Bronze Age people from Ireland had steppe ancestry and R1b

From the paper:

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

and:

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

PNAS doi: 10.1073/pnas.1518445113

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

Lara M. Cassidy, Rui Martiniano et al.

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

Link

Neolithic boom and bust in Ireland

Journal of Archaeological Science doi:10.1016/j.jas.2013.08.009

Neolithic agriculture on the European western frontier: the boom and bust of early farming in Ireland

Nicki J. Whitehouse et al.

A multi-disciplinary study assessing the evidence for agriculture in Neolithic Ireland is presented, examining the timing, extent and nature of settlement and farming. Bayesian analyses of palaeoenvironmental and archaeological 14C data have allowed us to re-examine evidential strands within a strong chronological framework. While the nature and timing of the very beginning of the Neolithic in Ireland is still debated, our results – based on new Bayesian chronologies of plant macro-remains – are consistent with a rapid and abrupt transition to agriculture from c. 3750 cal BC, though there are hints of earlier Neolithic presence at a number of sites. We have emphatically confirmed the start of extensive Neolithic settlement in Ireland with the existence of a distinct ‘house horizon’, dating to 3720-3620 cal BC, lasting for up to a century. Cereals were being consumed at many sites during this period, with emmer wheat dominant, but also barley (naked and hulled), as well as occasional evidence for einkorn wheat, naked wheat and flax. The earliest farmers in Ireland, like farmers elsewhere across NW Europe, were not engaged in shifting cultivation, but practised longer-term fixed-plot agriculture. The association between early agriculture and the Elm Decline seen in many pollen diagrams shows that this latter event was not synchronous across all sites investigated, starting earlier in the north compared with the west, but that there is a strong coincidence with early agriculture at many sites. After this early boom, there are changes in the nature of settlement records; aside from passage tombs, the evidence for activity between 3400-3100 cal BC is limited. From 3400 cal BC, we see a decrease in the frequency of cereal evidence and an increase in some wild resources (e.g. fruits, but not nuts, in the records), alongside evidence for re-afforestation in pollen diagrams (3500–3000 cal BC). Changes occur at a time of worsening climatic conditions, as shown in Irish bog oak and reconstructed bog surface wetness records, although the links between the various records, and assessment of causes and effects, will require further investigation and may prove complex. This period seems to have been one of environmental, landscape, settlement and economic change. The later 4th millennium BC emerges as a period that would benefit from focused research attention, particularly as the observed changes in Ireland seem to have parallels in Britain and further afield.

Link

Irish Travellers are Irish

Am J Phys Anthropol DOI: 10.1002/ajpa.22191

Genetic drift and the population history of the Irish travellers

John H. Relethford, Michael H. Crawford

Abstract

The Irish Travellers are an itinerant group in Ireland that has been socially isolated. Two hypotheses have been proposed concerning the genetic origin of the Travellers: (1) they are genetically related to Roma populations in Europe that share a nomadic lifestyle or (2) they are of Irish origin, and genetic differences from the rest of Ireland reflect genetic drift. These hypotheses were tested using data on 33 alleles from 12 red blood cell polymorphism loci. Comparison with other European, Roma, and Indian populations shows that the Travellers are genetically distinct from the Roma and Indian populations and most genetically similar to Ireland, in agreement with earlier genetic analyses of the Travellers. However, the Travellers are still genetically distinct from other Irish populations, which could reflect some external gene flow and/or the action of genetic drift in a small group that was descended from a small number of founders. In order to test the drift hypothesis, we analyzed genetic distances comparing the Travellers to four geographic regions in Ireland. These distances were then compared with adjusted distances that account for differential genetic drift using a method developed by Relethford (Hum Biol 68 (1996) 29–44). The unadjusted distances show the genetic distinctiveness of the Travellers. After adjustment for the expected effects of genetic drift, the Travellers are equidistant from the other Irish samples, showing their Irish origins and population history. The observed genetic differences are thus a reflection of genetic drift, and there is no evidence of any external gene flow.

Link

GWAS study of pigmentation in four European countries

From the paper:

Males (M) have consistently lighter pigmentation (lower scored) than females (F) in all four countries. Among countries, the largest pigmentation difference is with Ireland, where, in our sample, individuals have lighter pigmentation or lower M index on average than in Poland, Italy, or Portugal. Hair pigmentation histogram (C) and boxplot by country (D) in 341 individuals showing the distribution of hair pigmentation and the differences among countries. In our sample, individuals from Northern European countries (Ireland, Poland) have on average lighter hair pigmentation than individuals from Southern European countries (Italy, Portugal). The distributions in males are similar to those in females in all countries except Ireland, where, in our sample, males have darker hair color than females (not shown). Eye pigmentation histogram (E) and boxplot by country (F) in 468 individuals showing the bimodal distribution of eye pigmentation and the differences among countries. Comparison with self-reported phenotypes shows that the two modes of the distribution correspond to blue and brown eye color, while individuals reporting green and hazel eye color have intermediate C’ values. As with hair pigmentation, in our sample, individuals from Northern European countries have on average lighter eye pigmentation than individuals from Southern European countries. 

...   

Interestingly, our analysis of variation in skin color in Europe demonstrates a consistent difference in skin color between the sexes. By the DermaSpectrometer M index measure, males are more lightly pigmented than females in each of the four European countries we studied. The same trend in M index was reported previously in a sample of European Americans [38]. Our results in populations of European ancestry contradict earlier anthropological studies that have concluded females are more lightly pigmented than males in most populations (reviewed in [2]). One potential reason for the conflicting results is the different instruments used. In early studies, which used the Evans Electric Limited (EEL) and Photovolt broad-spectrum spectrophotometers, skin pigmentation estimates may be confounded by the hemoglobin level to a greater extent than for the DermaSpectrometer used in the present study [46].

Some data (lower = lighter):

One thing of interest is that while Irish males/females are both lighter-eyed than other Europeans, including Poles from northern Europe, Irish females appear to be lighter-haired than Irish males (96.3 vs. 106.7), but no such substantial sex difference exists in the Poles in this trait (107.5 vs. 109.5). Sexual dimorphism seems to lean in the direction of lighter male skins and lighter female hair across the four countries.

Peter Frost has offered the theory that "gentlemen prefer blondes" because during the Ice Age boreal hunters lived a harsh lifestyle that killed many of them, but the remainder could not adopt a polygynous lifestyle, because provisioning for a wife was expensive. As a result, women had to compete for the remaining men, and men could be picky, preferring those with a "rare color advantage." It is not immediately clear to me how this might explain the Ireland vs. Poland differentiation, assuming it reflects a broader NW/NE trend, since NE Europeans are more likely to be descended from hunter-gatherers of the tundra-steppe.

PLoS ONE 7(10): e48294. doi:10.1371/journal.pone.0048294

Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations

Sophie I. Candille et al.

Pigmentation of the skin, hair, and eyes varies both within and between human populations. Identifying the genes and alleles underlying this variation has been the goal of many candidate gene and several genome-wide association studies (GWAS). Most GWAS for pigmentary traits to date have been based on subjective phenotypes using categorical scales. But skin, hair, and eye pigmentation vary continuously. Here, we seek to characterize quantitative variation in these traits objectively and accurately and to determine their genetic basis. Objective and quantitative measures of skin, hair, and eye color were made using reflectance or digital spectroscopy in Europeans from Ireland, Poland, Italy, and Portugal. A GWAS was conducted for the three quantitative pigmentation phenotypes in 176 women across 313,763 SNP loci, and replication of the most significant associations was attempted in a sample of 294 European men and women from the same countries. We find that the pigmentation phenotypes are highly stratified along axes of European genetic differentiation. The country of sampling explains approximately 35% of the variation in skin pigmentation, 31% of the variation in hair pigmentation, and 40% of the variation in eye pigmentation. All three quantitative phenotypes are correlated with each other. In our two-stage association study, we reproduce the association of rs1667394 at the OCA2/HERC2 locus with eye color but we do not identify new genetic determinants of skin and hair pigmentation supporting the lack of major genes affecting skin and hair color variation within Europe and suggesting that not only careful phenotyping but also larger cohorts are required to understand the genetic architecture of these complex quantitative traits. Interestingly, we also see that in each of these four populations, men are more lightly pigmented in the unexposed skin of the inner arm than women, a fact that is underappreciated and may vary across the world.

Link

Genetic differences between five European populations (Moskvina et al. 2010)

Notice (on the left) the number of SNPs with significant (p=0.05) differences between population varies between a low for the Scotland-Ireland pair to a high for the Sweden-Portugal one.

The supplementary material is also interesting. In Supp. Fig. 2 you can see the occurrence of 4 distinct clusters corresponding to the four corners of Europe, and also a barely perceptible tilting of Scotland toward Sweden relative to Ireland, within the NW cluster. As always, we should not interpret this as a lack of distinctiveness of the two populations, as such distinctiveness may hide in either higher-order dimensions, or a combination of more markers/individuals to be able to discern it. We could, however, say, as common sense would also dictate that these two populations are very close to each other in the European context.

Human Heredity Vol. 70, No. 2, 2010

Genetic Differences between Five European Populations

Valentina Moskvina et al.

Abstract

Aims: We sought to examine the magnitude of the differences in SNP allele frequencies between five European populations (Scotland, Ireland, Sweden, Bulgaria and Portugal) and to identify the loci with the greatest differences. Methods: We performed a population-based genome-wide association analysis with Affymetrix 6.0 and 5.0 arrays. We used a 4 degrees of freedom χ2 test to determine the magnitude of stratification for each SNP. We then examined the genes within the most stratified regions, using a highly conservative cutoff of p less than 10–45. Results: We found 40,593 SNPs which are genome-wide significantly (p ≤ 10–8) stratified between these populations. The largest differences clustered in gene ontology categories for immunity and pigmentation. Some of the top loci span genes that have already been reported as highly stratified: genes for hair color and pigmentation (HERC2, EXOC2, IRF4), the LCT gene, genes involved in NAD metabolism, and in immunity (HLA and the Toll-like receptor genes TLR10, TLR1, TLR6). However, several genes have not previously been reported as stratified within European populations, indicating that they might also have provided selective advantages: several zinc finger genes, two genes involved in glutathione synthesis or function, and most intriguingly, FOXP2, implicated in speech development. Conclusion: Our analysis demonstrates that many SNPs show genome-wide significant differences within European populations and the magnitude of the differences correlate with the geographical distance. At least some of these differences are due to the selective advantage of polymorphisms within these loci.

Link

R1b founder effect in Central and Western Europe

Post will be updated after I read the paper. (Last Update: Aug. 29)

UPDATE I:

From the paper:

The ages of various haplogroups in populations were estimated using the
methodology described by Zhivotovsky et al,30 modified according to Sengupta
et al,10 using the evolutionary effective mutation rate of 6.9 x 10^-4 per 25 years.
The accuracy and appropriateness of this mutation rate has been independently
confirmed in several deep-rooted pedigrees of the Hutterites.

Of course readers of the blog are aware that I disagree with the use of the evolutionary rate. My comments on the Hutterites paper will be posted separately after I read it. I will simply say that there are numerous cases where the use of the genealogical rate makes better sense of the evidence than use of the "evolutionary" rate. Off the top of my head, the genealogical rate harmonizes with the Genghis Khan cluster, the expansion of Na-Dene speakers into the Americas, the expansion of Balto-Slavic, the Bronze Age spread of Semitic speakers, in accordance with the linguistic evidence, the expansion of Bantu in Angola, more recent British surnames, the formation of Arabian kingdoms, Greek colonization of Sicily, and the Bronze Age origin of Indo-Aryans and Finno-Ugrians (and I skipped a few).

UPDATE II (Aug 26):

Here is the phylogeny of R-M207 from the paper. For reference, the R-M207 page from ISOGG.


UPDATE III (Aug 26):

Going through the material in this paper in a systematic manner is not easy, so I will probably do a potpourri of updates covering various topics of interest.



As noted in the other recent paper, and shown in the above Figure from the current one, R-U106 peaks in northern Europe. Its frequency (including the R-U198 sublineage) is 36.8% in the Netherlands, 20.9% in Germany and Austria, 18.2% in Denmark, 18.2% in England, 12.6% in Switzerland, 7.5% in France, 6.1% in Ireland, 5.9% in Poland, 5.6% in north Italy 4.4% in Czech Republic and Slovakia, 3.5% in Hungary, 4.8% in Estonia, 4.3% in south Sweden, 2.5% in Spain and Portugal, 1.3% in eastern Slavs, 0.8% in south Italy, 0.6% in Balkan Slavs, 0.5% in Greeks (i.e. 2 of 193 Cretans, and no mainland Greeks), 0.4% in Turks, 0% in Middle East.

The age of R-U106 is estimated by the authors as 8.7ky BP, which translates to about 2.5ky BP with the germline rate. The existence of R-U106 as a major lineage within the Germanic group is self-evident, as Germanic populations have a higher frequency against all their neighbors (Romance, Irish, Slavs, Finns). Indeed, highest frequencies are attained in the Germanic countries, followed by countries where Germanic speakers are known to have settled in large numbers but to have ultimately been absorbed or fled (such as Ireland, north Italy, and the lands of the Austro-Hungarian empire). South Italy, the Balkans, and West Asia are areas of the world where no Germanic settlement of any importance is attested, and correspondingly R-U106 shrinks to near-zero.

UPDATE IV (Aug 26):

Another informative lineage, as noted in the other recent paper as well is R-U152:


Of interest is the fact that while R-U152 has a clear French-Italian center of weight, the locations exhibiting highest STR variance are Germany and Slovakia, i.e., Central Europe. My guess is that R-U152 originated in Central Europe spreading to the west and south, perhaps with Italo-Celtic speakers or some subset thereof. In its home territory of Central Europe, its frequency decreased by the introduction of the Germanic and Slavic speaking elements which dominate the region.

Irrespective of what the ultimate origin of R-U152 is, it provides us with a good diagnostic marker for population movements out of the French-Italian area. In Italy for example it is noted at 26.6% for the north and 10.5% in the south. It would be extremely interesting to see its occurrence in Balkan Vlachs, as this would confirm/disprove the Italian component in their origin. However, R-U152 occurs in 7.3% of Cretans, suggesting introgression Y-chromosomes of North Italian (Venetian) origin, from the 4-century period of Venetian rule of the island. It also occurs in 4.1% of Greeks, where it might come from any period since the Roman annexation of the Hellenistic states to the Vlachs. However, its presence at only 1.8% of Romanians makes a large Italian contribution to the Romanian population unlikely. Balkan R-U152 chromosomes should be better resolved to determine when they arrived from the northwest.

The paucity of R-U152 in Turks (0.6%) make tales of wandering Galatians less likely to be true. There is no doubt that Galatians settled in Anatolia, but they were probably so few in numbers that they did not permanently alter the population. Knowledgeable readers should chime in about the Lebanese Christian R1b which was posited as a signature of the Crusades a couple of years ago, and its position in the phylogeny.

UPDATE V (Aug 26):

The most commong R1b subgroup in Europe is R-M269 and the most common subgroup is R-L23 which encompasses the vast majority of European R-M269 chromosomes. It is interesting to see where R-M269(xL23) is concentrated. In Europe I see cases in Germany, Switzerland, Slovenia, Poland, Hungary, Russia, the Ukraine. It is most prominent, however, in the Balkans, where every population except Croatia mainland (N=108) possesses it. In the Caucasus it does not exist except in the northeast. In Turkey and Iran there is some, albeit it is not clear in which regions.

UPDATE VI (Aug 27):

The authors write with respect to haplogroup R-V88:

With the exception of rareincidences of R1b-V88 in Corsica, Sardinia13 and Southern France(Supplementary Table S4), there is nearly mutually exclusive patterning of V88 across trans-Saharan Africa vs the prominence of P297-related varieties widespread across the Caucasus, Circum-Uralic regions, Anatolia and Europe. The detection of V88 in Iran, Palestine and especially the Dead Sea, Jordan (Supplementary Table S4) provides an insight into the back to Africa migration route.

Haplogroup R-V88 has been the subject of a recent study and was associated with the migration of Chadic speakers in Africa. It is difficult to say whether or not the authors' results really provide any insight into an alleged movement of this haplogroup from Asia to Africa, as it occurs in only a single Palestinian, and a single Iranian. Neither is the higher frequency (13.7%) observed in the Amman and Dead Sea area of Jordan really evidence of its antiquity there.

Neither the aforementioned paper nor the current one presents any evidence (e.g., Y-STR variance) for any great antiquity of the Asian R-V88 with respect to the African one. Indeed, with the exception of the aforementioned Jordanian sample, R-V88 is rare in Asia, while it is widespread in African Berbers. I see no clear reason at present to think that it migrated to Africa from Asia, and not to think of it as a relic of an older, widely dispersed R1b population leading to R-V88 in Africa itself.

UPDATE VII (Aug 28):

The paper repeats the standard claims about the origin of R1b and its main sublineage R-M269 in Asia, but presents no new information that would support this claim. With the state of the evidence, I see no real reason to prefer a West Asian to a Southeastern European origin for this haplogroup.

I don't give much credence to small differences in Y-STR variance, due to the large confidence intervals associated with such estimates, and it is interesting that the authors do not present an argument from Y-STR variation about the origin of R1b, preferring to make broad statements about Mesolithic-Neolithic movements into Europe.

A study of supplementary table S2 which gives coalescent times reveals that there is no clear pattern of greater Asian diversity within haplogroup R1b or its subclades. And, while Central-Western Europe does appear to be an outgrowth of R1b rather than a place of origin (with the dominance of derived R-M412 lineages) there is nothing in the paper that would make one prefer West Asia to Southeastern Europe as a place of origin.

Personally I think the issue cannot be settled yet, but there are reasons to prefer the latter option. An Asian origin of R1b has a major parsimony hurdle: it would require a seemingly directed drang nach westen for R1b, into Europe, and into North Africa, with a paucity of R1b in the opposite direction (among Arabians and to the south and in South Asia) and a scattering of very young R-M73 and R-M269 to the east of Europe.

UPDATE VIII (Aug 29):

R-S116 shows maximum Y-STR diversity in France and Germany but maximum frequency in Iberia and the British Isles. In the latter region it is represented mainly by R-M529 with the R-M222 subclade being particularly prominent in Ireland but also North England. It would be interesting to see data for Scotland, and I do not doubt that R-M222 would be prominent there as well. R-S116 also shows signs of being a Celtic, or Celtiberian-related lineage.

European Journal of Human Genetics doi: 10.1038/ejhg.2010.146

A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe

Natalie M Myres et al.

The phylogenetic relationships of numerous branches within the core Y-chromosome haplogroup R-M207 support a West Asian origin of haplogroup R1b, its initial differentiation there followed by a rapid spread of one of its sub-clades carrying the M269 mutation to Europe. Here, we present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles. Although this frequency pattern closely approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past ≤10 thousand years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.

Link

Guess their origin (answer: Irish)

Here are readers' guesses:

See page 45 for explanation.

Population structure in Ireland and Britain (O'Dushlaine et al. 2010)

From the paper:

Eigensoft PCA analysis across all seven of our European and European-ancestry populations broadly identified four sub-groups consisting of (i) Bulgarian, (ii) Portuguese, (iii) Swedish and (iv) Irish/British/Utah populations (see Figure 1a, Supplementary Figure S1). The first two principal components (PCs) separate out northern from southern, and western from eastern European ancestry, respectively. The Europe-wide PCA analysis positions the Scottish population (Aberdeen) intermediate between the Irish and English populations. We further explored this observation by restricting our PC analysis to residents of Ireland, Scotland (Aberdeen) and south/southeast England (Figure 1b, Supplementary Figure S1). This analysis confirms the observation that the Scottish population is intermediate between the Irish and English cohorts on the first principal component(this time dividing west from east). Although more subtle, the Scottish cohort is also shifted slightly from the other two on PC2.

The distinction between Britons and Swedes was also noted in an earlier study. It's nice to see Bulgarians and Portuguese sampled, as they have been rather neglected in genomic studies, but, unfortunately none of their neighbors or any other intermediate populations were included, which is understandable as the study focused on British Isles populations. Bulgarians and Portuguese served as "anchor points" to re-create the well-known correlation of the first two PCs of European genetic variation with longitude/latitude.

The intermediate position of Scottish populations relative to the Irish and English is not surprising, given the Gaelic connection between Scotland and Ireland.

The paper also has haplotype diversity data that can be compared with those recently published by Auton et al.

The authors observe:

In summary, our results illustrate a subtle genetic structure across Britain and Ireland in the context of the comparatively homogenous nature of the European genetic pool. We have observed slightly elevated levels of LD and genome-wide homozygosity in Ireland and Sweden compared with neighbouring British and European populations, although these levels do not approach those of traditional population isolates. Similarly, we have illustrated a decrease in HD in Britain and Ireland, more so in Scotland and Ireland than in England.

Finally, the authors present results of frappe analysis (Figure S2):


At K=2 we see a distinction between northern and southern Europeans.

At K=3 a distinction between British Isles and Sweden appears. The absence of the Western European component in Bulgarians is noteworthy and expected.

At K=4 the Bulgarian component is identified.

At K=5 a Portuguese component is identified.

British Isles populations are dominated by the "Northwestern" green component with variable "Scandinavian" white (which is higher in England as expected) and both "Iberian" and "Balkan" minority elements.

European Journal of Human Genetics doi: 10.1038/ejhg.2010.87

Population structure and genome-wide patterns of variation in Ireland and Britain

Colm T O'Dushlaine et al.

Abstract

Located off the northwestern coast of the European mainland, Britain and Ireland were among the last regions of Europe to be colonized by modern humans after the last glacial maximum. Further, the geographical location of Britain, and in particular of Ireland, is such that the impact of historical migration has been minimal. Genetic diversity studies applying the Y chromosome and mitochondrial systems have indicated reduced diversity and an increased population structure across Britain and Ireland relative to the European mainland. Such characteristics would have implications for genetic mapping studies of complex disease. We set out to further our understanding of the genetic architecture of the region from the perspective of (i) population structure, (ii) linkage disequilibrium (LD), (iii) homozygosity and (iv) haplotype diversity (HD). Analysis was conducted on 3654 individuals from Ireland, Britain (with regional sampling in Scotland), Bulgaria, Portugal, Sweden and the Utah HapMap collection. Our results indicate a subtle but clear genetic structure across Britain and Ireland, although levels of structure were reduced in comparison with average cross-European structure. We observed slightly elevated levels of LD and homozygosity in the Irish population compared with neighbouring European populations. We also report on a cline of HD across Europe with greatest levels in southern populations and lowest levels in Ireland and Scotland. These results are consistent with our understanding of the population history of Europe and promote Ireland and Scotland as relatively homogenous resources for genetic mapping of rare variants.

Link

ESHG 2009 abstracts

ESHG 2009 is in two weeks, and there are some very interesting abstracts, including a tantalizing new study on Y-chromosome haplogroup R1b1b2 (R-M269).

Phylogeography of human Y chromosome haplogroup R1b1b2 (R-M269) in Europe

F. Cruciani et al.

The human Y chromosome haplogroup R1b1b2 (R-M269) displays an extremely wide geographic distribution within Europe, with a decreasing frequency cline from Iberia (frequencies up to 90%) towards the Balkans (usually less than 10%). Previous studies have proposed that the observed R1b1b2 frequency cline is due to a population expansion from an Iberian Ice-age refugium after the LGM (Malaspina et al. 1998; Semino et al. 2000).

In this study, we explored the phylogeography of the human Y chromosome haplogroup R1b1b2 by analyzing more than 2,000 males from Europe. The haplogroup-defining marker M269 (Cruciani et al. 2002), and two additional internal markers (U106 and U152, Sims et al 2007) which identify internal branches (R1b1b2g and R1b1b2h) were analyzed. The paragroup R1b1b2*(xR1b1b2g, R1b1b2h) and the haplogroups R1b1b2g and R1b1b2h showed quite different frequency distribution patterns within Europe, with frequency peaks in the Iberian Peninsula, northern Europe and northern Italy/France, respectively. The overall frequency pattern of R1b1b2 haplogroup is suggestive of multiple events of migration and expansion within Europe rather than a single and uniform spread of people from an Iberian Ice-age refugium.

References:

Malaspina et al. (1998) Am J Hum Genet 63:847-860
Semino et al. (2000) Science 290:1155-1159
Cruciani et al. (2002) Am J Hum Genet 70:1197-1214
Sims et al. (2007) Hum Mutat 28:97

Note that in the abstract below, the authors refer to Slavopaionians, not Macedonians.

Y chromosome haplogroup R1a is associated with prostate cancer risk among Macedonian males

D. Plaseska-Karanfilska et al.

Prostate cancer (PC) is one of the most common male-specific cancers. Its incidence varies considerably between populations. Recent surveys suggest that PC is influenced by both genetic and environmental factors, although the etiology of the disease remains unknown in the majority of cases. Certain Y chromosomal lineages have been suggested to predispose individuals to prostate cancer in Japanese population, but no association has been found among Korean and Swedish patients. The aim of this study was to investigate the association between Y chromosomal haplogroups and predisposition to prostate cancer in Macedonian men. We studied 84 PC patients and 126 males from the general population of Macedonian ethnic origin. A total of 28 markers have been studied by multiplex PCR and SNaPshot analysis. Nineteen different Y haplogroups were determined; the most frequent being I1b-P37b, E3b1-M78, R1a-SRY 1532, R1b-P25 and J2b1a-M241. The frequency of R1a was significantly higher in PC patients (20.2%) in comparison with the controls (9.5%) [p=0.027; OR=2.41 (1.09-5.36)]. When stratified according to age, even stronger association was observed between haplogroup R1a and prostate cancer in patients of >65 years of age [p=0.004; OR=3.24 (1.41-7.46)]. Our results suggest that Y chromosome haplogroup R1a is associated with an increased prostate cancer risk in Macedonian men.

The genetic position of Western Brittany (Finistère, France) in the Celtic Y chromosome landscape

K. Rouault et al.

Brittany, a large peninsula located at the western part of France, is of particular interest because of its historical settlement and its relative geographic and cultural isolation. Brittany was invaded by waves of migration from Britain and Ireland between the 4th and 7th centuries and, therefore, belongs to the Brythonic branch of the Insular Celtic language. We have focused our study on the department of Finistère, the most western territorial unit of Brittany, and its administrative and historical areas. To explore the diversity of the Y-chromosome, we analyzed a total of 348 unrelated males using a combination of 23 biallelic markers and 12 microsatellite loci. The molecular analysis revealed that 82.2% of the Y chromosomes fell into haplogroup R1b, placing Finistère within the Western European landscape. Interestingly, at a microgeographical level, differences were detected by the haplogroup R1a* being confined to the south of the department, while haplogroups E3b, F, G, J2, K and R1a1 were found in the north. Nevertheless, geographical distribution of haplogroups and haplotypes suggested territorial homogeneity inside Finistère. Most of the Y-chromosomal gene pool in Finistère is shared with European, especially British, populations, thus corroborating the historical reports of ancient migrations to Brittany. Finally, the results are consistent with those obtained from classic genetic markers and support the Celtic paternal heritage of the Finistère population.

Mitochondrial Genome Diversity in Tungusic-speaking Populations (Even and Evenki) and Resettlement of Arctic Siberia After the Last Glacial Maximum

I. O. Mazunin et al.

The present study includes the Even/Evenki, hunters and reindeer-breeders, sampled from a few localities scattered across their vast geographic range encompassing low Yana-Indigirka-Kolyma in the west and the Sea of Okhotsk coast in the east. The mtDNA data show a very close affinity of the Even/Evenki with the Yukaghir, typical reindeer hunters, dominating in extreme northeastern Siberia until the middle of 18th century but now being on the brink of extinction. We found that the majority of mtDNA diversity in the Tungusic-speaking populations was accounted for by Siberian-East Eurasian lineages C2, C3, D2, D3, D4-D9 and G1. The similarity in the haplogroup C and D mtDNA intrinsic variation between the Even and Yukaghir populations is pronounced and indicates that the Even/Evenki harbor an essential portion of the ancestral Yukaghir pool. The phylogeography of the D4-D9 point to an early Neolithic phase expansion initiated northward to the northern and eastern perimeters of former Beringia. Concerning unique D2* lineage (Volodko et al. 2008), the network analysis encompassing four complete sequences, three of the Yukaghir from the low Indigirka-Kolyma region and one of the Evenk from the upper reaches of the Aldan River would suggest that the founding haplotype (1935-8683-14905) for D2* originated within western part of former Beringia. In the meanwhile, the core of the Even/Evenki mtDNA pool residing in the midst of the Yukaghir ancient territory would represent a recent amalgamation of the remnants of the Yukaghir and northern Tungusic-speakers (Even/Evenki) originated in the mid-Amur region.

X-chromosomal haplotypes in global human populations

V. A. Stepanov, I. Y. Khitrinskaya;

To reconstruct the origin and evolution of X-chromosomal lineages in global human populations we investigated the genetic diversity in 23 population samples (about 1500 individuals totally) using SNP markers in a single linkage disequilibrium region of ZFX gene. About sixty haplotypes belonging to 3 phylogenetic branches (A, B, and F) originated from the single African root were found in the total sample. Branch A includes mostly African haplotypes, whereas four major haplotypes belonging to different sub-branches of B (haplotype E8) and F (haplotypes H4, I3 and I11) were present in Eurasia. Major haplotype of the older branch B (E8) is almost evenly distributed among Eurasian populations. Haplotypes of the younger phylogenetic branches demonstrates clinal distribution with the sharp frequency changes from East to West. Haplotype H4 is presumably “Eastern-Eurasian”. It reaches the highest frequency in Eastern and South-Eastern Asians. Haplotypes I3 and I11 in the contrary show the clear frequency gradient from West to East with the highest frequency in Europeans, moderate frequency in Central Asia, and the minimal frequency in North-East and South-East Asia. The total level of genetic differentiation of global human populations estimated by the analysis of molecular variance of X-chromosomal haplotypes (Fst = 9.1%) is quite high and roughly corresponds to those measured for most other types of genetic markers except Y-chromosomal haplogroups which are characterized by the much higher level of between-population differences.

Dissecting the genetic make-up of Central Eastern Sardinia using a high density set of sex and autosomal markers

L. M. Pardo

Genetic isolates are valuable for identifying genetic variations underlying complex traits. However, prior knowledge of the genetic structure of the isolate is fundamental for carrying-out genome-wide association studies (GWAS) in these populations. The Sardinian population is currently the target of GWAS because of its ancient origin and long-standing isolation. To perform GWAS in Sardinia, we aim to characterize a subpopulation from the archaic area of Central-Eastern Sardinia at the genomic level. We used sex-specific markers (Y-chromosome and mtDNA) to assess the heterogeneity of the founder lineages and the divergence from other populations. In addition, we used a dense set of autosomal markers (SNP 5.0 array, Affymetrix) to investigate genome-wide Linkage Disequilibrium, to construct a Copy Number Variation map and to estimate pair-wise kinship and inbreeding.We first determined Y-chromosome lineages in 256 unrelated Sardinians using biallelic and microsatellite markers. Our analysis showed that the frequency of the major Y haplogroups clearly sets this population apart from other European haplogroups. The analysis of microsatellite markers revealed a high degree of gene diversity. Pairwise kinship and inbreeding were estimated in 113 subjects using 77709 autosomal SNP markers. We found that 16% of the subject pairs shared identical-by descent alleles more often than expected by chance. Furthermore, 60% of the subjects had low inbreeding coefficient values. Our preliminary results confirm that Sardinia is genetically different from other populations, as shown by Y-chromosome markers. The kinship and inbreeding estimates indicate some degree of relatedness among Sardinians, as expected for an isolated population.

Genetic differences between four European populations

V. Moskvina et al.

Population stratification can distort the results of genome-wide association studies (GWAS). One approach to deal with this inflation of the statistic is to estimate the inflation factor and adjust the detection statistic accordingly. However, the evolutionally forces work with different strength in some regions of the human genome, e.g. around the lactase gene (LCT) and the HLA region, making such an adjustment inappropriate.

We examined the population differences in four European populations (Scotland, Ireland, Sweden and Bulgaria) using data from GWAS performed with the Affymetrix 6.0 array at the Broad Institute. We show that there are >20,000 SNPs which are highly (p less than 10-6) significantly stratified between the four populations, after genome wide Bonferroni correction for multiple testing. We then examined the top 20 stratified regions to see what genes might have caused the top differences, using a highly conservative cut-off of p less than 10-40. Some of the loci span genes reported before: hair colour and pigmentation (HERC2, EXOC2), the LCT gene, genes involved in NAD metabolism, and genes involved in immunity (HLA and the Toll-like receptor genes TLR10, TLR 1, TLR 6). Among the top hits were several genes which have not yet been reported as stratified within European populations, indicating that they might also provide a selective advantage. Some involve other immunity genes (CD99, ILT6), but others show no obvious effect on positive selection: several zinc fingers, and most intriguingly, FOXP2, implicated in speech development. Future GWAS should take into consideration any positive associations with these genes.

Genomic runs of homozygosity: population history and disease

R. McQuillan

Runs of homozygosity (ROH), resulting from the inheritance from both parents of identical haplotypes, are abundant in the human genome. ROH length is determined partly by the number of generations since the common ancestor: offspring of cousin matings have long ROH, while the numerous shorter ROH reflect shared ancestry tens and hundreds of generations ago. In studies of European populations we show that Froh, a multipoint estimate of individual autozygosity derived from genomic ROH, distinguishes clearly between subpopulations classified in terms of demographic history and correlates strongly with pedigree-derived inbreeding coefficients. In a global population dataset, analysis of ROH allows categorisation of individuals into four major groups, inferred to have (a) parental relatedness in the last 150 years (many south and west Asians), (b) shared parental ancestry arising hundreds to thousands of years ago through population isolation and restricted effective population size (Ne), but little recent inbreeding (Oceanians, African hunter-gatherers, some European and south Asian isolates), (c) both ancient and recent parental relatedness (Native Americans), and (d) only the background level of shared ancestry relating to continental Ne (east Asians, urban Europeans; African agriculturalists). Long runs of homozygosity are therefore a widespread and underappreciated characteristic of our genomes which record past consanguinity and population isolation and provide a unique record of individual demographic history. Individual ROH measures also allow quantification of the disease risk arising from polygenic recessive effects. We present preliminary data from a survey of the effects of ROH on quantitative disease-related traits and disease risk.

European Lactase Persistence Allele is Associated With Increase in Body Mass Index

J. A. Kettunen et al.

The global prevalence of obesity, usually indexed by body mass index (BMI) cut-offs, has increased significantly in the recent decades, mainly due to positive energy balance. However, the impact of a selection for specific genes cannot be excluded. Here we have tested the association between BMI and one of the best known genetic variants showing strong selective pressure: the functional variant in the cis-regulatory element of the lactase gene. We tested this variant since it is presumed to provide nutritional advantage in specific physical and cultural environments. We found that the variant responsible for lactase persistence among Europeans was also associated with higher BMI in a Nordic population sample (p = 1.3*10-5) of 15 209 individuals, the size of the effect being close to that of FTO. We tested the effect of population stratification and concluded that the association was not due to population substructure.

Supplement on "Geographical structure and differential natural selection amongst North European populations" (McEvoy et al. 2009)

From the supplemental material of a paper I covered in March, here are a couple of PCA plots of the first two principal components of the studied populations, with or without the Finns.


In the plot without the Finns, we see the expected British Isles -> Continental Europe differentiation in the order of Ireland, UK, Netherlands, along PC1. Swedes, and to a much lesser extent Danes deviate from this gradient in an orthogonal direction.
When Finns are included, PC1 now captures the major difference between them and the other Celto-Germanic populations which appear strikingly homogeneous along this component. The reason for the Swedes' divergence is now clear, as they are seemingly drawn towards the Finns, although the two clusters can be cleanly separated by a line at around PC1=-0.03.

It is fairly clear by now, that in northern Europe, there are two major distinctions (in that order): (i) between the Finns, and Finno-Ugrian influenced populations on the one hand, and the rest, and (b) a less important West-East gradient from Ireland to the Baltic.

The fact that factor (i) is the most important one pretty much vindicates the views of traditional physical anthropology since the time of Deniker at least. Despite the lack of data and statistical knowledge available at his time, Deniker, in the late 19th century, divided the light-pigmented northern European xanthochrooi of earlier classifications into two: the race nordique, associated primarily with the Germanic peoples, and the race orientale associated primarily with the eastern Slavs and Finns.

This classification scheme was continued by the better writers that followed, e.g., as razza nordica and razza baltica by Renato Biasutti, and as Атланто-балтийская раса (Atlanto-Baltic race) and Беломорско-балтийская раса (White Sea-Baltic race) in works written in Russian.

Genetic structure in northern Europe revisited

The results of the STRUCTURE analysis are quite interesting. When Finland is included (B), it is the first one to be separated from other Northern Europeans, confirming previous results. Sweden, and to a lesser degree Denmark seems to possess some admixture with the Finnish-related (red) element. The next split (blue vs. green) differentiates continental Germnics (esp. Scandinavians, and somewhat less Dutch) from Irish-British and Australians of largely British ancestry.

When Finland is not included (C) and for K=4, it becomes obvious that the UK population includes three components ("Dutch" green, "Scandinavian" red, and "British Isles" blue).
See also a previous study on the topic.

Genome Research doi:10.1101/gr.083394.108

Geographical structure and differential natural selection amongst North European populations

Brian P McEvoy et al.

Abstract

Population structure can provide novel insight into the human past and recognizing and correcting for such stratification is a practical concern in gene mapping by many association methodologies. We investigate these patterns, primarily through principal component (PC) analysis of whole genome SNP polymorphism, in 2099 individuals from populations of Northern European origin (Ireland, UK, Netherlands, Denmark, Sweden, Finland, Australia and HapMap European-American). The major trends (PC1 and PC2) demonstrate an ability to detect geographic substructure, even over a small area like the British Isles, and this information can then be applied to finely dissect the ancestry of the European-Australian and -American samples. They simultaneously point to the importance of considering population stratification in what might be considered a small homogenous region. There is evidence from FST based analysis of genic and non-genic SNPs that differential positive selection has operated across these populations despite their short divergence time and relatively similar geographic and environmental range. The pressure appears to have been focused on genes involved in immunity, perhaps reflecting response to infectious disease epidemic. Such an event may explain a striking selective sweep centered on the rs2508049-G allele, close to HLA-G gene on chromosome 6. Evidence of the sweep extends over 8Mb/3.5cM region. Overall the results illustrate the power of dense genotype and sample data to explore regional population variation, the events that have crafted it and their implications in both explaining disease prevalence and mapping these genes by association

Link

Ancient mtDNA from Iceland

From the paper:

Using the sequence data described in Table 1, we obtained an estimate of 58% ancestry from Scotland and Ireland for contemporary Icelanders (95% C.I.: 44.6–71.2%). In comparison, the IEMS [DP: Iceland Early Medieval Sample] yielded an estimate of 64.7% (95% C.I.: 36.8–90.3%), indicating a similar excess of matrilineal ancestry from Scotland and Ireland.

PLoS Genetics doi: 10.1371/journal.pgen.1000343

Sequences From First Settlers Reveal Rapid Evolution in Icelandic mtDNA Pool

Agnar Helgason et al.

Abstract

A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations. Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. Here, we show that a sample of mitochondrial DNA (mtDNA) control region sequences from 68 early medieval Icelandic skeletal remains is more closely related to sequences from contemporary inhabitants of Scotland, Ireland, and Scandinavia than to those from the modern Icelandic population. Due to a faster rate of genetic drift in the Icelandic mtDNA pool during the last 1,100 years, the sequences carried by the first settlers were better preserved in their ancestral gene pools than among their descendants in Iceland. These results demonstrate the inferential power gained in ancient DNA studies through the application of population genetics analyses to relatively large samples.

Link

ISBA3 abstracts

Many abstracts from the International Symposium on Biomolecular Archaeology.

Various DNA / Technology

Human ancient DNA analysis within The Genographic Project: a project update and preliminary results from two powerful multiplex SBE typing methods

Wolfgang Haak1, Juan J Sanchez2, Clio Der Sarkissian1, Christina Adler1 & Alan Cooper1

1 The Australian Centre of Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia
2 National Institute of Toxicology and Forensic Science, Canary Islands Delegation, 38320 Tenerife, Spain.

The Australian Centre of Ancient DNA (ACAD) is one of 11 Regional Centres of The Genographic Project (TGP), and the only centre dedicated solely to ancient human DNA analyses. Our aim is to provide a temporal perspective to the movements and presence of prehistoric and historic populations through ancient DNA, and establish a time depth to the detailed genetic landscape being generated from the largescale modern human population data of TGP. We will present an update on the current activities and an overview of the protocols and strategies used in the ACAD. The retrieval of authentic human ancient DNA is plagued by methodological problems, and to deal with these we are relying on state-of-the-art methods ranging from sample collection through to data generation. We are using SPEX and multiplex PCR assays followed by SBE typing to analyse both mtDNA coding region markers and nuclear NRY markers. New multiplex assays were designed to amplify highly degraded DNA with an average amplicon length of 60-80bp, targeting 22 mtDNA SNPs and 25 NRY SNPs - to match the core marker panel used within TGP. Preliminary results show that the SBE typing protocols are robust and prove to be highly efficient in targeting minute amounts of suriving aDNA. In addition, the main advantage of SBE has proven to be the detecting power of omnipresent (background) contamination. We conclude that the mtDNA and NRY SBE assays, in combination with sequence data from the mtDNA control region (backed up by cloning and SPEX), and specialised sample collecting systems, provide a powerful means to effectively generate largescale (pre-)historic population data from ancient human samples.

What colour was Attila the Hun’s horse?: genetic signatures of phenotypic traits in archaeological materials

Mim A. Bower¹, Michael G. Campana², Diane Lister¹, Mark Whitten³, Kathy M. Dominy⁴, Angela M. Murphy⁵, Paula Jenkins⁶, Richard Sabin⁶, Michael Akam⁷, Robert Asher⁷ & Matthew Binns⁵.

¹ McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK.

² Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3DZ, UK.

³ Comparative Population Linguistics Group, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.

⁴Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, London, SE1 9RT, UK.

⁵Department of Veterinary Basic Sciences, the Royal Veterinary College, Royal College Street, London, NW1 0TU, UK.

⁶ Department of Zoology, Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK

⁷Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.

Studying the phenotype, i.e. what a plant or animal looked or behaved like, is perhaps the next “Holy Grail” in ancient DNA research. If we could trace the genes responsible for particular characters in archaeological specimens, it would open the door to some highly relevant and interesting questions in archaeology; the least of which may be the elusive “domestication gene”, but could cover more basic questions, such as: did people in mediaeval Europe prefer cows that had a tendency to lay down fat or muscle? When and where did a particular genetic disorder enter a domestic population? Was the spread of agriculture influenced by adverse environmental conditions? Or what colour was Attila the Hun’s horse? We could begin to understand past approaches to animal and plant husbandry, the expression of past human choice and selection, and past understanding of biological processes such as heredity. Fortunately, molecular biology is fast uncovering the genes responsible for particular phenotypic traits – the only problem, and a significant one perhaps, is looking for these genetic signatures in ancient DNA, known to be a recalcitrant material for analysis.

Here we present the results of our research on phenotypic loci in various historic and archaeological materials (bones, teeth, parchment, hide, seeds), and discuss the potential for future of phenotypic research in archaeogenetics.

Greece & Italy

Aristophanes and Stable Isotopes: Comparing literary and isotopic evidence of diet in Classical Thebes, Greece.

Efrossini Vika ^1,2, Mike Richards^3,4, Holger Schutkowski² and Vassilis Aravantinos⁵

¹ School of Conservation Sciences, Bournemouth University, BH12 5BB, UK

² Division of Archaeological, Geographical and Environmental Sciences, University of Bradford, BD7 1DP, UK

³ Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, DE

⁴ Department of Archaeology, Durham University, DH1 3LE, UK

⁵ IX Ephorate of Prehistoric and Classical Antiquities, Thebes 60200, GR

The greatest advantage for an archaeologist working with historically dated material is the existence of literary sources, which can complement scientific analyses in archaeology. The present study compiles a dietary profile for the inhabitants of Classical Thebes, using δ¹³C and δ¹⁵N isotope analysis, comparing this evidence with information on diet as presented in Aristophanes’ comedies (Acharnians, Plutus, Wasps).

Aristophanes’ work is abundant in satirical scenes, which emphasize personal attributes and local characteristics. Within this realm, it is possible to extract information on dietary habits, trade and economy in the Classical times. Merchants from Thebes oftentimes appear in his work, reflecting the city’s wealth. Among the goods deriving from this region, eels feature prominently, and are praised as an exceptional delicacy.

Stable isotope analyses of bone collagen were carried out for individuals from the Classical burials of the Northeastern cemetery of Thebes. Results show a remarkable increase of the nitrogen values relative to the previous periods, which is not accompanied by an analogous enrichment of the carbon values. This profile can partly be explained by an increased consumption of freshwater sources in Thebes during the Classical times, such as Aristophanes’ famous eels.

The results demonstrate how the integration of isotopic and literary evidence can provide novel information about Classical society in Thebes.

Greek myths

Terry Brown
Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, UK

The Greek Bronze Age is the time of the Homeric legends and the Greek myths. The work of Schliemann, Tsountas, Wace and others revealed the material remains of the Mycenaean civilisation that was dominant in the Aegean during the 17th to 12th centuries BC, these remains including human skeletons, some buried with rich grave goods. Biomolecular archaeologists have been attracted to the Greek Bronze Age because there are interesting kinship questions for the burials at several sites, and because aDNA could throw light on the impact of diseases such as malaria on these societies. Addressing these questions clearly requires that aDNA is preserved in the relevant material, and our conclusion after ten years of work is that largely it is not. We have found no indication of aDNA at Lerna, Antron Grave Circles A and B and Mycenae Grave Circle A. At Mycenae Grave Circle B, we detected mitochondrial aDNA in just four of the 22 skeletons that we studied. Only at Kouphovouno have we have obtained sufficient aDNA results to attempt any kind of archaeologically relevant study. The distinguishing feature of Kouphovouno is that we obtained skeletal samples immediately after their excavation. We used optimised PCR systems in order to maximise our chances of detecting aDNA if it was present, but we also used a high containment facility and took scrupulous care to remove surface contamination from the bone samples and to prevent cross-contamination with PCR products from previous experiments. We also confirmed that our negative results were not due to inhibition of PCRs by substances co-purifying with aDNA. Negative results tend not to get widely publicised – we would have preferred positive ones but not if they lead to new Greek myths.

Late Bronze Age Diet in the Greek Peloponnese

E.I.Petroutsa1 & M.P.Richards2

1.20 Koundouriotou str., Exarcheia, 10683 Athens, Greece

2.Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany


In this paper we present the results of an isotopic study of bone collagen samples from four Late Bronze Age cemeteries from the Northern Peloponnese in Greece: Voudeni, Aghia Triada, Almyri and Kritika. Through isotope analyses we sought to characterise the general diets in these four sites, especially the amounts of marine protein, as well as animal vs. plant proteins in diets. We also compared the isotopic results from these sites with other Bronze Age sites, including Mycenae. Despite the coastal location of most of the sites we could not find evidence of any significant consumption of marine foods. Instead, most human diets are based on a mixture of plant and animal protein, from C3 terrestrial resources.

Preliminary results of C and N isotope analyses and 14C dating of prehistoric humans and animals from the Mesolithic-Neolithic site of Grotta dell’Uzzo, Sicily, Italy

Marcello A. Mannino1, Sahra Talamo1, Rosaria Di Salvo2, Vittoria Schimmenti2, Marcello Piperno3, Sebastiano Tusa4, Antonio Tagliacozzo5, Michael P. Richards1,6

(1) Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig (Germany)

(2) Museo Archeologico Regionale ‘Antonino Salinas’, Via Bara all’Olivella 24, 90133 Palermo (Italy)

(3) Dipartimento di Scienze Storiche, Archeologiche ed Antropologiche dell’Antichità, Sezione di Paletnologia, Università di Roma ‘La Sapienza’, Via Palestro 63, 00185 Roma (Italy)

(4) Soprintendenza del Mare, Palazzetto Mirto, Via Lungarini 9, 90133 Palermo (Italy)

(5) Museo Nazionale Preistorico Etnografico ‘L. Pigorini’, Piazzale Guglielmo Marconi 14, 00144 Roma E.U.R. (Italy)

(6) Department of Archaeology, University of Durham, South Road, DH1 3LE Durham (United Kingdom)

Grotta dell’Uzzo is one of the key sites in the Mediterranean for the study of the changes in subsistence that took place in the transition from hunter-gatherer (Mesolithic) to agro-pastoral (Neolithic) economies. The cave is also important because 13 Mesolithic humans have been unearthed from 11 burials excavated within it. In order to study the diets of these humans, C and N isotope analyses were undertaken on skeletal remains recovered in the burials and from different trenches excavated at the cave. The preliminary results of these analyses suggest that the main sources of dietary protein were terrestrial and probably originated from the consumption of mammalian herbivores such as red deer (the most commonly exploited animal for much of the cave’s occupation). The contribution of marine resources to human diet at Grotta dell’Uzzo was probably not very significant in absolute terms. This finding might appear to be in contrast with the results of the archaeozoological studies, which have demonstrated that there was an intensification in shellfish collecting and in fishing from the end of the Mesolithic to the inception of the Neolithic. However, given that on the basis of the chronological data currently available the burials predate the end of the Mesolithic, the results of the isotope analyses are in line with the findings of the archaeozoological studies and of the seasonality studies, which have shown that marine resources (mainly represented by shellfish) were not exploited throughout the year before the final stages of the Mesolithic.

Plants

Phylogeographic analysis of barley (Hordeum vulgare) landraces shows that the distribution of lineages retains an imprint from the initial patterns of agricultural spread through Europe.

Huw Jones1, James Cockram1, Lydia M Smith1, Ian MacKay1, Robin G Allaby2, Terrence A Brown3, Wayne Powell1

1 National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE

2 Warwick HRI , Wellesbourne, Warwick , CV35 9EF

3 Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester, M1 7DN

In the 8000 years since barley was first introduced into the continent of Europe, the evolution of this crop species has been subject to selection under biotic and abiotic pressures. European farmers will have influenced the distribution of barley ecotypes by the movements of early farmers and by their selection of preferred types. The evolution of barley in Europe will also reflect the differing environments in which it has been grown. Modern barley cultivars from across Europe can be seen to differ in their morphology and growth habits. We have attempted to dissect the origins of these different forms by examining the landraces and assess the relative importance of human and environmental selection on modern barley lineages.

We have sampled barley landraces from Europe and discovered their population structure by microsatellite genotyping and statistical analysis. We have used passport data from germplasm collections to characterise the 2-row / 6-row head morphology, hulled / naked grain morphology and the spring / winter growth habit of these sub-populations. The genetic variation underlying key adaptive traits controlling flowering time has been explored by re-sequencing the photoperiod response gene Ppd-H1 and by haplotype analysis at the spring / winter vernalisation genes Vrn-H1 and Vrn-H2. These studies were designed to run alongside analysis of ancient DNA and historic DNA from barley and emmer wheat collected from across Europe.
The population structure we have discovered divides barley landraces into a number of sub-populations each with a distinct geographic distribution. Our genetic data for key adaptive traits allows us to understand the environmental influence on the geographic distribution of each lineage. Where lineages with a similar adaptive profile have distinct geographic distributions we see the imprint of early dispersal by ancient farmers.

Stable isotope evidence for the consumption of millet in Bronze Age Italy

Mary Anne Tafuri1, Oliver Craig2 & Alessandro Canci2
1 Dipartimento di Biologia Animale e dell’Uomo, Sapienza Università di Roma, P.le A. Moro, 5, 00185 Roma. Italy – email: maryanne.tafuri@uniroma1.it

2 Department of Archaeology, University of York, BioArch Biology, S Block PO Box 373 York YO10 5YW, UK

3 Dipartimento di Storia e Tutela dei Beni Culturali, Università degli Studi di Udine, Via Palladio, 8, 33100 Udine. Italy


This study presents, via carbon and nitrogen stable isotope analysis on human and animal bone collagen, new data on diet and subsistence strategies at northern and southern Italy Early and Middle Bronze Age sites, which clearly indicate the direct or indirect consumption of C4 plants. On the basis of paleobotanic data available and as suggested by previous similar studies, we argue here that the isotopic signal obtained can be associated with the consumption of millet (P. miliaceum and Setaria italica). If such an interpretation were true, while we wait for further paleobotanical and isotopic studies, we should consider the results obtained as the earliest evidence of millet consumption in prehistoric Europe. We thus suggest a possible pattern of distribution in the Peninsula of the practice of production and consumption of millet, while setting a new agenda on food security and subsistence strategies in prehistoric Italy

Cattle & Goats

A PCR system free of contaminating DNA for the amplification of bovine DNA from bovine fossils

Camille Berthelot, Sophie Champlot, Marie Liouville, Thierry Grange, Eva-Maria Geigl

Institut Jacques Monod CNRS UMR 7592, Universités Paris 6 et 7, Tour 43, 2, Place Jussieu, 75251 Paris cedex 05, France

Palaeogenetic analyses of bovine bone remains from many Neolithic sites in Europe and in Southwest Asia suffer from poor DNA preservation in these bones that increases the risk of amplification of contaminating modern bovine DNA. Indeed, trace amounts of contaminating bovine DNA occur ubiquitously. In particular, they can be found at low quantities in biochemical reagents used to extract and amplify DNA. These contaminating molecules mimic ancient DNA molecules. Indeed, the contamination rate often resembles the success rate of ancient DNA studies from bovine remains and the length of the contaminating DNA fragments is often comparable to ancient DNA fragments. We elaborated a decontamination protocol for PCR reagents combining various treatments to reduce contamination towards zero. This system significantly increases the reliability of ancient DNA results from bone remains of domesticated animals.

Detecting selection in ancient cattle remains: Pre industrial selection in Bos Taurus and SNP typing in medieval cattle remains

Emma Svensson1, Anders Götherström1

1 Evolutionary Biology, Evolution Genomics & Systematics, Uppsala University, 752 36 Uppsala, Sweden

Historic and prehistoric animal breeding is an enigmatic topic, complicated to approach with conventional genetics and osteology. Questions like when it started, and how strict it was, are of general interest, but it is also complicated to generate a suitable dataset for such questions. By tracing changes in genetic diversity with serial data we can find out how cattle has changed since the domestication of the aurochs to become the array of breeds seen today. Cattle are likely to have been subjected to selection predating the 18th century but the information is scarce. Using a 12plex SNP stream system alongside pyrosequencing we typed up to eight coding and six neutral SNPs in 142 ancient and 216 modern Bos Taurus from Northern Europe. We found a significant decrease in total heterozygosity over time for the coding SNPs which are presumably associated with phenotypic traits such as milk quality and coat colour while neutral markers on the other hand don’t show any significant change over time. This suggests that the decline in diversity is caused by artificial selection and not other genetic processes. The medieval period was a dynamic time in northern European history. The society was moving toward a higher degree of specialization in general, and a number of towns based on trade arouse in Scandinavia. Our findings of early selection fit well with the more sophisticated farming and higher degree of animal breeding that likely occurred at this time.

Using new and old approaches to study bovid systematics and evolution across Eurasia

Alan Cooper¹, Kefei Chen¹, Beth Shapiro²

¹ The Australian Centre of Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia

² Department of Biology, The Pennsylvania State University, 326 Mueller Laboratory, University Park PA 16802, USA

Ancient DNA studies of bovid remains from Europe have detected four main taxa: Bison bonasus (the European Bison); Bison priscus (Steppe bison), Bos primigenius (Aurochs); and early Bos taurus (Daisy). Studies of bones recovered from caves in the Urals and Caucasus, and from material dredged from the North Sea, have revealed a fifth European bovid – the Caucasus bison. Previously recognised only as a sub-species of European bison, this taxon appears to represent a separate species, with more genetic diversity than Beringian populations of Bison priscus, suggesting a long evolutionary history and stable population size. It has changed ecological dominance with Bison priscus at several points in the Pleistocene, which appear to be related to climatic and environmental change.

We have been using emulsion PCR and high-throughput hybridisation-based SNP screening systems that can simultaneously analyse 50,000 bovid SNPs to explore the genomic evolution of ancient bovids during the Pleistocene and subsequent domestication. We have been concentrating on pre-domestic Bos taurus specimens, as well as representatives of the other Pleistocene bovid species. This approach holds enormous promise for fine-scale temporal analyses of evolution in response to climate and environmental change, as well as archaeology and domestication.

The process of cattle domestication during the Neolithic as revealed by a large-scale palaeogenetic study

Eva-Maria Geigl, Mélanie Pruvost, Marie Liouville, Camille Berthelot, Reinhard Schwarz, Sophie Champlot, Thierry Grange, Virginia Bessa-Correia, Hans-Peter Uerpmann, Lamys Hachem, Hitomi Hongo, Séverine Braguier

Institut Jacques Monod CNRS UMR 7592, Universités Paris 6 et 7, Tour 43, 2, Place Jussieu, 75251 Paris cedex 05, France

Several disciplines can contribute to the elucidation of the processes of animal domestication during the Neolithic, such as archaeology, archaeozoology, and, more recently, isotope and genetic studies. The processes of domestication leave genetic signatures in the genomes of the domesticated animals that can be explored via the combination of both genetic analyses of extant domesticates and palaeogenetic analyses of bone remains of the first generations of domesticated animals and of their wild ancestors. We adopted this approach to shed light on the domestication of the aurochs. We studied roughly 250 Bos bone remains from Southwest Asia, according to archaeological and archaeozoological evidence the presumed centre of cattle domestication, and from France, the region where the two Neolithic migration currents mingled. To obtain authentic palaeogenetic results, several methodological difficulties related to poor DNA preservation and reagent contamination had to be solved. We will present both the methodological challenge that we encountered and overcame and the results of our large-scale study.

Cattle domestication and the troublesome aurochs

Cecilia Anderung1, Jurgita Baubliene2, Daniel Makowiecki3, José Miguel Carratero4, Linas Daugnora2, Juan Luis Arsuaga5 and Anders Götherström6

1Palaeontology Department, Natural History Museum, Cromwell road, London SW7 5BD, Great Britain.
2Department of Anatomy and Histology, Lithuanian Veterinary Academy, Tilžes str. 18, LT-3022, Kaunas, Lithuania
3Institute of Archaeology, Nicolaus Copernicus University, Podmurna 9/11 87-100 Toruń, Poland
4Laboratorio de Evolución Humana, Departamento Ciencias Históricas y Geografía Edificio I+D+I Plaza de Misael Bañuelos s/n, 09001, Burgos, Spain
5Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos c/ Sinesio Delgado Nº 4 Pabellón 14, 28029 Madrid, Spain
6Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden

A number of genetic studies relating to the origin of modern cattle have been published recently. In particular the extinct European aurochs (Bos primigenius), progenitor of the modern domesticated form, has attracted a lot of attention. European aurochs bones that have yielded mitochondrial DNA are genetically clearly different from modern cattle. This genetic data, in combination with the genetic patterns observed in modern cattle, has led to the suggestion that modern cattle have a single origin in the Near East, and that the European aurochs population had little to do with their domestication.

However, we ask the question: could this picture of European cattle domestication be too simple?

Here we present results from an investigation of published and novel aurochs sequences from Lithuania, Spain, Poland, and Britain, giving special attention to the Spanish sequences. We looked at the mitochondrial DNA variation in Iberian aurochs remains and searched for aurochs sequences in a domestic context. We find that cattle and aurochs mitochondrial sequences from Iberia deviate from the pattern observed in sequences from Central and Eastern Europe.

In the light of this data, we discuss the possibility of local aurochs domestication events in Europe.

High mtDNA diversity among cattle and goats from the earliest Neolithic settlements on the European continent

Amelie Scheu1,2, Norbert Benecke2 and Joachim Burger1
1 AG Palaeogenetik, Institut für Anthropologie, Johannes Gutenberg-Universität, 55099 Mainz, Germany

2 Deutsches Archäologisches Institut, Eurasienabteilung, 14195 Berlin, Germany

The process of domestication includes a decline in genetic variability. Additional homogenisation occurs due to subsequent colonisation events, such as the Neolithisation of Europe. Our previous studies have shown genetic uniformity even among early Neolithic European cattle (Bollongino et al. 2006). But modern goats also share more than 90% of the same mtDNA haplogroup.

To find out exactly when and where this genetic bottleneck arose during the Neolithisation of Central Europe, we investigated remains of early domesticates on the border between Asia and Europe, i.e. at the origin of the trans-Danubian route of Neolithisation. That region, particularly the area around the Bosphorus and the transit country of Bulgaria, plays a crucial role.

We found higher mtDNA diversity among Neolithic and Bronze Age domesticated cattle East and West of the Black Sea (haplogroups T, T2 and T3) than in Central European populations. Among goats, we found the two different mtDNA haplogroups A and G. G had previously been found among modern goats only near the Fertile Crescent (Naderi et al. 2007).

Our results argue for large and genetically more diverse herds imported to this area and/or for intense trade. Furthermore, they indicate that a second wave of expansion in the direction of Central Europe is responsible for the final loss of mtDNA diversity.

Ice man Schnidi’s trousers: insight into prehistoric goat diversity

Angela Schlumbaum1, Serge Volken 2, Marquita Volken 3, Jörg Schibler4, Peter Suter 5 Kathrin Glauser6 & Albert Hafner 7

1 Institute of Prehistory and Archaeological Science, University of Basel, Spalenring 145, 4055 Basel, Switzerland

2 Gentle Craft, Rue du Rôtillion, 10, 1001 Lausanne, Switzerland

3 Gentle Craft, Rue du Rôtillion, 10, 1001 Lausanne, Switzerland

4 Institute of Prehistory and Archaeological Science, University of Basel, Spalenring 145, 4055 Basel, Switzerland

5 Archaeological Service of the Canton Bern, Brünnenstrasse 66, 3001 Bern, Switzerland

6 Archaeological Service of the Canton Bern, Brünnenstrasse 66, 3001 Bern, Switzerland

7 Archaeological Service of the Canton Bern, Brünnenstrasse 66, 3001 Bern, Switzerland
Since 2003 more than 300 prehistoric remains were discovered in the vicinity of a melting ice patch of the Schnidejoch (2750 m; Bernese Alps, Switzerland), paralleling the finds accompanying the Iceman from the Tisenjoch (Oetztal Alps, Italy/Austria; “Oetzi”). One leg of a Neolithic leather trouser was found and 14C dated to 2900 – 2600 BC. The morphological identification of the animal skin was ambiguous because of the bad preservation of diagnostic features. Based on grain patterns of the skin the leather was made either from sheep or goat.

Because of the importance of the object, a genetic identification of the animal species was attempted. After DNA extraction with QiAmp DNA Mini Kit a 70bp fragment of the mitochondrial cytochrome b gene was amplified in the diluted extract. The leather was made of goat skin (Capra hircus). Six geographically broadly distributed goat lineages are recognized based on mitochondrial d-loop variation, of these lineage A and C were identified by others in prehistoric goat bones from France. The “trouser’s goat” however, belongs to lineage B, which is common in Asia, but extremely rare in Europe today.

An Ancient DNA study from The Farm Beneath the Sand

Martin Bay Hebsgaard1

1 Dept. of Biology, University of Copenhagen, Universitetsparken 15, Denmark
Applying ancient DNA techniques on samples from the archaeological site “The Farm Beneath the Sand” (GUS) near Nuuk in Southwest Greenland is the first attempt to extract DNA from these relative young but novel samples. The sample site highlight the dramatic landscape changes that resulted in floodplain aggradations that eventual buried the site fixing the site under perma-frozen conditions.
The Farm beneath the Sand is situated on a plain surrounded by low mountains ca. 80 km east of Nuuk. When the building remains were found they were overlain by ca. 1,5 m thick layers of sand and gravel, and today the plain in front of the farmhouse appears as a sandy dessert intersected by meandering watercourses that are draining off the icecap.

All together the samples yielded DNA from humans, cattle, sheep, goat and reindeer. Quantification shows approximately 16 times more DNA from cattle than from sheep. Goat DNA was undetectable using Quantitative PCR. The amount of cattle DNA declines over time while sheep DNA probably reflects background variation.
Thanks to thick layers of sand and gravel that may have protected the DNA in the anthropogenic layers ancient DNA is usable in an archaeological context in the reconstruction of the past. In this example ancient DNA research has helped to refine and define archaeological interpretations of the Norse life by adding information not seen by the naked eye. In the future ancient DNA have the capacity to be used more vigorously to investigate the diet of the Norse and show what function specific farms may have had during the settlement. As in this study the future research is not limited to animal DNA but DNA from plant and humans can be used to address different questions.

Horses

Pleistocene Horses genetics before and after the last glacial maximum

Sebastian Lippold¹ and Michael Hofreiter¹

¹ Dept. Evolutionary Genetics, MPI for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany

We are investigating how the last glacial period affected the genetic composition of populations, particularly the horse (Equus spec.). Vast climatic changes that occurred between 30,000 and 12,000 years BP resulted in dynamic mammalian population structures. Restriction and expansion events during this period influenced both the genetic distribution and variability of a variety of mammals. We focus on western European horse populations, and try to characterize their genetic diversity and phylogeographic patterns both before and after the last glacial maximum. We sequence 600 bp of mtDNA from the mitochondrial D-Loop of different individuals obtained from different locations. Our initial results indicate tremendous genetic diversity, but no phylogeographic pattern within this marker. The genetic distribution of these ancient samples also falls within the broad diversity range apparent in recent horses. Because of this finding, we started screening the DNA samples for additional nuclear markers. Our comparison of these different markers has enabled us to reconstruct several scenarios for horse population dynamics during this period.

Investigating Eneolithic horse exploitation in northern Kazakhstan, via compound-specific stable carbon and deuterium isotope analysis of pottery.

Natalie A. Stear1, David Chivall1, Alan K. Outram2 and Richard P. Evershed1 1Organic Geochemistry Unit, School of Chemistry, University of Bristol, Clifton, BS8 1TS, UK 2 Department of Archaeology, SoGAER, University of Exeter,Laver Building, North Park Road, Exeter, EX4 4QE, UK The Eneolithic site of Botai in northern Kazakhstan has been the centre of much debate regarding its role in early horse domestication (Levine, 1999; Olsen, 2003). The faunal assemblage from this remarkable site was almost entirely comprised of horse (99%); however it has remained unknown whether any of these horses were domesticated. Horse domestication is extremely difficult to detect morphologically from skeletal remains and consequently it is necessary to establish a reliable proxy for detecting ancient domestic horse populations. Fermented mare’s milk (Kumyss) is commonly consumed in rural communities in Kazakhstan, a tradition dating back to prehistory. It is not clear if the milking of horses began (i) in the Eneolithic, during the height of the horse centred communities of the Botai culture; (ii) in the Bronze Age, in response to the milking of ruminants or, (iii) much later. If mare’s milk were identified in ancient pottery it would serve as conclusive evidence for the presence of domestic horses and enable a chronology of horse exploitation to be established. Equine fat residues can be identified in potsherds using compound-specific stable carbon isotope analysis, but unlike ruminant fats, equine milk and adipose fats are indistinguishable from one another based on δ13C values. However, we show that it is possible to further classify equine fats as either milk or adipose, based upon the δD values of their C16:0 and C18:0 fatty acids which are determined using GC-thermal conversion-IRMS (GC-TC-IRMS). This new proxy has been applied to organic residues extracted from potsherds from Botai as part of a large scale investigation of Eneolithic and Bronze Age pottery from sites in northern Kazakhstan. Using the δ13C and δD values obtained from the Botai residues we have been able to detect equine milk residues preserved within the pottery and consequently, we provide the first direct evidence for the presence of domestic horses at Botai during the Eneolithic.

Anatolia

Detecting dairying with stable calcium isotope ratios (δ44/42Ca) of bones and teeth

Linda M. Reynard^1,2, Robert E.M. Hedges¹ & Gideon M. Henderson²

¹ Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, United Kingdom

² Department of Earth Sciences, University of Oxford, Parks Road, Oxford, OX1 3PR, United Kingdom

The use of dairy products in antiquity is an important part of the development of agriculture and pastoralism in Eurasia. They offer advantages of more efficient land use, improved nutrition, and more reliable and constant access to protein. Understanding the adoption of dairy, its timing, and geographical spread is relevant to developing a fuller understanding of changes in subsistence from the Neolithic.

Detecting and quantifying dairy product consumption in antiquity has, to date, relied on indirect evidence such as the age and sex structure of faunal remains and potsherd lipid residues.. To complement these methods, we have measured stable calcium isotope ratios (δ^44/42Ca) of bones and teeth which allows the direct detection of dairy consumption by prehistoric humans. Dairy products have lower δ^44/42Ca than other dietary calcium inputs, and this results in lower δ^44/42Ca of the dairy consumer. We have measured the δ^44/42Ca of human and animal bones from a range of archaeological sites by MC-ICP-MS. Results from the Mesolithic to the Neolithic at the key Near Eastern site of Abu Hureyra, Syria (11,100 –7,300 BP) show a δ^44/42Ca signal attributable to dairy consumption by ancient humans, with a changing pattern through time. Work on intra- and inter-tooth δ^44/42Ca variability is in progress as this material is expected to form a robust archive of in vivo isotope ratios.


Britain

An investigation into origins of individuals from a mass grave in Roman Gloucester, UK: strontium and stable isotope evidence

Carolyn Chenery^1,2, Gundula Müldner¹, Jane Evans², Louise Loe³, Nicholas Márquez Grant³, Hella Eckardt¹ Stephanie Leach¹, Mary Lewis¹

¹ Department of Archaeology, University of Reading, Reading, Berkshire.

² NERC Isotope Geoscience Laboratory, British Geological Survey, Keyworth, Nottingham.

³ Oxford Archaeological Unit Ltd, Janus House, Osney Mead, Oxford.

Contrary to popular assumptions, Britain under Rome was truly multi-cultural, with historical and epigraphic evidence recording the voluntary and forced migration of Gaulish, Germanic and North African individuals into the British provinces refs. This paper presents the results an isotopic investigation of population diversity in 1^st to the 4^th century Roman Gloucester; focusing on individuals found in a late 2^nd century mass burial pit and comparing them to those found in single graves.

The results suggest that the majority of the individuals buried in the London Road Cemetery were from areas within the UK. However, the isotope data has identified a number of individuals whose origins lay in a region with a warmer climate than the UK. Whether these were soldiers, their followers or merchants cannot be determined.

On Rome’s Northern Frontier: Multi-isotopic investigations into cultural diversity in Roman York

Gundula Müldner1, Carolyn Chenery1,2, Stephany Leach1, Mary Lewis1 & Hella Eckardt1

1 Department of Archaeology, University of Reading, Whiteknights, PO Box 227, Reading RG6 6AB, England

2 NERC Isotope Geoscience Laboratory, British Geological Survey, Keyworth, Nottingham, NG12 5GG, England

Britain under Rome was a multi-cultural society, with historical and epigraphic evidence attesting to the presence of migrants from continental Europe, North Africa and the Middle East. Here, we combine isotope analysis for the reconstruction of diet (C,N) and mobility (Sr, O) with skeletal (craniomorphometric) and archaeological data, in order to investigate diversity in Roman York, the political, military and administrative centre of the North. The results show a heterogenous population and highlight the varied life-histories of individuals in the northernmost provincial capital of the Empire; however, they also show that skeletal and isotopic evidence are not always easily correlated. It is suggested that a diet high in marine protein was used to demonstrate a “Roman” identity.

Investigating Marine Food Consumption in Prehistoric Humans via the δ13C values of Collagen Amino Acids

Philip Dunn1, Richard P. Evershed1 & C. Joshua Pollard2
1 School of Chemistry, University of Bristol, Organic Geochemistry Unit, School of Chemistry, Cantock's Close, Bristol, BS8 1TS, UK

2 Department of Archaeology and Anthropology, 43 Woodland Road, Clifton, Bristol BS8 1UU, UK

The current debate concerning the importance of marine foods in the diets of prehistoric peoples has stimulated interest in refining analytical approaches based on stable isotopes. An alternative to the widely bulk collagen approach is to investigate the stable carbon isotope composition of human bone collagen at the amino acid level. Our investigations of prehistoric humans from the Western Cape, South Africa, have shown that the Δ13CGlycine-Phenylalanine values for bone collagen amino acids correlate strongly with bulk δ15N values and provide a new proxy for marine food consumption. We are currently applying this new approach to human skeletal remains from northern Europe.
The tomb at Isbister lies on the south west coast of South Ronaldsay and is one of a number of Neolithic cairns found in the Orkney Islands. During excavation in 1976, the stalled main chamber and three side chambers were found to contain some 16,000 human bones and bone fragments deriving from a minimum of 341 individuals along with a wide range of faunal remains. Previous analyses of bone collagen from the human remains have shown that the tomb was in use from 4,500 to 3,800 BP and bulk collagen stable isotope values for 5 individuals lay in the range -19.9 to -21.2 ‰ indicating a predominantly terrestrial diet, which is surprising for people that lived so close to the coast.
We have now employed the recently introduced LC-IRMS technique to determine the δ13C values of bone collagen amino acids from 22 individuals from Isbister. The results will be compared to those obtained by GC/C/IRMS. The derived Δ13CGlycine-Phenylalanine values give enhanced insights into the dietary habits of the people of Isbister.

Northern Europe

Large-scale FLX-sequencing and the Swedish Neolithic

Helena Malmström1,2, Anna Linderholm3, M. Thomas P. Gilbert2, Mikael Brandström1, Jan Storå4, Petra Molnar4, Christian Bendixen5, Gunilla Holmlund6, Kerstin Lidén6, Anders Götherström1, Eske Willerslev2

1Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden

2Ancient DNA and Evolution Group, Biological Institute, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark

3Archeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden

4Osteoarchaeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden

5Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences Research Centre Foulum, K25 PO Box 50, DK-8830 Tjele, Denmark

6National Board of Forensic Medicine, Department of Forensic Genetics and Forensic Toxicology, Artillerigatan 12, SE-587 58 Linköping, Sweden

The relationship between the contemporary hunter-gatherer Pitted Ware Culture (PWC) and the farming Funnel Beaker Culture (TRB) in Middle Neolithic (3300-2500 B.C.) Sweden has been debated for more than a century. We approach this issue by determining the genetic signatures of skeletal remains from both complexes. Initially, we generated large amounts of “cloned” ancient mitochondrial DNA (mtDNA) PCR amplicons using a single run of the Genome Sequencher FLX System, and a recently described primer tagging protocol. Our data set consisted of Hypervariable Region I (HVRI) amplicons derived from bleach pre-treated powdered bone from Neolithic humans as well as from a large number of negative controls (animal samples, extraction and PCR blanks). We compared the ‘clone’ data with sample quality indicators, such as the number of PCR starting template molecules and the degradation ratio of DNA in the sample (number of long/short fragments). The data shows distinct patterns that differ between high and low quality extracts. After establishing the efficacy of the large scale sequencing approach, additional high-quality PWC and TRB samples (based on collagen preservation) were sequenced in a second FLX run. The compiled data yielded unambiguous HVRI sequences for approximately 40 Neolithic human samples, each compiled from cloned, duplicate PCR amplicons derived from overlapping HVRI fragments. F-statistics and AMOVA revealed significant genetic differences between the PWC and TRB samples, indicating that they indeed comprise of two distinct groups.

Allele frequencies of the lactase gene in Scandinavian Neolithic populations, hunter-gatherers vs. farmers

Anna Linderholm1, Helena Malmström2, 5, Love Dalén3, Kerstin Lidén1, Jan Storå4, Petra Molnar4, M. Thomas P. Gilbert5, Eske Willerslev5, Gunilla Holmlund6, Anders Götherström2
1Archeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden

2Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden

3Marie Curie Fellow, School of Biological Sciences, University of London, United Kingdom

4Osteoarchaeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden

5Ancient DNA and Evolution Group, Biological Institute, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark

6National Board of Forensic Medicine, Department of Forensic Genetics and Forensic Toxicology,Artillerigatan 12, SE-587 58 Linköping, Sweden

Genetics and culture are believed to interact, but it has been difficult to find direct evidence for the process. One example that has been put forward as a candidate is lactase persistance in adulthood, i.e. the ability to continue drinking milk. This genetic trait is believed to have evolved within a short space of time in connection with the emergence of farming cultures. Here we investigate certain Scandinavian Neolithic populations and their allele status with respect to the gene responsible for lactase persistance. We find that the allele responsible for lactase persistance was common and not significantly different from modern Swedish populations among Neolithic farmers, whereas Neolithic hunter-gatherers had a lower frequency of the allele.

aDNA analysis of human population samples from the Danish past – what have we learned?

L.C. Melchior¹, N. Lynnerup² and J.Dissing¹.

¹Research Laboratory, Institute of Forensic Medicine, University of Copenhagen, Denmark, ²Laboratory of Biological Anthropology, Institute of Forensic Medicine, University of Copenhagen, Denmark.

During an ongoing survey of the Danish genetic past we analyzed mtDNA from teeth from human remains from a range of burial sites from medieval times to the Stone Age. To ensure the highest possible degree of reliability generally accepted authentication criteria (including sequencing of multiple clones and replication by different researchers) as well as additional precautions (e.g. testing of laboratory performance) were observed.

Unequivocal assignment of mtDNA haplotypes was possible for more than 50 ancient subjects; however, the success rate varies substantially between sites. The highest success rate (11 out 11) was obtained with freshly excavated Viking Age subjects (ca AD 1,000), but good results were also obtained for recently excavated Iron Age sites (AD 0-400). Poor results were found with highly manipulated subjects (contamination) and with most of the Stone Age samples (4,500-5,000 YBP).

While laboratory related contamination can effectively be prevented by the abovementioned precautions, the most serious challenge to authenticity is caused by pre-lab contamination. This problem was tackled using several approaches including analysis of DNA damage patterns, haplotyping of archaeologists, phylogenetic testing and as the most efficient measure, sampling from the ancient subjects during exhumation. We show that reliable retrieval and analysis of DNA from ancient humans is indeed a possible undertaking.

A high degree of nucleotide diversity was observed in the ancient populations, and at four out of six locations the diversity was considerable higher than among modern Danes. Also, we observed a consistently higher abundance of Hg I (10-20%) than among modern Danes (~3%).The effect of the Black Death has been suggested as a possible explanation for a similar decline in the English genetic diversity. Interestingly, we found the highest genetic diversity in a 15^th century population sample long after the major outbreak in the14^th century.

NspI typed transition within PRNP gene (A385G / Met129Val) confirms rapid shift in allele frequencies during The Second Millennium

Henryk W. Witas1, Magdalena Kołodziejczak1, Paweł P. Liberski2
1 Dept. of Molecular Biology, Medical University of Lodz, 91-738 Lodz, Sporna 36/50, Poland

2 Dept. of Molecular Pathology and Neuropathology, Medical University of Lodz, 92-216 Łódź, Pomorska 251, Poland

Although precise biological role of prion proteins (PrPC) is still a subject of extensive study and debate, a few suggestions of their involvement in cellular processes have been described, including involvement in biology of synapse, short-term memory formation and long-term memory consolidation. Prion proteins became commonly recognizable as a cause of some human transmissible spongiform encephalopathies (TSE). Among a number of SNPs, A385G / Met129Val is assumed as a factor involved in the pathogenesis of TSEs (e.g. kuru) and a marker of memory efficiency as well. Although frequency of Met129Val alleles are precisely characterised for modern populations and its significance discussed, no data for historic and prehistoric populations to compare are available.

Specimens came from seven medieval cemeteries located throughout today’s Poland, and have been excavated recently. Teeth stored at low temperature underwent procedures generally accepted for aDNA isolation, performed automatically (MagNa Pure, Roche) at least two times on different teeth of each individual. Only the samples represented by collagen quantity above 2% dry weight, negative result of appropriate mock controls throughout isolation and amplification procedures, with successfully cloned (Amersham) and sequenced (AB 310) PCR products have been considered as authentic ancient templates. Moreover, we have applied NspI restriction analysis as a method for recognition and retrieval of undamaged ancient sequences.

The results show rapid increase in PRNP allele A frequency (Met 129) since the beginning of the Second Millennium (0.51 v. 0.65), accompanied by slight drop in heterozygotes (0.49 v. 0.39) and significant rise in Met homozygotes (0.27 v. 0.45).

As compared to present Polish as well as present European PRNP alleles frequency, medieval specimens provided the data which suggest altered mode of PRNP alleles transmission within last 35-40 generations. Although the nature of mechanism leading to observed changes is unclear, the impact of demographic factors is probably the most pronounced one affecting the process of local fluctuations of Met allele spreading out. However, the effect of selection processes should also be considered. This work is being supported by grant from Ministry of Science and Higher Education

Mice and Vikings

Eleanor Jones1
1 Department of Biology, University of York, Heslington, YO10 5DD, United Kingdom
Originally native to the northern Indian subcontinent and the Middle East, house mice (Mus musculus) have spread to their current near global distribution by exploiting a commensal niche with humans, originally in agrarian settlements. Mice also owe their current distribution pattern to human movements: they have reached the areas they now inhabit by being accidentally transported with grain and livestock foods. This close association between mice and humans means we can use information from the current genetic distribution of house mice to make inferences about past human colonisations and cultural linkages. In this study, we used mitochondrial DNA sequences from modern house mice in Great Britain, France, Ireland, Iceland, the Faeroe Islands and Norway to identify patterns in the their distribution, and tie these in to historic human migrations. The mice appear to be telling us about Norse Viking colonisations, and add a useful source of information to complement archaeological and historical data.

East Asia & Pacific

Genetic relationship of Human Skeletal Remains from an archaeological cemetery

Sang Hyun Jee 1, Yun Ji Kim 1, Yong Jae Chung1 & Min Seok Seo 1

1 Conservation Science Division, National Research Institute of Cultural Heritage, 472 Munji-dong, Yuseong-gu, Daejeon, 305-380, South Korea

We carried out genetic analyses of human skeletal remains from cemetery of a historic site, Myeong-arm-ri of Asan in South Korea. According to archaeological evidences, this site had been constructed from the Neolithic Age to the Joseon Dynasty. Twenty one human skeletons excavated from thirty pit tombs that have outer coffin build up into plaster dated to the Joseon Dynasty (14-19th century). To identify the genealogy and traditional burial pattern were assessed using mitochondrial DNA (mtDNA) and Y chromosomal STRs. We take cautious to avoid erroneous recombination by the segmental and modern contaminations were derived from researchers and all experimental stages. We sequenced the segmental amplicons of the hyper variable regions (HVRs) of mtDNA, and appointed relevant haplogroups according to the sequence polymorphism using the known mtDNA database. We also applied variable short tandem repeat (STR) marker in Y chromosome to understand paternal lineage and kinship among the burials. Especially, we interested in the four burying together and examined genetic relationship more closely between two individuals.

Not quite in the bag: A systematic bioarchaeological approach to the question of South American chickens origins

Greger Larson
1 Dept. of Archaeology, Durham University, South Road, DH1 3LE, UK

Though chickens were undoubtedly introduced into the American continents by the Spanish after their arrival in the 15th century, there is an ongoing debate as to the possible that Polynesians traveling across the Pacific introduced chickens to South America before Europeans did so. A recent publication concluded on the basis of ancient DNA extracted from an archaeological Chilean chicken bone that domestic fowl were present in a pre-Columbian context and that those chickens possessed a Polynesian genetic signature. In order to test this hypothesis, we generated mitochondrial DNA control region sequences from 41 modern, native Chilean specimens and analyzed them within a database consisting of both the published ancient DNA sequences and ~1,000 globally distributed modern domestic chicken sequences. Our modern Chilean sequences cluster closely with haplotypes predominantly distributed amongst European, Indian, and Southeast Asian chickens, consistent with a European genetic origin. The previously published, apparently pre-Columbian, Chilean specimen and seven pre-European Polynesian specimens, also cluster with the same European/Indian subcontinental/Southeast Asian sequences, providing, at this stage, no support for a Polynesian introduction of chickens to South America. Ancient DNA sequences from two archaeological sites on Easter Island, however, cluster with chickens found in Island Southeast Asia, and may represent a genetic signature of an early Polynesian dispersal as far as Easter Island. Lastly, we modeled the potential marine carbon contribution to the Chilean archaeological specimen (thus revising the derived date of the specimen) which cast doubt on the pre-Columbian age of the chicken remains. Definitive proof of a pre-Columbian introduction will require excavating more chicken bones, and further analyses of ancient DNA and radiocarbon data from Chilean and Polynesian archaeological excavations.

A New Bioarchaeological Clue for the DongHu Nationality

ZHANG Quan-chao, CHANG E，ZHU Hong

( Research Center f or Chinese Frontier A rchaeology , Jilin University , Changchun , Jilin , 130012 , China)

Abstract: DongHu nationality is a branch the Hu population who acted actively in the northeast of Yan. Whilst the remains of DongHu had not been confirmed for a long time, The tombs discovered in linxi Jinggouzi site in 2002 suggested a new clue for exploring the remains of Donghu in Chifeng area. These tombs not only meet the condionons in relation to DongHu in the aspects of time and region, but also conformed to DongHu characteristics of economic style and ethic features. In this article, human remains unearthed from the Spring and Autumn-Warring states cemetery at the Jinggouzi site in Linxi county, Inner Mongolia were studied. The morphological features of Jinggouzi group crania show that the racial type is closely related to the modern North Asiatic Mongoloids, and some physical characteristics of these skulls are closer to the ancient XianBei population in the north China and the modern Mongol. Ancient DNA sequences from ancient human remains have provided very important information on human evolution, blood relationship and migration, making ancient DNA research an important field of molecular anthropology. This study illustrates ancient DNA extraction, amplification and sequencing of five individuals of an ancient population buried in the west cemetery at Jinggouzi site in Inner Mongolia. A phylogenetic tree, a two-dimensional PC plot and MDS plot are constructed using mtDNA sequences from the ancient population and several modern Eurasian populations. However, the application of the techniques of ancient DNA allows us to explore the fasten source of the ancient population. Therefore, the genetic evidence raise the important meaning for the study of archeological culture in the east of Inner Mongolia during Spring and Autumn-Warring states. In addition, this new study which based on genetics and traditional archaeology on the development of populations from the north steppes of our country during Spring and Autumn-Warring states, provides precious data. In this study, we examine Jinggouzi population paleodiet using stable isotope ratios of carbon and nitrogen in bone collagen. Nitrogen isotope ratios of bone collagen show that Jinggouzi ancient population in primarily ate animal products with only a small amount of plant products. Carbon isotope ratios of bone collagen show that most plant products come from C₄ plant.

Physical anthropology

Obtaining population genetics data via non-destructive means: a three-dimensional analysis of human craniofacial morphology

Sabrina B. Sholts1, Sebastian Wärmländer2, & Phillip L. Walker3
1 Department of Anthropology, University of California at Santa Barbara, Department of Anthropology, University of California, Santa Barbara, CA 93106, USA

2 Division of Biophysics, Arrhenius Laboratories for Natural Science, Stockholm University, 10691 Stockholm, Sweden

3 Department of Anthropology, University of California at Santa Barbara, Department of Anthropology, University of California, Santa Barbara, CA 93106, USA

In this study, shapes extracted from the human craniofacial skeleton were used to investigate the genetic heritabilities of morphological traits. Three-dimensional point data was collected from human crania with a 3D laser scanner and used to render complete 3D surface models of the original skeletal material. 3D data analysis software was used to digitally slice the cranial models with geometric planes defined by traditional craniometric landmarks. The cross-sections produced by these planes yielded contours of cranial outlines for different craniofacial features. Using elliptical Fourier transforms, the contours were parametrized into series of Fourier coefficients, which, due to their inherent orthogonality, form suitable input parameters for statistical analysis. Principal components analysis (PCA) was employed to differentiate population groups based on shape differences in various aspects of cranio-facial skeletal morphology. This method can yield population genetics data and information on probable ancestral affinity using non-destructive analysis of human remains and with greater accuracy than with traditional craniometric studies of metric and non-metric traits. The application of this method to human skeletal collections can elucidate genetic relationships in past populations and improve our understanding of their archaeological contexts. This non-invasive method also offers a viable alternative for determining ancestral affinities between groups and individuals in cases where DNA testing is not possible, due to either the necessary destruction of bone required for DNA analysis or the degraded condition of the material.