Wednesday, May 10, 2017

Big Ancient DNA Paper Preprints

The Bell Beaker Behemoth Paper


The biggest news from the Bell Beaker Behemoth paper is that Iberian Bell Beaker individuals have almost no genetic overlap with central European Bell Beaker individuals.

The Iberians were local Neolithic farmers who evolved in material culture, which was adopted culturally by people with high proportions of steppe ancestry outside of Iberia. 

The non-Iberians had predominantly Y-DNA R1b-S116 and considerable steppe ancestry, with higher levels of hunter-gatherer ancestry than the Iberians and central-Northern European Neolithic ancestors, although proportions of steppe ancestry varied greatly. But, British Neolithic ancestry and Southern French Neolithic ancestry was from Iberia.

Still as Bell Beaker blogger notes in his commentary:
* Beaker appears to have come directly from the Pontic-Caspian steppe while absorbing LBK-like or admixed ancestry. Census estimates and other data supports this.
* Many of their mito-profiles look steppic. . . .
* Skin, eyes and LP basically identical to Yamnaya, changes over time. (Which I still don't get)
* Not a trickle of people. Waves of immigrants first into Europe, then the isles with massive population increases following (older papers below).
The Paper

The Bell Beaker ancient DNA paper is expected here. The abstract is as follows:
Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200-1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. 
In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900-1200 BCE. 
British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion. 
Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain's Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.
I. Olalde, et al., "The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe" (May 9, 2017).

This abstract adds surprisingly little to the abstract of a previously announced conference paper by the same authors about which I made a number of observations.

The Y-DNA Results
We determined Y-chromosome haplogroups for the 54 male Beaker-associated individuals (Supplementary Table 3). Individuals from the Iberian Peninsula carried Y haplogroups known to be common across Europe during the earlier Neolithic period such as I2a (n=3) and G2 (n=1) (Supplementary Table 3). In contrast, Beaker-associated individuals outside Iberia (n=44) largely carried R1b lineages (84%), associated with the arrival of Steppe migrants in central Europe during the Late Neolithic/Early Bronze Age. For individuals in whom we could determine the R1b subtype (n=22), we found that all but one had the derived allele for the R1b-S116/P312 polymorphism, which defines the dominant subtype in western Europe today. Finding this early predominance of the R1b-S116/P312 polymorphism in ancient individuals from central and northwestern Europe suggests that people associated with the Beaker Complex may have had an important role in the dissemination of this lineage throughout most of its present-day distribution.
mtDNA Results

The mtDNA Atlas blog notes some of the interesting mtDNA results from today's papers:
-A high frequency of K1(mostly K1c) in Mesolithic Serbia/Romania. Recall that K1b2 was found in Mesolithic Lithuania a few months ago and K1c was found in Mesolithic Greece a few years ago. 
-High frequency U5a and hg I in British Bell Beaker and British Bronze age. Low frequency of H in British Bell Beaker and British Bronze age. 
-High frequency of H1 and K1a in British, Iberian Neolithic. 
-Several examples of H1b in Eastern European Neolithic (Poland, Ukraine). 
-Middle Eastern mHG R0a1 in Bulgarian Yamnaya. This individual genetically clusters between the Middle East and other Yamnaya individuals.   
The British population turnover
our results imply a minimum of 93±2% local population turnover by the Middle Bronze Age (Supplementary Information, section 6). Specifically, for individuals from Britain around 2000 BCE, at least this fraction of their DNA derives from ancestors who at 2500 BCE lived in continental Europe. An independent line of evidence for population turnover comes from Y-chromosome haplogroup composition: while R1b haplogroups were completely absent in the Neolithic samples (n=25), they represent 95% and 75% of the Y-chromosomes in Beaker Complex-Early Bronze Age and Middle Bronze Age males in Britain, respectively (Fig. 3b; Supplementary Table 3).
Pertinent to this finding is another key paper from a couple of years ago cited by Rob in comments at the Bell Beaker blog:
This paper rewrites the early history of Britain, showing that while the cultivation of cereals arrived there in about 4000 cal BC, it did not last. Between 3300 and 1500 BC Britons became largely pastoral, reverting only with a major upsurge of agricultural activity in the Middle Bronze Age. This loss of interest in arable farming was accompanied by a decline in population, seen by the authors as having a climatic impetus. But they also point to this period as the time of construction of the great megalithic monuments, including Stonehenge. We are left wondering whether pastoralism was all that bad, and whether it was one intrusion after another that set the agenda on the island.
Chris J. Stevens and Dorian Q Fuller, Did Neolithic farming fail? The case for a Bronze Age agricultural revolution in the British Isles (January 2, 2015).

Phenotype associated genetics
Derived alleles at rs12913832 (SLC45A2) and rs16891982 275 (HERC2/OCA2), which contribute to reduced skin and eye pigmentation in Europeans, dramatically increased in frequency during the Beaker and Bronze Age periods (Extended Data 277 Fig. 5). Thus, the arrival of migrants associated with the Beaker Complex significantly altered the pigmentation phenotypes of British populations. 
However, the lactase persistence allele at SNP rs4988235 remained at very low frequencies in our dataset both in Britain and continental Europe, showing that the major increase in its frequency in Britain, as in mainland Europe, occurred in the last 3,500 years.
The very late and thus even harder than expected sweep of the lactase persistence allele is very surprising. The widespread assumption was that the selective fitnesses enhancing effect of this gene rode piggyback on the Bell Beaker expansion or even was present in the seed Bell Beaker population from the steppe. This evidence, pretty convincingly, says no. The sweep hasn't even really started as of about 1500 BCE and it wasn't a result of the population replacement in Britain and much of Western Europe with steppe-like people.

Moreover, we know that after 1500 BCE the gene pool of Western Europe was substantially similar to what it is today, although there were differences in detail.* This hard sweep has become even more of a mystery than it was before this study came out. And, this hard sweep had to have been propelled almost entirely by its intrinsic selective fitness enhancing properties without otherwise disrupting the population structure of Europe. It seems likely that there is some unknown phenotypic property of the LP genes which is European specific and incredibly fitness enhancing. My best guess at this point is that the LP gene in pregnant women greatly reduces the odds of miscarriage and lowers infant mortality for their children and greatly reduces maternal mortality because it enhances the health of the pregnant woman.

* As Razib notes:
In the context of this paper the Anglo-Saxon migrations tackled by the PoBI paper are minor affairs because the two populations were already genetically rather close. Additionally, the PoBI paper found that the German migrations were significant demographic events, but most of the ancestry across Britain does date to the previous period.
Razib states that this is consistent with the result in Iain Mathieson, et al., "Eight thousand years of natural selection" (October 10, 2015). That paper says:
The strongest signal of selection is at the SNP (rs4988235) responsible for lactase persistence in Europe. Our data strengthens previous reports that an appreciable frequency of lactase persistence in Europe only dates to the last four thousand years. The allele’s earliest appearance in our data is in a central European Bell Beaker sample (individual I0112) that lived between approximately 2300 and 2200 BCE. 
The frequency of the derived LP gene is currently 75%. It was about 1% in Neolithic Britons and not more than about 5% in the Bell Beaker people.

Razib also notes that there is significant late Bronze Age/post-Bronze Age selection for SLC45A2 (associated with light skin color) and HERC2-OCA2 (associated with blue eyes) in the post-Bell Beaker era of the last 4,000 years, because while the ancestral darker skin, brown eyed versions of these alleles was less common in the steppe folk than in the Neolithic British, the ancestral versions were still much more common then than they are today.

Derived HERC2 was present in about 20% of the Neolithic British, 65% of the Bell Beaker British, and about 80% of the modern British.  About 4% of the Neolithic British had blue eyes. About 45% of the Bell Beaker British had blue eyes. About 64% of the modern British have blue eyes.

SLC45A2 was present in about 25% of the Neolithic British, about 68% of the Bell Beaker British, and about 96% or more of the modern British. (It is 82% in Iberians and a bit lower in Sardinians according to Razib.) More than half of the Neolithic would have been much darker skinned, about one in nine Bell Beaker British would have been much darker skinned, and about one in 2,500 or less of the ancestrally European British are that dark skinned now.  A study from a year ago by Field, et al., finds selection on this gene within the last 2,000 years.

Autosomal genetics
We grouped Beaker Complex individuals based on geographic proximity and genetic similarity (Supplementary Information, section 4), and used qpAdm2 to model their ancestry as a mixture of western European hunter-gatherers (WHG), northwestern Anatolian farmers, and Yamnaya steppe pastoralists (the first two of which contributed to earlier European farmers; Supplementary Information, section 6). 
We find that the great majority of Beaker Complex individuals outside of Iberia derive a large portion of their ancestry from Steppe populations (Fig. 2a), whereas in Iberia, such ancestry is absent in all sampled individuals, with the exception of two (I0461 and I0462) from the Arroyal I site in northern Spain. We detect striking differences in ancestry not only at a pan-European scale, but also within regions and even within sites. Unlike other individuals from the Upper Alsace region of France (n=2), an individual from Hégenheim resembles previous Neolithic populations and can be modelled as a mixture of Anatolian Neolithic and western hunter-gatherers without any Steppe-related ancestry. Given that the radiocarbon date of the Hégenheim individual is older (2832–2476 cal BCE) (quoting 95.4% confidence intervals for this and other dates) (Supplementary Information, section 1) than other samples from the same region (2566–2133 cal BCE), the pattern could reflect temporal differentiation. At Szigetszentmiklós in Hungary, we find Beaker Complex- associated individuals with very different proportions (from 0% to 74%) of Steppe ancestry but  overlapping dates.  . . .
there is genetic affinity to Iberian Early Neolithic farmers in Iberian Middle Neolithic/Copper Age populations, but not in central and northern European Neolithic populations (Fig. 2b), which could be explained by differential affinities to hunter-gatherer individuals from different regions (Extended Data Fig. 2). A new finding that emerges from our analysis is that Neolithic individuals from southern France and Britain also show a greater affinity to Iberian Early Neolithic farmers than to central European Early Neolithic farmers (Fig. 2b), similar to previous results obtained in a Neolithic farmer genome from Ireland. By modelling Neolithic populations and WHG in an admixture graph framework, we replicate these results and further show that they are not driven by different proportions of hunter-gatherer admixture (Extended Data Fig. 3; Supplementary Information, section 5). Our results suggest that a portion of the ancestry of the Neolithic farmers of Britain was derived from migrants who spread along the Atlantic coast. Megalithic tombs document substantial interaction along the Atlantic façade of Europe, and our results are consistent with such interactions reflecting movements of people. . . . .
For Beaker Complex individuals from Iberia, the best fit was obtained when Middle Neolithic and Copper Age populations from the same region were used as a source for their Neolithic farmer-related ancestry, and we could exclude central and northern European populations (P < 4.69E-03) (Fig. 2c). Conversely, the Neolithic farmer-related ancestry in Beaker Complex individuals outside Iberia was most closely related to central and northern European Neolithic populations with relatively high hunter-gatherer admixture (e.g. Globular_Amphora_LN, P = 0.14; TRB_Sweden_MN, P = 0.29), and we could significantly exclude Iberian sources (P < 3.18E-08) (Fig. 2c). These results support largely different origins for Beaker Complex individuals, with no discernible Iberia-related ancestry outside Iberia. 
Data From The Portugal Paper

Another ancient DNA from Portugal paper also came out today:
We analyse new genomic data (0.05-2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200-3500 BC) to the Middle Bronze Age (1740-1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. 
While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. 
Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature.
Rui Martiniano, et al., "The Population Genomics Of Archaeological Transition In West Iberia"(May 10, 2017).

Linguistic Implications

The hypothesis that Vasconic languages, of which the last survivor is Basque, is derived from a language of the first farmers of Iberia, or maybe even remotely possibly a Mesolithic language of the Franco-Cantabrian refuge, looks stronger than it did yesterday. 

These discoveries also cast doubt on the linguistic character of non-Iberian Bell Beaker people. Yes, there was a definite shift to Bell Beaker relics, but was this accompanied by language shift, or not? 

Of course, even if they did speak Indo-European languages, this still doesn't solve the problem that the Celtic language family is too young to have arrived ca. 2500 BCE to 2000 BCE, when the population turnover took place and there was no doubt language shift of some kind in the British Isles and much of the rest of Western Europe accompanying a 91%-95% population turnover.

The Southeast European Ancient DNA Paper

The genomic history of Southeast Europe is expected here. The abstract is as follows:
Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. However, the dynamics of the interaction between the first farmers and the indigenous hunter-gatherers remain poorly understood because of the near absence of ancient DNA from the region. We report new genome-wide ancient DNA data from 204 individuals-65 Paleolithic and Mesolithic, 93 Neolithic, and 46 Copper, Bronze and Iron Age-who lived in southeastern Europe and surrounding regions between about 12,000 and 500 BCE. 
We document that the hunter-gatherer populations of southeastern Europe, the Baltic, and the North Pontic Steppe were distinctive from those of western Europe, with a West-East cline of ancestry. 
We show that the people who brought farming to Europe were not part of a single population, as early farmers from southern Greece are not descended from the Neolithic population of northwestern Anatolia that was ancestral to all other European farmers.  
The ancestors of the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but we show that some groups that remained in the region mixed extensively with local hunter-gatherers, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that we show prevailed later in the North and West. 
After the spread of farming, southeastern Europe continued to be a nexus between East and West, with intermittent steppe ancestry, including in individuals from the Varna I cemetery and associated with the Cucuteni-Trypillian archaeological complex, up to 2,000 years before the Steppe migration that replaced much of northern Europe's population.
I. Mathieson, et al., "The Genomic History Of Southeastern Europe" (May 9, 2017).

Hat tip for the links to Eurogenes, and to Razib for the strong hint that they are coming this week.

1 comment:

bellbeakerblogger said...

Varna I had some steppe ancestry? Makes sense..and wow!