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Friday, September 12, 2014

Spanish-like Celts and Finnish-like Anglo-Saxons


Update 9/10/2014: Analysis of an ancient genome from Hinxton

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This is arguably one of the most intriguing abstracts from next month's ASHG 2014 conference:

Insights into British and European population history from ancient DNA sequencing of Iron Age and Anglo-Saxon samples from Hinxton, England. S. Schiffels, W. Haak, B. Llamas, E. Popescu, L. Loe, R. Clarke, A. Lyons, P. Paajanen, D. Sayer, R. Mortimer, C. Tyler-Smith, A. Cooper, R. Durbin.

British population history is shaped by a complex series of repeated immigration periods and associated changes in population structure. It is an open question however, to what extent each of these changes is reflected in the genetic ancestry of the current British population. Here we use ancient DNA sequencing to help address that question. We present whole genome sequences generated from five individuals that were found in archaeological excavations at the Wellcome Trust Genome Campus near Cambridge (UK), two of which are dated to around 2,000 years before present (Iron Age), and three to around 1,300 years before present (Anglo-Saxon period). Good preservation status allowed us to generate one high coverage sequence (12x) from an Iron Age individual, and four low coverage sequences (1x-4x) from the other samples. By providing the first ancient whole genome sequences from Britain, we get a unique picture of the ancestral populations in Britain before and after the Anglo-Saxon immigrations. We use modern genetic reference panels such as the 1000 Genomes Project to examine the relationship of these ancient samples with present day population genetic data. Results from principal component analysis suggest that all samples fall consistently within the broader Northern European context, which is also consistent with mtDNA haplogroups. In addition, we obtain a finer structural genetic classification from rare genetic variants and haplotype based methods such as FineStructure. Reflecting more recent genetic ancestry, results from these methods suggest significant differences between the Iron Age and the Anglo-Saxon period samples when compared to other European samples. We find in particular that while the Anglo-Saxon samples resemble more closely the modern British population than the earlier samples, the Iron Age samples share more low frequency variation than the later ones with present day samples from southern Europe, in particular Spain (1000GP IBS). In addition the Anglo-Saxon period samples appear to share a stronger older component with Finnish (1000GP FIN) individuals. Our findings help characterize the ancestral European populations involved in major European migration movements into Britain in the last 2,000 years and thus provide more insights into the genetic history of people in northern Europe.

So in other words, the Iron Age Britons, presumably of Celtic origin, share inflated levels of rare (ie. low frequency) alleles with Spaniards. Assuming these are pre-Roman samples, and it does seem that way, then the results suggest there were direct genetic ties between the British Celts and Mediterranean populations even before the Romans crossed the channel. I wonder if this is the Bell Beaker pimp juice talking?

Conversely, the Anglo-Saxons are more Finnish-like. But I wouldn't read too much into this result, because Finns are the only northern European population from east of England in the 1000 Genomes project, so they're probably just acting as a proxy for gene flow from the far north of what is now Germany.

Interestingly, these signals aren't all that difficult to pick up in present-day English genomes. Below, for instance, are two sets of Eurogenes K15 ancestry proportions for English samples from Cornwall and Kent, respectively.

Note that both groups are typically Northwest European. However, the English from Cornwall are clearly more West Med, while those from Kent slightly more North Sea, Baltic and Eastern Euro. The West Med component peaks in Sardinia, but also occurs at relatively high frequencies in Iberia, while the North Sea, Baltic and Eastern Euro components are well represented among the Finns.

These differences aren't jaw dropping, but they're certainly noticeable. They also make prefect sense in the light of the ancient genomic data, because Cornwall is arguably one of the regions of the UK least affected by the Anglo-Saxon invasions. Kent, on the other hand, was settled by the Jutes during the 5th century. These people weren't Anglo-Saxons, but nonetheless a very similar Germanic tribe from the Jutland Peninsula.

English from Cornwall

North_Sea 35.22
Atlantic 28.94
Baltic 9.69
Eastern_Euro 8.02
West_Med 11.16
West_Asian 3.55
East_Med 1.82
Red_Sea 0.59
South_Asian 0.54
Southeast_Asian 0.05
Siberian 0.03
Amerindian 0.07
Oceanian 0.19
Northeast_African 0.11
Sub-Saharan 0.03

English from Kent

North_Sea 35.52
Atlantic 29.86
Baltic 9.89
Eastern_Euro 8.36
West_Med 8.77
West_Asian 3.35
East_Med 2.5
Red_Sea 0.33
South_Asian 0.58
Southeast_Asian 0.03
Siberian 0.05
Amerindian 0.35
Oceanian 0.31
Northeast_African 0.06
Sub-Saharan 0.03

See also...

Corded Ware Culture linked to the spread of ANE across Europe

Wednesday, September 10, 2014

Corded Ware Culture linked to the spread of ANE across Europe


A news feature on the Lazaridis et al. preprint has just appeared at Science. The full text is behind a pay wall, but the freely available intro and graphic, of the Corded Ware horizon at its maximum extent, betray the main points of the article.

Three-part ancestry for Europeans: Eurasian “ghost lineage” contributed to most modern European genomes

Lazaridis et al. has been online for almost a year, so it's not exactly breaking news, but the Science feature is actually based on a talk by one of the paper's co-authors, Dr. Johannes Krause, at the recent SMBE 2014 conference in Basel.

The interesting thing is that in both drafts of Lazaridis et al. the authors keep well clear of attributing the post-Neolithic spread of Ancient North Eurasian (ANE) admixture (ie. the Eurasian "ghost lineage") into Western and Central Europe to any specific archeological culture or linguistic group. But according to the Science article, Krause thinks that the Corded Ware Culture (CWC) might have been responsible. Indeed, the article adds that Dr. Wolfgang Haak expressed the same opinion in another SMBE talk.

Keep in mind that Haak has already published a paper on uniparental markers from CWC remains (see here). So perhaps he wasn't just speculating that CWC people pushed ANE deep into Europe? Maybe he already knew after sequencing a CWC genome? Or not, but in any case, we're certainly due for an ancient genome from the critically important Late Neolithic/Early Bronze Age period of European prehistory.

Update 11/09/2014: It looks like my hunch was right. Haak and others have managed to sequence genome-wide data from CWC skeletons, and a paper is in the works. The authors are presenting their findings at the ASHG 2014 conference next month.

Capture of 390,000 SNPs in dozens of ancient central Europeans reveals a population turnover in Europe thousands of years after the advent of farming. I. Lazaridis, W. Haak, N. Patterson, N. Rohland, S. Mallick, B. Llamas, S. Nordenfelt, E. Harney, A. Cooper, K. W. Alt, D. Reich.

To understand the population transformations that took place in Europe since the early Neolithic, we used a DNA capture technique to obtain reads covering ~390 thousand single nucleotide polymorphisms (SNPs) from a number of different archaeological cultures of central Europe (Germany and Hungary). The samples spanned the time period from 7,500 BP to 3,500 BP (Early Neolithic to Early Bronze Age periods) and most of them were previously studied using mtDNA (Brandt, Haak et al., Science, 2013). The captured SNPs include about 360,000 SNPs from the Affymetrix Human Origins Array that were discovered in African individuals, as well as about 30,000 SNPs chosen for other reasons (that are thought to have been affected by natural selection, or to have phenotypic effects, or are useful in determining Y-chromosome haplogroups). By analyzing this data together with a dataset of 2,345 present-day humans and other published ancient genomes, we show that late Neolithic inhabitants of central Europe belonging to the Corded Ware culture were not a continuation of the earlier occupants of the region. Our results highlight the importance of migration and major population turnover in Europe long after the arrival of farming.

Update 11/02/2015: Massive migration from the steppe is a source for Indo-European languages in Europe (Haak et al. 2015 preprint) .

See also...

Corded Ware people: more versatile and healthier than Neolithic farmers

Wednesday, September 3, 2014

First I1-M253 from prehistoric Europe


A preprint at bioRxiv reports on ancient DNA from the Balkans and Carpathian Basin. STA stands for Starčevo Culture, LBK for Linearbandkeramik Culture, and LBKT for LBK in Transdanubia.

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]. 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, comprising the majority of mtDNA variation in each culture (STA=86.36%, LBKT=61.54%, LBK=79.63%). In contrast, hunter-gatherer haplogroups are rare in the STA and both LBK groups (Table 1).

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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).

So nothing really surprising there, as far as I can see. Y-haplogroup G2a has been found in plenty of other European Neolithic remains, so its status as the main Y-haplogroup of the men who introduced the Neolithic package from the Near East into Europe remains unchallenged. The I1 and I2 probably belonged to the descendants of indigenous European foragers who were incorporated into the ranks of the early farmers as they made their way north from Anatolia.

But the I1-M253 is interesting, because this is the first time that this haplogroup has been reported from prehistoric remains. I probably don't have to remind anyone that it's the most common Y-haplogroup in Scandinavia today, and yet it was missing from two sets Scandinavian forager remains analyzed recently by Lazaridis et al. and Skoglund et al. This perhaps suggests that it did not enter Scandinavia until the Neolithic, or even later.

Citation...

Anna Szécsényi-Nagy, Guido Brandt, Victoria Keerl, et al., Tracing the genetic origin of Europe's first farmers reveals insights into their social organization, bioRxiv, first posted online September 3, 2014, doi: http://dx.doi.org/10.1101/008664.