Lack of significant population structure in Spain

I took the Iberian Spanish (IBS) regional populations, and ran multidimensional scaling on them (left). Most of the populations form a tight cluster, with Basques and Canary Islanders having averages further removed from the main cluster.

It should be noted that the Canarias sample consists of only two individuals (big red dots): one removed from the main cluster, one in the midst of individuals from Castilla Y Leon (small red dots).

MCLUST analysis using 1 dimension, reveals 2 clusters: one consisting of Pais Vasco individuals (blue dots), the other of everyone else, with one Aragonese and one Cantabrian individual showing mixed probabilities between the two clusters.

The overall impression is that there may be additional population structure here (e.g., for Canarians or Galicians), but the sample sizes are not sufficient to make additional clusters unambiguously evident, except in the case of Basques vs. non-Basques.

ASHG 2010 abstracts

The 2010 meeting of the American Society of Human Genetics is in November. Here are some interesting abstracts that caught my eye:

It's nice to finally see a genomic study on the Greek population.
P. Paschou et al. Evaluation of the HapMap dataset as reference for the Greek population.

The HapMap project has provided a unique tool for the analysis of human genetic variation, providing reference information for allele frequency and genotype distributions as well as linkage disequilibrium patterns of Single Nucleotide Polymorphisms (SNPs) across the entire genome. The latest release of HapMap phase 3 data provides genotypes for millions of SNPs in 11 populations from around the world, with Europe being represented by the CEU (originating from Northwestern Europe) and the TSI populations (Tuscan Italians from Southern Europe). Although initial studies support the fact that the CEU can be used as reference for the selection of tagging SNPs in other European populations, a critical step in the design of genetic association studies, this hypothesis has not been extensively studied across Europe and in particular in Southern Europe. We set out to explore the extent to which the HapMap populations can be used as reference for a previously unstudied population of South-Eastern Europe, the Greek population. To do so we studied genomic variation in 1,813 SNPs, genotyped by our group in 56 individuals of Greek origin, and compared them to the CEU and TSI genotypes (1,813 SNPs from the CEU HapMap dataset and 1,205 from the TSI dataset). The studied SNPs are spread over 13 autosomal chromosomes and 26 regions, ranging in size from 120Kb to more than 4Mb. Genotype, allele frequency, and pairwise LD measures were compared across all three populations. PCA was used in order to identify those markers that are responsible for the observed inter-sample variance. Tagging SNPs were selected in the CEU and TSI samples and their transferability to the Greek population was tested, using both the r2 metric as well as the efficiency of genotype imputation of the non-selected SNPs. Our results demonstrate that, although the CEU population can to some extent be used as reference for the Greek population, it is preferable to use as reference a European population of closer genetic ancestry, like the TSI. These results are applicable in medical genetics, in order to inform the design of genetic association studies, as well as in studies of evolutionary relationships of Southern European populations.

One of the great problems of Eurasian anthropology is whether the Uralic populations are simply variable admixtures of Caucasoids and Mongoloids or they contain a tertium quid in the form of a Proto-Uralic element. The latter need not be distinct from the other two, as it can also be an old or stabilized blend of the two major Eurasian races that later admixed with more recent groups on either side. The abstract does not seem promising in this respect, i.e., in identifying a common core of ancestry among Uralic speakers in addition to their variable east-west admixture, but it would be nice to see if anything like that exists in the paper.

K. Tambets et al. Haploid and autosomal variation within a linguistic continuum of the Uralic-speaking people of Eurasia.

For about last two decades the examination of uniparentally inherited genetic marker systems revealing the variation embedded in mtDNA and Y chromosome has been the main tool in the studies of human genetic origins. Within few recent years the analysis of the genome-wide SNP data of individuals from different populations has started to give promising new insights in the field of human population genetics. The uniparentally inherited markers have shown slightly different demographic scenarios for the maternal and paternal lineages of North Eurasian, particularly of European Uralic-speaking populations. The geographical location of a population has evidently been the most important component that dictates the proportion of western and eastern mtDNA types in the gene pool of Uralic-speakers. Thus, the palette of maternal lineages of the Uralic-speakers resembles that of their geographically close European or Western Siberian Indo-European and/or Altaic-speaking neighbours, respectively. At the same time, the most frequent North Eurasian Y chromosome type N1c, that is also a common link between almost all Uralic-speakers, is with few exceptions rare, if present at all, among Indo-European-speakers of Western and Southern Europe. Here we combine genome-wide high density SNP data (650 000 SNPs, Illumina) with uniparentally inherited mtDNA and Y-chromosome variation of 16 Uralic-speaking populations to assess their place on the genetic landscape of North Eurasia. By the use of principal component and structure-like analysis on the autosomal data we show that the proportions of western and eastern ancestry components among the Uralic-speakers are determined mostly by geographical factors. The westernmost populations from Europe, both Uralic- and Indo-European speakers, are similar in their pattern of ancestry components and show low levels (less than 10%) of the eastern component. Conversely, the eastern ancestry component is dominant (60-70%) in the gene pool of the Siberian Uralic-speakers. In general, the genome-wide analyses corroborate the results of mtDNA analysis and do not reflect the common genetic characteristics between western and eastern Uralic-speakers at the level seen in case of N1c. Interestingly, among Saami from North Europe, who are often considered as „outliers“ in genetic studies, the dominant western component is accompanied by 30% of eastern component making them more similar to Volga-Uralic populations than to their closest neighbours.

This seems to validate my thoughts on relics and their importance in age estimation.

U. A. Perego et al. The Initial Peopling Of The Americas: An Ever-Growing Number Of Founding Mitochondrial Genomes From Beringia

Genetic evidence based on mitochondrial DNA (mtDNA) has recently revealed the existence of additional founding lineages that have contributed to the first peopling of America’s double-continent in addition to the more popular five Native American haplogroups (A2, B2, C1, D1 and X2a), and has demonstrated as well the need for additional sampling and analysis to be performed for some of the already known but poorly characterized lineages. One paradigmatic example is represented by the pan-American haplogroup C1. Two of its sub-branches (C1b and C1c) harbor ages and geographical distributions that are indicative of an early arrival from Beringia about 15-17,000 years ago, concomitantly with the other currently accepted Paleo-Indian founders. However, the estimated age of C1d - the third Native American subset of C1 - is only 8-10,000 years, which is suggestive of a much later entry and spread in the Americas. In this study, we shed light on the origin of this enigmatic Native American branch of C1 by completely sequencing a large number of C1d mitochondrial genomes from a wide range of geographically diverse, mixed and indigenous American populations. The revised phylogeny shows that the age previously reported for C1d was heavily underestimated and indicate that C1d is ancient enough to be among the founding Paleo-Indian mtDNA lineages. Moreover, our results reveal that there were two C1d founder genomes for Paleo-Indians that most likely arose early (~16kya), either in the dynamic Beringian gene pool, or at a very initial stage of the Paleo-Indian southward migration. This brings the recognized maternal founding lineages of Native Americans to the unexpected number of 15, and indicates that the overall number of Beringian or Asian founder mitochondrial genomes will probably continue to increase as more Native American haplogroups reach the same level of phylogenetic resolution as we obtained here for C1d. Additionally, we have confirmed a nearly identical geographic distribution pattern for haplogroup C1d when comparing samples collected in the general mixed population with those from native tribal groups, as it was also reported previously for haplogroups X2a and D4h3. This substantiates the validity of searching large public mtDNA databases (such as the one available through the Sorenson Molecular Genealogy Foundation, www.SMGF.org) for novel founder candidates able to reveal unknown details concerning the ancient human history of the Americas.

Another interesting abstract. I've written before about the association of Y-chromosome haplogroups with the spread of Semitic speakers and the agreement with language phylogenetics.

N. Al-Zahery et al. The male gene pool of the contemporary Mesopotamia marsh population supports their Semitic origin.

The origin of the modern Mesopotamia marsh people, which are locally called “Ma’dan” or “Marsh’s Arabs”, is a question of great interest. Based on their life-style (living in reed houses, grazing of water buffalo and other aspects) and local archaeological sites, many historians and archaeologists believe they may have Sumerian ancestry. Although little is known about the origin of Sumerians themselves, two main hypotheses have been advanced in this regard. According to the first, Sumerians were a group of populations which migrated from the “South East” following a seashore route through the Arabian Gulf, and settled down in the southern marshes of Iraq. According to the second, the advancement of the Sumerian civilization is the result of migration from the mountainous area of Anatolia to the southern marshes of Iraq where they settled, adsorbing previous populations. In order to shed some light on the genetic origin of the Mesopotamia marsh population, we investigated the male gene pool of 145 DNA samples of modern Mesopotamia people, still living in marshes in the south of Iraq. The analyses of Single Nucleotide Polymorphisms (SNPs) and Short Tandem Repeats (STRs) of the paternally transmitted Male Specific region of the Y chromosome (MSY) revealed that more than 80% of marsh Y chromosomes belong to (Hg) J1-M267, the autochthonous haplogroup of Middle Eastern/Semitic speakers with possible recent expansion and/or founder effect reflected by the reduced STRs variability. In particular, 90% of them were assigned to the J1e-M267-PAGE08 sub-haplogroup, which is the predominant Y chromosome lineage among Middle Eastern Arab populations (Yemen, Qatar, UAE, and Levant). Thus, these findings testify, at least from the paternal side, a strong Semitic Arabian component in the contemporary Mesopotamia marshes population, whereas no clear Anatolian and/or South Asian genetic evidence has been detected.

The finding of haplogroup I in China is surprising, as I is not generally found that far away from Europe. It would be interesting to see what the actual haplotypes are.
Y. Lu et al. Western Eurasian Y chromosomes found in the Chinese Salar ethnic group

Salar is a small Western-Turkish-speaking population living mostly in Qinghai province of China. The most similar languages to Salar are all far in Turkmenistan. Historical records suggested that they may be descendants of the Turkic nomadic tribes in Central Asia. In this study, 141 Salar Y chromosomes were analyzed for 39 SNP and 14 STR markers to investigate the potential imprints of their western ancestors. The most frequent haplogroup (hg) in this population sample is Hg R, comprising 40% of all Y chromosomes. Most of these Hg R samples belong to R1a1 (M17), which distributes in a wide geographic region including South Asia, East Europe, Central Asia, and South Siberia. Other four Western Eurasian haplogroups (G-2%, H-5%, I-3%, J-3%) were also found in Salar Y chromosome gene pool. These paternal lineages of Salar are absent in their East Asian neighbors but frequent in Central Asia. Y-STR-based analyses also grouped Salar to Central Asians. On the other side, Salar also has low frequencies of the East Asian specific Hg D and Hg O, suggesting possible gene flow from their neighboring populations. This Y chromosome study demonstrated that Salar well keeps the Western Eurasian paternal lineages of their Central Asian ancestors although they may have migrated to Central China for about 800 years.

I wish that more "people pairs" would be studied this way, as it would give us some good insight of how migration affects gene pools (allele frequency changes, founder effects, possible social selection etc.)

M. Davis et al. Ancient and recent demographic events influence mitochondrial DNA diversity in an immigrant Basque population

The Basques are an ancient people, considered by many anthropologists to represent the oldest extant European population. Because of this, they have been the subject of numerous sociological and biological investigations. The Basque Diaspora, a relatively recent demographic expansion of the Basque population, has until now been overlooked in genetic studies. Samples were taken from 53 individuals with Basque ancestry in Boise, Idaho, and the mitochondrial DNA (mtDNA) sequence variation of the first and second hypervariable regions were determined. Thirty-six mtDNA haplotypes were detected in the sample. Comparing the genetic diversity in the Idaho sample with other Basque populations, signatures of founder effects were observed, consistent with both the recent and ancient history of Basque mitochondrial lineages. There has been a marked alteration of haplogroup frequency and diversity, and there is a slight reduction in other measures of diversity in the NW Basque population compared to the native Basque population. We have found a relatively high percentage of the Cambridge Reference Sequence (rCRS) haplotype for hypervariable regions I and II, which is absent in previous studies of Basque mtDNA, and rare in other Spanish populations. The amount of nucleotide diversity is consistent with a sample that is predominantly haplogroup H, which is especially common in the Basque regions of Europe, due to ancient migrations and expansions out of glacial refugia. This is the first report of mtDNA diversity in an immigrant Basque population, and we find that the diversity in NW Basques can be explained by the recent history of migration, as well as the phylogeography and diversity of the major European haplogroups.

W. S. Watkins et al. Admixture in New World populations: an analysis of Y-chromosome, mtDNA, and genome-wide microarray data

The first major interaction between Native Americans and Europeans is documented historically and occurred less than 550 years ago. This recent time frame provides an excellent opportunity to investigate the effects of admixture between two populations that were previously separated for hundreds of generations. To characterize European admixture in Native American populations, we sampled and analyzed a group of isolated Totonac agriculturists from tropical Mexico near Veracruz and a group of native Bolivians predominantly from the mountainous region near La Paz, Boliva. Mitochondrial sequencing of HVS1 showed that all samples had pre-Columbian mtDNA haplogroups (A, B, C, and D). Using a panel of 48 STRs or 12 Y-chromosome SNPs, Totonac Y-chromosomes lineages were all assigned to the pre-Columbian haplogroup Q1a3a, and Bolivian Y-chromosome lineages were assigned to haplogroups Q1a3a, R1, and J2. Haplogroups R1 and J2 are common in European populations. Principal components analysis (PCA) using >800K autosomal SNPs typed in 24 Totonacs and 23 Bolivians showed that all Totonacs and 14 Bolivians clustered distinctly from Eurasian individuals. Nine Bolivians, however, were positioned between the New World and European PCA clusters. Admixture analysis showed that these nine samples had 21 - 33% European admixture using a European reference population. All three observed Y-chromosome haplogroups, including the well-studied pre-Columbian haplogroup Q1a3a, occurred in the admixed individuals. Two of the nine admixed individuals had pre-Columbian mtDNA and Y-chromosome haplogroups but 21-23% European ancestry. This result demonstrates that Y-chromosome and mtDNA haplogroups are only partial indicators of an individual’s complete ancestry.

Readers of the blog know that I don't agree with the scenario presented in the followin abstract. The serial founder effect idea is used by geneticists to explain the overall reduced genetic diversity of our species (that we appear to be young, in evolutionary terms). Personally, I don't see how a smart, expanding species that all of the sudden had access to the resources of the landmass of Eurasia went through these extreme bottlenecks.
I think that the alternative of a larger human population, genetic diversity reduced across the species by ongoing climate- and culture-mediated selection, and admixture within Africa itself -where a particular expanding H. sapiens group must've co-existed with pre-existed hominids, anatomically modern or not- has merit.
J. Long et al. Evidence for archaic admixture in contemporary non-African human populations

Analyses of large-scale genetic data sets show evidence for a series of founder effects that occurred as modern humans left Africa and settled the rest of the world. Nonetheless, research on modern humans has not ruled out the possibility that other processes, such as local gene flow, or mixing between archaic and modern humans, have also contributed to modern human diversity. Recent analyses of the Neanderthal genome make archaic admixture a salient issue because they show evidence for mixing between Neanderthals and out-of-Africa migrants. The present study examines evidence for archaic admixture in genotypes for 619 microsatellite loci collected from over 2,000 individuals from 100 human populations. We obtained these data from the Marshfield Clinic collection. The populations analyzed represent all inhabited continents of the world. In our analysis, we formulate the serial founder effects (SFE) model as a special case of a phylogenetic model promoted by Cavalli-Sforza and his associates. In this light, the SFE process makes four predictions: 1) A tree of descent according to the pattern of fissions. 2) The root of the tree lies in Africa. 3) The length of each branch is proportional to ratio of evolutionary time to effective population size. 4) The gene identity between all pairs of populations that share the same most recent common ancestor is equal in expectation. Using hypothesis tests based on generalized hierarchical statistical models, we find good agreement between the SFE predictions and diversity within and between African populations, and we find good agreement between the SFE predictions and diversity between non-African populations. However, there is more diversity within the non-African populations than the SRE model can account for. This makes for greater genetic distance between Africans and non-Africans than otherwise expected. How and where did the non-Africans obtain this diversity? A simple explanation for the finding is that the earliest migrants out-of-Africa mixed with an archaic population such as Neanderthals prior to their expansion throughout Europe and Asia. Coalescent based computer simulations of the SFE model with mixing support our interpretation. The time and place that we detect mixing coincides perfectly with that detected in a recent examination of Neanderthal genome sequences. Our study shows that genomic diversity in modern humans still reflects ancient events and processes.

C. Flores et al. Using EuroAIMs to measure admixture proportions in atypical European populations: the case of Canary Islanders

Using ancestry informative markers (AIMs) allows reducing the number of makers needed for population stratification adjustments in association studies. As few as 100 AIMs are sufficient to adjust for the largest European axis of differentiation (i.e. EuroAIMs). However, their use for ancestry inference and adjustment in association studies in atypical European populations such as the Canary Islanders, a recently African-admixed population from Spain, needs to be addressed. We aimed to explore whether EuroAIMs were suitable both for the inference of Spanish and Northwest African admixture proportions and for ancestry adjustments in association studies including samples from Canary Islanders. We analyzed samples from Canary Islanders, mainland Spanish (IBE) and Northwest Africans (NWA) for 93 EuroAIMs and compared the data with CEU and YRI from HapMap, Basques and Mozabite from HGDP, as well as from previously analyzed European samples. The major genetic difference was observed between NWA and all European populations, preserving the northwest-to-southeast differentiation of European populations in the second axis. Analyses revealed that Canary Islanders were intermediate between IBE and NWA, and that direct sub-Saharan African influences were negligible. Assessment of individual admixtures without prior population information clearly identified two subpopulations corresponding to NWA and IBE, while Canary Islanders were admixed with an average of 17.4% Northwest African contribution varying largely among individuals (range 0-95.7%). As few as 23 EuroAIMs correctly estimated population membership to IBE and NWA, while 69 EuroAIMs were required to accurately estimate individual admixture proportions in Canary Islanders. Ancestry estimates based on a subset of 69 EuroAIMs also controlled significant allele frequency differences between IBE and Canary Islanders. These data suggest that a handful of EuroAIMs would be useful to control false-positives in association studies performed in Spanish populations. Supported by FUNCIS 23/07 and grants from the Spanish Ministry of Science and Innovation PI081383 and EMER07/001 to CF.

As I have I mentioned before, the Maasai (and many other east Africans in various degrees) are intermediate between Negroids and Caucasoids, and hence admixture estimates considering Yoruba Nigerians would tend to underestimate the African element. It's important to remember that extant Africans are not uniform, ranging from Caucasoids to Negroids, Pygmies, and Khoi-San, with multiple identifiable clusters within the major Negroid group itself, and all sorts of between-group gene flow in a regional basis. It is always useful (as is the case e.g., with African Americans) to both use historical knowledge about population sources, and also to validate historical narratives with the genetic evidence.
R. L. Raaum et al. Autosomal African admixture in Yemeni populations.

Approximately 30% of mtDNA lineages in South Arabian samples are African L haplotypes, whose origin has usually been attributed to migration and assimilation of African females into the Arabian population over approximately the last 2,500 years. Few In contrast, few Y chromosome lineages of clear recent sub-Saharan African origin have been found in Southern Arabian populations. This bias in maternal and paternal lineages is in accord with historical accounts of the female bias in the Middle Eastern slave trade. In order to evaluate autosomal African ancestry, we collected high-resolution SNP genotype data from a geographically representative set of 62 Yemenis selected from a collection of 552 samples acquired in the Spring of 2007. The ancestry of chromosomal segments in the Yemeni population was estimated using a haplotype-based local ancestry estimation method, HAPMIX. The HAPMIX method is based on a two way admixture model that requires two phased reference populations; we used the HapMap Yoruba in Ibadan, Nigeria (YRI), Luhya in Webuye, Kenya (LWK), Maasai in Kinyawa, Kenya (MKK), and CEPH US residents with ancestry from northern and western Europe (CEU) samples. The three African reference populations include two Bantu-speaking groups (YRI and LWK) and one Nilotic-speaking group (MKK). We estimated local ancestry in the Yemeni sample with all three European-African reference population combinations (CEU-YRI, CEU-LWK, CEU-MKK). The correlations among African ancestry calculated using all three reference population combinations are high (r > 0.98 in all pairwise correlations). Furthermore, there is no significant difference between the average proportion of African ancestry in Yemenis calculated using either of the two Bantu-speaking reference populations: CEU-YRI (mean 0.062, sd 0.044) and CEU-LWK (mean 0.076, sd 0.049) (p=0.13, two-tailed Welch two sample t-test). However, the average African ancestry calculated using the Maasai reference population (CEU-MKK, mean 0.148, sd 0.060) is significantly greater from that calculated using either the Yoruba or Luhya reference populations (p less than 0.0001 in both comparison, two-tailed Welch two sample t-test). These data suggest that the source population for the African ancestry of the Yemeni population is more similar to the contemporary Maasai population than either the Luhya or Yoruba.

The next abstract seems fun; it's always nice to see something that isn't like everything that came before it.
T. Rzeszutek et al. Music as a novel marker in the study of prehistoric human migrations.

The study of prehistoric human population history is often fraught with controversy owing to incongruent evidence among various markers of present-day genetic and cultural diversity. While archaeological evidence can be used to calibrate the conclusions drawn from present-day diversity, the fickle nature of the fossil record leaves some migration histories unresolved. Our work analyzes the potential of music - in particular, vocal music - to serve as novel migration marker, bolstering established migration work and shedding light on regions of the world whose settlement history is contested. One such migration is the recent expansion of Austronesian-speaking peoples across the Pacific within the last 6000 years. The dominant hypothesis posits a recent origin in Taiwan, with a rapid movement southwards and eastwards to populate Polynesia during the following 3500 years. While this model is strongly supported by both archaeological evidence and the present-day distribution of linguistic diversity, our goal was to analyze whether music could serve as a novel line of evidence in the study of Pacific prehistory. A critical concern regarding any migration marker is its time depth. In order to examine this for music, we analyzed correlations between musical diversity and mitochondrial-DNA diversity in 9 Taiwanese aboriginal tribes for which both types of data were available. A sample of 226 choral songs was analyzed using 39 binary characters representing significant structural features of music (e.g., rhythm, interval size, melodic contour, etc.). The musical samples were restricted to ritual musics, which constitute the most conservative (i.e., slowly changing) component of a culture’s repertoire. Mantel tests showed a significant correlation between musical distance and genetic distance among these 9 tribes, suggesting that music may have a time depth comparable to widely-used genetic markers like mitochondrial DNA. This work demonstrates that music has the potential to enrich the conclusions drawn from other markers, and establishes methods for employing it as a tool in the study of prehistoric human movements throughout the world. At the same time, we want to capitalize on music’s own unique dynamics of change over time and place, particularly its capacity for admixture. In other words, music might not only be able to support the narratives told by other migration markers but shed new light on the histories of population movement and cultural contact.

The bolded part in the following abstract makes sense, as it indicates (i) the distinctiveness of Ashkenazi Jews compared to CEU Europeans, and (ii) the fairly recent widespread formation of admixed individuals (in the last couple of generations) which generated individuals that are 1/4 1/2 and 3/4 AJ genomically.

V. Vacic et al., Admixture in Ashkenazi Jewish cohorts and implications for association studies.

Studies of complex genetic disorders may benefit from focusing on population isolates, such as Ashkenazi Jews (AJ). However, in order to truly exploit the advantages of reduced genetic diversity the self-declared AJ ancestry of study participants should be independently confirmed with available genetic data. We investigate whether the AJ cohorts display genetic heterogeneity, such as e.g. different rate of admixing in cases and controls, which could potentially confound disease association studies. We applied principal component analysis (PCA) to AJ cohorts ascertained in Israel and the US East Coast with the goal of characterizing population structure. As described previously, when compared to the HapMap samples with CEU, YRI and CHB/JPT ancestry, virtually all AJ samples cluster with the CEU. Similar analysis done on CEU and Jewish HapMap samples from Ashkenazi, Sephardic and Middle Eastern Jewish communities revealed that 97.8% of AJ samples cluster along the AJ-CEU axis, with modes at AJ and CEU cluster centers and at approximately quartile distances between them. We postulate that these groups correspond to 100-0, 75-25, 50-50, 25-75, and 0-100% AJ-CEU admixtures. Notably, only 91.7% of self-reported AJ individuals fall into the reference JHapMap panel AJ cluster, with 1.6, 3.3, 0.5 and 0.7% in the admixed modes ordered by decreasing fraction of AJ ancestry. We also observe admixing with the non-AJ Jewish communities: 0.7% of samples fall within the non-AJ clusters and 1.4% at a subgroup approximately halfway between the AJ and non-AJ cluster centers. In our dataset we found that when compared to the sample as a whole or only to controls, individuals with Crohn’s disease (CD) show significantly more admixing: 78.1, 3.1, 8.5, 2.0 and 0.9% in the 100, 75, 50, 25 and 0% AJ subgroups respectively. Also, CD samples show more admixing with non-AJ groups (2.8 and 1.0% in the 50-50 and 0-100 AJ-non-AJ subgroups). Isolates typically exhibit a greater amount of cryptic relatedness compared to outbred populations, which motivates an orthogonal method for verifying AJ ancestry based on identity-by-descent (IBD). The high background level of IBD within the Ashkenazi Jewish community can be used to estimate degree of AJ ancestry by averaging the IBD between a sample under study and the AJ individuals in the JHapMap panel. Our preliminary results show that this method recapitulates the high-level results from the PCA analysis and provides better resolution.

Ancient Y chromosomes from the Canary Islands

On the aboriginal remains (ABO):

Aboriginal remains were clearly pre-conquest for all the analyzed islands: Tenerife (2210 ± 60 to 1720 ± 60 BP), Gomera (1743 ± 40 to 1493 ± 40 BP), Hierro (1740 ± 50 to 970 ± 50 BP) and Gran Canaria (1410 ± 60 to 750 ± 60 BP) [33].

It is clear that the aboriginal population was dominated by haplogroups E-M81, E-M78, J-M267. In the historical period (a few centuries ago) new haplogroups make their appearance (e.g., R1a) and a massive increase in the frequency of R1b is observed.

UPDATE (Aug 5):

There are several interesting observations one could make based on these results:

1. The idea of European-descended fair-haired Guanches has taken a hit, as the aboriginal population looks largely like North African Berbers in terms of their Y-chromosomes. No real need to invoke mythical "Nordic" tribes as some have attempted to do.
2. The common view about the dispersal of J-haplogroup in the West has been of early Neolithic dispersal of J2 agriculturalists, followed by J1 dispersal of Arabs, Jews, etc. This paper pretty much destroys that picture.
   
3. The two most conspicuous "missing" haplogroups in the clearly pre-Indo-European population of the Canary Islands are J2 and R1a,.
   

BMC Evolutionary Biology 2009, 9:181 doi:10.1186/1471-2148-9-181

Demographic history of Canary Islands male gene-pool: replacement of native lineages by European

Rosa Fregel et al.

Abstract (provisional)

Background

The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th-18th century remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Y-chromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times.

Results

Autochthonous (E-M81) and prominent (E-M78 and J-M267) Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17th-18th centuries than today.

Conclusions

The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts.

Link (provisional pdf)

Purifying selection and the mtDNA clock (Soares et al. 2009)

This paper deals with the problem of a time-varying mutation rate due to purifying selection, i.e., the removal of harmful variation from the mtDNA gene pool.

From the paper:

Thus, it estimates the coalescence time of the mtDNA tree overall at ~160,000 kya, L3 (the clade that evolved within Africa and gave rise to the three major non-African haplogroups—sometimes termed ‘‘macrohaplogroups’’— M, N, and R) at 65 kya, and M, N, and R themselves at 40–50 kya.

...

In any event, L3 probably expanded ~70 kya, possibly associated with an improvement of the climatic conditions around that time after a long period of drought.103 There are no ‘‘pre-M’’ or ‘‘pre-N’’ clades extant either within or outside Africa, so the out-of-Africa event could be as early as the coalescence time of L3. These data render an outof- Africa dispersal prior to the Toba eruption in Sumatra at ~74 kya less likely.

...

the age of haplogroup M in India, at 49.4 (39.0; 60.2) kya, is significantly lower than in East Asia, at 60.6 (47.3; 74.3) kya (both are lower in r but the proportional
difference is similar; see Table 3).

...

Europe was first settled by modern humans ~45 kya, and it is believed that one of the branches of U, U5 or a genetically close ancestor to U5, arose among the first settlers. The ML estimate of haplogroup U5 is 36.0 (25.3; 47.2) kya, and lower with r at 30.7 (21.4; 40.5) kya and 33.0 (13.3; 52.8) with our synonymous rate. [...] The closest link in the tree with the Near East is the root of haplogroup U, placing any early migration into Europe involving U5 or its ancestors between ~55 kya and ~30 kya.

The new chronology of human mtDNA. As you can see, about 2/3 of the age of mtDNA represents within-Africa variation. L3 Africans and Eurasians are much closer related (matrilineally) than they are with any other Africans. The next closest relation is with L2 Africans, separated by L3's by ~43ky.



American Journal of Human Genetics doi:10.1016/j.ajhg.2009.05.001

Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock

Pedro Soares et al.

Abstract

There is currently no calibration available for the whole human mtDNA genome, incorporating both coding and control regions. Furthermore, as several authors have pointed out recently, linear molecular clocks that incorporate selectable characters are in any case problematic. We here confirm a modest effect of purifying selection on the mtDNA coding region and propose an improved molecular clock for dating human mtDNA, based on a worldwide phylogeny of > 2000 complete mtDNA genomes and calibrating against recent evidence for the divergence time of humans and chimpanzees. We focus on a time-dependent mutation rate based on the entire mtDNA genome and supported by a neutral clock based on synonymous mutations alone. We show that the corrected rate is further corroborated by archaeological dating for the settlement of the Canary Islands and Remote Oceania and also, given certain phylogeographic assumptions, by the timing of the first modern human settlement of Europe and resettlement after the Last Glacial Maximum. The corrected rate yields an age of modern human expansion in the Americas at 15 kya that - unlike the uncorrected clock - matches the archaeological evidence, but continues to indicate an out-of-Africa dispersal at around 5570 kya, 520 ky before any clear archaeological record, suggesting the need for archaeological research efforts focusing on this time window. We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses.

Link

Ancient mtDNA from La Palma (Canary Islands)

Related posts:

• Origin of Canary Islanders
• mtDNA from 17th-18th c. Tenerife

European Journal of Human Genetics doi:10.1038/ejhg.2009.46

The maternal aborigine colonization of La Palma (Canary Islands)

Rosa Fregel et al.

Abstract

Teeth from 38 aboriginal remains of La Palma (Canary Islands) were analyzed for external and endogenous mitochondrial DNA control region sequences and for diagnostic coding positions. Informative sequences were obtained from 30 individuals (78.9%). The majority of lineages (93%) were from West Eurasian origin, being the rest (7%) from sub-Saharan African ascription. The bulk of the aboriginal haplotypes had exact matches in North Africa (70%). However, the indigenous Canarian sub-type U6b1, also detected in La Palma, has not yet been found in North Africa, the cradle of the U6 expansion. The most abundant H1 clade in La Palma, defined by transition 16260, is also very rare in North Africa. This means that the exact region from which the ancestors of the Canarian aborigines came has not yet been sampled or that they have been replaced by later human migrations. The high gene diversity found in La Palma (95.2 +/- 2.3), which is one of the farthest islands from the African continent, is of the same level than the previously found in the central island of Tenerife (92.4+/-2.8). This is against the supposition that the islands were colonized from the continent by island hopping and posterior isolation. On the other hand, the great similarity found between the aboriginal populations of La Palma and Tenerife is against the idea of an island-by-island independent maritime colonization without secondary contacts. Our data better fit to an island model with frequent migrations between islands.

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.