of Europe

Full text is free:

The extent to which the transition to agriculture in Europe was the result of biological (demic) diffusion from the Near East or the adoption of farming practices by indigenous hunter–gatherers is subject to continuing debate. Thus far, archaeological study and the analysis of modern and ancient European DNA have yielded inconclusive results regarding these hypotheses. Here we test these ideas using an extensive craniometric dataset representing 30 hunter–gatherer and farming populations. Pairwise population craniometric distance was compared with temporally controlled geographical models representing evolutionary hypotheses of biological and cultural transmission. The results show that, following the physical dispersal of Near Eastern/Anatolian farmers into central Europe, two biological lineages were established with limited gene flow between them. Farming communities spread across Europe, while hunter–gatherer communities located in outlying geographical regions adopted some cultural elements from the farmers. Therefore, the transition to farming in Europe did not involve the complete replacement of indigenous hunter–gatherer populations despite significant gene flow from the Southwest Asia. This study suggests that a mosaic process of dispersal of farmers and their ideas was operating in outlying regions of Europe, thereby reconciling previously conflicting results obtained from genetic and archaeological studies.

Jean M comments:

Their results are remarkably neat, showing two clearly distinct lineages, with comparatively little inter-mixture, confirming the picture from the archaeology of the LBK, for example, which seems to indicate that farmers and foragers kept to their own zones.

This helps to explain why the presumed Neolithic Y-DNA haplogroups G, E and J do not dominate Europe today, and decline in frequency the further one moves from the Mediterranean. The farming pioneers in Europe, though initially successful, eventually encountered problems which led to population crashes. Then after the Neolithic, Europe had two great bursts of migration, both from fringe regions where farming had been adopted by foragers. One came from the European steppe in the Copper and Bronze Ages. The other was the spread of their Germanic and Slavic descendants in the Migration Period.

Victor Mair talk on Tarim Basin Mummies

Part of a series of lectures related to the "Secrets of the Silk Road" exhibition at the University of Pennsylvania Museum of Archaeology and Anthropology. The mummy and artifacts abruptly pulled from the exhibition by the Chinese government before it opened are back for now.

Norwegian foundation plans ancient DNA analysis of Rollo descendants

The Explico Historical Research Foundation:

will attempt to find out if Rollo the Viking [male line ancestor of William the Conqueror] was Danish or Norwegian to settle a dispute that has been going on for centuries in Scandinavia. This we will do by retrieving DNA from corpses of his descendants.

They say they "hope to be able to perform our analysis by Easter 2011." The foundation's other projects include searching for remnants of the Celts in Turkey and Goths north of the Black Sea. More:

- Successfully conducted research on the Easter Island, proving South American origin for parts of the Easter Island population through genomic HLA typing. This research indicates strongly that some of the original Easter Island inhabitants some how migrated to the island from the east, from South America, and not only from Polynesia in the west, which has been the official story of Easter Island immigration. The research report by professor Erik Thorsby can be read here.

- On the Canary Islands contributed to the understanding of how the Canary Islands were originally settled and by whom (Pereira et al: Population expansion in the North African Late Pleistoscene signalled by mitochondrial DNA haplogroup U6. BMC Evolutionary Biology 2010 10:390). Also, DNA from a Royal Native lineage on the Canary Island La Gomera proves a connection most likely with the Basque, North Portugal or a British 'Celtic' connection.

- In Normandy, in our search for famous historical figures, closed in the lead on the patriach of William the Conqueror, the great Viking giant Rollo, in order to solve a close to thousand year old riddle about his origin. To be continued..

- In the Ukraine on Crimea and the Black Sea coast of Azov our successful 2006 expedition work is now continued in the labs, hopefully providing us with new vital knowledge on the ancient Greeks, who they were and whom today are most closely related to them.

- In the Caribbean we have worked hard on finding the DNA and especially the Y-chromosome lineage of Christopher Columbus' heritage. This work now seems to have paid off, giving us the opportunity to make new revelations about one of the worlds greatest explorers.

- Established good contact and made all preparations ready for field work in Northern Africa. We are awaiting the neccesary permissions to continue our scientific work in the Atlas Mountains.

- Continued our work in the different fields of expertise involving new technologies and our constant search for new discoveries. We are currently involved in projects in the Caribbean, the Ukraine, in Peru, Russia, Spain, France, Turkey, on Greenland and in Scandinavia. The new technologies we continue to make use of are foremost DNA and the mapping of Human Migrations and Georadar instruments for discovering treasures underground.

(Via the GENEALOGY-DNA list.)

The Denisova hominin need not be an out of Africa story

I had a similar reaction when the original article was published, but this piece in the Journal of Human Evolution makes a much more extensive and better-argued case:

The recent retrieval of a complete mitochondrial (mt) DNA sequence from a 48–30 ka human bone from Denisova (Siberia) (Krause et al., 2010) is a remarkable achievement fully deserving international acclaim. Without wishing to detract from this feat, however, we wish to challenge their conclusion that the Denisova hominin “derives from a hominin migration out of Africa [ca. 1.0 Ma] distinct from that of the ancestors of Neanderthals and of modern humans” (Krause et al., 2010: 894). In addition, we challenge their assumption that the ancestors of the Neanderthals left Africa between 500–300 ka. In our view, alternative interpretations of the evidence are available and should be considered.

Longer excerpts below:

CF mutant heterozygote advantage in heavy metal exposure

Teeth and leg bones from Iron Age people are showing a 21st century scientific-research team that there might be an evolutionary silver lining to the gene defects that cause cystic fibrosis (CF)

DNA analysis of ancient archeological finds is revealing that some CF gene defects may protect those who carry them from lead and other metal poisoning, or perhaps tuberculosis. [. . .]

Since the protective CF gene mutation is so common among people living in or coming originally from central and Western Europe, Farrell suspects that the mutation first arose in that part of the world, very likely in early Celtic populations. [. . .]

To understand what in the environment could cause the mutated CF gene to occur in the first place, Farrell turned to ancient burial remains. Evidence from his earlier studies already showed that transgenic mice carrying the gene might be resistant to lead toxicity. He wanted to see if there were links to people living in Europe during the Iron and Bronze Ages.

“This was an era in which people were exposed to toxic heavy metals for the first time in history,” he says. [. . .]

The first analyses are showing that specimens containing CF gene defects were not affected by lead or other metal poisoning, hinting at the mutation’s protective advantage. The specimens also contained very little tuberculosis. The scientists can’t pinpoint exactly where the first CF carrier may have lived, but they think current day Austria is a good candidate.

Via Jean M. The manuscript is freely available at Nature Precedings: Discovery of the Principal Cystic Fibrosis Mutation (F508del) in Ancient DNA from Iron Age Europeans

Middle-eastern milk drinkers?

A Der Spiegel article makes a case for the role of mass migration in shaping the European gene pool, while failing to mention the evidence for large-scale post-Neolithic population replacement. Jean M is unclear on whether the attempt to link lactase persistence to the LBK rests on unpublished aDNA results or questionable computer models. Greg Cochran on the latter eventuality:

Judging from the comment about lactose tolerance in Austria/Slovakia/Hungary, they may be relying on a paper that came out of Mark Thomas's lab last year: "The Origins of Lactase Persistence in Europe".
The authors of that paper tried to estimate the region of origin using simulations - but one of the inputs was the current distribution of that allele. Which is reasonable, except that they did not use the actual distribution of that allele, but rather a truncated distribution - their map is centered on central Europe and stops halfway through the Ukraine. That ensured that they would find an origin in somewhere in middleuropa.

The allele doesn't stop there, though: it has a second region of fairly high frequency in northern India. Before Mongols and Turks took over the Eurasian steppe, the frequency of that allele may have been high in those steppe regions. Scythians are described as milk-drinkers quite a while ago - in the Iliad. And my sources claim that the royal guard of the Hittites also 'drank sweet milk'...

Checking out ancient DNA from Kurgan burials in that region might clarify this.

I think it is difficult to imagine a historical process that moves a lot of people from Bavaria to the Punjab: it is easier to imagine one that expands to both regions from somewhere in-between.
Which would explain the distribution of the Indo-European languages, also.

When you think about it, it may not be easy for German researchers to talk about this hypothesis. I think they have trouble saying "Aryan" nowadays.

John Hawks agrees:

Problem is: from the standpoint of ancient DNA samples, the lactase persistence mutation was also absent within the early Neolithic! The article is full of details that are wrong or misleading. [. . .]

The [mtDNA] differences between early Neolithic and later Europeans suggests that post-Neolithic migrations -- real Völkerwandurung -- actually had a major impact on the European gene pool. What we see today is not a pattern established 6000 years ago, but a palimpsest richly painted with strokes from successive migrations.

One aspect of this scenario: There's no reason to link the early Neolithic with Indo-European languages. There were many later widespread population movements that might have carried this language family, and we know that these later movements were genetically decisive -- at least, as concerns the maternal genealogy. The relation of Y chromosome haplogroups with mtDNA haplogroups is a critical question, but even more necessary is the development of an effective means of testing these hypotheses with nuclear genotype data.

The horse, the wheel, and language

It appears someone took the liberty of uploading David Anthony's book on Indo-European origins to scribd. Read and discuss if you wish.

Ptolemy map of ancient Germania deciphered

Berlin Researchers Crack the Ptolemy Code

All this offers up rather exciting prospects, since it makes half the cities in Germany suddenly 1,000 years older than previously believed. "Our atlas is a treasure map," team member Andreas Kleineberg says proudly, "and the coordinates lead to lost places in our past."

Archaeological interest in the map will likely be correspondingly large. Archaeologists' opinions on the Germanic tribes have varied over the years. In the 19th century, Germany's early inhabitants were considered brave, wild-bearded savages. The Nazis then transformed them into great heroes, and in the process of coming to terms with its Nazi past, postwar Germany quickly demoted the early Germanic peoples to proto-fascist hicks. [. . .] More recent research proves this view to be complete invention.

Stone Age Atlantis (2010)

A National Geographic documentary (watch online) on Doggerland, which I haven't watched yet.

Two old papers on Tarim Basin mummies / crania

Now available online at the Sino-Platonic Papers website.

Dolkun Kamberi, "The Three Thousand Year Old Charchan Man" Sino-Platonic Papers, 44 (January, 1994)

The male would have been two meters tall when living (see color plates I and IIa); the corpse was lying on its right side with legs bent and propped up by a small piece of wood (perhaps to promote preservation by means of circulation of air around the corpse). The hair, eyelashes, beard and chest hair were intact and traces of makeup (ocher spiral sun-symbols) could be seen on the face. The presence in the tomb of two small bone spoons with dried ocher pigment in them may indicate that the makeup was applied after death. The male's head hair was yellowish brown half gone to white;

Note: More recent estimates put Cherchen Man's height closer to 5'9".

HAN Kangxin: "The Study of Ancient Human Skeletons from Xinjiang, China" Sino-Platonic Papers, 5 1 (November, 1994)

Between 1920 and 1940, only three foreign scientists published completed research in this area. They are: Arthur Keith of England (1929), Carl-Herman Hjortsjo and Ander Walander of Germany (1924) and A.N. Iuzefovich of the USSR (1949). A total of twenty skulls were described. Five came from the northern part of the Taklamakan Desert and Keith thought they characterized the "Loulan racial type." Eleven skulls were collected by Sven Hedin from near Luobubo (Lopnor) in 1928 and 1934, and have been subdivided into three groups (Nordic, Chinese, and Alpine) by Hjortsjo and Walander. The remaining skulls also came from the Luobubo (Lopnor) area and exhibit Mongoloid characteristics. Iuzefovich considered these to be of Tujue (Turkish) origin (Keith, A., 1929; Hjortsjo, C.H. and A. Walander, 1942; Iusefovich, A.N., 1949). [. . .]

Chinese scientists have conducted systematic excavations in this region since 1940. I have studied all the skeletal material housed at the Institute of Archeology of Xinjiang and analyzed the physical and racial characteristics of these human bones. The materials included about 274 skulls which were collected from nine ancient cemeteries in Xinjiang. The cemeteries range in age from about 1800 B.C.E. to 300 C.E.

Ancient French megalithic mtDNA

Sample size is three:

We reproducibly retrieved partial HVR-I sequences (nps 16,165 to 16,390) from three human remains (Prisse´ 1, 2, and 4, Table 1), one adult and two children deposited during different stages of use of the burial chamber. Corresponding sequences could be unambiguously assigned to haplogroups X2, U5b, and N1a

Marie-France Deguilloux et al. News from the west: Ancient DNA from a French megalithic burial chamber. American Journal of Physical Anthropology DOI: 10.1002/ajpa.21376.

Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that in the Neolithic period the mtDNA haplogroup N1a, previously only known in central Europe, was as widely distributed as western France. Alternative scenarios are discussed in seeking to explain this result, including Mesolithic ancestry, Neolithic demic diffusion, and long-distance matrimonial exchanges. In light of the limited Neolithic ancient DNA (aDNA) data currently available, we observe that all three scenarios appear equally consistent with paleogenetic and archaeological data. In consequence, we advocate caution in interpreting aDNA in the context of the Neolithic transition in Europe. Nevertheless, our results strengthen conclusions demonstrating genetic discontinuity between modern and ancient Europeans whether through migration, demographic or selection processes, or social practices.

On the origins of the alphabet

Brian R. Pellar. On the Origins of the Alphabet. Sino-Platonic Papers, 196. December 2009. (pdf):

In addition, Petrie’s pre-Egypt theory of the early development of the alphabet needs to be taken more seriously. Based on the discovery that the small alphabet loop is also seen in Mesopotamia, and on the proto-writing glyphs being found in Tartaria, Karanovo, and China (such as found in Dawenkou,8 Shandong Province, and in Jiahu, Henan Province), it appears that there might have already existed a culture/tradition of proto-alphabetic signs based on theo-astronomical observations/rituals that not only pre-dated Egypt, Sumeria, and China, but that also had its roots in Northern Europe. Given Marshak’s findings that Cro-magnon man in Europe appeared to keep track of lunar appearances via vertical scratches/marks on bone (Marshak 1972), it seems that writing was perhaps a natural, southern and then eastern extension/maturation of the observations/notations of the moon and sun moving through the sky via what they perceived to be divine forces. This early and sophisticated dependence on the sky for information seems inevitable, as Krupp noted that the stars and constellations provided “practical services: timekeeping, season marking, calendrics, weather signs, concentrations of supernatural power, and symbolic containment of important cultural data” (Krupp 2000: 58).

Small River Cemetery Number 5

A New York Times article from last month on Ördek's Necropolis:

All the men who were analyzed had a Y chromosome that is now mostly found in Eastern Europe, Central Asia and Siberia, but rarely in China. The mitochondrial DNA, which passes down the female line, consisted of a lineage from Siberia and two that are common in Europe. Since both the Y chromosome and the mitochondrial DNA lineages are ancient, Dr. Zhou and his team conclude the European and Siberian populations probably intermarried before entering the Tarim Basin some 4,000 years ago.

The Small River Cemetery was rediscovered in 1934 by the Swedish archaeologist Folke Bergman and then forgotten for 66 years until relocated through GPS navigation by a Chinese expedition. Archaeologists began excavating it from 2003 to 2005. Their reports have been translated and summarized by Victor H. Mair, a professor of Chinese at the University of Pennsylvania and an expert in the prehistory of the Tarim Basin. [. . .]

Several items in the Small River Cemetery burials resemble artifacts or customs familiar in Europe, Dr. Mair noted. Boat burials were common among the Vikings. String skirts and phallic symbols have been found in Bronze Age burials of Northern Europe.

Folke Bergman's 1939 report, Archaeological Researches in Sinkiang, is available online at the Digital Archive of Toyo Bunko Rare Books, along with expedition records from Sven Hedin, Aurel Stein, and others. Ördek was Sven Hedin's Turkish servant, who after being inspired by what he saw working for Hedin discovered the cemetery on a tomb robbing expedition in search of buried treasure. From Bergman:

STEIN emphasizes the non-Mongolian features of the Lop-nor mummies, and I have been able, on the whole, to confirm his statement. One or two of the mummified heads at Cemetery 5 had, however, broad cheek-bones giving them a "Mongolian" look, but this might be due to the individual variations that occur in every race or type