PoBI paper BTFO

We next analyzed UK Biobank population structure in conjunction with ancient DNA samples. Modern European populations are known to have descended from three ancestral populations: Steppe, Mesolithic Europeans and Neolithic farmers 21,22 . We projected ancient samples from these three populations as well as ancient Saxon samples 24 onto the UK Biobank PCs (Figure 3, Supplementary Figure 4, see Online Methods). These populations were primarily differentiated along PC1 and PC3, indicating higher levels of Steppe ancestry in northern UK populations.

Additionally, the lack of any ancient sample correlation with PC2 suggests that Welsh populations are not differentially admixed with any ancient population in our data set, and likely underwent Welsh-specific genetic drift. We confirmed these findings by projecting pan- European POPRES 26 samples onto the UK Biobank PCs (see Online Methods, Supplementary Figure 5) noting that of the continental European populations, Russians (who have the most Steppe ancestry) lie on one side and Spanish and Italians (who have least) 22 lie on the other side along PC1 and PC3, and that none of the continental European populations projected onto the same regions as the Welsh on PC2 and PC5.

In addition to the impact of ancient Eurasian populations, we know that the genetics of the UK has been strongly impacted by Anglo-Saxon migrations since the Iron Age 24 , with the Angles arriving in eastern England and the Saxons in southern England. The Anglo-Saxons interbred with the native Celts, which explains much of the genetic landscape in the UK. We analyzed a variety of samples from Celtic (Scotland and Wales) and Anglo-Saxon (southern and eastern England) populations from modern Britain in conjunction with the PoBI samples 20 and 10 ancient Saxon samples from eastern England 24 in order to assess the relative amounts of Steppe ancestry. [. . .] We consistently obtained significantly positive f4 statistics, implying that both the modern Celtic samples and the ancient Saxon samples have more Steppe ancestry than the modern Anglo-Saxon samples from southern and eastern England. This indicates that southern and eastern England is not exclusively a genetic mix of Celts and Saxons. There are a variety of possible explanations, but one is that the present genetic structure of Britain, while subtle, is quite old, and that southern England in Roman times already had less Steppe ancestry than Wales and Scotland.

Population structure of UK Biobank and ancient Eurasians reveals adaptation at genes influencing blood pressure. Kevin Galinsky, Po-Ru Loh, Swapan Mallick, Nick J Patterson, Alkes L Price doi: http://dx.doi.org/10.1101/055855

Note: I find it unlikely the pattern they observe is a holdover from Roman times. I suspect it will turn out the decrement of Steppe ancestry in England stems from a continual trickle of continental genes into England over the past 1000 years (from which the fringes of the British Isles were comparatively isolated).

Also supports my impression that the Wellcome Trust paper still overestimated the degree of Iron Age British admixture in modern England (given that the authors had assumed a simple two-way admixture, while the authors of the above preprint provide evidence "southern and eastern England is not exclusively a genetic mix of Celts and Saxons").

Related:

• People of the British Isles project paper
• Iron Age and Anglo-Saxon genomes from East England reveal British migration history

More ancient DNA from Britain supporting significant later Anglo-Saxon genomic impact

Genomic signals of migration and continuity in Britain before the Anglo-Saxons:

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (~1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.

The full text is freely accessible. More:

Ancient sample ancestry within Britain

To place our ancient genomes within a detailed British context, we next plotted these in a background PCA using 3,075 published genotypes from British3, Irish23 and southern Netherlands samples24. The modern samples were analysed using SNP genotypes at ~250,000 loci and projected into a single plot using smartpca (Fig. 3a). As in Burton et al.3 the first component of the variation was informative for the structure within Britain. Given the close ancestral relationships between these populations and their well-known history of migrational exchange, a substantial overlap between regional groups was both expected and observed. However, by considering median values, one can see a clear progression from Irish samples at one pole through Scottish, Welsh, English to the Dutch cohort at the other extreme. In this plot the York Romans cluster centrally close to the modern Welsh median value, along with the Iron-Age genome. The local Anglo-Saxon is placed differently, closest to modern East Anglians between the English and Dutch medians.

This first component also offers an opportunity to compare within the English sample. Figure 3b shows a boxplot of PC1 values for each subsample and structure is evident, with higher median values in Eastern regions such as East Anglia, East Midlands, intermediate values in the southern and western parts and lower values in the north and northwest. This pattern is more clearly seen in a geographical plot of interpolated values (Fig. 5a). When the York Romans are compared together with each modern cohort, they are most similar to the Welsh distribution of PC1 values and differ significantly from all other regional groups, apart from those from North and Northwest England (Mann–Whitney test; Fig. 3b, Supplementary Note 2 and Supplementary Table 13). An interesting difference is the marked one between the Driffield Terrace ancient and contemporary Yorkshire samples (P=0.003), implying regional discontinuity. It is also worth noting that the PC1 coordinate of the Anglo-Saxon individual is closer to the median PC1 value of East Anglians, possibly reflecting a more pronounced contribution of Germanic immigrants to eastern British populations. However, we note the inherent uncertainty in drawing inference from a single sample.

Population genetic differentiation of height and body mass index across Europe

From Visscher and colleagues:

Population genetic differentiation of height and body mass index across Europe

Across-nation differences in the mean values for complex traits are common1, 2, 3, 4, 5, 6, 7, 8, but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95 × 10−4), and we find an among-population genetic correlation for tall and slender individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P < 0.001), but environmental differences across Europe masked genetic differentiation for BMI (P < 0.58).

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

A preprint on some ancient DNA work in England is up. Researchers sequenced samples from seven early and middle Anglo-Saxon period and three late Iron Age (presumably Celtic) skeletons.

We  generated  a  principal  component  plot  of  the  ten  ancient  samples  together with  relevant  European  populations  selected  from  published  data 10,11  (Extended data  Figure  3).  The  ancient  samples  fall  within  the  range  of  modern  English  and Scottish  samples,  with  the  Iron  Age  samples  from  Hinxton  and  Linton  falling closer  to  modern  English  and  French  samples,  while  most  Anglo-­Saxon  era samples  are  closer  to  modern  Scottish  and  Norwegian  samples.  Overall,  though, population  genetic  differences  between  these  samples  at  common  alleles  are very  slight.

While  principal  component  analysis  can  reveal  relatively  old  population structure,  such  as  generated  from  long-­‐term  isolation-­‐by-­‐distance  models 12 , whole  genome  sequences  let  us  study  rare  variants  to  gain  insight  into  more recent  population  structure. [. . .]

There are  striking  differences  in  the  sharing  patterns  of  the  samples,  illustrated  by  the ratio  of  the  number  of  rare  alleles  shared  with  Dutch  individuals  to  the  number shared  with  Spanish  individuals  (Figure  2a).   The  middle  Anglo-­‐Saxon  samples from  Hinxton  (HS1,  HS2,  HS3)  share  relatively  more  rare  variants  with  modern Dutch  than  the  Iron  Age  samples  from  Hinxton  (HI1,  HI2)  and  Linton  (L).  The early  Anglo-­‐Saxon  samples  from  Oakington  are  more  diverse,  with  O1  and  O2 being  closer  to  the  middle  Anglo-­‐Saxon  samples,  O4  exhibiting  the  same  pattern as  the  Iron  Age  samples,  and  O3  showing  an  intermediate  level  of  allele  sharing, suggesting  mixed  ancestry.  The  differences  between  the  samples  are  highest  in low  frequency  alleles  and  decrease  with  increasing  allele  frequency.  This  is consistent  with  mutations  of  lower  frequency  on  average  being  younger, reflecting  more  recent  distinct  ancestry,  compared  with  higher  frequency mutations  reflecting  older  shared  ancestry.  

Comparing the relative number of rare alleles shared with the Dutch and Spanish samples, the researchers estimate 30% Anglo-Saxon admixture in the present-day East English and 20% in the Scottish and Welsh.

We  also  examined  using  the  same  method  30  modern  samples  from  the  UK10K project   16 ,  10  each  with  birthplaces  in  East  England,  Wales  and  Scotland.  Overall, these  samples  are  closer  to  the  Iron  Age  samples  than  to  the  Anglo-­‐Saxon  era samples  (Figure  2a).  There  is  a  small  but  significant  difference  between  the  three modern  British  sample  groups,  with  East  English  samples  sharing  slightly  more alleles  with  the  Dutch,  and  Scottish  samples  looking  more  like  the  Iron  Age samples.  To  quantify  the  ancestry  fractions,  we  fit  the  modern  British  samples with  a  mixture  model  of  ancient  components,  by  placing  all  the  samples  on  a linear  axis  of  relative  Dutch  allele  sharing  that  integrates  data  from  allele  counts one  to  five  (Figure  2b).  By  this  measure  the  East  England  samples  are  consistent with  30%  Anglo-­‐Saxon  ancestry  on  average,  with  a  spread  from  20%  to  40%, and  the  Welsh  and  Scottish  samples  are  consistent  with  20%  Anglo-­‐Saxon ancestry  on  average,  again  with  a  large  spread  (Supplementary  Table  2).  An alternative  and  potentially  more  direct  approach  to  estimate  these  fractions  is  to measure  rare  allele  sharing  directly  between  the  modern  British  and  the  ancient samples.  While  being  much  noisier  than  the  analysis  using  Dutch  and  Spanish outgroups,  this  yields  consistent  results  (Extended  Data  Figure  4  and Supplementary  Table  2).  In  summary,  this  analysis  suggests  that  only  20-­‐30%  of the  ancestry  of  modern  Britons  was  contributed  by  Anglo-­‐Saxon  immigrants, with  the  higher  number  in  East  England  closer  to  the  immigrant  source.  The difference  between  the  three  modern  groups  is  surprisingly  small  compared  to the  large  differences  seen  in  the  ancient  samples,  although  we  note  that  the UK10K  sample  locations  may  not  fully  reflect  historical  geographical  population structure  because  of  recent  population  mixing.

I have not thought about it deeply, but the rare variant comparison method used by the authors seems like it should produce reasonable results, at least for the relatively straightforward admixture estimates (with the understanding that Anglo-Saxons and Iron Age Britons are not the only two possible source populations for the modern British). I will say I was surprised to see Britain sharing a branch with Finland in this plot (even though it's a short one) to the exclusion of Denmark and Netherlands:

I've seen a few people interpret this study's estimates as a vindication of the ridiculous admixture estimates featured in the People of the British Isles project paper. For me, the ancient DNA results confirm my initial impression: the methods the POBI authors used to generate their estimates of ancient admixture were useless for divining what they thought they could divine.

That this 30% estimate informed by ancient DNA falls within the range of estimates suggested by the POBI authors is primarily a testament to the extremely broad range of possible admixture estimates they offered up (spanning 10% to 50%, depending on what one subjectively deemed "likely"). The POBI authors themselves were pushing for ~10% Anglo-Saxon admixture in the 19th-century Central and South English population (and if I recall correctly ~0% in the Welsh). POBI volunteers were primarily middle-aged or older people who could document four grandparents all born in particular locations. The UK10K modern British samples appearing in the ancient DNA paper are not screened in a similar manner, but are simply classified based on the sample donor's birth place. This means at least a couple generations (and probably disproportionately important generations, at that, as concerns mobility) of additional homogenization will have taken place.

So I have little doubt POBI samples from East Anglia (proxies for 19th-century East Anglians) would produce higher estimates of Anglo-Saxon admixture than "East England" UK10K samples (though apparently at present only microarray data, and not the whole genome sequencing data that would be necessary for the rare variant comparisons, is available for POBI samples). Levels up to 40% or higher Anglo-Saxon admixture in 19th-century East Anglians would not surprise me. And whatever the 19th-century number turns out to be, Anglo-Saxon admixture in England likely would have been progressively higher going back in time toward before the Norman conquest.

Gene flow into England over the past millennium (from Wales, Scotland, Ireland, and France) will have tended to make the English look less Anglo-Saxon and more "Iron Age". The Scandinavian component in the Normans and particularly their followers was probably outweighed by the French; and subsequently France probably remained one of the main sources of continental immigrants into England at least down to the Huguenots. It's said around 50,000 Huguenots came to England (against a 17th-century English population of around 5 million). 1% does not sound like an especially large wave (and it's certainly not by the standards of modern mass immigration), but these immigrants were concentrated in south and east England:

Huguenot settlement was concentrated in London and the south, East Anglia and the Fens

Even a relative trickle of continental immigrants over the past 1000 years might have had a noticeable cumulative effect on the English gene pool, and Scottish, Welsh, and Irish gene flow into England over the past millennium is likely even more significant. 24% of British claim Irish ancestry recent enough to be aware of, including 77% of those in London. Around 10% of the UK population is estimated to have an Irish grandparent.

Filtering recent Irish immigration into Scotland might also lead to higher estimates of Anglo-Saxon admixture there, as well (though recent English immigration too would need to be excluded). Recent English immigration into Wales may mean the 20% Anglo-Saxon admixture estimate is significantly inflated (though going off the 20% estimate for modern Welsh I would guess 19th-century Welsh speakers had at least ~10% Anglo-Saxon-like admixture).

According to the authors:

The  genetic  analyses  described  above  add  significantly  to  our  picture  of  Anglo-­Saxon  migration  into  Britain.   In  the  cemetery  at  Oakington  we  see  evidence  even in  the  early  Anglo-­Saxon  period  for  a  genetically  mixed  but  culturally  Anglo-­Saxon  community ^21,22 ,  in  contrast  to  claims  for  strong  segregation  between newcomers  and  indigenous  peoples ⁷ .  The  genomes  of  two  sequenced  individuals are  consistent  with  them  being  of  recent  immigrant  origin,  from  different continental  source  populations,  one  was  genetically  similar  to  native  Iron  Age samples,  and  the  fourth  was  an  admixed  individual,  indicating  intermarriage.   Despite  this,  their  graves  were  conspicuously  similar,  with  all  four  individuals buried  in  flexed  position,  and  with  similar  grave  furnishing.  Interestingly  the wealthiest  grave,  with  a  large  cruciform  brooch,  belonged  to  the  individual  of native  British  ancestry  (O4),  and  the  individual  without  grave  goods  was  one  of the  two  genetically  “foreign”  ones  (O2),  an  observation  consistent  with  isotope analysis  at  West  Heslerton  which  suggests  that  new  immigrants  were  frequently poorer   ^23,24 .  Given  this  mixing  apparent  around  500CE,  and  that  the  modern population  is  no  more  than  30%  of  Anglo-­Saxon  ancestry,  it  is  perhaps  surprising that  the  middle  Anglo-­Saxon  individuals  from  the  more  dispersed  field  cemetery in  Hinxton  all  look  genetically  consistent  with  unmixed  immigrant  ancestry.  One possibility  is  that  this  reflects  continued  immigration  until  at  least  the  Middle Saxon  period.  

In fact, there's nothing really inconsistent with the "Anglo-Saxon apartheid" paper in the mixed earlier samples and unmixed later samples. The Anglo-Saxon period samples tested here are all female. It's easy to imagine intermarriage rates may have been higher among the earliest Anglo-Saxon settlers, when their fraction of the total British population would have been smallest -- especially if females were to any degree underrepresented among the incoming Anglo-Saxons.

From the "Anglo-Saxon apartheid" paper (Evidence for an apartheid-like social structure in early Anglo-Saxon England):

We have only considered the effects of differences in ethnic reproductive advantage and inter-ethnic marriage rate on patterns of genetic variation. If there were no sex bias in the intermarriage rate, then we would expect these effects to be equal for the different genetic systems (mitochondrial DNA, Y-chromosome, X-chromosome, autosomes). However, part of the motivation for this study was to seek an explanation for the discrepancy between archaeological estimates of the size of the Anglo-Saxon migration (Härke 1998, 2002; Hills 2003) and estimates based on Y-chromosome data (Weale et al. 2002; Capelli et al. 2003). There are three further factors that could exacerbate replacement of indigenous Y-chromosomes. The first is that when intermarriage does occur the offspring may be more likely to assume the identity of the father, thus reducing the effective intermarriage rate, as it would affect patterns of Y-chromosome diversity. The second is that forced extra-marital matings are more likely to occur between Anglo-Saxon men and native British women than the reverse since, as the law codes of Ine indicate, the degree of punishment was determined by the social status of the victim. The third is based on the theory that relatively ‘good condition’ males tend to out-reproduce females of a similar condition, whereas relatively ‘poor condition’ females tend to out-reproduce their male counterparts (Trivers & Willard 1973). From this, a strategy of sex-biased parental investment, whereby relatively wealthy parents favour wealth transfer to their sons, should emerge (Hartung 1976). Such a phenomenon is supported by genealogical data (Boone 1986) and should lead to an asymmetric increase in the population frequency of Y-chromosomes carried by wealthy men, when compared to the other genetic systems.

The motivation for this study was to reconcile the discrepancy between, on the one hand, archaeological and historical ideas about the scale of the Anglo-Saxon immigration (Hills 2003), and on the other, estimates of the genetic contribution of the Anglo-Saxon immigrants to the modern English gene pool (Weale et al. 2002; Capelli et al. 2003). We have shown that this discrepancy can be resolved by the assumption of an apartheid-like social structure within a range of plausible values for interethnic marriage and socially driven reproductive advantage following immigration (Woolf 2004). Perhaps most strikingly, our model indicates that, by using plausible parameter values, the genetic contribution of an immigrant population can rise from less than 10% to more than 50% in as little as five generations, and certainly less than fifteen generations. Similar processes are likely to have shaped patterns of genetic variation in other ‘conquest societies’ of the period, and perhaps more recently (Carvajal-Carmona et al. 2000).

People of the British Isles Project talk

(I'm not convinced by the approach they took to estimating Anglo-Saxon admixture proportions; but the intra-UK clustering discussed starting around ~14:30 should be objective enough.)

Garrett Hellenthal - The Genetic History of the United Kingdom: the POBI project

Garrett presents results from the People of the British Isles (POBI) project, an exploration of the fine-scale genetic architecture of the United Kingdom. Using the DNA of individuals sampled across England, Northern Ireland, Scotland and Wales, Garrett illustrates the striking correlation between an individual's genetics and their geographic origins. Furthermore, by comparing the DNA of UK individuals to that of individuals sampled from continental Europe, we identify clear differences in ancestry among different geographic regions of the UK, reflecting the genetic imprint of the Anglo-Saxon and Norwegian Viking migrations from several centuries ago.

People of the British Isles project paper

After long delays, the main PoBI paper has finally been published. At this point, it comes as something of an anticlimax (particularly since it appears access to the underlying data will be restricted, when researchers had previously implied it would be openly accessible).

In the past, it's been said this publication was held up because reviewers had problems with the dating and attribution of the various clusters by the authors. I'd presumed such reviewers must be anti-migrationist holdouts motivated by politics. But now that I've read the paper, I can't say I'm impressed with the authors's methods or conclusions.

After the Saxon migrations,the language,place names,cereal crops and pottery styles all changed from that of the existing(Romano-British) population to those of the Saxon migrants. There has been ongoing historical and archaeological controversy about the extent to which the Saxons replaced the existing Romano-British populations. Earlier genetic analyses, based on limited samples and specific loci, gave conflicting results. With genome-wide data we can resolve this debate. Two separate analyses (ancestry profiles and GLOBETROTTER)show clear evidence in modern England of the Saxon migration, but each limits the proportion of Saxon ancestry, clearly excluding the possibility of long-term Saxon replacement. We estimate the proportion of Saxon ancestry in Cent./SEngland as very likely to be under 50%, and most likely in the range of 10–40%.

A more general conclusion of our analyses is that while many of the historical migration events leave signals in our data, they have had a smaller effect on the genetic composition of UK populations than has sometimes been argued. In particular, we see no clear genetic evidence of the Danish Viking occupation and control of a large part of England, either in separate UK clusters in that region, or in estimated ancestry profiles, suggesting a relatively limited input of DNA from the Danish Vikings and subsequent mixing with nearby regions, and clear evidence for only a minority Norse contribution (about 25%) to the current Orkney population.

We saw no evidence of a general ‘Celtic’ population in non-Saxon parts of the UK. Instead there were many distinct genetic clusters in these regions, some amongst the most different in our study, in the sense of being most separated in the hierarchical clustering tree in Fig.1. Further,the ancestry profile of Cornwall (perhaps expected to resemble other Celtic clusters) is quite different from that of the Welsh clusters, and much closer to that of Devon, and Cent./S England. However, the data do suggest that the Welsh clusters represent populations that are more similar to the early post-Ice-Age settlers of Britain than those from elsewhere in the UK.

An example of their reasoning:

The observation (Fig.2 and Supplementary Table 4) that particular European groups(for example, GER3, FRA12, FRA17) contribute substantially to the ancestry profiles of some, but not all, UK clusters strongly suggests that at least some of the structure we observe in the UK results from differential input of DNA to different parts of the UK: the absence in particular UK clusters of ancestry from specific European groups is best explained by the DNA from those European groups never reaching those UK clusters. A critical observation which follows is that groups which contribute significantly to the ancestry profiles of all UK clusters most probably represent, at least in part, migration events into the UK that are relatively old, since their DNA had time to spread throughout the UK. Conversely, groups that contribute to the ancestry profiles of only some UK clusters most probably represent more recent migration events, with the resulting DNA not yet spread throughout the UK by internal migration. ‘Old’ and ‘recent’ here are relative terms—we can infer the order of some events in this way but not their absolute times. Although we refer to migration events, we cannot distinguish between movements of reasonable numbers of people over a short time or ongoing movements of smaller numbers over longer periods.

Thus, their estimate of Anglo-Saxon admixture comes from picking which of their "European groups" -- which do not, of course, represent actual ancient European groups but are merely synthetic clusters generated on data from present-day continental Europeans -- to associate with Anglo-Saxons. Going with the authors's approach, estimates of the Anglo-Saxon contribution can range from 10% to over 50%, depending on what one deems "likely".

Personally, I deem it unlikely they're picking up any signals dating back to "the early post-Ice-Age settlers of Britain". I would guess that most of their clusters are influenced by more recent patterns of migration and isolation than the authors tend to assume. More credible estimates of, e.g., Anglo-Saxon admixture in Britain will await sequencing of large amounts of ancient DNA.

ESHG 2014: Genomic description of the Generation Scotland Cohort: a large family base genetic study

Title: P17.29-S - Genomic description of the Generation Scotland Cohort: a large family base genetic study
Keywords: Genetic introgression; Principal Component Analysis; GS:SFHS
Authors: C. Amador1, J. Huffman1, H. Trochet1, A. Campbell1, D. Porteous1, G. Scotland1, N. Hastie1, V. Vitart1, C. Hayward1, P. Navarro1, C. S. Haley1,2; 1MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom, 2Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, United Kingdom.

Abstract: Generation Scotland’s Scottish Family Health Study (GS:SFHS) includes over 24,000 participants from across Scotland with records for health-related traits and environmental covariates, 10,000 genotyped for ~700K SNPs. The cohort represents an important resource for the study of complex traits and diseases. We have analysed the genomic structure of GS:SFHS as a preliminary step towards choosing appropriate subsets of individuals and statistical techniques for future studies. Initially we merged the GS:SFHS data with 1092 individuals of diverse ancestries from the 1000 Genomes project and estimated genomic relationships using the ~700K SNPs. A Principal Component Analysis on the resulting relationships facilitated identification of a group of 70 individuals of likely Italian ancestry and a number of individuals with African or Asian ancestry. We characterised the amount of genetic introgression and were able to differentiate between individuals with a few small exogenous regions in their genome, and those with long exogenous haplotypes covering a large part of the genome. We found that the pattern of homozygosity was very similar to that of other European populations and identified an individual carrying a chromosome 1 uniparental disomy. Overall, there is very limited evidence for geographic differentiation or stratification of the GS:SFHS sample within Scotland. These findings provide a genomic perspective on the history of the Scottish population, and have implications for further analyses, such as studying the contributions of common and rare variants to trait heritabilities and evaluation of genomic and phenotypic prediction of disease.

A model of social class from BBC survey data

A New Model of Social Class? Findings from the BBC’s Great British Class Survey Experiment (pdf):

We analyse the largest survey of social class ever conducted in the UK, the BBC’s 2011 Great British Class Survey, with 161,400 web respondents, as well as a nationally representative sample survey, which includes unusually detailed questions asked on social, cultural and economic capital. Using latent class analysis on these variables, we derive seven classes. We demonstrate the existence of an ‘elite’, whose wealth separates them from an established middle class, as well as a class of technical experts and a class of ‘new affluent’ workers. We also show that at the lower levels of the class structure, alongside an ageing traditional working class, there is a ‘precariat’ characterised by very low levels of capital, and a group of emergent service workers. We think that this new seven class model recognises both social polarisation in British society and class fragmentation in its middle layers, and will attract enormous interest from a wide social scientific community in offering an up-to-date multi-dimensional model of social class.

More:

Next PoBI paper should be more interesting

Another ICHG/ASHG 2011 abstract:

People of the British Isles: An analysis of fine-scale population structure in a UK control population. S. Leslie1, B. Winney1, G. Hellenthal2, S. Myers2, A. Boumertit1, T. Day1, K. Hutnik1, E. Royrvik1, D. Lawson3, D. Falush4, P. Donnelly2, W. Bodmer1 1) Department of Oncology, University of Oxford, Oxford, United Kingdom; 2) Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; 3) Department of Mathematics, University of Bristol, Bristol, United Kingdom; 4) Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

There is a great deal of interest in fine scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it is likely to play a significant part in the next generation of studies designed to search for rare variants. A powerful means of detecting such structure is to control and document carefully the provenance of the samples involved. Here we describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK control population that can be used as a resource by the research community as well as providing fine scale genetic information on the British population. So far, some 4000 samples have been collected, the majority of which fit the criteria of coming from a rural area and having all four grandparents from approximately the same area. Three thousand samples were genotyped on the Illumina 1.2M and Affymetrix v6.0 platforms as part of WTCCC2. Using a novel clustering algorithm that takes into account linkage disequilibrium structure, approximately 3000 of the samples were clustered, using these comprehensive genotyping data, into more than 50 groups purely as a function of their genetic similarities without any reference to their know locations. When the appropriate geographical position of each individual within a cluster is plotted on a map of the UK, there is a striking association between clusters and geography, which reflects to a major extent the known history of the British peoples. Thus, for example, even individuals from Cornwall and Devon, the two adjacent counties in the southwestern tip of Britain, fall into different, but coherent clusters. Further details of this comprehensive analysis of the genetic structure of the People of the British Isles, together with a description of the provenance of the samples, will be give in the presentation. We believe that this is the first time that such a detailed fine scale genetic structure of a population of generally very similar individuals has been possible. This has been achieved through, on the one hand, a careful geographically structured collection of samples and, on the other hand, an approach to analysis that takes into account fully the linkage disequilibrium structure of the population.

Was there ever a Ruling Class? 1000 years of Social Mobility

According to Gregory Clark, because of regression to the mean and the lack of any (e.g., racial) barrier preventing gene flow across classes, there was never a persistent ruling class in England.

Notes from a presentation by Clark last year containing "work in progress from a planned book on social mobility over the long run" (pdf):

What is the fundamental nature of human society? Is it stratified into enduring layers of privilege and want, with some mobility between the layers, but permanent social classes? Or is there, over generations, complete mobility between all ranks in the social hierarchy, and complete long run equal opportunity? [. . .]

This book systematically exploits a new method of tracing social mobility over many generations, surnames, to measure the persistence of classes over as much as 800 years, 24 generations. It looks at societies where surnames are inherited, unchanged, by children from fathers. In such cases they thus serve as a tracer of the distant social origins of the modern population (and interestingly also as a tracer of the Y chromosome).

In this role surnames are a surprisingly powerful instrument for measuring long run social mobility. The results they reveal are clear, powerful, and a shock to our casual intuitions.

(1) In England, where we can trace social mobility back to 1066 using surnames, there were never any long persistent ruling and lower classes for the indigenous population: not in medieval England, and not now. About 5-6 generations were, and are, enough to erase most echoes of initial advantage or want. For the English class is, and always was, an illusion. Histories such as those of the Stanley family turn out to be rare exceptions, not the rule.

(2) Paradoxically, while England reveals complete long run mobility, the rates of social mobility per generation, better measured by looking over multiple generations, turn out to be lower than is conventionally estimated. But the mathematics of mobility is such that even such slow regression to the mean, over time, will completely erase initial advantage and want.

(3) The rate of social mobility in England was as high in the middle ages as it is now. The arrival of the whole apparatus of free public education in the late nineteenth century, and the elimination of nepotism in government and private firms, has not improved the rate of social mobility.

(4) The extraordinarily complete long run mobility of England is likely typical of other western European societies. But other countries, in contrast, do exhibit persistent social classes over hundreds of years. In the US, for example, the Black population has persisted at the bottom of the social order, and the Jewish population at the top. In Chile surname evidence shows the indigenous population has remained at the bottom since the Spanish conquest of 1541. [. . .]

(7) Though parents at the top of the economic ladder in any generation in preindustrial England did not derive any lasting advantage for their progeny, there was one odd effect. Surname frequencies show was that there was a permanent increase in the share of the DNA in England from rich parents before 1850. After 1850 a frequency effect operated, but in reverse. Surname frequencies show the DNA share of families in England who were rich in 1850 declined relative to that of poor families of the same generation by 2010. [. . .]

What is the meaning and explanation of these results? This is a much more contentious and difficult area. The book argues for the following conclusions:

A. Why can’t the ruling class in a place like England defend itself against downwards mobility? If the main determinants of economic and social success were wealth, education and connections then there would be no explanation of the consistent tendency of the rich to regress to the society mean. Only if genetics is the main element in determining economic success, if nature trumps nurture, is there a built-in mechanism that ensures the observed regression. That mechanism is the intermarriage of the rich with those from the lower classes. Even though there is strong assortative mating, since this is based on the phenotype created in part by chance and luck, those of higher than average innate talent tend to systematically mate with those of lesser ability and regress to the mean.

B. Racial, ethnic and religious differences allow long persisting social stratification through the barriers they create to this intermarriage. Thus for a society to achieve complete social mobility it must achieve cultural homogeneity. Multiculturalism is the enemy of long run equality.

On the Normans:

Editorial and preliminary paper on People of the British Isles project

Both freely accessible.

A British approach to sampling:

The acronym ‘PoBI’ may not yet be familiar to human geneticists in the way that ‘HGDP’, ‘WTCCC’ or ‘HapMap’ are, but a paper in this issue of EJHG1 that introduces the ‘People of the British Isles’ project to the scientific community aims to change this. The PoBI project will collect up to 5000 DNA samples from diverse regions of the British Isles, taking great care to sample individuals with several generations of ancestry in rural locations. These samples are intended to serve as controls for future medical genetic studies, and to provide insights into the peopling of the British Isles over the last few millennia. [. . .] Although readers will have to wait for future publications to discover the insights from these large-scale genetic analyses, the current paper describes the sampling strategy and initial 3865 samples in some detail, outlines an approach to investigating fine-scale population structure using surnames, and presents some preliminary genetic analyses of a handful of chosen loci. [. . .]

In addition to collecting blood, the project recorded surnames. Using data from a census performed in 1881, these were classified as ‘local’ or ‘non-local’, and the two classes examined separately. The authors then modelled a population such as that from central England as a mixture between south-western (taken to represent Ancient Britons) and eastern (Anglo Saxon) populations, and estimated the contribution of each population to the central England autosomal genotypes. These contributions differed between the local surname class (mostly eastern) and the non-local class (half and half), which the authors take as evidence of subtle population structure. Published genetic analyses using much larger numbers of markers have already detected low, but significant levels of genetic structure within Britain in more straightforward ways,4, 5 even with less stringently ascertained samples (Figure 1): Europe-wide south-east to north-west gradients extend into the British Isles. We can look forward to deeper insights into genetic differentiation and its causes when large-scale genetic analyses of the PoBI samples are available.

[. . .] anthropological and evolutionary geneticists should rejoice in the assembly of this resource, the foresight of The Wellcome Trust in funding the project over a decade or so, and hope that resources are available for establishing more cell lines and performing more genome-wide sequencing, so that both the full set of samples and their sequences can be made widely available.

It is obvious why British people interested in their ancestry, and medical geneticists working with British subjects should welcome PoBI, but why should others pay attention? PoBI will not provide information about global genetic diversity in the way that HGDP7 and HapMap8 do, but its microcosmic survey of genetic variation in a set of small islands off the western coast of the Eurasian continent is revealing the level of differentiation that builds up over millennia via events well documented by archaeology and history, so these alternative data sets can be compared to address questions about the initial peopling of the area, and its subsequent reshaping by internal and external forces. And if the characteristics of the British – politeness, eccentricity, or drunken loutishness, according to your viewpoint and experience – have any genetic basis, perhaps PoBI can provide a starting point for identifying it! 

People of the British Isles: preliminary analysis of genotypes and surnames in a UK-control population:

There is a great deal of interest in a fine-scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it is likely to have a significant part in the next generation of studies designed to search for rare variants. A powerful way of detecting such structure is to control and document carefully the provenance of the samples involved. In this study, we describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK-control population that can be used as a resource by the research community, as well as providing a fine-scale genetic information on the British population. So far, some 4000 samples have been collected, the majority of which fit the criteria of coming from a rural area and having all four grandparents from approximately the same area. Analysis of the first 3865 samples that have been geocoded indicates that 75% have a mean distance between grandparental places of birth of 37.3 km, and that about 70% of grandparental places of birth can be classed as rural. Preliminary genotyping of 1057 samples demonstrates the value of these samples for investigating a fine-scale population structure within the UK, and shows how this can be enhanced by the use of surnames.

Ethnic background of the British Royal family

From the website of genealogist William Addams Reitwiesner, who died last year. The Ethnic ancestry of Prince William (b. 1982):

Every so often, someone will state that the British Royal Family is "not British", that they are instead "German" or "Foreign". Since this belief seems to be somewhat wide-spread, and since the genealogy of many members of the British Royal Family is fairly well known, it seemed to me that it would be fairly easy to quantify precisely how "British" or "non-British" the British Royal Family is. This webpage shows the results of my work.

Further update on People of the British Isles project

From their most recent newsletter (pdf):

We are pleased to tell you that we have just submitted our first scientific paper about the project. The main function of this paper is to announce PoBI to the scientific world and in it we show that, even with a relatively small number of samples and a few genetic markers, the samples we collected should be sufficient to detect genetic differences across the UK. [. . .]

One aspect that is of particular interest is the surnames we collected and we have spent some time with our collaborators at UCL (Professor Paul Longley and his group) dividing them into local and non-local surnames. The figure on the left shows a couple of examples. The idea is that individuals whose surname is local to an area are more likely to have family in that area for many generations than individuals whose surnames are found all over the country. This is obviously a generalisation, but it does seem that there are some genetic differences between sets of volunteers with local surnames and sets with non-local surnames and we are really looking forward to analysing all the data rather than just the small subset we have been studying so far. [. . .]

Our next priority is to analyse the 1.3 million genetic markers that have been typed on 3,000 of our volunteers [. . .] The data we analyse from these samples should shed light on the genetic impact of the different historical incursions into Britain. It is an extremely large data set and so it will take a while to analyse and write up. As mentioned in our last newsletter, 100 of our samples are having their complete DNA sequenced by the 1,000 Genomes Project (www.1000genomes.org) and it should not be too long before that very valuable information becomes available to us. [. . .]

As you will know from the last newsletter, the Wellcome Trust has given us funding for a further five years to look for genes involved in normal traits. The main focus is on facial features, but other traits include handedness, taste perception and skin colour. We have been going back to our volunteers to collect these data. We take 3D photographs of each volunteer’s face in order to identify genes involved in the control of particular facial features. Over the last 18 months, we have collected 475 such photographs and are beginning to analyse them with our collaborators in Surrey (Professor Josef Kittler and his group).

Last newsletter (pdf):

There is a great deal of interest in the genetics of facial features and, in addition, the frequency of genetic variants for facial features may well differ significantly between different parts of the UK. We will also be collecting data on a variety of other normal features including height, hair and skin colour, handedness, milk tolerance, musical preferences and perfect pitch, taste and smell preferences and features of the hand.

DNA USA: A Genetic Biography of America

Apparently not due out for another year, but here's what Bryan Sykes has been working on:

The best-selling author of The Seven Daughters of Eve now turns his sights on the United States, one of the most genetically variegated countries in the world. From the blue-blooded pockets of old-WASP New England to the vast tribal lands of the Navajo, Bryan Sykes takes us on a historical genetic tour, interviewing genealogists, geneticists, anthropologists, and everyday Americans with compelling ancestral stories. His findings suggest: Of Americans whose ancestors came as slaves, virtually all have some European DNA. Racial intermixing appears least common among descendants of early New England colonists. There is clear evidence of Jewish genes among descendants of southwestern Spanish Catholics. Among white Americans, evidence of African DNA is most common in the South. European genes appeared among Native Americans as early as ten thousand years ago. An unprecedented look into America's genetic mosaic and an impressive contribution to how we perceive race, this is a fascinating book about what it means to be American.

Also of possible interest: Viking DNA: The Wirral and West Lancashire Project (Stephen Harding, Mark Jobling, Turi King); Surnames, DNA, and Family History (George Redmonds, Turi King, David Hey).

Twenty-eleven

I'll skip the predictions (you're welcome to post your own), and just post a bit more information on a few projects that should be announcing results this year:

(1) Otzi genome. Here's a 9 minute podcast from Life Technologies containing a few more details:
- "above 5X coverage"
- "looking at potentially medically-relevant SNPs"
- "this individual living over 5000 years ago would represent an ancestor for, we think, a significant proportion of the European population."
- "looking at his ancestry and indeed trying to determine exactly where is he from"

(2) People of the British Isles Project. A movie from the Wellcome Trust:



Most interestingly, the project is now collecting phenotypic data, including skin color, and taking 3-d facial photographs. Bodmer: "The next stage of our study, we're now taking pictures of people's faces so we can analyze components statistically [. . .] and then look for the genetic features behind that. What are the genes, what are the variations that determine facial features. Will it be possible to reconstruct from a piece of DNA what a person really looked like."

(3) 1000 Genomes Project. Another short film by the Wellcome Trust:



Chris Tyler-Smith: "[The project has] told us that natural selection has influenced virtually every part of our genome [. . .] we've now got a catalog of some thousands of genes that we think have been specifically positively selected in our fairly recent history."

Update on People of the British Isles project

A reader forwarded me this message, posted to a mailing list by a third party:

One of my project members wrote to one of the organisers of the People of the British Isles Project to find out a few more details. He was told the following:

"The data will be made publicly available after we have done some analyses, and so anyone should be able to get hold of it when it is!

As for SNPs, we have had 3,000 samples typed on a large scale (about 1.2M SNPs, of which something like 2,000 are on the Y-chromosome). There are about 150 or so that are on the y-chromosome consortium tree, so hopefully we should get quite a lot of information out of the analyses!"

That should make a big difference to Population Finder and all the other admixture tests. Perhaps those of us who already know that we are of 100% British origin might then actually get some meaningful results. The Orkney Islands are not exactly a good proxy for the entire British Isles!

The website is showing a total of 4214 samples collected.

Puritan intelligence: the ideological background to IQ

Anti-IQ academic "blames" intelligence testing and eugenics on Puritans and Quakers.

John White. Puritan intelligence: the ideological background to IQ. Oxford Review of Education, Volume 31, Issue 3 September 2005 , pages 423 - 442.

Given well-known difficulties in justifying the Galtonian conception of intelligence as innate general intellectual capacity, a historical explanation is required of why this problematic notion became so prominent in Britain and in the USA in the late nineteenth and twentieth centuries. Parallels are drawn between it and various features of the thought-world of the Puritans, including ideas of predestination, the elect, salvation, vocation, and intellectual education. An examination of the family backgrounds of the leading pioneers of intelligence and intelligence testing reveals that most, if not all, of them had puritan roots. A final section focuses on the tight connexion made between Galtonian intelligence and abstract thinking. It suggests that this may be linked with the central role of logic in puritan thought and its alliance with 'pneumatology', the forerunner of scientific psychology.

More excerpts within:

Iron Age Scottish written language?

DiscoveryNews reports:

The ancestors of modern Scottish people left behind mysterious, carved stones that new research has just determined contain the written language of the Picts, an Iron Age society that existed in Scotland from 300 to 843.

The highly stylized rock engravings, found on what are known as the Pictish Stones, had once been thought to be rock art or tied to heraldry. The new study, published in the Proceedings of the Royal Society A, instead concludes that the engravings represent the long lost language of the Picts, a confederation of Celtic tribes that lived in modern-day eastern and northern Scotland.

The paper ("Pictish symbols revealed as a written language through application of Shannon entropy") is open access.

Fine-Scale Population Structure in Humans

Biswas et al. Genome-wide Insights into the Patterns and Determinants of Fine-Scale Population Structure in Humans. The American Journal of Human Genetics, Volume 84, Issue 5, 641-650 15 May 2009 doi:10.1016/j.ajhg.2009.04.015

Studying genomic patterns of human population structure provides important insights into human evolutionary history and the relationship among populations, and it has significant practical implications for disease-gene mapping. Here we describe a principal component (PC)-based approach to studying intracontinental population structure in humans, identify the underlying markers mediating the observed patterns of fine-scale population structure, and infer the predominating evolutionary forces shaping local population structure. We applied this methodology to a data set of 650K SNPs genotyped in 944 unrelated individuals from 52 populations and demonstrate that, although typical PC analyses focus on the top axes of variation, substantial information about population structure is contained in lower-ranked PCs. We identified 18 significant PCs, some of which distinguish individual populations. In addition to visually representing sample clusters in PC biplots, we estimated the set of all SNPs significantly correlated with each of the most informative axes of variation. These polymorphisms, unlike ancestry-informative markers (AIMs), constitute a much larger set of loci that drive genomic signatures of population structure. The genome-wide distribution of these significantly correlated markers can largely be accounted for by the stochastic effects of genetic drift, although significant clustering does occur in genomic regions that have been previously implicated as targets of recent adaptive evolution.

Link; supplementary material; press release.

Y chromosome diversity and patrilineal surnames

New paper on British surnames and Y DNA.

Most heritable surnames, like Y chromosomes, are passed from father to son. These unique cultural markers of coancestry might therefore have a genetic correlate in shared Y chromosome types among men sharing surnames, although the link could be affected by mutation, multiple foundation for names, nonpaternity, and genetic drift. Here, we demonstrate through an analysis of 1678 Y-chromosomal haplotypes within 40 British surnames a remarkably high degree of coancestry that generally increases as surnames become rarer. On average, the proportion of haplotypes lying within descent clusters is 62%, but ranges from zero to 87%. The shallow time-depth of many descent clusters within names, the lack of a detectable effect of surname derivation on diversity, and simulations of surname descent suggest that genetic drift through variation in reproductive success is important in structuring haplotype diversity. Modern patterns therefore provide little reliable information about the original founders of surnames some 700 years ago. A comparative analysis of published data on Y diversity within Irish surnames demonstrates a relative lack of surname frequency dependence of coancestry, a difference probably mediated through distinct Irish and British demographic histories including even more marked genetic drift in Ireland.

[Turi E. King , and Mark A. Jobling
Founders, drift and infidelity: the relationship between Y chromosome diversity and patrilineal surnames
MBE Advance Access published on February 9, 2009, DOI 10.1093/molbev/msp022. ]

This sounds interesting:

We are currently undertaking genomewide SNP analysis of men whose Y chromosomes belong to descent clusters, with the aim of determining the proportion of the genome identical-by-descent among these distantly, but unambiguously, related individuals.