A dynastic elite in monumental Neolithic society

Abstract

The nature and distribution of political power in Europe during the Neolithic era remains poorly understood¹. During this period, many societies began to invest heavily in building monuments, which suggests an increase in social organization. The scale and sophistication of megalithic architecture along the Atlantic seaboard, culminating in the great passage tomb complexes, is particularly impressive². Although co-operative ideology has often been emphasised as a driver of megalith construction¹, the human expenditure required to erect the largest monuments has led some researchers to emphasize hierarchy³-of which the most extreme case is a small elite marshalling the labour of the masses. Here we present evidence that a social stratum of this type was established during the Neolithic period in Ireland. We sampled 44 whole genomes, among which we identify the adult son of a first-degree incestuous union from remains that were discovered within the most elaborate recess of the Newgrange passage tomb. Socially sanctioned matings of this nature are very rare, and are documented almost exclusively among politico-religious elites⁴-specifically within polygynous and patrilineal royal families that are headed by god-kings^5,6. We identify relatives of this individual within two other major complexes of passage tombs 150 km to the west of Newgrange, as well as dietary differences and fine-scale haplotypic structure (which is unprecedented in resolution for a prehistoric population) between passage tomb samples and the larger dataset, which together imply hierarchy. This elite emerged against a backdrop of rapid maritime colonization that displaced a unique Mesolithic isolate population, although we also detected rare Irish hunter-gatherer introgression within the Neolithic population.

Extended Data Fig. 1. Genomic affinities of the Irish Neolithic.

a, ADMIXTURE plot (K = 14) for ancient Irish and British populations (first row), other ancient Eurasians (second and third rows) and global modem populations (fourth row). For components that reach their maximum in modem populations, the five individuals with highest values were selected for representation. If the majority of these individuals corne from a single population the block is labelled as such; otherwise, it is labelled using the general geographic region from which these individuals originate. Three components reach their maximum in ancient populations, and we label these ‘European_HG’ (red), Early_Farmer (orange) and ‘Steppe’ (teal). b, Box plot (Tukey method) showing the distribution of the European_HG component among British and Irish Neolithic shotgun-sequenced individuals (n = 50). c, Normalized haplotypic length contributions, estimated with ChromoPainter, from Early Neolithic populations to later Neolithic and Chalcolithic individuals. The top two donors are outlined in black for each individual. Given the unsupervised nature of the analysis, regional differences in overall haplotypic donation levels should be ignored, as larger populations have more opportunity for within-group painting.

Extended Data Fig. 2. Haplotypic structure among ancient populations

a, ChromoPainter principal component analysis of diverse ancient genomes (n = 149) generated using the output matrix of haplotypic lengths. The colour and shape key for the Irish samples follows Fig. 1. b, fineSTRUCTURE dendrogram derived from the same matrix as in a, with the passage tomb cluster highlighted. Dotted branches are shown at a quarter of their true length.

Extended Data Fig. 3. Inferring the relationship between the parents of NG10.

a, Whole-genome plot of heterozygosity in NG10, revealing extreme runs of homozygosity. b, Nine mating scenarios (coloured Unes) that can lead to an inbreeding coefficient of 25%. c, Number and average lengths of homozygous-by-descent (HBD) segments for each of these simulated scenarios (500 iterations) and the same values observed for the NG10 genome. Box plots follow Tukey’s method. Scenarios in the subpanels i and ii best fit the homozygous-by-descent distribution of NG10; ii is less parsimonious than i when anthropological and biological factors are taken into consideration.

Extended Data Fig. 4. Levels of inbreeding through time in ancient populations.

Inbreeding coefficients for imputed ancient samples estimated by measuring the proportion of the genome that is homozygous by descent. Box plots follow Tukey’s method. Individuals are binned according to archaeological period. UP-MS, Upper Palaeolithic to Mesolithic (n = 24); EN, Early Neolithic (n = 13); MN-CA, Middle Neolithic to Chalcolithic (n = 69); BA, European Bronze Age (n = 12); IA-MA, Iran Age to Medieval (n = 21); Steppe CA-BA, steppe Chalcolithic to Bronze Age (n = 14). Outliers of note are labelled. The inferred degrees of relatedness between the parents of an individual are marked.

Extended Data Fig. 5. Detecting recent shared ancestry between pairs of British and Irish Neolithic samples.

a, lcMLkin kinship coefficients between pairs of Irish and British Neolithic samples, jittered by a height of 0.00018 and width of 0.00036 for visualization. Optimized duplicate tests are linked by dotted Unes. Several standalone values are also shown (italics), in which one duplicate did not meet the threshold of overlapping sites (>20,000). The MB6 and car004 pairing (19,850 sites) is shown as a translucent point. An inset is shown for lower values of pi-HAT. Pairs over 5er from the mean pi-HAT and K₀ for subpanel ii (marked with a line) are highlighted using thesame colour and shape key as in Fig. 1. Combined symbols are used for inter-site pairs, b, Total haplotypic lengths donated between all pairs (n = 2,162) of British and Irish samples from the ChromoPainter analysis of diverse ancient samples (Extended Data Fig. 2). Outlying pairs (4α above the mean) are labelled. c, Outgroup f3-statistics measuring shared drift between pairs (n = 2,236) of Irish and British Neolithic samples (>25,000 informative sites). d, Total haplotypic lengths donated between all pairs of ‘passage tomb cluster’ (pink; n = 42) and ’ British—Irish cluster’ (grey; n = 1,190) samples from the ChromoPainter analysis of genomes from the Atlantic seaboard (Fig. 1d, e). Single members from the outlying pairs in b were removed for this analysis. Positions of passage tomb pairs are marked along the x axis, with two outlying pairs from Carrowkeel highlighted.

Extended Data Fig. 6. Regional-scale diversity in the Irish Neolithic.

a, Nitrogen stable-isotope values (an indicator of trophic level) plotted across time for samples from the neighbouring sites of Poulnabrone (blue) and Parknabinnia (yellow). For male samples, the Y chromosome haplogroup is given. Distant kinship connections are marked with a dotted line, and a closer (about fourth degree) relationship is highlighted with a solid line, b, Box plot (Tukey’s method) of nonnalized read coverage aligning to chromosome 21 for shotgun-sequenced ancient samples (n = 188), with a single outlier from Poulnabrone (representing an infant with trisomy).

Extended Data Fig. 7. Subclade distributions of Y chromosome haplogroup I2a1 in Ireland, Britain and Europe from the Mesolithic to the Bronze Age.

a, Y haplogroups observed for Neolithic individuals (jittered) in Britain and Ireland. Shape indicates the approximate time period within the Neolithic (based on ref. ), and colour indicates haplogroup and follows the same keys as in b-d. b-d, Approximately 94% of the British and Irish Neolithic samples belong to haplogroups I2a1b1 (45%), I2alal (14%) and I2ala2 (35%). Incidences (jittered) of these haplogroups in European individuals from the Mesolithic to the Bronze Age are shown for I2albl (b), I2a1a1 (c) and I2a1a2 (d). Haplogroup colour keys are shown with respect to phylogenetic placement; thosehaplogroups observed within Britain and Ireland are shown in bold. European individuals who share an identical set of haplotypic mutations (for sites covered) to an Irish Neolithic individual are highlighted with a black outline in c (for I2a1a1) and d (for I2a1a2).

Extended Data Fig. 8. Geographic and genomic distributions of northwestern European hunter-gatherer ancestry among British and Irish Neolithic individuals.

a, Geographic distribution of northwestern European hunter-gatherer introgression in Britain and Ireland across 103 Neolithic samples. Box plot (Tukey’s method) highlights four outliers, three from the Early-to-Middle Neolithic of Argyll and one from Ireland (Parknabinnia675 (PB675)). The next highest value is also from Parknabinnia (individual PB754). b, The same Z)-statistic run on separate chromosomes for individuals of sufficient coverage (n = 86). Outlying individuals are marked for each chromosome. Irish outliers follow the same shape and colour key as in Fig. 1. Outliers who are also outliers inthe box plot in a are marked in bold. c, Box plot (Tukey’s method; n = 86) of sample standard deviations across the chromosomes for the same D-statistic. Four outliers with high variance across the chromosomes are marked, including three samples from Parknabinnia, two of whom are also top hits in a. d-f, Haplotypic affmities of imputed Irish and British Neolithic individuals (n = 47) to Irish hunter-gatherers, relative to other northwestem European hunter-gatherers (Bichon, Loschbour and Cheddar Man). Colour and shape key follows Fig. 1. The outlying individual PB675 shows a preference for Irish hunter-gatherer haplotypes in all measures. Regression Unes are shown with 95% confidence interval shaded (sample size = 47). PB675 shows a higher-than-expected number of Irish hunter-gatherer haplotypes (d), has the highest overall hunter-gatherer haplotypic length contribution, with a ratio skewed towards Irish hunter-gatherers (e) and displays the longest average length of Irish-hunter-gatherer haplotype chunks (f).

Extended Data Fig. 9. SNP-sharing analyses of autosomal structure in Neolithic populations of the Atlantic seaboard.

a, Principal component analysis created using an identical sample (n = 57) and set of SNPs (about 488,000 sites; pseudo-haplodized) to that presented in Fig. 1d, e. b, Outgroup f3-statistics for all combinations of samples in a, using a reduced set of SNPs (about 270,000 sites; pseudo-haplodized). Results are presented in a heat map and corresponding dendrogram.

Extended Data Fig. 10. Imputation accuracies for chromosome 22 of the high-coverage NE1 genome, downsampled to 1X.

The levels of accuracy seen across all SNPs (solid line) (n= 204,316 for no minor allele frequency (MAF) filter and genotype probability of 80) is compared to that seen for transversions only (dashed line) (n = 62,374 for no minor allele frequency filter and genotype probability of 80). Accuracies at different genotype probability thresholds and minor allele frequency filters are shown for the three different genotype categories. Minor allele frequency filters are based on overall frequency in the 1000 Genomes phase 3 dataset.

Fig. 1. Fine-scale haplotypic and dietary structure in the Neolithic.

a, Timeline of analysed Irish genomes with inbreeding coefficients are shown for those with sufficient coverage. All dates are direct and calibrated, excluding that for individual CAK534 (translucent). The key for the sample sites is given in c. The earliest widespread evidence of Neolithic activity (house horizon) is marked with a black line. The Irish Neolithic ends at about 2500 BC. NA, not applicable, b, Stable isotope values for samples from the Irish and British Neolithic (n = 292). The key for the Irish samples is given in c, and samples included in the ancient DNA anatysis are outlined in black. British samples are shown as hollow shapes; black, Scotland; grey, England or Wales; circles, pre-3400 BC; squares, post-3400 BC. An infant with Down syndrome (PN07) is labelled; this individual showed isotope values consistent with a high trophic level. c, Site locations for Irish individuals sampled or included in this study coloured by burial type: yellow, court tomb; blue, portal tomb; green, Linkardstown-type; magenta, passage tomb and related; light pink, natural sites; and light blue, the unclassified Baltynahatty megalith. Sites outlined in black were included in ancient DNA anatysis. d, ChromoPainter principal component (PC) anatysis of individuals from the Atlantic seaboard of majority Early_Farmer ancestry (n = 57), generated using a matrix of haplotypic length-sharing. Passage tomb outliers in Fig. 2d are labelled. e, fineSTRUCTURE dendrogram derived from the same matrix as in d with five consistent clusters.

Fig. 2. Genomic signals of dynasty among focal passage tomb interments.

a, Front elevation and interior of the Newgrange passage tomb. Photographs by Failte Ireland; Photographic Unit, National Monuments Service, b, Plan of chamber, redrawn after ref. . Scale bar, 6 m. c, The coefficient of relatedness (pi-HAT) between car004 (an interment from the central monument at Carrowmore), and 38 British and Irish Neolithic samples, with the top 5 hits labelled (CAK68 and CAK530 are equal in value), d, Average length of donated haplotypic chunks between all reciprocal pairs of the ‘passage tomb cluster’ (pink; n = 42) and British-Irish cluster’ (grey; n = 1,190) as defined by fineSTRUCTURE in Fig. 1e. The highest values for passage-tomb-cluster pairs are marked along the x axis, with an excess of longer chunks shared between the inferred kin of car004 (CAK533, MB6 and NG10) in c. Darker lines link reciprocal donations. Combined symbols are used for inter-site pairs, e, A sliding window of heterozygosity is plotted for transversions along selected chromosomes ofNGIO, revealing extreme runs of homozygosity. Scale bar, 50 Mb.

Fig. 3. Origins and Legacy of the Irish Mesolithic.

a, a, Right, the maps show the estimates of shared drift between Irish and British or continental hunter-gatherers (HG) (jittered) from the Mesolithic and Upper Palaeolithic (triangles, Magdalenian culture). Left, the top ten hits with sufficient coverage are cross-compared with one another and with Irish hunter-gatherers in a heat map using the statistic f3(Mbuti; HG1, HG2), in which HG1 and HG2 represent all possible pairs, b, Short and long runs of homozygosity (ROH) spectra in modem and ancient genomes. Hollow shapes indicate direct (rather than imputed) diploid calls. For four Irish samples, both imputed and direct data are presented, showing close agreement. c, Normalized haplotypic length donations from hunter-gatherer populations to Neolithic individuals, arranged by their geographic region (labelled). The top three hunter-gatherer donors are outlined for each individual. Donor hunter-gatherer population colours are as in b; British and northwestem European hunter-gatherers are merged into one donor population (blue).