Tuesday, October 7, 2014

Tracing The Genetic Roots Of Western Europe With Megalithic Ancient DNA


Today, the predominant Y-DNA haplogroup of Western Europe (and a fair amount of Northern Europe), inherited via patrilines, is R1b, and the predominant mtDNA haplogroup in Europe, which is inherited from one's matrilineal ancestor, is H. The question, which turns out to be fairly hard to answer, is when Europe's current population genetics took their current form.

If you know when this happened, then the already well developed archaeological history of Europe can point you to the archaeological culture that appeared when the last major demic migration in history shaped the gene pool of Western Europe.

Western and Northern Europe were depopulated during the Last Glacial Maximum (ca. 20,000 years ago) outside two Western European refuges of hunter-gather people, the Franco-Cantabrian refuge, and Italian Penninsula (there was another refuge in the Caucasus  region).  This was followed by the repopulation of Europe during the Mesolithic era (early Holocene ca. 8,000 BCE), followed by the first wave Neolithic revolution (in most of Western Europe, the megalithic culture ca. 5000-3000 BCE), then the Bell Beaker culture and cultures derived from it (ca. 2900-1200 BCE), and then Celtic and Germanic Indo-European cultures (ca. 1300 BCE) which persisted until the expansion of the Roman Empire as far as Iberia, France and England.

If you know which of these archaeological culture was responsible, you are much further along in answering an even deeper and more primal question:
Who are the deep prehistoric ancestors of Western Europeans who are themselves the ancestors of most European-Americans.
Astonishingly, in the last few years, it has been possible to come up with some pretty solid answers to these questions by comparing the DNA left behalf by members of archaeological cultures are various time depths from many thousands of years ago, and comparing them to contemporary populations.

Once the preliminaries are out of the way, this post will focus on trying to determine if the modern gene pool of Western Europe mostly took shape as part of the Atlantic Megalithic culture, which is an undersampled community of first farmers and first herders in this part of Europe who raised monuments like Stonehenge. This was the most intense demographic event of the last few thousand years in Europe, so it is a natural place to look.

But, it could have happened earlier, with current European population genetics resembling that of the Western European hunters and gathers who roamed Europe before the first farmers arrived, who have made a major autosomal genetic contribution (probably more than a third of autosomal ancestry) to the modern Western European gene pool.[1]

Or, it could have happened later, in the Copper Age and Bronze Age, perhaps, even later, in the wake of Bronze Age collapse and the advent of the Iron Age.

What We Know About Ancient DNA In Various Archaeological Cultures

We know from a variety of ancient DNA sources that Y-DNA I2 and mtDNA U were predominant in much of Europe in the Mesolithic, although it isn't entirely clear that the far Atlantic coast region is fully typical of this trend.[2]

There may be mtDNA V in the Atlantic Mesolithic as well. Today mtDNA V is found among Berbers, the Saami of Finland, coastal Atlantic populations and people in or near Basque Country. There are some indications of mtDNA H and HV in Iberia and/or the Italian refugia in the Mesolithic as well.

 This suggests that this common genetic affinity arose from a dispersal sometime before these populations acquired languages from four different language megafamilies (Uralic, Indo-European, Basque and Afro-Asiatic), although the are competing theories about its origins.[3][4]

But, these linguistic limitations aren't necessarily all that powerful given the likelihood that the Uralic language was adopted by the Saami around 1500 BCE, that Indo-European languages arrived in the coastal Atlantic area ca. 800 BCE, that the Vasconic languages probably arrived in Europe ca. 2900 BCE, and that the time at which the Berber's adopted their language is not well established but could have been as recent as the domestication of the camel (camels were domesticated in Arabia ca. 3000 BCE, but were present in the Levant and in North Africa where Berber languages are spoken only ca. 1000 BCE - 900 BCE).

The high frequency of mtDNA V in the Saami favors a founders effect in this population in the Mesolithic era, but one can't rule out a source, for example, from the including of Finland all of the way up to places north of the Arctic Circle (when a rapid expansion of the Saami population as a result of its adoption of food production technology from the Indo-European Corded Ware Neolithic culture that preceded their adoption of a Uralic language could make it possible for founder effects from the people who integrated Saami hunter-gatherers into their herding and farming communities at the time to greatly influence the post-expansion gene pool. The Saami integration of mtDNA V into its gene pool could have been independent, but roughly contemporaneous with a source of mtDNA V in all of the other locations where it is found, perhaps as a much lower frequency component of the mtDNA mix of an initial Bell Beaker population which had a much larger effective, than the percentage of the founding Neolithic population that merged with the pre-Saami, which might have had a much smaller effective population size size than the Bell Beaker people.

The first wave Neolithic in most of Europe is Y-DNA G2a and a mix of mtDNA types with less mtDNA H than there is now.[2][5] But see [6] (reporting continuity between Neolithic mtDNA from Northeast Spain ca. 3500 BCE and modern Iberian mtDNA, in contrast to the results in LBK samples of [5] from ca. 5500 BCE). First wave Neolithic populations everywhere crashed after a population bubble and there was a significant population rebound at some point after this crash which is a likely source of the post-first wave Neolithic, pre-Iron Age shift in European population genetics.[7]

The only ancient DNA from Bell Beaker, from Central Europe, has the Y-DNA R1b and mtDNA H at high levels that is the typical of Western Europe.[8] But, this is just a single sample at the fringe of the Bell Beaker area.  It is also equally consistent with an Atlantic megalithic or Mesolithic source for Y-DNA R1b in Europe that was present on a continuous basis since those time and into the Bell Beaker era.  Indeed, conventional assumptions based on archaeology about the demic impact of the Bell Beaker people on the places they came to settle would have expected just this kind of continuity.

But, as we will see later in this post, despite the existence of dozens of ancient Y-DNA samples from early Neolithic and Mesolithic individuals in the territory where the Bell Beaker culture or its cultural successors extended, there is not a single instance where a Y-DNA R1b individual has been identified.  Not in European hunter-gatherer populations (where Y-DNA I2 is predominant), not in LBK or Cardial Pottery Neolithic populations including Southern France and Spain  (where Y-DNA G2 is predominant).  A specifically identified ancient mtDNA sample from an Atlantic megalithic site further North in France, likewise has a mix of halogroups much more consistent with other first wave Neolithic sites than with the mix in the Bell Beaker era and at all subsequent times.

Ancient DNA evidence establishes that the predominant source of R1a and mtDNA H in Central and Eastern Europe is almost certainly the Corded Ware culture that followed the collapse of the first wave Neolithic archaeological cultures, such as the Linear Pottery aka LBK culture, and its successors, in the region.[9][10]

Interestingly, there there is great affinity between sea faring, non-Indo-European, Minoan's of Crete who incorporated contests with bulls into their culture and modern Western European populations in both Y-DNA and mtDNA).[11][12] These links and the fact that the Bell Beaker and Minoan civilizations were roughly contemporaneous suggest that they could have a connection, although the material culture connections between the two cultures isn't necessarily all that compelling.

Minoan Crete, in turn, shows stronger ancient DNA genetic ties to Anatolia than to the Balkans (which is the area with more of an affinity for the remainder of Greece).[13] But, this was not always the case. A review of 15 ancient mtDNA samples from 8000 BCE at the dawn of the Fertile Crescent Neolithic favor a migration route of the first wave of farmers from the Fertile Crescent into Europe via Cyprus, Crete and the Aegean rather than Anatolia.[14]

The population genetic impact of Indo-Europeans in Western Europe was probably modest. I estimate that the impact was probably on the order of 5%-15%,

This is based upon taking the Basque population as representative of the Northern Iberian population immediately prior to the arrival of the Indo-Europeans, and then looking at the haplogroups found in areas that subsequently became Celtic (which were probably Vasconic before the arrival of the Celts), but are not found in Basque populations, as an order of magnitude estimate of the Indo-European population genetic impact, since population genetics in Western Europe have been largely stable since the Indo-Europeans arrived in Western Europe.

The fact that the two populations aren't all that different, even though they are somewhat distinct, suggests that the Indo-Europeans who arrived in Western Europe predominantly in the Iron Age, had a quite modest impact on the region's gene pool.

Contemporary Population Genetics

These days, the most basal forms of Y-DNA R1b are found in Iran [15], the eastern Caucasus [16], Armenia [17], and Turkey[18]. So, ultimately, it seems very likely that Western Europeans can trace their roots to a migration sometime during the Holocene area (i.e. that last 10,000 years) from the highlands of West Asia.

Y-DNA R1a, the dominant Y-DNA haplogroup in the rest of Europe which expanded to become common where it is found today at approximately the same time as the R1b expansion, also probably originates in eastern Turkey or Iran,[19]

Linguistic Conjectures

Geographically, this region where R1b orignated corresponds fairly closely to the geographic range of the copper age Kura-Araxes culture (ca. 3400 BCE to 2700-2000 BCE)[20][21] which archaeological evidence demonstrates had longstanding and sustained trade ties (at least) to the Sumerian Uruk culture (ca. 4000 BCE to 3100 BCE).[22] It isn't clear to what extent the Kura-Araxes culture's metal working technologies derived from the Sumerians who neighbored it to the South, or the Maikop culture, who were its Northern neighbors.

The Kura-Araxes culture probably spoke a language belonging to the now extinct the Hurro-Urartian language family.[23] Linguistic overlaps between the Hurro-Uratian and Sumerian languages, which are statistically significant at approximately the p=0.02 level, suggest that the languages are related to each other in some way.[23] But, the words that they have in common are not a good fit to either borrowing of loan words, or to a model in which both languages share of proto-language.[23] Instead, it seems likely that either a Hurro-Uratian population was in the process of adopting a Sumerian superstrate language which was aborted before it could run its course, or that alternately, a Sumerian population was in the process of adopting of Hurro-Uratian superstrate language and that process was aborted before it was completed, as the pattern of shared words is similar to the small number of cases where that scenario is attested.[23]

Hurrian was spoken in Mesopotamia, and eastern and southern Anatolia ca. 2200 BCE to 1000 BCE. The language of the Kassite people (ca. 1500 BCE to 1100 BCE) in an area that overlaps heavily with the region of the Kura-Araxes culture's extent, was probably also a part of the Hurro-Uratian language family.[24]  Uratian which is widely acknowledge to share a language family with Hurrian was spoken in what is now eastern Turkey and modern Armenia at least between 900 BCE and 600 BCE.  The strongest candidate for a modern family of living languages related to Hurro-Uratian is the Northeast Caucasian language family.

Thus, Minoan civilization may have been the result of an intrusive Copper Age Anatolian population's migration to the island, perhaps related to the non-Indo-European Hattic culture that preceded the Indo-European Hittite civilization that began its conquest of Anatolia and the northern Fertile Crescent at a historically attested date after 2000 BCE, in the wake of the highly disruptive 4.2 kiloyear climate event that was also probably pivotal in the fall of the Sumerian language to the Semitic Akkadian language in Mesopotamia.

The Hattic language shows similarities to the Northwest Caucasian and South Caucasian languages, and to the thinly attested languages of the Kaskians of northeastern Bronze Age Anatolia, in the mountains along the Black Sea coast, who may be the ancestors of the Northwest Caucasian Circassian people today. This language family is also a likely candidate for the language of the Maikop culture.

Proposals to link the Northeastern and Northwestern Caucasian languages into a North Caucasian language family have received serious consideration, and if well founded, would link almost all of the non-Indo-European languages of the Copper Age region in which Y-DNA R1a and R1b in Europe both have their likely origins into one linguistic family that probably also would include the Basque language and Minoan.

Minoan may also have been part of the same language family as the non-Indo-European substrate language of Greek, and of other known non-Indo-European languages of the Aegean and Italy such as Lemnian (spoken through about 600 BCE on the island of Lemnos near the Anatolian coast in the Aegean sea that was annexed to Greece in 1912, the Etruscan language spoken in early Roman times (through about 0 CE) in what is now Tuscany, and the Raetic language of the Italian-Austrian Alps that was part of the same language family as Etruscan and survived somewhat longer (no relation to the Indo-European language of the same name now spoken in Switzerland).

Y-DNA R1a, the dominant Y-DNA haplogroup in the rest of Europe which expanded to become common where it is found today at approximately the same time as the R1b expansion, also originated to the north of the historically attested copper age Elamite civilization of Iran and the contemporaneous Sumerian culture of Mesopotamia.[19]

This would put it in the vicinity of both the Kura-Araxes culture and the Maikop culture (aka Maykop culture) (ca. 3700 BCE-3000 BCE) immediately to the north of the Kura-Araxes culture in the Northern Caucasus mountains. The Maikop culture, under cultural influences from Iran and South Central Asia developed metal working technology independently of the Sumerians or the Balkan-Anatolian copper age cultures.[22] The Maikop culture also invented the Kurgan burial practices that would later spread (along with its metal working technology) to the probably proto-Indo-European Yamna culture of the Pontic Steppe (ca. 3500 BCE to 2200 BCE) where these burial practices would become the litmus test for Indo-European cultural affinities.[25] The Maikop culture itself, however, may very well not have been Indo-European linguistically.

But, can be do better to pin down the time and place of the predominant genetic ancestors of Western Europeans?

The Big Open Questions

The source of Y-DNA R1a and mtDNA H in Central and Eastern Europe was very likely the Indo-European Corded Ware culture, not so far from an Indo-European homeland on the Pontic Caspian Steppe whose antecedents started to gel around 4000 BCE.

The predominant source of Y-DNA R1b and mtDNA H in Western Europe is more controversial.

1. Does R1b originate in the Paleolithic hunter-gatherers from the Franco-Cantrabrian refugium or Northwest Africa? This hypothesis was advanced, for example, in a 2013 paper.[26]

2. Does R1b have its source in the first wave megalithic Neolithic?  This is not true in the case of other first wave Neolithic populations in Europe, whose closest match among modern populations are the people of the island of Sardinia whose ancient DNA and physical anthropology show continuity from Neolithic times to the present.[1][27][28]

3. Does it come after them, with the Bell Beaker culture and its immediate successors of the Copper Age and early Bronze Age?

4. Does it come with the late Bronze Age/early Iron Age Indo-European Celts?

5. Or, does this happen when later ruling powers like the Romans (whose Italic family language is also Indo-European and closely related to Celtic), arrive.

Increasingly, it is my view that the answer is choice number 3.  Western European ancient DNA starts to look very modern from this point onward, but the hints we have gotten about the genetics of the Atlantic megalithic culture appears to resemble other first wave Neolithic cultures (whose genetics are quite distinct from modern Europeans) rather than modern Western Europeans.

Did Y-DNA R1b and mtDNA H Become Common In The Megalithic Era Or Metal Age Age In Western Europe?

If Y-DNA R1b and mtDNA H either expanded in the Mesolithic and was incorporated heavily into the first wave Neolithic culture of the Atlantic megalithic culture, or if the Atlantic megalithic culture, rather than later metal age cultures in Western Europe, were the source of Y-DNA R1b and mtDNA H in Europe, then the population genetics of the Atlantic megalithic people should be significantly different from first wave Neolithic populations in Central and Eastern Europe (LBK) and Southern Coastal Europe (Cardium Pottery).

If Y-DNA R1b and mtDNA H are scarce or absent in Atlantic megalithic ancient DNA, in contrast, then there has to be a major metal age migration of people that is the source of these population genetic components in Western Europe, and this increasingly looks like it must be Bell Beaker and associated cultures, which were probably linguistically Vasconic (i.e. part of the language family that includes Basque and some extinct Iberian languages), because if Indo-Europeans were the source of these genetic components, the pre-Indo-European Basque people would not be extremely high in Y-DNA R1b and mtDNA H.

Fortunately, in the last few years, some ancient Atlantic megalithic ancient DNA samples have been sequences allowing us to finally make progress towards answering some of these questions.

As set forth in detail below, the limited available data is consistent with the Atlantic megalithic culture being a first wave Neolithic culture that is very similar to that of first wave Neolithic cultures elsewhere in Europe from a population genetic perspective, and is inconsistent to the extent that we have data, with the Atlantic megalithic culture being the main source of Y-DNA R1b and mtDNA H in modern Western Europe.

In contrast, the limited data that is available is consistent with Y-DNA R1b and mtDNA H being spread in Western Europe by the Bell Beaker culture, despite a once mainstream view that the Bell Beaker culture did not have a major demic impact and largely had an impact on Western Europe through the dissemination of technology and trade goods. There is simply no other archaeological culture that can fit the ancient DNA facts as well.

Some Key Data Points

One substantial sample comes from Saint-Jean-et-Saint-Paul in inland Southern France ca. 3000 BCE, although this is arguably more in the Cardium Pottery Neolithic than the Atlantic megalithic cultural area.[29] This sample is very typical of first wave Neolithic populations in the LBK and at other Cardium Pottery sites with lots of Y-DNA G2a (20 men) and Y-DNA I2a (2 men) and no Y-DNA R1b. There was diversity of mtDNA that is not particularly heavy in mtDNA H. Specifically,
[Researchers obtained mtDNA haplotypes for] 29 of the 53 individuals tested. They were classified into 13 different haplotypes, which yielded a relatively high haplotype diversity . . . of 0.8966 ± 0.0354. . . . the 13 haplotypes previously found could be classified in 11 different haplogroups or subhaplogroups: H1, H3, HV0, V, K1a, T2b, U, U5, U5b1c, X2, and J1.
Another ancient DNA study with the same lead author looked at a first wave Neolithic sample from Spain ca. 5000 BCE, which found Y-DNA G2a and E1b1b1a1b and typical diverse early Neolithic mix of mtDNA halotypes (as opposed to an mtDNA H dominated sample), but again, no Y-DNA R1b [30]:
The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the fifth millennium B.C. Thanks to a “multimarkers” approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the biogeographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7,000 years ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. . . .

These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated.

Presently, few ancient data are available on the Neolithic period, and most of them consist of mitochondrial DNA data, which are only informative for the maternal origin. These have revealed a particularly high frequency of haplogroup N1a, a haplogroup quite rare currently in central European and in Atlantic coast Neolithic specimens, whereas this last was never found in southern European samples. These furthermore suggested a probable genetic continuity between ancient southern Neolithic specimens and current populations located in the same areas, whereas the ancient central European plains samples would share a greater affinity with the modern-day Near East and Anatolia. The findings deduced from the study of maternal genetic lineages seemed consistent with the archeological evidences of the existence of two distinct routes of neolithization: one along the central plains of Europe and another along the Mediterranean coasts.
A clearly relevant ancient data point comes from an Atlantic megalithic burial chamber in western France ca. 4200 BCE.[31]
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.
I don't have access to the full text of the article and it does not have Y-DNA samples, but it is not dominated by mtDNA H, or apparently, by mtDNA U, to an extent that would be notable in the abstract of the paper.

A fourth sample provides ancient mtDNA from an early Neolithic Iberian population, which is also a Cardial Pottery culture.[32]
The Neolithic transition has been widely debated particularly regarding the extent to which this revolution implied a demographic expansion from the Near East. We attempted to shed some light on this process in northeastern Iberia by combining ancient DNA (aDNA) data from Early Neolithic settlers and published DNA data from Middle Neolithic and modern samples from the same region. We successfully extracted and amplified mitochondrial DNA from 13 human specimens, found at three archaeological sites dated back to the Cardial culture in the Early Neolithic (Can Sadurní and Chaves) and to the Late Early Neolithic (Sant Pau del Camp). We found that haplogroups with a low frequency in modern populations—N* and X1—are found at higher frequencies in our Early Neolithic population (∼31%). Genetic differentiation between Early and Middle Neolithic populations was significant (FST∼0.13, P < 10−5), suggesting that genetic drift played an important role at this time. To improve our understanding of the Neolithic demographic processes, we used a Bayesian coalescence-based simulation approach to identify the most likely of three demographic scenarios that might explain the genetic data. The three scenarios were chosen to reflect archaeological knowledge and previous genetic studies using similar inferential approaches. We found that models that ignore population structure, as previously used in aDNA studies, are unlikely to explain the data. Our results are compatible with a pioneer colonization of northeastern Iberia at the Early Neolithic characterized by the arrival of small genetically distinctive groups, showing cultural and genetic connections with the Near East.

The first wave Neolithic revolution Atlantic megalithic people of Western Europe, so far as the limited available ancient DNA evidence can tell us, bore a strong genetic resemblance to all of the other first farmers of Europe, about whom we have better ancient DNA data.

We know for a fact that across the board, although not always in precisely the same places at precisely the same times, the unprecedented population surge produced by the introduction of farming and herding to Western Europe was followed by an epic population crash that would put the Bubonic Plague to shame.

The modern European gene pool took its shape as the next major archaeological cultures, in the Copper and Bronze Ages, filled much of the vacuum created when the farming and herding economy collapsed the first time around, and expanded in a way that was effectively permanent.

In Eastern and Central Europe, this was the Indo-European Corded Ware culture.  But, in Western and Northern Europe, its technological equal, the Bell Beaker civilization and its immediate successors, held the Corded Ware culture at bay for a thousand years, until ultimately the climatic events of that precipitated the Bronze Age collapse tipped the balance in favor of Indo-European people - the linguistically Italic people in Italy (along with migrant Indo-European Greek colonies), the Celts in most of Western Europe and the British Isles, and the Germanic people in Northern Europe and Scandinavia.

Notwithstanding archaeological interpretations of the Bell Beaker culture as a thin superstrate of traders, metal workers and perhaps religious leaders.  The hard evidence from ancient and modern DNA, points strongly towards a major demic impact from these people in the 3rd millenium BCE, as they expanded their numbers at a record rate and evolved physically in a way that exploited their dairy farming prowess.

The subsequent Iron Age Celtic peoples conquered the region and had a moderate demic impact, while producing a language shift to their Vasconic substrate influenced Indo-European language in much of Europe.  The Romans and other waves of migrants that followed them had even less of a population genetic impact, although most of the people of the Celtic world ultimately came to speak another family of Indo-European languages under subsequent conquests, either Latin derived languages with a source in Rome, Italy, or Proto-Germanic derived languages that expanded and diversified out of origins Denmark.

Of course, suppose that we can conclude that the Bell Beaker people were the last and strongest force in shaping the modern Western European gene pool.

Suppose also that we can say with some comfort that the ultimate place of origin of Y-DNA haplotype R1b was in the highlands of West Asia.

The story of how the Bell Beaker people reached a secondary expansion focal point in Southern Portugal and went on to sweep Western Europe in the Copper Age and early Bronze Age remains an unsolved question although we have some tantalizing hints that have been suggested in this post, and previous posts at this blog.


[UPDATE: The references in this post have been significantly updated from the original post date through October 10, 2014, together with very minor changes in the body text.]

[1] Iosif Lazaridis, et al., "Ancient human genomes suggest three ancestral populations for present-day Europeans," (bioRxiv, Posted December 23, 2013) (examining autosomal DNA).
[2] Anna Szécsényi-Nagy et al., "Tracing the genetic origin of Europe's first farmers reveals insights into their social organization" (bioRxiv 2014).
[3] Doron M. Behar et al., "A 'Copernican' Reassessment of the Human Mitochondrial DNA Tree from its Root," (The American Journal of Human Genetics, Volume 90 (2012), supplement) (arguing for a Neolithic dispersal, possibly from the Near East).
[4] Antonio Torroni et al., "mtDNA Analysis Reveals a Major Late Paleolithic Population Expansion from Southwestern to Northeastern Europe," (American Journal of Human Genetics, vol. 62 (1998)) at pp. 1137–1152 (arguing for a Mesolithic dispersal from a Franco-Cantabrian refugium).
[5] Wolfgang Haak et al,, "Ancient DNA from the First European Farmers in 7500-Year-Old Neolithic Sites" (Science, Vol 310, Issue 5750, 1016-1018 , 11 November 2005) (the study looked at 24 mtDNA samples from members of the LBK culture ca. 5500 BCE from multiple locations)
[6] Sampietro ML, et al., "Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe." (Proc Biol Sci. 2007 Jun 26; Epub ahead of print) (the study looked at mtDNA from "11 Neolithic remains from Granollers (Catalonia, northeast Spain) dated to" 3500 years BCE).
[7] Timpson et al, "Reconstructing regional population fluctuations in the European Neolithic using radiocarbon dates: a new case-study using an improved method" (Journal of Archaeological Science 2014).
[8] Lee EJ, et al. "Emerging genetic patterns of the european neolithic: Perspectives from a late neolithic bell beaker burial site in Germany" (American Journal of Physical Anthropology 2012).
[9] Wolfgang Haak et al. "Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age" (PNAS 2008).
[10] I. Lazaridis, et al., "Capture of 390,000 SNPS in dozens of ancient central Europeans reveals a population turnover in Europe thousands of years after the advent of farming.", American Society of Human Genetics (ASHG) 2014 Conference Abstracts (to be delivered October 18-22, 2014) (via Dienekes Anthropology Blog).
[11] Jeffery R. Hughey, et al., "A European population in Minoan Bronze Age Crete", (Nature Communications 2013) (sample size N=37).
[12] Laisel Martinez, et al., "Paleolithic Y-haplogroup heritage predominates in a Cretan highland plateau" (European Journal of Human Genetics advance online publication 31 January 2007).
[13] King RJ, et al., "Differential Y-chromosome Anatolian influences on the Greek and Cretan Neolithic" (2008 Ann Hum Genet 72:205–214).
[14] Eva Fernandez, et al., "Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands" (PLOS Genetics June 5, 2014)
[15] Viola Grugni et al., "Ancient Migratory Events in the Middle East: New Clues from the Y-Chromosome Variation of Modern Iranians" (PLoS ONE 2012).
[16] Bayazit Yunusbayev et al., "The Caucasus as an asymmetric semipermeable barrier to ancient human migrations" (Mol Biol Evol 2011)
[17] Kristian J Herrera, et al., "Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists" (European Journal of Human Genetics 16 November 2011)
[18] Ömer Gokcumen et al., "Biological Ancestries, Kinship Connections, and Projected Identities in Four Central Anatolian Settlements: Insights from Culturally Contextualized Genetic Anthropology" (2011 American Anthropologist Volume 113, Issue 1, pages 116–131) (about 10% of Y-DNA is R1b in this Central Anatolian region, but one must observe that many ethnically Greek and Armenian people who had Y-DNA R1b and once lived in Anatolia were exiled or exterminated in recent history).
[19] Underhill, et al., "The phylogenetic and geographic structure of Y-chromosome haplogroup R1a" (Eur J Hum Genet. 2014 Mar 26).
[20] I.M. Diakonoff, "The early Trans-Caucasian culture" (1984) (suggesting a demise of the culture ca. 2000 BCE).
[21] Edens, Christoper, "Transcaucasia at the End of the Early Bronze Age" (Bulletin of the American Schools of Oriental Research Aug–Nov 1995) (suggesting a demise of the culture ca. 2700-2600 BCE).
[22] Mariya Ivanova, "Kaukasus und Orient: Die Entsthung des "Maikop-Phanomens" im 4. Jahrausend .Chr.", 87(1) Prahistorische Zeitschrift 1-28 (2013) (in German) (abstract translated at Dienekes Anthropology Blog).
[23] Alexei Kassian, "Lexical Matches between Sumerian and Hurro-Urartian: Possible Historical Scenarios" (Cuniform Digital Library Journal Preprint October 3, 2014).
[24] Arnaud Fournet, "The Kassite Language In a Comparative Perspective with Hurrian and Urartean" (The Macro-Comparative Journal 2010).
[25] Konstatine Pitskhelauri, "Uruk Migrants in the Caucuasus", (6(2) Bulletin of the Georgian National Academy of Sciences 2012)
[26] Vankan P., "Prevalence gradients of Friedreich's ataxia and R1b haplotype in Europe co-localize, suggesting a common Palaeolithic origin in the Franco-Cantabrian ice age refuge" (J Neurochem. August 2013).
[27] D'Amore G, et al., "Craniofacial morphometric variation and the biological history of the peopling of Sardinia." (Homo. 2010 Oct 25 Epub ahead of print) (skull shape in Sardinia shows continuity from the Neolithic era through the Bronze Age and into the present and are distinct from Etruscan skulls and have skulls more distinct from modern Italian skulls than from early Neolithic Italian skulls).
[28] Silvia Ghirotto et al., "Inferring Genealogical Processes from Patterns of Bronze-Age and Modern DNA variation in Sardinia" (Molecular Biology and Evolution 2009) (Bronze Age mtDNA in Sardinia N=23 shows strong continuity with modern mtDNA variation in Sardinia).
[29] Marie Lucan, et al, "Ancient DNA reveals male diffusion through the Neolithic Mediterranean route" (PNAS open access June 14, 2011).
[30] Marie Lucan, et al., "Ancient DNA suggests the leading role played by men in the Neolithic dissemination" (PNAS open access November 8, 2011).
[31] Marie-France Deguilloux, et al., "News from the west: Ancient DNA from a French megalithic burial chamber" (American Journal of Physical Anthropology August 17, 2010).
[32] C. Gamba, "Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers" (Molecular Ecology January 2012).


spagetiMeatball said...

Aren't we pretty sure now that both haplogroups R1b and R1a originate from a Ancient North Eurasian population (ANE) from Siberia, because of Mal'ta boys R* ?

andrew said...


First off, we have no clear idea what kind of range Y-DNA R had at the time of Malt'ta boy. There could have been a spread of thousands of miles at that point.

We know that F=>K=>P=>R=>R1 and R2 and that R1=>R1a and R1b.

Our best guess is that F arose in South Asia, K in inland SE Asia, and that P, R and its sister clade Q arose somewhere to the North of the Himalayas and Tibet, somewhere between the Black Sea and the Pacific, but not too clearly where.

The place where R1 and R2 broke off from each other is not entirely clear (perhaps Afghanistan since R2 is South Asian and R1 is West Asian before it reaches Europe), and the place where R1 broke into R1a and R1b is probably in Iran or nearby in highland West Asia.

spagetiMeatball said...

I think IJ* also broke up into I and J somewhere between west asia and europe, right?

Since J is clearly native to the middle east, and I to europe. What is strange about this is that I2 is associated with WHG, or west european hunter gatherers, which is missing from the middle east or present in very low levels. But that doesn't make sense, because an ancestral population should have which the guy who had IJ* belonged to, right?

spagetiMeatball said...

Sorry last sentence came out jumbled: There should have been an ancestral population to which the IJ* man belonged, and that population should be related to the WHG group.

terryt said...

"Aren't we pretty sure now that both haplogroups R1b and R1a originate from a Ancient North Eurasian population (ANE)"

I used to be convinced R1b was Paleolithic because it is so common at the western extremity of Europe but I have been forced to accept it's arrival is post farming. My guess is that R1b, although not the first Neolithic, carried in the surviving Early European Farmer genes (EEF) and R1a carried in the Ancient North Eurasian genes (ANE).

"There should have been an ancestral population to which the IJ* man belonged, and that population should be related to the WHG group".

IJ obviously belonged to some population but that need not have been WHG. Haplogroup I probably became WHG only once it had entered Europe.

"I think IJ* also broke up into I and J somewhere between west asia and europe, right?"

I think we can narrow it down to somewhere immediately south of the Caucasus Mountains. That means that Andrew's comment would not be quite correct:

"Our best guess is that F arose in South Asia"

The three haplogroups now classified as some sort of 'F' are primarily South Asian (F2 is on the border with East Asia) but several basal haplogroups within the F-M89 clade certainly are not South Asian. For example G is also most likely Anatolian/Iranian in origin, as may be the newly defined H1/H2, H2 being the old SW Asian 'F3'. I have no idea where the newly-defined H3 is found although for some reason I suspect SE Asia. If that is the case H would be split geographically from west (H2), through South Asia ((H1), to SE Asia (H3). All this strongly suggests the F-M89 haplogroup as a whole originated west of South Asia but moved rapidly into and through it leaving branches behind as it went.

"P, R and its sister clade Q arose somewhere to the North of the Himalayas and Tibet, somewhere between the Black Sea and the Pacific, but not too clearly where".

Your next comment provides some sort of answer I think:

"The place where R1 and R2 broke off from each other is not entirely clear (perhaps Afghanistan since R2 is South Asian and R1 is West Asian before it reaches Europe)"

Which indicates to me that P travelled back west through South Asia before emerging into Iran/West Asia.

"the place where R1 broke into R1a and R1b is probably in Iran or nearby in highland West Asia".

Agreed. And probably the same for Q.

terryt said...

Sorry, I forgot to mention: well done Andrew. Great post.

"Increasingly, it is my view that the answer is choice number 3".

Yes. The reason:

" looks like it must be Bell Beaker and associated cultures, which were probably linguistically Vasconic (i.e. part of the language family that includes Basque and some extinct Iberian languages), because if Indo-Europeans were the source of these genetic components, the pre-Indo-European Basque people would not be extremely high in Y-DNA R1b and mtDNA H".

terryt said...

You might both be interested in this 2000 paper, if you're not already familiar with it:



"Using this relationship, we estimated that hg 1 frequencies
follow a cline within Europe,
extending from the Near East (1.8% in Turkey) to a peak in the Spanish Basque country (89%) in the west. This cline mirrors other genetic gradients in Europe and is best explained by the migration of Neolithic farmers from the Near East. When the surname-divided Irish data are appended to this cline, it continues to the western edge of Europe, with hg 1 — the putative pre-Neolithic western European variant — reaching its highest frequency in Connaught (98.3%)".

Since I first read this paper I have assumed my Y-DNA is 'hg 1', currently called R1b1a2a1a2-P312. My surname is Gaelic Irish and my Great Grandfather came from Cork. Because Maju claims to be Basque I mentioned to him years ago that we might be related, as 89% of Basques are also R1b1a2a1a2-P312. His reaction led me to believe that, unlike me, he actually knew his haplotype, and it wasn't R1b1a2a1a2-P312. We've never established a cordial relationship since. But it turns out that my basic assumption, formed from this paper, was correct. Basques and West Coast Irish are quite closely related although speaking entirely different languages.