team which has been assembled include leading European geneticists, anthropol ogist and archaeologists. This cross-disciplinary team is involved in the following:
a. The identification, accessibility and collection of key archaeological samples
b. Providing anthropological and anthropometric data
c. Combining accurate absolute dating and isotope analysis within the archaeological context
d. Obtaining human aDNA data in a contamination free environment
e. Using new capture/NGS methods
f. Applying new population genetic model-testing and simulation methods
The Project will have several major impacts on scientific, technological, and scholarly horizons. From a technological and scientific perspective, it is the first project to combine hypothesis driven bioarchaeology, including accurate dating and isotope analysis, with a systematic exploration of the genetic structure of prehistoric Europeans using new genome-wide approaches and an appropriate modelling and simulation approach to analyze these data.
a. Identify and model the effect of the LGM and Holocene onset on the population history of AMH in Europe between 45,000-4,500 BP
b. Provide a new precise and comprehensive chronology of AMH in Europe between 23,000 and 6,000 BP
c. Detect any anthropometric and genetic evidence for equal and/or sex-biased hunter-farmer admixture in southeast, central, northern and western Europe
d. Test the best fit of the obtained genetic and morphometric data to a new set of agricultural dispersal models using spatial simulations (taking into account the findings in aim 3)
e. Study spatial and temporal genetic variation associated with (a) pigmentation, (b) infectious disease resistance and mendelian disorders, and (c) other genetic loci that show high Fst values among major geographical groups. Of particular importance will be (d) the study of variation within genes associated with dietary adaptations following the onset of the Neolithic. These include: lactase deficiency, deficiency in sucraseiomaltase, gluten-intolerance, and alcohol metabolism
f. Detect (a) specific palaeopathological conditions and (b) changes in cranial and post-cranial morphology and to investigate links between aims 5, 7
g. Assess genetic variation within individuals this can provide information on past mating networks and demography (by providing evidence for endogamy)
Sampling and dating
Bone samples of <2.5g are taken from specimens which are to be dated and analysed for isotope ratios and aDNA. These were selected on the basis of archaeological (provenance, quality of excavation, etc.) and anthropological criteria. In order to minimise destruction only small samples will be collected using a portable dental drilling set.
Carbon and oxygen isotope fractionations are analysed at Oxford and is analysed by the team.
(i) Craniometry: Geometric morphometrics methods to landmark data are applied by the team. Several portable 3D MicroScribe digitizers are used to collect landmark and semi-landmark data which best captures the dimensionality and robusticity of the skull and at the same time allows to obtain the traditional set of craniometric distances.
(ii) The age and sex of each individual will be determined according to standard anthropological methods.
(iii) Cranial robusticity is assessed by means of scoring the set of non-metric traits as and by digitising a set of landmarks and contours on the cranial vault, base and cranio-facial regions. Morphometric data is collected on post-cranial remains using a measurement system which will provide data to compare body size and physique, patterns of childhood growth, and skeletal biomechanics. The latter will be supplemented through the study of long-bone cross-sectional geometry using a new non-invasive method based on silicone moulds of diaphyseal dimensions developed by J. Stock and others.
(iv) Analysis of (a) skeletal markers of occupational stress and (b) musculoskeletal stress markers (MSM) is performed by the team.
(v) The health profiles of popula
DNA is extracted in a clean room environment at the specialised laboratories in Trinity College Dublin and York. Within this controlled environment libraries for NGS sequencing are created using ligation of indexed adapters.
mitochondrial DNA sequences and capture assays are obtained by sequencing
Solexa libraries, which are in essence whole sample amplifications. The greater
part of these consists of environmental DNA and on average best archaeological
samples yield ~20% or less endogenous DNA. Importantly, the mtDNA data and
duplication of procedures in both labs give strong indication of sample
suitability for NGS analysis and authenticity.
Y chromosome sequencing is pursued by first performing a simple PCR test using a few small Y specific DNA fragments to sex test samples. SNPs will be typed by capture as above.
In the case of samples with good endogenous yields, we focus on the following:
1. The analysis of priority gene sequences which code for important phenotypic traits many of which are postulated to have changed and/or undergone strong selection in European prehistory. These include 100 genes in categories of (a) pigmentation, (b) dietary change, e.g. lactase persistence (c) genes known to be involved in susceptibility to infectious diseases, e.g. CCR5, TLRs and mendelian disorders eg
CFTR, HFE; (d) genes emerging from GWAS studies suspected to be involved in physical traits such as stature, e.g. GPR133, HMGA1, HMGA2. Note that the data that emerges from the 1000 genomes project will give a rich context within which to analyse these results.
2. We are particularly interested in the study of Single Nucleotide Polymorphisms (SNPs) with strong phylogeographical structure. A strong worldwide data collec tion is available, particularly from European populations. This provides a very rich context for ancient work especially as analyses show that such data gives excellent resolution of genetic-geography structure at the level of individual samples.
Examination of ancient bones with similar data enables interrogation of the time depth of European genetic structure and is also a tool for complementing other analyses of migration