Bronze Age people from Ireland had steppe ancestry and R1b

From the paper:

We were able to deduce that Neolithic Ballynahatty had a dark hair shade (99.5% probability), most likely black (86.1% probability), and brown eyes (97.3% probability) (46). Bronze Age Rathlin1 probably had a light hair shade (61.4%) and brown eyes (64.3%). However, each Rathlin genome possessed indication of at least one copy of a haplotype associated with blue eye color in the HERC2/OCA2 region.

and:

Third, we followed the methods described in Haak et al. (9), which use a collection of outgroup populations, to estimate the mixture proportions of three different sources, Linearbandkeramik (Early Neolithic; 35 ± 6%), Loschbour (WHG; 26 ± 12%), and Yamnaya (39 ± 8%), in the total Irish Bronze Age group. These three approaches give an overlapping estimate of ∼32% Yamnaya ancestry.

PNAS doi: 10.1073/pnas.1518445113

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

Lara M. Cassidy, Rui Martiniano et al.

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

Link

British origins (with ancient data)

Related:

• British Origins (Leslie et al. 2015)

bioRxiv http://dx.doi.org/10.1101/022723

Iron Age and Anglo-Saxon genomes from East England reveal British migration history

Stephan Schiffels, Wolfgang Haak, Pirita Paajanen, Bastien Llamas, Elizabeth Popescu, Louise Lou, Rachel Clarke, Alice Lyons, Richard Mortimer, Duncan Sayer, Chris Tyler-Smith, Alan Cooper, Richard Durbin

British population history has been shaped by a series of immigrations and internal movements, including the early Anglo-Saxon migrations following the breakdown of the Roman administration after 410CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences generated from ten ancient individuals found in archaeological excavations close to Cambridge in the East of England, ranging from 2,300 until 1,200 years before present (Iron Age to Anglo-Saxon period). We use present-day genetic data to characterize the relationship of these ancient individuals to contemporary British and other European populations. By analyzing the distribution of shared rare variants across ancient and modern individuals, we find that today’s British are more similar to the Iron Age individuals than to most of the Anglo-Saxon individuals, and estimate that the contemporary East English population derives 30% of its ancestry from Anglo-Saxon migrations, with a lower fraction in Wales and Scotland. We gain further insight with a new method, rarecoal, which fits a demographic model to the distribution of shared rare variants across a large number of samples, enabling fine scale analysis of subtle genetic differences and yielding explicit estimates of population sizes and split times. Using rarecoal we find that the ancestors of the Anglo-Saxon samples are closest to modern Danish and Dutch populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

Link

More Y-chromosome super-fathers

The time estimates are based on a mutation rate of 1x10-9 mutations/bp/year which is ~1/3 higher than mutation rate of Karmin et al.  So the values on the table may be a little lower.

There may be additional founders with recent time depths than shown in the table, e.g., a very shallow clusters within E-M35 (probably E-V13?) and a couple of shallow clusters within I-P215

Also of interest is the fact that Greeks and Anatolian Turks do not show evidence of the recent Y-chromosomal bottleneck:

The plots are consistent with patterns seen in the relative numbers of singletons, described above, in that the Saami and Palestinians show markedly different demographic histories compared with the rest, featuring very recent reductions, while the Turks and Greeks show evidence of general expansion, with increased growth rate around 14 KYA. A different pattern is seen in the remaining majority (13/17) of populations, which share remarkably similar histories featuring a minimum effective population size ~2.1–4.2 KYA (considering the 95% confidence intervals (CIs) reported in Supplementary Table 4), followed by expansion to the present.

Related:

• Y chromosome super-fathers 
• Bottleneck in human Y-chromosomes in the last 10,000 years

Nature Communications 6, Article number: 7152 doi:10.1038/ncomms8152

Large-scale recent expansion of European patrilineages shown by population resequencing

Chiara Batini, Pille Hallast et al.

The proportion of Europeans descending from Neolithic farmers ~10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ~2.1–4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.

Link

A story of 69 ancient Europeans

A new study on the bioRxiv includes data on 69 ancient Europeans (remember when we got excited in anticipation for the single genome of the Iceman? that was only three years ago) and adds plenty of new info to chew on for those of us interested in prehistory. 

Two Near Eastern migrations into Europe

In 2011, I observed that West Eurasian populations were too close (measured by Fst) to allow for long periods of differentiation between them. By implication, there must have been a "common source" of ancestry uniting them, which I placed in a "womb of nations" of the Neolithic Near East. I proposed that migrations out of this core area homogenized West Eurasians, writing:

In Arabia, the migrants would have met aboriginal Arabians, similar to their next door-neighbors in East Africa, undergoing a subtle African shift (Southwest_Asians). In North Africa, they would have encountered denser populations during the favorable conditions of MIS 1, and by absorbing them they would became the Berbers (Northwest_Africans). Their migrations to the southeast brought them into the realm of Indian-leaning people, in the rich agricultural fields of the Mehrgarh and the now deserted oases of Bactria and Margiana. Across the Mediterranean and along the Atlantic facade of Europe, they would have encountered the Mesolithic populations of Europe, and through their blending became the early Neolithic inhabitants of the Mediterranean and Atlantic coasts of Europe (Mediterraneans). And, to the north, from either the Balkans, the Caucasus, or the trans-Caspian region, they would have met the last remaining Proto-Europeoid hunters of the continental zone, becoming the Northern Europeoids who once stretched all the way to the interior of Asia.

The new paper confirms the last two of these migrations. The remainder involve parts of the world from which no ancient DNA has been studied.

The first migration (early Neolithic) is already uncontroversial, but the paper includes data from Spanish early farmers that are also Sardinian- and LBK-like. The "Sardinian" Iceman was no fluke. It is now proven that not only the LBK but also the Spanish Neolithic came from the same expansion of Mediterranean populations which survives in Sardinia. The authors write:

Principal components analysis (PCA) of all ancient individuals along with 777 present-day West Eurasians4 (Fig. 2a, SI5) replicates the positioning of present-day Europeans between the Near East and European hunter-gatherers4,20, and the clustering of early farmers from across Europe with present day Sardinians3,4,27, suggesting that farming expansions across the Mediterranean to Spain and via the Danubian route to Hungary and Germany descended from a common stock.

The second migration went into eastern Europe:

The Yamnaya differ from the EHG by sharing fewer alleles with MA1 (|Z|=6.7) suggesting a dilution of ANE ancestry between 5,000-3,000 BCE on the European steppe. This was likely due to admixture of EHG with a population related to present-day Near Easterners, as the most negative f3-statistic in the Yamnaya (giving unambiguous evidence of admixture) is observed when we model them as a mixture of EHG and present-day Near Eastern populations like Armenians (Z = -6.3; SI7).

The EHG (Eastern European Hunter-Gatherers) are likely Proto-Europeoid foragers and the Yamnaya (a Bronze Age Kurgan culture) were a mixture of the EHG and something akin to Armenians.The "attraction" of later groups to the Near East is clear in the PCA: hunter-gatherers on the left side, the Near East (as grey dots) on the right side, and Neolithic/Bronze Age/modern Europeans in the middle. The second migration may very well be related to the Uruk expansion and the presence of gracile Mediterranoids and robust Proto-Europeoids in the Yamna:

The Yamna population generally belongs to the European race. It was tall (175.5cm), dolichocephalic, with broad faces of medium height. Among them there were, however, more robust elements with high and wide faces of the proto-Europoid type, and also more gracile individuals with narrow and high faces, probably reflecting contacts with the East Mediterranean type (Kurts 1984: 90).

The authors present a table of Fst values which confirms the homogenizing influence of migrations from the Near East. The WHG group has an Fst=0.086 with Armenians, but the LBK farmers have only 0.023. The EHG group has an Fst=0.067 with Armenians, but the Yamnaya steppe people have only 0.030. Someone might argue that it is the Armenians that are receiving genes from Europe, but the same pattern holds even for the Bedouins, for which admixture with Europeans seems far-fetched: 0.106 to 0.043 and 0.093 to 0.060. It is now clear that the "glue" that did not allow West Eurasian populations to drift very far apart were migrations from the Near East.

The (partial) demise of the farmers

It seems that the legacy of the early farmers suffered two hits, which is why only in Sardinia and (to a lesser degree) in southern Europe that they have persisted as the major component of ancestry. The first blow came during the Neolithic:

Middle Neolithic Europeans from Germany, Spain, Hungary, and Sweden from the period ~4,000-3,000 BCE are intermediate between the earlier farmers and the WHG, suggesting an increase of WHG ancestry throughout much of Europe.

And the coup de grâce after the 5kya mark:

We estimate that these two elements each contributed about half the ancestry each of the Yamnaya (SI6, SI9), explaining why the population turnover inferred using Yamnaya as a source is about twice as high compared to the undiluted EHG. The estimate of Yamnaya related ancestry in the Corded Ware is consistent when using either present populations or ancient Europeans as outgroups (SI9, SI10), and is 73.1 ± 2.2% when both sets are combined (SI10). [...] The magnitude of the population turnover that occurred becomes even more evident if one considers the fact that the steppe migrants may well have mixed with eastern European agriculturalists on their way to central Europe. Thus, we cannot exclude a scenario in which the Corded Ware arriving in today’s Germany had no ancestry at all from local populations.

Confirmation of the Bronze Age Indo-European invasion of Europe

In 2012 I had used the paltry data on a handful ancient DNA samples to observe that in ADMIXTURE modern Europeans had a West Asian genetic component (peaking in "Caucasus" and "Gedrosia") that pre-5kya Europeans didn't. I proposed that the Bronze Age migration of the Indo-Europeans spread this component:

But there is another component present in modern Europe, the West_Asian which is conspicuous in its absence in all the ancient samples so far. This component reaches its highest occurrence in the highlands of West Asia, from Anatolia and the Caucasus all the way to the Indian subcontinent. [...] Nonetheless, some of the legacy of the earliest Indo-European speakers does appear to persist down to the present day in the genomes of their linguistic descendants, and I predict that when we sample later (post 5-4kya) individuals we will finally find the West_Asian piece that is missing from the European puzzle.

This prediction is now confirmed:

This pattern is also seen in ADMIXTURE analysis (Fig. 2b, SI6), which implies that the Yamnaya have ancestry from populations related to the Caucasus and South Asia that is largely absent in 38 Early or Middle Neolithic farmers but present in all 25 Late Neolithic or Bronze Age individuals. This ancestry appears in Central Europe for the first time in our series with the Corded Ware around 2,500 BCE (SI6, Fig. 2b, Extended Data Fig. 1).

I was a little puzzled with the "Ancient North Eurasians" recently proposed as a "third ancestral population" for Europeans: it seemed to be a tertium quid that spread after 5kya, but very different geographically than the "West Asian" component. But:

These results can be explained if the new genetic material that arrived in Germany was a composite of two elements: EHG and a type of Near Eastern ancestry different from that which was introduced by early farmers (also suggested by PCA and ADMIXTURE; Fig. 2, SI5, SI6).

So, it seems that there is no contradiction after all and both EHG (which is related to "Ancient North Eurasians") and another type of Near Eastern ancestry (=West_Asian) arrived after 5kya.

1939 strikes back

It is amazing how well this was anticipated by Carleton Coon in 1939. Back then much of West Eurasia was an archaeological/anthropological terra incognita, there was no radiocarbon dating, no DNA, no computers, not even serious multivariate statistics. And yet:

We shall see, in our survey of prehistoric European racial movements, 8 that the Danubian agriculturalists of the Early Neolithic brought a food-producing economy into central Europe from the East. They perpetuated in the new European setting a physical type which was later supplanted in their original home. Several centuries later the Corded people, in the same way, came from southern Russia but there we first find them intermingled with other peoples, and the cul-tural factors which we think of as distinctively Corded are included in a larger cultural equipment. [...] On the basis of the physical evidence as well, it is likely that the Corded people came from somewhere north or east of the Black Sea. The fully Neolithic crania from southern Russia which we have just studied include such a type, also seen in the midst of Sergi's Kurgan aggregation. Until better evidence is produced from elsewhere, we are entitled to consider southern Russia the most likely way station from which the Corded people moved westward.

And in 2015:

Our results support a view of European pre-history punctuated by two major migrations: first, the arrival of first farmers during the Early Neolithic from the Near East, and second of Yamnaya pastoralists during the Late Neolithic from the steppe (Extended Data Fig. 5).

In 1939:

Linguistically, Indo-European is probably a relatively recent phenomenon, which arose after animals had been tamed and plants cultivated. The latest researches find it to be a derivative of an initially mixed language, whose principal elements were Uralic, called element A, and some undesignated element B which was probably one of the eastern Mediterranean or Caucasic languages. 5 The plants and animals on which the Somewhere in the plains of southern Russia or central Asia, the blending of languages took place which resulted in Indo-European speech. This product in turn spread and split, and was further differentiated by mixture with the languages of peoples upon whom it, in one form or other, was imposed. Some of the present Indo-European languages, in addition to these later accretions from non-Indo-European tongues, contain more of the A element than others, which contain more of the B. The unity of the original " Indo- Europeans," could not have been of long duration, if it was ever complete. 

In 2015:

These results can be explained if the new genetic material that arrived in Germany was a composite of two elements: EHG and a type of Near Eastern ancestry different from that which was introduced by early farmers (also suggested by PCA and ADMIXTURE; Fig. 2, SI5, SI6). We estimate that these two elements each contributed about half the ancestry each of the Yamnaya (SI6, SI9), explaining why the population turnover inferred using Yamnaya as a source is about twice as high compared to the undiluted EHG.

The EHG is still flimsy as it's only two individuals from Karelia and Samara who are very similar to each other. It's hard not to imagine that the hunter-gatherer from Russian Karelia (outside any proposed PIE homeland) would be speaking a similar language as his Samara counterpart. Did they both speak "element A" and was PIE formed when the "southern" steppe hunter-gatherers came into contact with "element B" people from the Caucasus? Short of a time machine, we can never say for sure. This might very well be an answer to the conundrum of Uralic/Proto-Kartvelian borrowings. There is simply no geographical locale in which these two language families neighbor each other: Northwest, Northeast Caucasian speakers and the pesky Greater Caucasus intervene. But, maybe there was no such locale, and these borrowings aren't due to some "PIE people" living adjacent to Uralic and Proto-Karvelian speakers but the "PIE people" being a mix of an element A (EHG) that was (or interacted with) Uralic and another element B (Armenian-like) that was (or interacted with) Proto-Kartvelian.

Urheimat (or not?)

The authors of the current paper are agnostic about the PIE homeland:

We caution that the location of the Proto-Indo-European9,27,29,30 homeland that also gave rise to the Indo-European languages of Asia, as well as the Indo-European languages of southeastern Europe, cannot be determined from the data reported here (SI11). Studying the mixture in the Yamnaya themselves, and understanding the genetic relationships among a broader set of ancient and present-day Indo-European speakers, may lead to new  insight about the shared homeland.

Whatever the ultimate answer will be, it seems that Coon was right that "The unity of the original " Indo- Europeans," could not have been of long duration, if it was ever complete." If PIE=EHG (as Anthony and Ringe suggest), then "from the crib", PIE got half its ancestry from a non-IE, Near Eastern source. Conversely, if PIE=Near East (as I suggested) then "from the crib", PIE got half of its ancestry from a non-IE, Eastern European source. The "Yamnaya" seems to max out in Norwegians at around half, which means that they are about a quarter Proto-Indo-European genetically, regardless of which theory is right.

These two possibilities (as well as the third one of PIE being neither-nor, but rather a linguistic mixture of the languages of the EHG and Near East) are testable. The Anthony/Ringe version of the steppe hypothesis predicts pre-Yamnaya expansions from the steppe. Whether these happened and what was their makeup can be tested: if they did occur and they did lack "Near Eastern" ancestry, then the steppe hypothesis will be proven. PIE in the Near East, on the other hand, predicts that some PIE languages (certainly the Anatolian ones) will be a "within the Near East" expansion. If such migrations did occur and they lacked "EHG" ancestry, then some variant of the Gamkrelidze/Ivanov model will be proven. Or, the truth might be that everywhere where Indo-Europeans arrive they carry a blend of "West Asian" and "EHG", supporting the third possibility. Time will tell.

In the interim, I am curious about how much Yamnaya ancestry existed in different parts of Europe (all of the post-5kya samples in this study come from Germany, with a couple from Hungary). In northern Europe, all populations seem to have less Yamnaya ancestry than the Corded Ware: there it must have declined. But, modern Hungarians have more than Bronze Age Hungarians: there it must have increased.

Germany and a slice of Hungary is a very narrow window through which to see the whole of Europe and these results must be tested by looking at samples from beyond the "heartland". I do hope that some kind of Moore's law operates in the world of ancient DNA, and in three more years we'll be reading studies about thousands of ancient individuals.

bioRxiv doi: http://dx.doi.org/10.1101/013433
Massive migration from the steppe is a source for Indo-European languages in Europe

Wolfgang Haak , Iosif Lazaridis , Nick Patterson , Nadin Rohland , Swapan Mallick , Bastien Llamas , GuidoBrandt , Susanne Nordenfelt , Eadaoin Harney , Kristin Stewardson , Qiaomei Fu , Alissa Mittnik , Eszter Banffy ,Christos Economou , Michael Francken , Susanne Friederich , Rafael Garrido Pena , Fredrik Hallgren , ValeryKhartanovich , Aleksandr Khokhlov , Michael Kunst , Pavel Kuznetsov , Harald Meller , Oleg Mochalov ,Vayacheslav Moiseyev , Nicole Nicklisch , Sandra L. Pichler , Roberto Risch , Manuel A. Rojo Guerra , ChristinaRoth , Anna Szecsenyi-Nagy , Joachim Wahl , Matthias Meyer , Johannes Krause , Dorcas Brown , DavidAnthony , Alan Cooper , Kurt Werner Alt , David Reich

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.

Link

Paternal lineages and languages in the Caucasus

An interesting new study on Y chromosome and languages in the Caucasus. The distribution of haplogroups is on the left. The authors make some associations of haplogroups with language families:

• R1b: Indo-European
• R1a: Scytho-Sarmatian
• J2: Hurro-Urartian
• G2: Kartvelian

Hum Biol. 2014 May;86(2):113-30.

Human paternal lineages, languages, and environment in the caucasus.

Tarkhnishvili D1, Gavashelishvili A1, Murtskhvaladze M1, Gabelaia M1, Tevzadze G2.

Abstract

Publications that describe the composition of the human Y-DNA haplogroup in diffferent ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with published data on haplogroup composition and location of other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical diffferences in frequencies of the Y-DNA haplogroups G2, R1a, R1b, J1, and J2. The analysis showed significant associations of (1) G2 with wellforested mountains, (2) J2 with warm areas or poorly forested mountains, and (3) J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a were significantly associated with Daghestanian and Kipchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among diffferent paternal lineages, arriving in the Caucasus in diffferent times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in the Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western Eurasia, and the East European Plain is plausible.

Link (pdf)

Recent radiation of R-M269 males in Europe

From the paper:

As such it is not possible to predict the subhaplogroup within R-M269 to which an individual belongs based on his YSTR haplotype, in contrast to the situation with higher level haplogroups for which haplotypes do have predictive power(Athey, 2005; Schlecht et al., 2008).

The explosion of R-M269 descendants who (seemingly) went from zero to a solid majority in much of Western Europe over the last few thousand years is probably one of the most interesting events in recent European history. Not many would have entertained such a possibility until a few years ago, but truth is often stranger than fiction.

Annals of Human Genetics DOI: 10.1111/ahg.12050

Recent Radiation within Y-chromosomal Haplogroup R-M269 Resulted in High Y-STR Haplotype Resemblance

Maarten H. D. Larmuseau et al.

Y-chromosomal short tandem repeats (Y-STRs) are often used in addition to Y-chromosomal single-nucleotide polymorphisms (Y-SNP) to detect subtle patterns in a population genetic structure. There are, however, indications for Y-STR haplotype resemblance across different subhaplogroups within haplogroup R1b1b2 (R-M269) which may lead to erosion in the observation of the population genetic pattern. Hence the question arises whether Y-STR haplotypes are still informative beyond high-resolution Y-SNP genotyping for population genetic studies. To address this question, we genotyped the Y chromosomes of more than 1000 males originating from the West-European regions of Flanders (Belgium), North-Brabant and Limburg (the Netherlands) at the highest resolution of the current Y-SNP tree together with 38 commonly used Y-STRs. We observed high resemblance of Y-STR haplotypes between males belonging to different subhaplogroups of haplogroup R-M269. Several subhaplogroups within R-M269 could not be distinguished from each other based on differences in Y-STR haplotype variation. The most likely hypothesis to explain this similarity of Y-STR haplotypes within the population of R-M269 members is a recent radiation where various subhaplogroups originated within a relatively short time period. We conclude that high-resolution Y-SNP typing rather than Y-STR typing might be more useful to study population genetic patterns in (Western) Europe.

Link

One to three men fathered most western Europeans?

It may sound far-fetched but it's certainly possible. After all, no R1b has been found in Europe before a Bell Beaker site from the 3rd millennium BC and today many Europeans (most in western Europe) belong to this haplogroup. As more Y chromosomes are sampled from ancient Europe, it will become clear if the R1b frequency actually shot from non-existence to ubiquity over a short span of time, and the Y chromosomes after the transition will be practically clones of each other.

Investigative Genetics 2013, 4:25 doi:10.1186/2041-2223-4-25

Modeling the contrasting Neolithic male lineage expansions in Europe and Africa

Michael J Sikora et al.

Abstract (provisional)

Background

Patterns of genetic variation in a population carry information about the prehistory of the population, and for the human Y chromosome an especially informative phylogenetic tree has previously been constructed from fully-sequenced chromosomes. This revealed contrasting bifurcating and starlike phylogenies for the major lineages associated with the Neolithic expansions in sub-Saharan Africa and Western Europe, respectively.

Results

We used coalescent simulations to investigate the range of demographic models most likely to produce the phylogenetic structures observed in Africa and Europe, assessing the starting and ending genetic effective population sizes, duration of the expansion, and time when expansion ended. The best-fitting models in Africa and Europe are very different. In Africa, the expansion took about 12 thousand years, ending very recently; it started from approximately 40 men and numbers expanded approximately 50-fold. In Europe, the expansion was much more rapid, taking only a few generations and occurring as soon as the major R1b lineage entered Europe; it started from just one to three men, whose numbers expanded more than a thousandfold.

Conclusions

Although highly simplified, the demographic model we have used captures key elements of the differences between the male Neolithic expansions in Africa and Europe, and is consistent with archaeological findings.

Link

House of Bourbon belonged to Y-haplogroup R1b1b2a1a1b* (R-Z381*)

Thus concludes a new study which conflicts with the identification of blood from a handkerchief presumed to be from the execution of Louis XVI and the presumed head of Henri IV.

It is nice that this study was made possible by the co-operation of three patrilineal Bourbon descendants. I've mentioned before that the European nobility is an untapped resource for historical/genetic studies, as they can often document much longer lines of descent than most others, so it's good to see that at least some descendants of kings are willing to contribute to this kind of research.


European Journal of Human Genetics advance online publication 9 October 2013; doi: 10.1038/ejhg.2013.211

Genetic genealogy reveals true Y haplogroup of House of Bourbon contradicting recent identification of the presumed remains of two French Kings

Maarten H D Larmuseau et al.

Genetic analysis strongly increases the opportunity to identify skeletal remains or other biological samples from historical figures. However, validation of this identification is essential and should be done by DNA typing of living relatives. Based on the similarity of a limited set of Y-STRs, a blood sample and a head were recently identified as those belonging respectively to King Louis XVI and his paternal ancestor King Henry IV. Here, we collected DNA samples from three living males of the House of Bourbon to validate the since then controversial identification of these remains. The three living relatives revealed the Bourbon’s Y-chromosomal variant on a high phylogenetic resolution for several members of the lineage between Henry IV and Louis XVI. This ‘true’ Bourbon’s variant is different from the published Y-STR profiles of the blood as well as of the head. The earlier identifications of these samples can therefore not be validated. Moreover, matrilineal genealogical data revealed that the published mtDNA sequence of the head was also different from the one of a series of relatives. This therefore leads to the conclusion that the analyzed samples were not from the French kings. Our study once again demonstrated that in order to realize an accurate genetic identification of historical remains DNA typing of living persons, who are paternally or maternally related with the presumed donor of the samples, is required.

Link

ESHG 2013 abstracts

A couple of weeks before the ESHG 2013 conference, here are a few abstracts that caught my eye. Feel free to point to more interesting presentations in the comments section.

• J16.05 - Checking the hypothesis of a Balkan origin of the Armenians
• P17.5 - Y chromosome haplogroup analysis to estimate genetic origin of Balts
• J16.27 - Armenian Highland as a transition corridor for the spread of Neolithic agriculturists
• J16.14 - In Search of the Origin of Haplogroup J1-P58
• J16.03 - Y-chromosome haplogroup analysis in the Besermyan ethnic group
• P17.4 - Mitochondrial DNA Analysis of the Southeast European Genetic Variation Reveals a New, Local Subbranching in Hg X2
• P16.085 - Population diversity and history of the Indian subcontinent: Uncovering the deeper mosaic of sub-structuring and the intricate network of dispersals
• J16.43 - Ancient mtDNA diversity in Bulgaria
• P16.072 - Mitochondrial DNA diversity in medieval and modern Romanian population
• P16.012 - Frequency analysis of the CCR5-Delta32 allele in medieval and modern Romanian population
• J16.78 - The gene pool of Argyn in the context of generic structure of Kazakhs according to data on SNP-Y-Chromosome markers.

Y chromosomes of Bulgarians (Karachanak et al. 2013)

Bulgaria had been something of a blank area in studies of uniparental markers, so it's nice to finally see a comprehensive Y-chromosome study of the country.

The dates in the paper are based on the "evolutionary mutation rate". I suspect that ancient DNA will be the final arbiter in this issue, because, for example, a Mesolithic TMRCA of E-V13 in Bulgaria implies that we'll find a lot of it in Neolithic contexts, whereas a Bronze Age one implies that we'll find a little if any of it, and a discontinuity across time.

Of interest is the occurrence of some E*(xM35, M2) in this sample in Burgas, Varna, and Plovdiv. It would be interesting to trace the ancestry of the bearers of these Y-chromosomes. I know that there still exists a minority-within-a-minority of Black Muslims in Greek Thrace, and it's not inconceivable that these Y-chromosomes may represent the legacy of a similar population; in any case, their haplotypes can be found in Table S5 for anyone wanting to investigate.

SNP Diversity within R seems substantial, and as always, it is difficult to say much, since this may be a consequence of either (i) a plausible role of the Balkans as a staging point of the likely invasion of Europe in late prehistory, or (ii) back-migration of derived R-bearers into the Balkans, be them Slavs or Goths or "eastern" folks of various stripes during history. Once again, I suspect that ancient DNA might solve this riddle, or, alternatively, routine high-coverage sequencing of the Y chromosome that might inform us, e.g., about the TMRCA of a Bulgarian and a German R-U152 or a Bulgarian and Polish R-M458.

PLoS ONE 8(3): e56779. doi:10.1371/journal.pone.0056779

Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry

Sena Karachanak et al

To better define the structure and origin of the Bulgarian paternal gene pool, we have examined the Y-chromosome variation in 808 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within the most informative haplogroups. We found that the Y-chromosome gene pool in modern Bulgarians is primarily represented by Western Eurasian haplogroups with ~ 40% belonging to haplogroups E-V13 and I-M423, and 20% to R-M17. Haplogroups common in the Middle East (J and G) and in South Western Asia (R-L23*) occur at frequencies of 19% and 5%, respectively. Haplogroups C, N and Q, distinctive for Altaic and Central Asian Turkic-speaking populations, occur at the negligible frequency of only 1.5%. Principal Component analyses group Bulgarians with European populations, apart from Central Asian Turkic-speaking groups and South Western Asia populations. Within the country, the genetic variation is structured in Western, Central and Eastern Bulgaria indicating that the Balkan Mountains have been permeable to human movements. The lineage analysis provided the following interesting results: (i) R-L23* is present in Eastern Bulgaria since the post glacial period; (ii) haplogroup E-V13 has a Mesolithic age in Bulgaria from where it expanded after the arrival of farming; (iii) haplogroup J-M241 probably reflects the Neolithic westward expansion of farmers from the earliest sites along the Black Sea. On the whole, in light of the most recent historical studies, which indicate a substantial proto-Bulgarian input to the contemporary Bulgarian people, our data suggest that a common paternal ancestry between the proto-Bulgarians and the Altaic and Central Asian Turkic-speaking populations either did not exist or was negligible.

Link

Algerian Y chromosomes and mtDNA

From the paper:

For the R-M343 subdivision, the Iberian Peninsula reflects a genuine European profile [45] except for the presence of one Sahel R-V88 type. In contrast, all R-M343 detected in W. Saharan-Mauritanian belong to sub-group R-V88, reaching a frequency of 7%, similar to those observed in other Sahel samples [40]. In the Maghreb countries, the frequency of R-V88 drops to around 1%. On the other hand, the presence in this area of representatives of the European sub-groups R-M412, R-S116, R-U152 and R-M529 points to North-South maritime contacts across the Mediterranean

It would be interesting to estimate the depth of common ancestry of the North African "European" Y chromosomes to determine the epoch during which they arrived there, i.e., whether the common ancestry stems from recent historical contacts (Roman Empire, Vandals, etc.) or from the early settlement of both Mediterranean coasts during the arrival of R-M269 into Europe.

A few observations on Y-haplogroup frequencies:

• The ubuquity of haplogroup Q at trace frequencies in most regions except North Africa (only a little in ALG) is interesting and it's high time that someone looked at the relationship between West Eurasian Q-bearers and their much more numerous East Eurasian cousins.
• I find the paucity of Y-haplogroup I in North Africa noteworthy; given its high levels in most of Western Europe, its relative absence might indicate that the people who brought "European" R-M269 into N Africa were not occasional recent migrants, but rather earlier settlers. 
• The relative absence of J2 is expected, given that neither of the two main strata of population ("Berber" and "Arab") may have possessed it initially; it has also not been found in a historical sample from the Canary Islands, whereas its J1 counterpart has.
• The paucity of haplogroup G, which is the European Neolithic lineage par excellence probably argues against the involvement of the people who colonized Europe during the Early Neolithic in similar events on the south shore of the Mediterranean.
• The further study of F chromosomes could also be further attempted, given their possible involvement in the Upper Paleolithic of Eurasia

The authors highlight that 80% of mtDNA is Eurasian vs. 90% of Y chromosomes. This might point to asymmetric gene flow from Sub-Saharan Africa. Alternatively, it might point to some mtDNA that is characterized as non-Eurasian (because it does not belong to the M, N macro-haplogroups) being in fact so. It is a persistent question whether lineages that have a wide frequency differential in two regions do so because of gene flow (from the high- to low-frequency area), or because of other processes.

PLoS ONE 8(2): e56775. doi:10.1371/journal.pone.0056775

Introducing the Algerian Mitochondrial DNA and Y-Chromosome Profiles into the North African Landscape

Asmahan Bekada et al.

North Africa is considered a distinct geographic and ethnic entity within Africa. Although modern humans originated in this Continent, studies of mitochondrial DNA (mtDNA) and Y-chromosome genealogical markers provide evidence that the North African gene pool has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. More recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North-South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the Maghreb. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population using mtDNA sequences and Y-chromosome biallelic polymorphisms, focusing on the fine dissection of haplogroups E and R, which are the most prevalent in North Africa and Europe respectively. The Eurasian component in Algeria reached 80% for mtDNA and 90% for Y-chromosome. However, within them, the North African genetic component for mtDNA (U6 and M1; 20%) is significantly smaller than the paternal (E-M81 and E-V65; 70%). The unexpected presence of the European-derived Y-chromosome lineages R-M412, R-S116, R-U152 and R-M529 in Algeria and the rest of the Maghreb could be the counterparts of the mtDNA H1, H3 and V subgroups, pointing to direct maritime contacts between the European and North African sides of the western Mediterranean. Female influx of sub-Saharan Africans into Algeria (20%) is also significantly greater than the male (10%). In spite of these sexual asymmetries, the Algerian uniparental profiles faithfully correlate between each other and with the geography.

Link

Y chromosome study of Italy (Brisighelli et al. 2012) incl. sample of Greek speakers from Salento

This is a wonderful new source of information on Y-chromosome variation in Italy, that also includes some samples of the linguistic minorities of Ladins and Griko speakers.

The latter is particularly interesting to me, because, these last Greeks of Magna Graecia are descended either from the ancient colonists or medieval Eastern Roman settlers, and as such may represent a group of Greek descendants that (i) may have admixed to some extent with local Italic speakers, but (ii) will not have had an opportunity to experience much post-medieval gene flow that may have affected Greeks from the Aegean.

There may be something wrong with the presentation of the haplogroup frequencies on the left; in particular, based on the text, I think that what appears as R1* is in fact R1*(xR1a1).

In any case, here are my observations on the Grecani Salentini sample:

• They, as well as the Messapi, possess the highest frequencies of E-M78. This ties them to the Balkans in a very obvious way; this haplogroup was also interpreted as a signal of Greek colonization in Sicily and Massalia. This seems like the most obvious explanation; note that Salento is in Messapia, so the high frequency in the non-Greek denizens of the region may be simply the result of language shift, since the remaining Greek speakers are presumably the last remnant of a once much more numerous population that was linguistically Italicized as have most other Greek speaking populations of Italy and Sicily.
• Their highest frequency haplogroups are R1*(xR1a1) and J2. Both are fairly common haplogroups in both Greece and Italy, so only a fine-scale analysis would be able to differentiate between what might be pre-Greek and what is Greek in origin. In any case, I have proposed that these two haplogroups were typical of (albeit not limited to) the Graeco-Phrygo-Armenian clade, so their occurrence in this sample is not surprising.
• There is an occurrence of I*(xM26) chromosomes. This requires finer phylogenetic resolution, but certainly the absence of M26 -which has a SW European distribution- is interesting to note.
• Haplogroup G-M201 again requires finer-scale resolution, and could be anything from a relative of the Neolithic Italians (having been found in the Tyrolean Iceman) to much more recent events.
• Within haplogroup J, the majority of the chromosomes belong to clade J2, with about a tenth of the frequency made up of J*(xM62, M172). Note that these are not necessarily J*(xJ1,J2) as indicated in the figure, since M62 defines only a part of the J1 lineage.
• The absence of haplogroup R1a1 in this sample is perhaps the most interesting finding. This occurs at a frequency of ~10% in Greek samples from Greece and is fairly variable. I have previously observed that it was absent in the south stream of Indo-European based on its paucity in Armenians, Albanians, and its uneven distribution in Greeks. Its absence in the Italian Griko sample reinforces this idea. A caveat, however, is that the origin of the Greek settlement of Italy can be traced to southern Greece and western Anatolia, so it's still possible that some R1a1 was present in other areas of the Aegean basin since pre-medieval times.

The authors of the paper use many conventional labels of what is "Neolithic" and what is not (e.g., R1*(xR1a1) is claimed as Mesolithic). But, certainly, both age estimation of modern chromosomes (e.g., Wei et al. 2012) and the ancient Y chromosome studies cast doubt on this association. I would say that rather than being predominantly pre-Neolithic, it might appear that the Y-chromosome gene pool of Italy may have been formed in late Neolithic to medieval times, with the only lineages that can convincingly trace their ancestry to the Neolithic or earlier epochs being G and I-M26.

As for the Ladins, the high frequency (67.7%) of R1*(xR1a1) is consistent with what I believe to have been the main Italo-Celtic lineage.

Finally, I should point out the occurrence of a couple of haplogroup L samples; this haplogroup is more typical of populations much to the east, being the "eastern" cousin of the more "western" haplogroup T within the LT clade. Certainly a finer-scale resolution of these two L samples might be informative about their potential origins and/or the ancient distribution of this rather mysterious haplogroup.

PLoS ONE 7(12): e50794. doi:10.1371/journal.pone.0050794

Uniparental Markers of Contemporary Italian Population Reveals Details on Its Pre-Roman Heritage

Francesca Brisighelli et al.

Abstract
Background

According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country.

Methods/Principal Findings

A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers.

Conclusions/Significance

Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.

Link

rolloff analysis of Lezgins as Sardinian+Burusho

I have carried out rolloff analysis of Lezgins, a Northeast Caucasian population that is of particular interest due to it being modal for the "Dagestan" component whose long-distance relationships with Western Europe and South Asia have triggered a great deal of followup investigation on my part.

The Lezgins are also interesting for other reasons: they may be one of the populations related to the Kura-Araxes culture; they possess a high frequency of Y-haplogroup R1b, so they may be related to the migration that brought this haplogroup into Europe from West Asia.

In my previous analysis of the French using the same reference populations, I speculated that their signal of admixture may involve admixture between a Sardinian-like and a West Asian population in Asia itself circa 7,000 years ago, followed by a later expansion into Europe. And, in my analysis of Lithuanians and Ukrainians, I discovered a somewhat less "old" signal of admixture involving South Asian+North European references with a mean value of 5.5-6.3ky for the various population pairs.

The exponential fit for the Lezgins can be seen below:

The admixture time estimate is 198.773 +/- 70.649 generations or 5,760 +/- 2,050 years. This is not very precise, but seems consistent with the two phenomena described above. It also seems to contrast with the much younger signal for Armenians.

3D laser scan of Stonehenge reveals axehead graffiti

Stonehenge up close: digital laser scan reveals secrets of the past

The first complete 3D laser scan of the stone circle has also revealed tool marks made 4,500 years ago, scores of little axehead graffiti added when the enormous slabs were already 1,000 years old, and damage and graffiti contributed by Georgian and Victorian visitors. 

...

Long after the monument was built, when Bronze Age burial mounds rich in grave goods began to be scattered across the plain around Stonehenge, and the archaeological evidence suggests those who could make or trade in metal goods had an almost shamanic status, people carved little images of daggers and axes, many now invisible to the naked eye, into the stones. Scores more have been revealed by the scan, including 71 new axe heads, bringing the total to 115 – doubling the number ever recorded in Britain.

"It is wonderful to have discovered so many more, but what is fascinating is that they are carved without regard to the importance or the siting of the stones – almost as if the people who carved them could no longer quite remember the significance of the monument and how it worked," Greaney said.

They probably could no longer remember, because they were Indo-European newcomers, and not the same people as the Megalithic folk who built Stonehenge.

A little history:

Craniologists of the time used a ratio based on length and width measurements, known as the cranial index, to divide skulls into two basic types: 'dolichocephalic', long and narrow in shape, and 'brachycephalic', broad and round in shape. Based on his observations at sites like Belas Knap, Thurnam established his famous axiom, 'long barrows, long skulls; round barrows, round skulls'. The long skulls were found in long barrows and never in association with metallic artefacts, while round skulls were found in round barrows sometimes with metalwork. 

... 

Thurnam's and Rolleston's theories gained considerable credibility in the late Victorian period and survived well into the earlier 20th century. Such racist theories failed to stand up, however, in the face of Gordon Childe's arguments for the definition of an archaeological culture based on shared social characteristics and material culture rather than race or biological type. In addition, the considerable moral repugnance felt towards Victorian anthropology and its role in the rise of fascist ideology in the 1930s caused the argument over long and round skulls to be sidelined and eventually dismissed. The identification of the Bronze Age incomers based on their material culture, including metalwork and Beaker pottery vessels, remained a more acceptable alternative.
In the 1990s, however, the archaeologist Neil Brodie took a fresh look at the craniological evidence and concluded that there was undeniably a difference between the shape of skulls from Neolithic long barrows and Bronze Age round barrows. A trend from long to round skull shape was clearly shown. 

The differences, he argued, could be caused by cultural practices, such as the binding of infants' heads, as well as by diet and a range of climatic or environmental factors. Looking at the totality of human history, he showed that head shape fluctuates in populations over long periods of time, and that extremes of head types occur in successive prehistoric populations as a matter of historical chance.

We don't have DNA evidence from British round barrows yet, but Beaker burials from Germany show the first R1b ever found, while Neolithic Western Europe shows a mix of I2a and G2a. Difference in material culture? check. Difference in physical anthropology? check. Difference in time of appearance? check. Difference in genetics? preliminary check.

So, it seems like a good bet that the people who carved axehead graffiti on Stonehenge were simply invaders who took over the site from the previous inhabitants, and, as is so often the case, used it for their own purposes.

rolloff analysis of South Indian Brahmins as Armenian+Chamar

The first analysis of this population showed that there were negative f3(Brahmin; X, Y) signals when X were a variety of West European, Balkan, and West Asian population, and Y either the Chamar or North Kannadi. In the first analysis I used Orcadians and North Kannadi. I have now carried out a new rolloff analysis on 470,559 SNPs, using Armenians_Y and Chamar_M as the reference populations.

The exponential fit can be seen below.

The admixture date is 142.814 +/- 15.010 generations, or 4,140 +/- 440 years, which seems to correspond quite well with commonly accepted dates for the formation of Indo-Iranian.

I have previously observed that:

These patterns can be well-explained, I believe, if we accept that Indo-Iranians are partially descended not only from the early Proto-Indo-Europeans of the Near East, but also from a second element that had conceivable "South Asian" affiliations. The most likely candidate for the "second element" is the population of the Bactria Margiana Archaeological Complex (BMAC). The rise and demise of the BMAC fits well with the relative shallowness of the Indo-Iranian language family and its 2nd millennium BC breakup, and has been assigned an Indo-Iranian identity on other grounds by its excavator. As climate change led to the decline and abandonment of BMAC sites, its population must have spread outward: to the Iranian plateau, the steppe, and into South Asia, reinforcing the linguistic differentiation that must have already began over the extensive territory of the complex.

Quite possibly, as the West Asian element began mixing with the Sardinian-like population in Greece, another branch of the Indo-Europeans made its appearance east of the Caspian, in the territory of the BMAC, admixing with South Asian-like populations. Thus, it might seem that the Graeco-Aryan clade of Indo-European broke down during the Bronze Age, with one branch heading off to the Balkans, and another to the east. 

This scenario would also explain how the likely J2-bearing population associated with the earliest Proto-Indo-Europeans may have acquired the contrasting pattern I have previously described: the western (cis-Caspian) population would have admixed with R1b-bearers who occupy the "small arc" west and south of the Caspian, while the eastern (trans-Caspian) populations would have admixed with R1a-bearers who occupy the "large arc" in the flatlands north and east of the Caspian. It would also explain how the "western" branch (Graeco-Armenian) would have picked up Sardinian-like "Atlantic_Med" admixture, which is absent in the "eastern" Indo-Iranian branch.

At the same time, this scenario would explain the lack of "North European" admixture in the "western" branch (since this was shielded by the Caucasus and Black Sea from the northern Europeoids who may have lived north of these barriers), and explain it in the "eastern" branch (since the BMAC agriculturalists were in contact with presumably northern Europeoid groups inhabiting the steppelands, unhindered by any major physical barriers). (The relative absence of this admixture in the Graeco-Armenian branch may be advanced on the strength of its absence in Armenians, the evidence of a Sardinian-like Iron Age individual from Bulgaria, and the historical-era timing of admixture for the Greek population.)

It would be interesting to carry out similar experiments on Iranian groups, to see if they, too, present a similar pattern of admixture.

Polish and German Y-chromosomes

I have often bemoaned the use of present-day populations as stand-ins for dealing with the subject of very old archaeological phenomena such as the Neolithic transition. Of course, I understand that until a few years ago, this was all we had to work with. But, this idea is now suspect, having been made so by a two-pronged attack. On the ancient DNA side, researchers have consistently discovered that for the better part of prehistory, ancient populations did not match modern ones: even if the constituent elements of later evolution could be identified, they were still in polarized non-admixed form as in the case of the Neolithic Swedes. On the recent side, researchers have used surnames or even toponyms to show that ethnic admixture in the recent historical past has shifted Y-chromosome frequencies around.

A new paper in EJHG follows on this tradition by comparing pre- and post-WWII patterns of Y chromosome variation in Germany and Poland. Y-haplogroup frequencies can be seen on top left. From the caption: "Phylogenetic relationship and frequencies of Y-chromosomal haplogroups in the studied populations. Ka Kaszuby; Ko Kociewie; Ku Kurpie; Lu Lusatia; Sl Slovakia; Me Mecklenburg; Ba Bavaria."

It is important to note that the researchers were able to study pre-war populations, because most everybody knows where their patrilineal ancestor lived less than 100 years ago. But, European history consists of many events whose effects on the current population are less known, because they occurred at an older time. In some cases, populations may have migrated (such as the Germans of eastern Europe following WWII), in others populations that have once existed there have almost disappeared, or become much less numerically significant (such as the Ashkenazi Jews due to persecution during WWII and after it through migration to Israel and elsewhere, or various Christian and Jewish communities that once flourished throughout the Middle East). Other, less known groups, such as the Old Prussians or the Jassic speakers of Hungary have been presumably absorbed by surrounding majorities, or through a process of elite dominance.

In many cases, the available information, in the form of linguistic, genealogical, or historical evidence, can be used to remove layers of admixture, migration, and extinction in history; but, the gap between the deep prehistoric past and the recent, historical one cannot be bridged by these methods alone. Ultimately, ancient DNA researchers must close in on the present by targeting more recent populations for analysis. As the realization of genetic change continues to amass on both sides of the divide, I suspect that this will come naturally, although I do expect some reticence to the findings as they begin to touch upon the most cherished origins traditions of the multitude of extant European nations.


European Journal of Human Genetics advance online publication 12 September 2012; doi: 10.1038/ejhg.2012.190

Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements

Krzysztof Rebala et al.

Abstract

Homogeneous Proto-Slavic genetic substrate and/or extensive mixing after World War II were suggested to explain homogeneity of contemporary Polish paternal lineages. Alternatively, Polish local populations might have displayed pre-war genetic heterogeneity owing to genetic drift and/or gene flow with neighbouring populations. Although sharp genetic discontinuity along the political border between Poland and Germany indisputably results from war-mediated resettlements and homogenisation, it remained unknown whether Y-chromosomal diversity in ethnically/linguistically defined populations was clinal or discontinuous before the war. In order to answer these questions and elucidate early Slavic migrations, 1156 individuals from several Slavic and German populations were analysed, including Polish pre-war regional populations and an autochthonous Slavic population from Germany. Y chromosomes were assigned to 39 haplogroups and genotyped for 19 STRs. Genetic distances revealed similar degree of differentiation of Slavic-speaking pre-war populations from German populations irrespective of duration and intensity of contacts with German speakers. Admixture estimates showed minor Slavic paternal ancestry (~20%) in modern eastern Germans and hardly detectable German paternal ancestry in Slavs neighbouring German populations for centuries. BATWING analysis of isolated Slavic populations revealed that their divergence was preceded by rapid demographic growth, undermining theory that Slavic expansion was primarily linguistic rather than population spread. Polish pre-war regional populations showed within-group heterogeneity and lower STR variation within R-M17 subclades compared with modern populations, which might have been homogenised by war resettlements. Our results suggest that genetic studies on early human history in the Vistula and Oder basins should rely on reconstructed pre-war rather than modern populations.

Link

East Eurasian-like admixture in Northern Europe (part 2)

This is a continuation of my earlier post. Please refer to it for the methodology. A new part 3 can be found here.

I have repeated the experiment with a much larger set of populations:

English_D, British_D, Ukranians_Y,  Karitiana, Spaniards, Sardinian,  Serb_D, Mordovians_Y, Irish_D,  French, Finnish_D, Chuvashs_16,  Romanian_D, N_Italian_D, French_Basque,  Austrian_D, Russian_D, Hungarians_19,  Kent_1KG, German_D, Belorussian,  Tuscan, Lithuanian_D, Orkney_1KG,  Dutch_D, TSI30, Ukrainian_D,  Bulgarians_Y, Bulgarian_D, Russian,  Swedish_D, Pais_Vasco_1KG, French_D,  Castilla_Y_Leon_1KG, Lithuanians, San,  Polish_D, Romanians_14, Orcadian,  Cornwall_1KG, Valencia_1KG, North_Italian,  FIN30, Norwegian_D, CEU30

I used Sardinians as the Caucasoid reference population, Karitiana for Mongoloids, and San for Africans. The latter two were chosen because they live at maximally opposite corners of the Earth (South America vs. South Africa).

A first plot of the f4 statistics used for f4 regression ancestry estimation is seen below:

Clearly, some evidence of a cline is present, but several populations appear to deviate from it. In order to get the cleanest possible cline, I carried out the following greedy procedure: I calculate the correlation coefficient of this set, and iteratively remove one population that leads to the maximum improvement of the correlation, until no further improvement takes place. The following populations were removed with this procedure:

Spaniards, Serb_D, Romanian_D, N_Italian_D, Tuscan, TSI30, Bulgarians_Y, Bulgarian_D, Castilla_Y_Leon_1KG, Romanians_14, Valencia_1KG

This seems to make sense, as all these are southern European populations. Note that their removal does not mean that they do not partake in the same phenomenon as northern Europeans: they also exhibit Karitiana-shift relative to the Sardinians, but there are probably other confounding factors that make them fall "off-cline". Including them would diminish the clarity of the cline for Northern European populations. The regression of the remaining populations can be seen on the right:

f4 regression ancestry estimation results are shown on the left. These appear to be much higher than was the case with the Han and Dai in the previous experiment.

I can't say that I've made any obvious mistakes, but these admixture proportions are substantial, and call for an explanation. Whatever their true levels, I am fairly confident on at least a few points:

First, it is evident that northern Europeans have higher levels of this element than southern Europeans; the latter are not altogether deficient in it, but they fall "off-cline", making estimation of their admixture proportions more difficult.

Second, within northern Europe, there is a fairly clear east-west cline of diminishing Amerasian-like admixture. The minimum occurs in Sardinians and secondarily in Southwest Europe. Romance, Celtic, and Germanic populations all have less of it than Balto-Slavic and Uralic ones. And, some populations of northeastern Europe seem to have a noticeable excess of it.

The groups with the most Amerasian-like admixture possess Y-haplogroup N, a clear trace of eastern ancestry that is not shared by most Europeans. The arrival of this haplogroup, either with Comb Ceramic of the Baltic Neolithic or later with Seima Turbino Bronze Age expansions is probably responsible for the local excess in Northeastern Europe. The Chuvash are, of course, a Turkic population but of Finno-Ugrian genetic origin.

But, the presence of this element even in Western Europe cannot be explained on the basis of typically Mongoloid elements which are almost completely lacking there. If Mesolithic Europeans were themselves Asian-shifted, then this would account for the presence of the element, but not necessarily for its clinal manifestation. The double (north-south and east-west) cline indicates every sign of an intrusive element. So, for the time being, I will propose that this is associated with late (e.g., Copper and Bronze Age) phenomena, such as the northern stream of the Bronze Age Indo-European invasion of Europe.

This may be due to the

• (i) northern Indo-European groups picking up some native east European or Siberian elements as they made their way into Europe, 
• or (ii), more likely, in my opinion, that the Y-haplogroup R1 group of people, whose closest relatives are in Central/South Asia (R2) , and whose more distant relatives (Q) are in Siberia and the Americas, were from the beginning an "intermediate population" between West and East Eurasia. The R1 group of people in its R1b and R1a varieties first appear in Europe during the Copper Age, and they are lacking in early Neolithic sites.

Eight years ago, and in a totally different context, I wrote:

Similarly, 9 out of 10 Basques are descended from a man who has also fathered 9 out of 10 Kets from Siberia and 9 out of 10 Maya Indians from America. That man, founder of haplogroup P thus has descendants who belong to two of the major human races (or three, if Amerindians are considered as separate from Asian Mongoloids)   

... 

In conclusion, human continental populations form groups of genetic and phenotypic similarity, and these groups can be considered races in the phenetic sense. However, these groups are not monophyletic, hence in the cladistic sense they should not be considered as valid taxa. Since the principle of common descent is generally applied in modern systematics (or at least it should!), I think it's best not to recognize human subspecies. 

If these data pan out, it may be revealed that the European branch of the Caucasoids is actually a product of admixture too, with at least two of its constituent elements being the "Palaeo-West Eurasians" (Y-haplogroups G, IJ, possibly LT) and the "Neo-NW Eurasians" (Y-haplogroups N1 and R1), with the "Neo-Afrasians" (Y-haplogroup E1b1b) forming a third element.

(A raw dump of fourpop output can be found here).

African Y chromosome news (E1b1a and R-V88)

European Journal of Human Genetics advance online publication 15 August 2012; doi: 10.1038/ejhg.2012.176

Evidence from Y-chromosome analysis for a late exclusively eastern expansion of the Bantu-speaking people

Naser Ansari Pour1, Christopher A Plaster1 and Neil Bradman1

Abstract

The expansion of the Bantu-speaking people (EBSP) during the past 3000–5000 years is an event of great importance in the history of humanity. Anthropology, archaeology, linguistics and, in recent decades, genetics have been used to elucidate some of the events and processes involved. Although it is generally accepted that the EBSP has its origin in the so-called Bantu Homeland situated in the area of the border between Nigeria and the Grassfields of Cameroon, and that it followed both western and eastern routes, much less is known about the number and dates of those expansions, if more than one. Mitochondrial, Y-chromosome and autosomal DNA analyses have been carried out in attempts to understand the demographic events that have taken place. There is an increasing evidence that the expansion was a more complex process than originally thought and that neither a single demographic event nor an early split between western and eastern groups occurred. In this study, we analysed unique event polymorphism and short tandem repeat variation in non-recombining Y-chromosome haplogroups contained within the E1b1a haplogroup, which is exclusive to individuals of recent African ancestry, in a large, geographically widely distributed, set of sub-Saharan Africans (groups=43, n=2757), all of whom, except one Nilo-Saharan-speaking group, spoke a Niger-Congo language and most a Bantu tongue. Analysis of diversity and rough estimates of times to the most recent common ancestors of haplogroups provide evidence of multiple expansions along eastern and western routes and a late, exclusively eastern route, expansion.

Link

European Journal of Human Genetics advance online publication 15 August 2012; doi: 10.1038/ejhg.2012.167

The genetic landscape of Equatorial Guinea and the origin and migration routes of the Y chromosome haplogroup R-V88

Miguel González1, Verónica Gomes1,2, Ana Maria López-Parra3, António Amorim1,4, Ángel Carracedo2, Paula Sánchez-Diz2, Eduardo Arroyo-Pardo3 and Leonor Gusmão1

Abstract

Human Y chromosomes belonging to the haplogroup R1b1-P25, although very common in Europe, are usually rare in Africa. However, recently published studies have reported high frequencies of this haplogroup in the central-western region of the African continent and proposed that this represents a ‘back-to-Africa’ migration during prehistoric times. To obtain a deeper insight into the history of these lineages, we characterised the paternal genetic background of a population in Equatorial Guinea, a Central-West African country located near the region in which the highest frequencies of the R1b1 haplogroup in Africa have been found to date. In our sample, the large majority (78.6%) of the sequences belong to subclades in haplogroup E, which are the most frequent in Bantu groups. However, the frequency of the R1b1 haplogroup in our sample (17.0%) was higher than that previously observed for the majority of the African continent. Of these R1b1 samples, nine are defined by the V88 marker, which was recently discovered in Africa. As high microsatellite variance was found inside this haplogroup in Central-West Africa and a decrease in this variance was observed towards Northeast Africa, our findings do not support the previously hypothesised movement of Chadic-speaking people from the North across the Sahara as the explanation for these R1b1 lineages in Central-West Africa. The present findings are also compatible with an origin of the V88-derived allele in the Central-West Africa, and its presence in North Africa may be better explained as the result of a migration from the south during the mid-Holocene.

Link