Remains of Richard III identified

From the paper:

Four of the modern relatives were found to belong to Y-haplogroup R1b-U152 (x L2, Z36, Z56, M160, M126 and Z192)13, 14 with STR haplotypes being consistent with them comprising a single patrilinear group. One individual (Somerset 3) was found to belong to haplogroup I-M170 (x M253, M223) and therefore could not be a patrilinear relative of the other four within the time span considered, indicating that a false-paternity event had occurred within the last four generations. 

... 

In contrast to the Y-haplotypes of the putative modern relatives, Skeleton 1 belongs to haplogroup G-P287, with a corresponding Y-STR haplotype. Thus, the putative modern patrilinear relatives of Richard III are not genetically related to Skeleton 1 through the male line over the time period considered. However, this is not surprising, given an estimated average false-paternity rate of ~1–2% (refs 12, 17, 18). The putative modern relatives and Richard III are related through a male relative (Edward III) four generations up from Richard III (Fig. 1a and Supplementary Fig. 2), and a false-paternity event could have happened in any of the 19 generations separating Richard III and the 5th Duke of Beaufort, on either branch of the genealogy descending from Edward III. Indeed, even with a conservative false-paternity rate18 (see Supplementary Methods) the chance of a false-paternity occuring in this number of generations is 16%.

Nature Communications 5, Article number: 5631 doi:10.1038/ncomms6631

Identification of the remains of King Richard III

Turi E. King et al.

Abstract

In 2012, a skeleton was excavated at the presumed site of the Grey Friars friary in Leicester, the last-known resting place of King Richard III. Archaeological, osteological and radiocarbon dating data were consistent with these being his remains. Here we report DNA analyses of both the skeletal remains and living relatives of Richard III. We find a perfect mitochondrial DNA match between the sequence obtained from the remains and one living relative, and a single-base substitution when compared with a second relative. Y-chromosome haplotypes from male-line relatives and the remains do not match, which could be attributed to a false-paternity event occurring in any of the intervening generations. DNA-predicted hair and eye colour are consistent with Richard’s appearance in an early portrait. We calculate likelihood ratios for the non-genetic and genetic data separately, and combined, and conclude that the evidence for the remains being those of Richard III is overwhelming.

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)

Y chromosomes and mtDNA of early farmers from Hungary

A new preprint has just appeared on the bioRxiv. It's free to read so I'll just summarize some results. First:

The haplotype of the Mesolithic skeleton from the Croatian Island Korčula belongs to the mtDNA haplogroup U5b2a5 (Dataset S3). The sub-haplogroup U5b has been shown to be frequent in pre-Neolithic hunter-gatherer communities across Europe [28–30,32,33,45,46]. 

But:

Contrary to the low mtDNA diversity reported from hunter-gatherers of Central/North Europe [28–30], we identify substantially higher variability in early farming communities of the Carpathian Basin  including the haplogroups N1a, T1, T2, J, K, H, HV, V, W, X, U2, U3, U4, and U5a (Table 1). Previous studies have shown that haplogroups N1a, T2, J, K, HV, V, W and X are most characteristic for the Central European LBK and have described these haplogroups as the mitochondrial ʻNeolithic packageʼ that had reached Central Europe in the 6th millennium BC [36,37]. Interestingly, most of these haplogroups show comparable frequencies between the STA, LBKT and LBK,

N1a is the "signature group" of the LBK based on previous publications and now it seems that it was also found in the Starcevo culture of Hungary. The mtDNA PCA plot (right) shows clearly that the Hungarian farmers are very similar to the German ones so it seems that the LBK is a direct outgrowth of the Carpathian Neolithic; some earlier models of "demic diffusion" argued that Neolithic farmers spread slowly across Europe, picking up hunter-gatherer ancestry as they went along, but now it seems that at least in the Hungary->Germany part of this journey interaction with hunter-gatherers was minimum.

mtDNA change over time in Europe is pictured in Figure 3 (left) showing a shared haplotype analysis. The Y-chromosome data genetic distance is shown on the right and shows the Balkan-Anatolian-Caucasian-Mesopotamian relationship of the early farmer Y-chromosomes. Practically, this is due to haplogroup G2a (and especially G2a2b), which has turned up in lots of ancient European farmers (including the famous Iceman):

Three STA individuals belong to the NRY haplogroup F* (M89) and two specimens can be assigned to the G2a2b (S126) haplogroup, and one each to G2a (P15) and I2a1 (P37.2) (Dataset S3, S5). The two investigated LBKT samples carry haplogroups G2a2b (S126) and I1 (M253). Furthermore, the incomplete SNP profiles of eight specimens potentially belong to the same haplogroups; STA: three G2a2b (S126), two G2a (P15), and one I (M170); LBKT: one G2a2b (S126) and one F* (M89) (Dataset S5).

I believe this is the first ancient finding of haplogroup I1 which attains a peak in modern Swedes. This might be useful to those who have tied this to Germanic migrations because of this, as it was already in Central Europe with the earliest farmers.

Interestingly:

Surprisingly, Y chromosome haplogroups, such as E1b1b1 (M35), E1b1b1a1 (M78), E1b1b1b2a (M123), J2 (M172), J1 (M267), and R1b1a2 (M269), which were claimed to be associated with the Neolithic expansion [23–25], have not been found so far in the 6th millennium BC of the Carpathian Basin and Central Europe. Intriguingly, R1a and R1b, which represent the most frequent European Y chromosome haplogroups today, have been reported from cultures that emerged in Central Europe during the 3rd/2nd millennium BC, while a basal R type has been reported from a Palaeolithic sample in Siberia [60] in agreement with a proposed Central Asian/Siberian origin of this lineage. In contrast, G2a has not been detected yet in late Neolithic cultures [42,43]. This suggests further demographic events in later Neolithic or post-Neolithic periods.

A cautionary tale against over-reliance on modern distributions to trace ancient origins.

Also:

Considering the entire set of 32 published NRY records available for Neolithic Europe thus far, the low paternal diversity is indeed quite remarkable: G2a is the prevailing haplogroup in the Central European and Carpathian Basin Neolithic, and in French and Iberian Neolithic datasets [36,40,41]. There are only two exceptions, namely one E1b1b (V13) [41] individual from the Avellaner cave in Spain (~5,000-4,500 BC), and two I2a [40] individuals from Treilles, France (~3,000 BC).

biorxiv http://dx.doi.org/10.1101/008664

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization

Anna Szécsényi-Nagy et al.

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's Hungary. However, the genetic background of the LBK genesis has not been revealed yet. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (7th/6th millennium BC) from the Carpathian Basin and south-eastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early farming south-eastern European and Carpathian Basin cultures on Central European populations of the 6th-4th millennium BC. Our comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through south-eastern Europe and the Carpathian Basin into Central Europe. Our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting patrilineal descent system and patrilocal residential rules among the early farmers.

Link

Afghan mega-paper (Di Cristofaro et al.)

The admixture results nicely presented on a map:

The authors note that none of the ancestral components peaks in Central Asia, concluding that this region has been a destination rather than a source of population movements. I certainly agree that Central Asia has a lot of recent history affecting it from virtually all directions. On the other hand, we should be cautious about interpreting geographical clines in terms of directionality of population movement; a good example is Sardinia which often emerges as a "focus" of Mediterranean ancestry, but this does not mean that it is the origin of such ancestry. It would certainly be interesting to remove the layers of more recent ancestry from Central Asia to see what was there before the last few thousand years.

The PCA based on autosomal data:

The Y-chromosome haplogroup data can be found in Figure S7. The authors comment:

94% of the chromosomes are distributed within the following 9 main haplogroups: R-M207 (34%), J-M304 (16%), C-M130 (15%), L-M20 (6%), G-M201 (6%), Q-M242 (6%), N-M231 (4%), O-M175 (4%) and E-M96 (3%). Within the core haplogroups observed in the Afghan populations, there are sub-haplogroups that provide more refined insights into the underlying structure of the Y-chromosome gene pool. One of the important sub-haplogroups includes the C3b2b1-M401 lineage that is amplified in Hazara, Kyrgyz and Mongol populations. Haplogroup G2c-M377 reaches 14.7% in Pashtun, consistent with previous results [31], whereas it is virtually absent from all other populations. J2a1-Page55 is found in 23% of Iranians, 13% of the Hazara from the Hindu Kush, 11% of the Tajik and Uzbek from the Hindu Kush, 10% of Pakistanis, 4% of the Turkmen from the Hindu Kush, 3% of the Pashtun and 2% of the Kyrgyz and Mongol populations. Concerning haplogroup L, L1c-M357 is significantly higher in Burusho and Kalash (15% and 25%) than in other populations. L1a-M76 is most frequent in Balochi (20%), and is found at lower levels in Kyrgyz, Pashtun, Tajik, Uzbek and Turkmen populations. Q1a2-M25 lineage is characteristic of Turkmen (31%), significantly higher than all other populations. Haplogroup R1a1a-M198/M17 is characterized by its absence or very low frequency in Iranian, Mongol and Hazara populations and its high frequency in Pashtun and Kyrgyz populations.

PLoS ONE 8(10): e76748. doi:10.1371/journal.pone.0076748

Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge

Julie Di Cristofaro et al.

Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.

Link

Y-chromosome and mtDNA of Henri IV

A recent paper had determined the Y-chromosome haplotype of Louis XVI of France from a handkerchief preserving his blood after his execution. A new study looks at the mummified head of Henri IV, the first Bourbon King of France. Even though only a limited number of Y-STRs were successfully typed, they match those of Louis XVI, who belonged to the not-so-frequent-anymore haplogroup G2a. So, while we cannot be entirely sure that the two Y-chromosomes were related in a genealogical time frame, the evidence is consistent with their known genealogical relationship and with the attribution of the two samples (mummified head/blood) to the respective kings.

Also of interest, Henri IV's mtDNA haplotype:

The majority of the clones generated show an U5b* mtDNA haplotype defined by three nucleotide changes at positions 16239T 16270T 16311C (see Supplementary material). The three HVR1 diagnostic positions were confirmed in two different amplifications of the L16185-H16378 HVR1 fragment, proving that the results are reproducible. This mtDNA haplotype is present so far in one single individual from France (originally published in [10]) in an in-house database of 22,807 published European sequences, and it is absent in all people involved in the laboratory analysis.

 If I followed the trail of ancestry correctly, this matrilineage leads all the way to a Tochter von Egisheim in the 11th century.

Forensic Science International Available online 30 December 2012

Genetic comparison of the head of Henri IV and the presumptive blood from Louis XVI (both Kings of France)

Philippe Charlier et al.

A mummified head was identified in 2010 as belonging to Henri IV, King of France. A putative blood sample from the King Louis XVI preserved into a pyrographically decorated gourd was analyzed in 2011. Both kings are in a direct male-line descent, separated by seven generations. We have retrieved the hypervariable region 1 of the mitochondrial DNA as well as a partial Y-chromosome profile from Henri IV. Five STR loci match the alleles found in Louis XVI, while another locus shows an allele that is just one mutation step apart. Taking into consideration that the partial Y-chromosome profile is extremely rare in modern human databases, we concluded that both males could be paternally related. The likelihood ratio of the two samples belonging to males separated by seven generations (as opposed to unrelated males) was estimated as 246.3, with a 95% confidence interval between 44.2 and 9729. Historically speaking, this forensic DNA data would confirm the identity of the previous Louis XVI sample, and give another positive argument for the authenticity of the head of Henri IV.

Link

The comings and goings of Near Eastern and European domestic pigs (Ottoni et al. 2012)

This is an excellent paper whose findings re: pig domestication seem to parallel many of my own observations regarding the flow of human populations. It is open access, so you can read it for yourselves, but the following figure illustrates the situation admirably:

The left-right arrangement of the columns corresponds to a west-east longitude across West Asia. It can be easily seen that some of the early domestic samples (yellow, bottom row) are concentrated in the west (Y1 haplotype), while others (blue, Arm1T) in the east.

Neolithic European samples possessed the Y1 haplotype, but lacked the Arm1T one. So, the authors conclude that:

The ancient Anatolian data presented here reveal that both wild and possibly domestic Neolithic pigs (identified using traditional metrics) possessed Y1 haplotypes ... The presence of these lineages corroborates the supposition that the earliest domestic pigs in Europe originated from populations originally domesticated in the Near East, conclusively linking the Neolithization of Europe with Neolithic cultures of western Anatolia (Larson et al. 2007a; Haak et al. 2010).

I have repeatedly highlighted the "puzzle" of the early European Neolithic: the signature Y-haplogroup G2a was unaccompanied by other common Near Eastern lineages, and the modal "West Asian" ancestral component in present-day West Asian populations seems to have been absent in early Neolithic samples, which were dominated by a "Sardinian-like" population. I have argued that this meant that the European Neolithic was drawn from a limited founder source that was more "Mediterranean/Southern" autosomally than "West Asian", at least in terms of the components identified by the Dodecad Project.

In Europe itself, the early Near Eastern domestic pigs were replaced by European ones:

Ancient DNA extracted from early Neolithic domestic pigs in Europe resolved this paradox by demonstrating that early domestic pigs in the Balkans and central Europe shared haplotypes with modern Near Eastern wild boar (Larson et al. 2007a). The absence of Near Eastern haplotypes in pre-Neolithic European wild boar suggested that early domestic pigs in Europe must have been introduced from the Near East by the mid 6th millennium BC before spreading to the Paris basin by the early 4th millennium BC (Larson et al. 2007a). 

By 3,900 BC, however, virtually all domestic pigs in Europe possessed haplotypes  from an indigenous European domestication process (Larson et al. 2007a) only found in European wild boar. This genetic turnover may have resulted from the accumulated introgression of local female wild boar into imported domestic stocks, or from an indigenous European domestication process (Larson et al. 2007a).

We have seen that early Neolithic domestic pigs came from Western Anatolia, but apparently these did not last, but were replaced in Europe by pigs carrying mtDNA of European wild boar. An additional possibility is that the European wild boar were better adapted to local conditions in Europe, so the stock of European farmers gradually became "local" due to artificial/natural selection favoring the local "European" type. It might also be that in accordance with Bergmann's rule, European-descended pigs were simply bigger, and thus more economically productive.

In any case, the interesting thing is that pigs carrying the "European" haplotype went the other way, crossing from Europe to Asia. The beginning of this process seems to have occurred in the Middle Bronze Age:

The temporal and geographic distribution of genetic haplotypes presented in our study demonstrates that the first AMS dated pig with European ancestry (haplotype A) appeared almost 1,000 years earlier than the Armenian samples in a Late Bronze Age context (~1,600-1,440 BC) at Lidar Höyük (fig. 1). An even earlier Middle Bronze Age specimen from the same site also possessed a European signature, but a direct
AMS date for this specimen could not be obtained.

I have written how increased mobility and long-range networks associated with the new metallurgical class facilitated commerce during the Bronze Age. The authors suggest the possibility of Minoan-Mycenaean/Hittite involvement during the Bronze Age, which are certainly plausible conduits for European pigs to have crossed the Aegean at this time. But, as you can see from the figure, the "European" pigs are still outliers during the Middle and Bronze Ages, but become common in the Iron Age sample from Lidar Höyük, and eventually replacing local types throughout Anatolia and Armenia, but, apparently, not Iran:

The frequency of pigs with European ancestry increased rapidly from the 12th century BC, and by the 5th century AD domestic pigs exhibiting a Near Eastern genetic signature had all but disappeared across Anatolia and the southern Caucasus. Though we did not detect European signatures in the ancient Iranian samples (fig. 1), the eastward spread of European lineages may have continued into Iran later than the Iron Age since European lineages have been found in wild caught modern Iranian samples (Larson et al. 2007a).

Of course a 12th century BC increase in European domestic pigs is entirely consistent -chronologically- with the Phrygian/Armenian settlement in Anatolia, and this association is further reinforced by the lack of European signatures in pigs from Iran where Phrygo-Armenians did not settle. The increase in European pigs could later be mediated by the Greek colonization, and the increase in trade during antiquity, just as trade would later introduce East Asian pig DNA into Europe.

The beautiful temporal transect presented in the Figure may also prove useful for students of ancient human DNA. I'd love to see how humans living close to sites #14-16, dominated by Arm1T haplotypes throughout history might differ from those of Neolithic West Anatolia, and whether the "mixed" Iron Age sample from Lidar Höyük shows evidence of the arrival of European-like human populations to accompany the European pigs.

Mol Biol Evol (2012) doi: 10.1093/molbev/mss261

Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics

Claudio Ottoni et al.

Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or appeared so as a result of admixture between introduced pigs and European wild boar. These pigs not only replaced those with Near Eastern signatures in Europe, they subsequently also replaced indigenous domestic pigs in the Near East. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria and Turkey. Our results firstly reveal the genetic signature of early domestic pigs in Eastern Turkey. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, nearly 1,000 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the demographic and societal changes during the Anatolian Bronze and Iron Ages.

Link

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.

The genetic history of Europeans (Pinhasi et al. 2012)

This is a nice paper with extensive references on the topic of European origins. Two of its co-authors, Joachim Burger, and Ron Pinhasi are leading a couple of exciting new ancient DNA projects that will probably flood us with interesting new data in the years to come.

From the paper:

Human evolutionary history includes all the complex demographic, natural selection, and stochastic processes that have shaped our species. Despite the limitations of genetic and archaeological data to inform on all the details of human evolution, they constitute an irreplaceable source of information to appraise the key episodes that are likely to have had major impacts on patterns of genetic, morphological, and cultural variation. When considering AMH in Europe, three such critical periods are apparent: (i) the expansion of AMH out of Africa and their colonization of Europe approximately 45 000 years ago (45 ka), (ii) the last glacial maximum (LGM) and the formation of uninhabitable areas in Europe between 27 and 16 ka, and (iii) the arrival of Neolithic culture in southeast Europe and its spread throughout the rest of the continent between 9 and 5 ka. Here we review genetic evidence describing these major demographic episodes in the context of archaeological and chronological data. 

I have postulated that there was at least one important post-5ka event affecting Europe. But, in order to understand how events played out before 5ka and the present, we must first understand the background of what was taking place in Europe before 5ka.

On the earliest settlement of Europe:

Until recently, the earliest date for the first appearance of AMH in Europe had been set to around 42 to 43 ka solely based on their proposed association with Aurignacian artifacts (Table 1) [5,6]. New direct radiocarbon dates of fossils support this view and indicate that AMH appeared in Europe by 44.2– 41.5 calibrated (cal.) ka BP at Kent’s Cavern in southern England [6] and by 45–43 cal. ka BP in Grotta del Cavallo, Italy [7], whereas Neanderthals did not survive in most of Europe and the Caucasus after 39 cal. ka BP [8,9].

These dates are so close to the MP/UP transition in the Levant (49-46 cal ky BP), with the Aurignacian appearing shortly thereafter in both Central Europe and Italy. It would appear that modern humans swiftly colonized Europe after they made the crucial UP leap. Of course, in my opinion, this population was ultimately descended from inhabitants of Arabia, escaping post-70ka climatic deterioration and pre-100ka with the archaeologically attested Nubian Complex. But, in any case, it is probably the last crucial step, when humans went into warp drive post-50ka that led to the first modern human colonization of Europe and ultimately the extinction (or absorption?) of the Neandertals.

But, the early colonizers were in for a rough patch of climate that last for several millennia, making whole parts of Europe uninhabitable, and allowing few ones to survive in the south of the continent:

After the disappearance of the Neanderthals and particularly during the LGM, the northern parts of Europe were covered by ice sheets, leaving humans to survive in poorly resourced environments [10,11]. Parts of northern Europe were either completely abandoned [12] or sparsely populated [13]. The archaeological record of this period catalogs a complex series of interrelated material cultures that vary in their geographic ranges and temporal durations (Table 1). Spatial patterns of material culture change have been interpreted as indicating colonization of regions up to 52 degrees N latitude during the Gravettian, followed by partial or complete retreat of most northern populations by 24 ka, and recolonization of these regions by 20–16 ka, with some continuity of occupation in more southern latitudes [14]. However, the extent to which material cultures correspond to distinct human populations, and to which their distribu- tion changes through time correspond to demographic pro- cesses, remains unclear. 

The following table presents a very useful summary of archaeological developments in west Eurasia:

So far, we have substantial autosomal data of modern humans only from the Mesolithic onwards (Iberia), but also mtDNA from much older specimens of the Gravettian in Italy and Russia.

Apparently, other people are looking to extract ancient genomic DNA from older remains as well:

A group led by evolutionary geneticist Johannes Krause of the University of Tubingen, Germany, is trying to remove and reassemble nuclear DNA from the bones of roughly 20,000-year-old people in Europe. If successful, that effort will provide the first look at whether Stone Age humans carried more Neandertal genes than people today do. “It’s a completely open question whether more interbreeding occurred in the past than what we’ve found so far,” Krause says.

But, let's see where things stand now.

Ancient mtDNA sequences recovered from three Upper Paleolithic and 14 Mesolithic and Neolithic hunter-gatherers all belong to the mtDNA haplogroup U [48], currently found at frequencies between 1 and 7% in most modern European populations, but at up to 20% in Baltic populations and around 40% in Saami. Interestingly, almost all pre-Neolithic hunter-gatherers from Central and Northeastern Europe sequenced to date, and the majority of European post-Neolithic hunter-gatherers, carry U-type mtDNA [48,49] (Figure 1a,c). There are three exceptions: two Italian individuals with N* and pre-HV types [50], and one from Sweden [46]; the latter dating to the late Neolithic and possibly being the result of an admix- ture event with incoming farmers. In all other hunter- gatherer samples, the now common mtDNA lineages H, T, K, and J are absent, suggesting that these mtDNA lineages were introduced during the Neolithic period. 

The mtDNA evidence is indeed the strongest argument for large-scale population replacement during the Neolithic, a scenario which has found support by the sequencing of Neolithic hunter-gatherers from Gotland Sweden and Mesolithic ones from Iberia.

The authors note that while early farming groups largely lacked mtDNA haplogroup U, the later ones possessed it to some extent:

Maps showing Europe in times slices and depicting the locations from which ancient mitochondrial DNA (mtDNA) sequences were retrieved. Squares represent hunter-gatherer individuals and circles represent farming individuals. Lineages belonging to the U-clade are shown in red. Other lineages are shown in yellow. (a) Paleolithic and Mesolithic hunter-gatherers 13 500–8300 BP (plotted on a map of Europe during the last glacial maximum ca 22 000 BP). All Pleistocene hunter-gatherers analyzed to date carry mitochondrial lineages that belong to one of the U-clades: U2, U4, or U5. (b) Early farmers 7600–6500 BP. The map illustrates the approximate arrival times and duration of the earliest Neolithic cultures (in years BP). Very few of the early farmers belong to one of the U-clade mtDNA haplotypes, indicating discontinuity between Paleolithic/Mesolithic hunter-gatherers and early farmers [48,64]. (c) Later hunter-gatherers 6500–4500 BP. Whereas early hunter-gatherers carry exclusively mitochondrial U-lineages, later hunter-gatherers show additional lineages that are also present in early farming groups (b), pointing to a possible admixture between the groups or a change in lifestyle of former farmers back to hunting-gathering in Northern Europe. (d) Later farmers 6500–4500 BP. Compared to the period of the first appearance of farmers, late farmers have a significantly higher frequency of U-lineages. This can be explained by increasing rates of admixture between farmer and hunter gatherer groups during this period and by the adoption of a farming lifestyle by hunter-gatherers. The maps are adapted from [69] and show datapoints from [46,48,51, 54–56,61,62,64,70,71]. Abbreviation: BP, before present. 

And, of course, we have the ubiquitous Y-haplogroup G2a as the lineage par excellence of the first European farmers:

In contrast to mtDNA, ancient Y-chromosome data has until recently been less informative, but a single Y-chro-mosome haplotype (G2a) in 20 of 22 male individuals from the Late Neolithic cave site at Treilles [62] led to the hypothesis that a small male founding population arrived in Southern France, probably by a maritime route from the eastern Mediterranean, in the early Neolithic. The same haplotype was also found in five of six individuals from the Avellaner Cave [61] and in one out of three Central Euro-pean LBK individuals [63]. If authentic, the presence of the Y-chromosome haplogroup G2a in 26 of 31 Neolithic individuals from Germany, France, and Spain is both surprising and intriguing, but this requires further examination. 

The only high coverage genome sequence of a prehistoric European individual is that of the Tyrolean Iceman, Oetzi, a 5300 year-old individual from South Tyrol, which was recently reported at 7-fold coverage [45]. Comparison with 1300 contemporary Europeans indicated closest genetic affinities with southern Europeans, particularly inhabi-tants of the Tyrrhenian Islands. Intriguingly, this is also the region where the Y-chromosome haplotype of the Ice-man is found at highest frequency, and this haplotype belongs to the same G2a haplogroup described above.

And of course:

Future research should also reveal the effects of post-Neolithic demographic processes, including migration events, which preliminary data suggest had a major impact upon the distribution of genetic variation. These include events associated with Bronze Age civilizations, Iron Age cultures, and later migrations, including those triggered by the rise and fall of Empires.

The recovery of the European past has only just begun.

Trends in Genetics doi:10.1016/j.tig.2012.06.006

The genetic history of Europeans

Ron Pinhasi, Mark G. Thomas, Michael Hofreiter, Mathias Currat, Joachim Burger

The evolutionary history of modern humans is characterized by numerous migrations driven by environmental change, population pressures, and cultural innovations. In Europe, the events most widely considered to have had a major impact on patterns of genetic diversity are the initial colonization of the continent by anatomically modern humans (AMH), the last glacial maximum, and the Neolithic transition. For some decades it was assumed that the geographical structuring of genetic diversity within Europe was mainly the result of gene flow during and soon after the Neolithic transition, but recent advances in next-generation sequencing (NGS) technologies, computer simulation modeling, and ancient DNA (aDNA) analyses are challenging this simplistic view. Here we review the current knowledge on the evolutionary history of humans in Europe based on archaeological and genetic data.

Link

Y chromosomes and mtDNA from late antique Bavaria

One of the papers in the aforementioned volume includes Y-STR and mtDNA data on a burial cemetery from Bavaria dating to the Imperial Roman age. I reproduce the DNA results below; the haplogroup assignments in red are my own and have been estimated with Whit Athey's haplogroup predictor using both Northwest European and Equal priors.

The number of Y-STRs is not sufficient to make very strong haplogroup assignments in some cases. Still, we can probably say that R1b, E1b1b, and I1 were present in the population. I1 might seem more likely than G2a in a few cases, but remember that a couple of G2a men were found in 7th c. Bavaria. E1b1b, another non-typical German haplogroup has also been found in Usedom from the medieval period.

Christina Sofeso, Marina Vohberger, Annika Wisnowsky, Bernd Päffgen, Michaela Harbeck, *

Verifying archaeological hypotheses: Investigations on origin and genealogical lineages of a privileged society in Upper Bavaria from Imperial Roman times (Erding, Kletthamer Feld)



During the years 2005 and 2006 approximately 2000 archaeological

finds ranging from the Neolithic Period to Late Antiquity 

were found on the Kletthamer Feld (Erding, Upper Bavaria). 

Out of this context a burial site was examined comprising 

13 individuals, some of them rich in precious grave goods. The 

inhumations were dated to the second half of the 4th to the first 

half of the 5th century – a time of upheavals in relation to the 

demographic structure of the former Roman province Raetia (today southern Bavaria).

The high proportion of male individuals within the skeletal population as well as the finding of a Roman fibula, which is seen as part of Roman military clothing, led to distinct hypotheses which we have attempted to support in this study. The hypothesis that the skeletal remains reflect a founder population from a Germanic region north of the Danube River could be rejected on the basis of stable isotope analyses. The theory of a buried family clan had to be dismissed as well, or rather, be extended to the scenario of several families being buried there with their servants. The results obtained fit the third presumption best, namely that the buried individuals were the members of a military unit interred with their families.

Major new paper on Y chromosome haplogroup G (Rootsi et al. 2012)

Haplogroup G is of substantial interest to prehistorians, because it has been sampled on multiple Neolithic locations from across Europe. A new paper updates the phylogeny of this important haplogroup (left), and studies its distribution. You can find information about the frequency of different haplogroup G subclades in the freely available supplementary material (Table 1).

From the paper:

First, we calculated haplogroup diversity using data in Supplementary Table S1 for the 52 instances when total population sample size exceeded 50 individuals and Z5 hg G chromosomes were observed. Then we applied a 10% overall hg G frequency threshold and the additional specification that both haplogroup G1 and G2 lineages also be present. In the ten remaining populations, haplogroup diversity spanned from a low of 0.21 in Adyghes, to highs of 0.88 in Azeris (Iran) and 0.89 in eastern Anatolia and 0.90 in Armenia. We estimate that the geographic origin of hg G plausibly locates somewhere nearby eastern Anatolia, Armenia or western Iran. The general frequency pattern of hg G overall (Figure 2a) shows that the spread of hg G extends over an area from southern Europe to the Near/Middle East and the Caucasus, but then decreases rapidly toward southern and Central Asia.

It is certainly interesting that the estimated region of origin of haplogroup G intersects my so-called "womb of nations", out of which I believe flowed populations after the inception of the Neolithic. The rapid diminution of this haplogroup in Central/South Asia may be compatible with the relative lack of the K=7 "Southern" autosomal component in populations of the area, in contrast to a couple of Neolithic European farmers (the Tyrolean Iceman and Gok4). The Iceman himself belonged to haplogroup G, and so did individuals from Derenburg LBK, and Treilles.

A couple of lineages of interest are M527 which is a low-frequency haplogroup which the authors associate with Greek colonization and the Sea Peoples, and L497 which they associate with the LBK. It would certainly be interesting to test for the latter in some of the existing ancient DNA samples.

Finally, the following is of interest:

Concerning the presence of hg G in the Caucasus, one of its distinguishing features is lower haplogroup diversity in numerous populations (Supplementary Table S1) compared with Anatolia and Armenia, implying that hg G is intrusive in the Caucasus rather than autochthonous. Another notable feature is its uneven distribution. Hg G is very frequent in NW Caucasus and South Caucasus, covering about 45% of the paternal lineages in both regions2 in this study. Conversely, hg G is present in Northeast Caucasus only at an average frequency of 5% (range 0–19%). Interestingly, the decrease of hg G frequency towards the eastern European populations inhabiting the area adjacent to NW Caucasus, such as southern Russians and Ukrainians,18,40 is very rapid and the borderline very sharp, indicating that gene flow from the Caucasus in the northern direction has been negligible.

Unfortunately, we currently lack ancient Y-DNA samples from West Asia. But, certainly, the samples we do have from Europe are indicative of shifts in West Asia as well, since the predominance of Y-haplogroup G in Neolithic Europe is hardly compatible with a haplogroup composition in the eastern source areas similar to today's.

Rather, it begins to appear that there once was a (roughly speaking) western-eastern-southern distribution of the G/R1/J2 lineages in the territory of West Asia; this would be compatible with both the Neolithic European G dominance, the paucity of G in Central/South Asia, and its NW/S vs. NE Caucasus differentiation.

European Journal of Human Genetics advance online publication 16 May 2012; doi: 10.1038/ejhg.2012.86

Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus

Siiri Rootsi et al.

Haplogroup G, together with J2 clades, has been associated with the spread of agriculture, especially in the European context. However, interpretations based on simple haplogroup frequency clines do not recognize underlying patterns of genetic diversification. Although progress has been recently made in resolving the haplogroup G phylogeny, a comprehensive survey of the geographic distribution patterns of the significant sub-clades of this haplogroup has not been conducted yet. Here we present the haplogroup frequency distribution and STR variation of 16 informative G sub-clades by evaluating 1472 haplogroup G chromosomes belonging to 98 populations ranging from Europe to Pakistan. Although no basal G-M201* chromosomes were detected in our data set, the homeland of this haplogroup has been estimated to be somewhere nearby eastern Anatolia, Armenia or western Iran, the only areas characterized by the co-presence of deep basal branches as well as the occurrence of high sub-haplogroup diversity. The P303 SNP defines the most frequent and widespread G sub-haplogroup. However, its sub-clades have more localized distribution with the U1-defined branch largely restricted to Near/Middle Eastern and the Caucasus, whereas L497 lineages essentially occur in Europe where they likely originated. In contrast, the only U1 representative in Europe is the G-M527 lineage whose distribution pattern is consistent with regions of Greek colonization. No clinal patterns were detected suggesting that the distributions are rather indicative of isolation by distance and demographic complexities.

Link

Serbian Y-chromosomes

Gene. 2012 Jan 31. [Epub ahead of print]

High levels of Paleolithic Y-chromosome lineages characterize Serbia.

Regueiro M, Rivera L, Damnjanovic T, Lukovic L, Milasin J, Herrera RJ.

Abstract

Whether present-day European genetic variation and its distribution patterns can be attributed primarily to the initial peopling of Europe by anatomically modern humans during the Paleolithic, or to latter Near Eastern Neolithic input is still the subject of debate. Southeastern Europe has been a crossroads for several cultures since Paleolithic times and the Balkans, specifically, would have been part of the route used by Neolithic farmers to enter Europe. Given its geographic location in the heart of the Balkan Peninsula at the intersection of Central and Southeastern Europe, Serbia represents a key geographical location that may provide insight to elucidate the interactions between indigenous Paleolithic people and agricultural colonists from the Fertile Crescent. In this study, we examine, for the first time, the Y-chromosome constitution of the general Serbian population. A total of 103 individuals were sampled and their DNA analyzed for 104 Y-chromosome bi-allelic markers and 17 associated STR loci. Our results indicate that approximately 58% of Serbian Y-chromosomes (I1-M253, I2a-P37.2, R1a1a-M198) belong to lineages believed to be pre-Neolithic. On the other hand, the signature of putative Near Eastern Neolithic lineages, including E1b1b1a1-M78, G2a-P15, J1-M267 and J2-M172 and R1b1a2-M269 accounts for 39% of the Y-chromosome. Furthermore, an examination of the distribution of Y-chromosome filiations in Europe indicates extreme levels of Paleolithic lineages in a region encompassing Serbia, Bosnia-Herzegovina and Croatia, possibly the result of Neolithic migrations encroaching on Paleolithic populations against the Adriatic Sea.

Link

Complete genome of the Tyrolean Iceman

I'll update this post once I read the paper. I could not locate a source for the data after a quick scan of the paper, but:

After genotyping, we merged both HapMap and 1,000 Genomes genotypes with the Popres/Iceman-merged dataset, resulting in a final analysis dataset containing 125,729 SNPs. PCA was then performed on all samples, excluding the five 1,000 Genomes samples, which were subsequently projected onto the PC space inferred from the rest of the dataset.

UPDATE: The Iceman's genome can be found at the http://icemangenome.net site.

UPDATE I (Y-chromosome):


From the paper:

We addressed this issue here by analysing the G2a4-defining L91 SNP in 7,797 chromosomes from 30 regions across Europe. Fig. 3d shows the spatial frequency distribution of G2a4 throughout Europe. The highest frequencies (25 and 9%) occur in southern Corsica and northern Sardinia, respectively, (Fig. 3e) while in mainland Europe the frequencies do not reach 1%.

UPDATE II (Autosomal DNA): 

In terms of autosomal DNA, the Iceman clearly clusters with modern Sardinians, and also appears slightly more removed than them compared to continental Europeans. Interestingly, at least as far as the PC analyssi shows, Sardinians appear to be intermediate between the Iceman and SW Europeans, rather than Italians. Perhaps, this makes sense if the Paleo-Sardinian language is indeed related to languages of Iberia.

I don't see a downloadable version of the Iceman's genome at the icemangenome.net site, but I've asked the corresponding author for a PLINK/EIGENSOFT version of it. I anticipate that, as I've predicted, this will appear to be largely "Mediterranean" according to Dodecad v3, or "Atlantic_Med" according to the newer K12b calculator. It appears that there has indeed been Sardinian continuity against a backdrop of European discontinuity.

UPDATE III (Sardinians):


The Iceman's genome also places the Sardinian genetic isolate into new light. Two explanations have been proposed for the fact that Sardinians appear genetically distinctive vis a vis continental Europeans:

1. Sardinians have lost due to drift alleles that were present in continental Europe
2. Continental Europeans have gained alleles that were not present in their Sardinian-like ancestors

The Iceman's genome argues strongly in favor of the latter hypothesis: continental Europeans, or, at least North Italians c. 5,300 years ago were more Sardinian-like, and they have become less Sardinian-like up to the present, probably due to an influx of new populations, carrying new alleles. As more ancient DNA is recovered, we will slowly witness the transformation of gene pools over time.

Nature Communications 3, Article number: 698 doi:10.1038/ncomms1701

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

Andreas Keller et al.

The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.

Link

Armenian Y-chromosomes revisited (Herrera et al. 2011)

Armenian Y-chromosomes have been a largely ignored since the publication of the classic Weale et al. (2001) paper a decade ago. The Armenian DNA Project has largely covered the void during the intervening years, but it is nice that the topic is revisited by academics.

Armenia is sandwiched between Anatolia, the Fertile Crescent, the Iranian plateau, the Caucasus, and the Black and Caspian seas, making the study of Armenian Y-chromosomes extremely interesting for the student of Eurasian prehistory.

Gene flow from the surrounding regions may have affected the Armenian population over historical time, but the remoteness of the Armenian highlands, coupled with the national church -- which distinguished Armenians from both the Orthodoxy of the Roman Empire, the Zoroastrianism of the Persians, and, later the Islam of Arabs and Ottomans -- may have prevented it.

My comments on the paper will follow below once I read it.

UPDATE I: The paper spends a lot of time on analysis of Y-STR variance; my opinion of Y-STRs as a tool for inferring past population movements is, to put it mildly, low. When Bahamian Y-STR variance is higher than African one, and E-V13, one of the youngest European Y-haplogroups (in terms of Y-STR variance) turns up in Spain in one of the earliest ancient DNA samples, it goes without saying that the burden of proof is on those who wish to continue to talk about Neolithic or other population movements to make the assumptions of their models clearer. Nonetheless, there is still some utility in Y-STRs, so I reproduce some tree diagrams from the paper (top left), and link to the supplementary info that has a collection of haplotypes that may be useful to genealogists.

From the paper:

However, owing to the contentions associated with the current calibrations of the Y-STR mutation rates,32,34,35,41 as well as the limitations of the assumptions utilized by the methodologies for time estimations, the absolute dates generated in this study should only be taken as rough estimates of upper bounds.

Indeed. We are at the point where Y-STRs are at the end of their utility, but the replacement technology of extensive Y-chromosome sequencing has not quite arrived in an economical way yet.

UPDATE II: I will have some additional thoughts on Y-chromosome distribution in the third update, but, for the time being, the two most important "nuggets" of information are: (i) the unusual haplogroup frequencies in Sasun (high R2 and T), which may be due to a founder effect, but it would be interesting if Armenian historians could find some explanation for their occurrence there, and (ii) the occurrence of R-M269*(xL23) in Ararat Valley. I invite more knowledgeable readers to comment on the issue; the haplotypes are in Table 2 of the supplement.

UPDATE III: The ubuiquity of haplogroup G2a in Neolithic Europe, coupled with the absence of other prominent present-day European haplogroups, has important implications about European discontinuity.

But, it also has implications about West Asian discontinuity. The Neolithic in Europe arrived by all accounts from either of two principal areas: Anatolia or the Levant. Today, in Anatolia and the Levant, we see a set of haplogroups of which haplogroup J is the most important and ubiquitous one. Haplogroup R1b is also quite frequent in Armenia, the east Caucasus, Anatolia, and Iran, but its frequency drops dramatically to the east and south. And, there is a whole assortment of other haplogroups with varying frequency.

Why didn't all these non-G2a haplogroups participate in the early Neolithic colonization of Europe? It could very well be that a very small founder population crossed the Aegean into Europe, one that happened to be G2a-dominated. But, that is ultimately not very satisfying: if there was plenty of J and R1b in West Asia at the time of the Neolithic expansion, why are these haplogroups so conspicuous in their absence -at least so far- from Neolithic Europe?

The case of haplogroup J is particularly problematic. If we had to guess, by looking at present-day distribution, which lineage tracks population movements from the Near East to Europe, there is simply no better candidate: every map of this haplogroup, and especially of its J2a sublineage shows an unambiguous pattern of radiation, with a core area consisting of Southern Italy, Greece, Anatolia, West Asia, Mesopotamia and the northern parts of the Levant. All these regions are crucial to the story of the Neolithic, so the absence of J in Neolithic Europe is perplexing.

And, the story has other complications. From the current paper:

The relative expansion times for haplogroup J2-M172 (Table 4) generally correspond with those yielded for R1b-M343, with the exception of Greece and Crete, which, unlike haplogroup R1b-M343, are slightly older than the dates yielded for several of the Near Eastern groups as well as the four Armenian populations.

As mentioned above, I don't give much weight on Y-STR evidence, but observations such as the above certainly add to the feeling of unease that something is not quite right with the default picture of prehistory.

Another observation on the Armenian population, is its very low frequency of haplogroup R1a1. Proponents of the Kurgan model of Indo-European dispersals sometimes associate this haplogroup with the Proto-Indo-European community, and it is strange why -if their ideas are right- Armenia is so lacking in this haplogroup, like its Caucasian neighbors. Why would these hypothetical migrants make such a huge impact in faraway India and barely a dent in nearby Armenia?

Finally, the occurrence of some I2, E-V13, and, perhaps, J2b in Armenia may point to Balkan contacts. But, when did these contacts occur? Are they traceable to the migration of Phrygians to Anatolia, according to the Herodotean account of Armenian origins, or can they be attributed to later contacts with Greeks or other Europeans?

The veil of mystery seems to be raised even higher by every new study: we may be less certain of what really happened today than in the days of happy ignorance, ten years ago. Ultimately it is new data, like the ones included in this paper, that will make every piece of evidence fit, and the grand puzzle of the history of Eurasia will be revealed in all its glory.

European Journal of Human Genetics , (16 November 2011) | doi:10.1038/ejhg.2011.192

Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists

Kristian J Herrera, Robert K Lowery, Laura Hadden, Silvia Calderon, Carolina Chiou, Levon Yepiskoposyan, Maria Regueiro, Peter A Underhill and Rene J Herrera

Abstract
Armenia, situated between the Black and Caspian Seas, lies at the junction of Turkey, Iran, Georgia, Azerbaijan and former Mesopotamia. This geographic position made it a potential contact zone between Eastern and Western civilizations. In this investigation, we assess Y-chromosomal diversity in four geographically distinct populations that represent the extent of historical Armenia. We find a striking prominence of haplogroups previously implicated with the Agricultural Revolution in the Near East, including the J2a-M410-, R1b1b1*-L23-, G2a-P15- and J1-M267-derived lineages. Given that the Last Glacial Maximum event in the Armenian plateau occured a few millennia before the Neolithic era, we envision a scenario in which its repopulation was achieved mainly by the arrival of farmers from the Fertile Crescent temporally coincident with the initial inception of farming in Greece. However, we detect very restricted genetic affinities with Europe that suggest any later cultural diffusions from Armenia to Europe were not associated with substantial amounts of paternal gene flow, despite the presence of closely related Indo-European languages in both Armenia and Southeast Europe.

Link

Y-haplogroups E-V13 and G2a in Neolithic Spain

I have not read the paper, so I can't comment in detail. Two quick comments:

• The discovery of G2a is added to the finds from Treilles, Derenburg, and the Alps. It is now virtually certain that the Neolithic transition in much of Europe, both inland, and coastal involved G2a-bearing men.
• The discovery of E-V13 in Spain is unexpected on a number of different reasons: there is relatively little of it there now; it had previously been associated with the inland route of the spread of agriculture, as well as the spread of the Greeks to Sicily and Provence, or Roman soldiers at a much later date.

While this Neolithic E-V13 may well have come from the Balkans, and the common ancestor of the very uniform present-day Balkan cluster may have lived after this Spanish find, it is now certain that E-V13 was established in Europe long before the Bronze Age. This highlights the need to avoid Y-STR based calculations on modern populations for inferring patterns of ancient history, and not to conflate TMRCAs with "dates of arrival": "In short: a particular TMRCA is consistent with either the arrival of the lineage long before and long after the TMRCA in a particular geographical area."

At least for now, three of the major players of the European genetic landscape (E-V13, G2a, and I2a) have made their Neolithic appearance. Hopefully, as more ancient DNA is published, and even from later dates, more of them will turn up.

I will comment more when I get to read the paper.

UPDATE I:

From the paper:

For the six male samples, two complete and four partial Y-STRs haplotypes were obtained (Table 3). They allowed classification of individuals into two different haplogroups: G2a (individuals ave01, ave02, ave03, ave05, and ave06, which seem to share the same haplotype) and E1b1b1 (individual ave07). The four markers chosen to confirm belonging to these haplogroups (Y-E1b1b1-M35.1, Y-E1b1b1a1b-V13, Y-G2-M287, and Y-G2a-P15) were typed with a rate of 66%, which permitted confirmation that four males were G2a and one was E1b1b1a1b (Table 3).

Analysis of shared haplotypes showed that the G2a haplotype found in ancient specimens is rare in current populations: its frequency is less than 0.3%(Table S3). The haplotype of individual ave07 is more frequent (2.44%), particularly in southeastern European populations (up to 7%). The Ave07 haplotype was also compared with current Eb1b1a2 haplotypes previously published (10–14). It appeared identical at the seven markers tested to five Albanian, two Bosnian, one Greek, one Italian, one Sicilian, two Corsican, and two Provence French samples and are thus placed on the same node of the E1b1b1a1b-V13 network as eastern, central, and western Mediterranean haplotypes (Fig. S1).

The ancient remains all appeared to lack the common European lactase persistence genotype.

On the mtDNA:

Mitochondrial HVS-I sequences were obtained for the seven individuals and can be classified into four different haplotypes (Table 2). All are still frequent in current European populations (Table S1), and three of them were also found in ancient Neolithic samples (Table S2). These haplotypes permitted the determination that the individuals ave01, ave02, and ave06 belonged to K1a, ave04 and ave05 to T2b, ave03 to H3, and ave07 to U5 haplogroups.

The supporting information (pdf) has a lot of additional information.

PNAS doi: 10.1073/pnas.1113061108

Ancient DNA suggests the leading role played by men in the Neolithic dissemination

Marie Lacan et al.

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 y 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.

Link

Sardinian continuity against a backdrop of European discontinuity

Ancient DNA research from Europe has tended to paint a picture of substantial population discontinuity. In a Neolithic sample from Derenburg, neither of the two major Y-chromosome haplogroups prevalent in Central-Northern Europe, R1 and I were found. The Tyrolean Iceman belongs to haplogroup G2a4, a minor lineage in modern-day Europeans. In a Neolithic site from the French south, Treilles, haplogroups G2 and I2 were found, the major R1 lineage again being absent. Megalithic mtDNA from France complements that from the Linearbandkeramik in suggesting a picture of discontinuity, or, at least, substantial change, in the occupation of Europe since the Neolithic. An upcoming study suggest that mtDNA haplogroup X2 did not arrive in Central Europe with the early LBK Neolithic, but with the later Bell Beaker folk. The picture of discontinuity, at least for the Mesolithic-Neolithic transition is supported from Scandinavia, as well as Luxembourg. To cap it all off, a pair of unexpected results from Hungary and Ukraine stretch the contact zone of West/East Eurasian populations well to the west of what has already been determined by ancient DNA work in the Tarim basin and Siberia.


There is, however, one population that stands as an outlier against the backdrop of discontinuity: Sardinians. Ghirotto et al. inferred population continuity in Sardinian mtDNA at least until the Bronze Age. Stories about the Tyrolean Iceman, confirmed in the NOVA TV documentary suggest that a 5,000-year old denizen of Central Europe was genetically closest to Sardinians. A study of craniofacial variation confirms population continuity in Sardinia since the Neolithic, with the population of peninsular Italy gradually diverging, consistent with the Iceman findings. Substantial frequencies of Y-haplogroups G and I are found in modern Sardinian newborns, the same two haplogroups detected in Neolithic southern France at Treilles. And, a study of European genetic isolates finds Sardinians to be lacking in some European polymorphic sites, suggesting a degree of genetic isolation compared to mainland Europeans; this is consistent with my own finding that Sardinians are maximally "western" along the east-west Eurasian axis.

Two cryptic bits of revealed information suggest that a major event may have happened in Europe. In an ICHG 2011 talk, David Reich revealed that his lab has unpublished work of ancient admixture in Europe and that "Europeans are anciently mixed just like South Asians." A blog post by Ewen Callaway suggests that Zink's Tyrolean Iceman investigators are asking "whether he and his kin died out and were replaced by migrants from elsewhere, such as the Middle East."

In the absence of concrete data, it is difficult to interpret such hints of things to come. But the idea of an episode of admixture in Europe from the East that would leave a South Asian-like cline of diminishing West Asian ancestry is supported by admixture studies of West Eurasians, showing that the Near-East to Atlantic-Baltic vector captures the principal aspect of variation in this region.


Interestingly, a "West Asian" ancestral component centered on the South Caucasus region has an Fst distance of 0.028 with the main European "Atlantic-Baltic" component, and of 0.058 with a "Southern" component present at non-trivial amount in southern populations from both sides of the Mediterranean and the Near East.

The possibility of a major east-west population movement into Europe that left Sardinians least affected is intriguing. At K=7 Sardinians have almost none of the "West Asian" ancestral component and most of the "Southern" one in Europe. This appears to be consistent with a population that was least affected by population movements from the northern parts of West Asia.

If I had to guess, I would propose that most extant Europeans will be discovered to be a 2-way West Asian/Ancestral European mix, just as most South Asians are a simple West Asian/Ancestral South Indian mix. In both cases, the indigenous component is no longer in existence and the South Asian/Atlantic_Baltic components that emerge in ADMIXTURE analyses represent a composite of the aboriginal component with the introduced West Asian one. And, like in India, some populations will be discovered to be "off-cline" by admixture with different elements: in Europe these will be Paleo-Mediterraneans like the Iceman, an element maximally preserved in modern Sardinians, as well as the East Eurasian-influenced populations at the North-Eastern side of the continent.


In a roundabout manner, the Caucasus and its environs may soon reclaim their position as the fons gentium that Blumenbach, more than two centuries ago, ascribed to them. More than one century ago, Italian anthropologist Giuseppe Sergi, proposed a model of the double origin of Europeans, supposing that the Mediterraneans of southern Europe (a branch of the "Eurafricans") were invaded by peoples from the east, the "Eurasiatics." Naturally, the ideas of Blumenbach and Sergi cannot be adopted today in their entirety, but they do well to remind us that inklings of truth can be found in the most unexpected of places.


And, when one reads this quote from Carleton Coon's classic 1939 synthesis The Races of Europe (section "The western Mediterranean Islands")... "Sardinia and Corsica were peopled at the beginning of the Neolithic by a race of short-statured, dolichocephalic, low-vaulted, brunet Mediterraneans, coming probably from several quarters, including the adjacent European coasts, North Africa, and the eastern Mediterranean. Subsequent immigrations of other Mediterranean peoples have affected the racial composition of these islands but little." ... one is inclined to say "Dr. Coon, you were right!"