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Durham Research Online Durham Research Online Deposited in DRO: 14 March 2016 Version of attached le: Supplemental Material Peer-review status of attached le: Peer-reviewed Citation for published item: Martiniano, Rui and Caell, Anwen and Holst, Malin and Hunter-Mann, Kurt and Montgomery, Janet and M¤uldner,Gundula and McLaughlin, Russell L. and Teasdale, Matthew D. and van Rheenen, Wouter and Veldink, Jan H. and van den Berg, Leonard H. and Hardiman, Orla and Carroll, Maureen and Roskams, Steve and Oxley, John and Morgan, Colleen and Thomas, Mark G. and Barnes, Ian and McDonnell, Christine and Collins, Matthew J. and Bradley, Daniel G. (2016) 'Genomic signals of migration and continuity in Britain before the Anglo-Saxons.', Nature communications., 7 . p. 10326. Further information on publisher's website: http://dx.doi.org/10.1038/ncomms10326 Publisher's copyright statement: Additional information: Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full DRO policy for further details. Durham University Library, Stockton Road, Durham DH1 3LY, United Kingdom Tel : +44 (0)191 334 3042 | Fax : +44 (0)191 334 2971 https://dro.dur.ac.uk Supplementary Information Genomic signals of migration and continuity in Britain before the Anglo­Saxons 1 2,3 2 4 Authors: Rui Martiniano ,​ Anwen Caffell ,​ Malin Holst ,​ Kurt Hunter­Mann ,​ Janet 3 ​ 5 ​ 1 ​ 1 ​ Montgomery ,​ Gundula Müldner ,​ Russell L McLaughlin ,​ Matthew D Teasdale ,​ Wouter ​ 6 6 ​ ​ 6 7 ​ van Rheenen ,​ Jan H Veldink ,​ Leonard H van den Berg ,​ Orla Hardiman ,​ Maureen 8 ​ 9 ​ 10 9 ​ 11 ​ 12 Carroll ,​ Steve Roskams ,​ John Oxley ,​ Colleen Morgan ,​ Mark G Thomas ,​ Ian Barnes ,​ ​ 4 ​ ​ 9 ​ 1 ​ ​ Christine McDonnell ,​ Matthew J Collins *,​ Daniel G Bradley *​ ​ ​ ​ Affiliations: 1 Smurfit​ Institute of Genetics, Trinity College Dublin, Dublin, Ireland; 2 York​ Osteoarchaeology Ltd, 75 Main St, Bishop Wilton, York, North Yorkshire YO42 1SR, UK 3 Department​ of Archaeology, Dawson Building, Durham University, South Road, Durham, DH1 3LE, UK 4 York​ Archaeological Trust for Excavation and Research Limited, 47 Aldwark, York YO1 7BX, UK 5 Department​ of Archaeology, University of Reading, Whiteknights PO Box 227, Reading RG6 6AB, UK 6 Department​ of Neurology, Neurogenetics Unit, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands 7 Academic​ Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin 2, Ireland 8 Department​ of Archaeology, University of Sheffield Northgate House, West Street, Sheffield S1 4ET UK 9 Department​ of Archaeology, University of York, York, UK 10 City​ of York Council, York, North Yorkshire, YO1 6GA, UK; 11 Research​ Department of Genetics, Evolution and Environment, University College London, London, UK 12 Department​ of Earth Sciences, Natural History Museum, London, UK. Supplementary Figures 3 Driffield Terrace Site North 27 39 29 True North 3DRIF-16 58 Skeleton number Decapitated Not Decapitated Infant / J uvenile Empty grave Orientation of body (arrow=head end) 54 48 Cremations 50 Intrusion 3DRIF-26 2011 watching brief 46 51 43 55 52 56 53 Site North 6 Driffield Terrace True North 6DRIF-23 6DRIF-18 6DRIF-21 6DRIF-22 6DRIF-3 3 Site North True North 6 Norton York Melton Supplementary Figure 1 - Location of Driffield Terrace, Norton on Tees and Melton Samples. ● 0.715 Other York Other Driff.Terrace Roman aDNA samples 0.714 ● ● ● 0.713 ● 0.712 ● Sr ● 86 0.711 Sr/ ● ● ● 87 ● ● ● ● ● ● ● ● ● ●●●● ● 0.710 ● ● ● 87 86 ● ● Sr/ Sr range for ● ● ● ● ● ● ● ●●● Vale of York ● ●● 0.709 ●● ● ● ●● ● ● ● ● ●● 0.708 ● 3DRIF−26 18 2SDδ Op range for British burials 0.707 14.0 15.0 16.0 17.0 18.0 19.0 20.0 21.0 22.0 18 δ Op (VSMOW) ‰ Supplementary Figure 2 - δ18O vs 87Sr/86Sr in tooth enamel carbonate from Driffield Terrace with samples selected for DNA highlighted and compared with other samples from Roman York. Current best estimates for the local 87Sr/86Sr and the British phosphate oxygen isotope (δ18Op) range are also indicated. British burials all periods Roman Period burials aDNA burials Supplementary Figure 3 - A biplot showing the distribution of strontium isotope and concentration data for archaeological human enamel excavated in Britain for: all periods; the Roman Period; and the seven individuals from Driffield Terrace, York analysed for aDNA. As the data are drawn from multiple sources 1–6 analytical uncertainty is estimated at +/- 0.002 % (2 SD) for 87Sr/86Sr (i.e. within symbol) and +/- 10 mg/kg for strontium concentration. 16.0 6DRIF-18 3DRIF-26 14.0 6DRIF-22 6DRIF-21 12.0 6DRIF-23 6DRIF-1 N 10.0 3DRIF-16 15 δ Driffield Terrace Bone Driffield Terrace Dentine 8.0 DNA-Samples Dentine Pigs DNA-Samples Bone York Mean (n=173) 6.0 Herbivores Analytical Error 4.0 -23.0 -22.0 -21.0 -20.0 -19.0 -18.0 -17.0 -16.0 -15.0 δ13C Supplementary Figure 4 - A biplot showing the distribution of strontium isotope and concentration data for archaeological human enamel excavated in Britain for: all periods; the Roman Period; and the seven individuals from Driffield Terrace, York analysed for aDNA. As the data are drawn from multiple sources 1–6 analytical uncertainty is estimated at +/- 0.002 % (2 SD) for 87Sr/86Sr (i.e. within symbol) and +/- 10 mg/kg for strontium concentration. Leptiminus, Tunisia 20.0 Dakhleh Oasis, Egypt Lower Nile, Egypt Kerma (N. Sudan) 18.0 Wadi Halfa (N. Sudan) Ya'amun (Jordan) 16.0 Gerasa(Jordan) Natfieh (Jordan) 14.0 Tell Barri (Syria) Sagalassos (Turkey) (‰) N Ephesos (Turkey) 15 12.0 Sourtara (Mainland Greece) δ Messene (Peloponnese) 10.0 Eleutherna (Crete) Rome 8.0 Portus Romae, Rome Velia, S Italy Ibiza 6.0 Croatia Øland, Swedish Baltic 4.0 Danish Baltic -22.0 -21.0 -20.0 -19.0 -18.0 -17.0 -16.0Northern -15.0 Poland Southern Germany 13 δ C(‰) York 3DRIF-26 Supplementary Figure 5 - Carbon and nitrogen stable isotope data from Driffield Terrace in comparison with mean values for fauna (±1SD) and humans (stepped error bars: ±2SD and ±3SD) from Roman York. Arrows connect isotope data from dentine (diet in late childhood/adolescence) and bone (adult diet) of the genotyped individuals. Data: 6–8. Roman Iron Age Anglo−Saxon >A changes >T changes − − G C 0.00 0.10 0.20 0.00 0.10 0.20 5 10 15 20 25 25 20 15 10 5 Distance from 5' end Distance from 3' end Supplementary Figure 6 - Comparison of aDNA misincorporation patterns at the 5′ end of sequencing reads (C to T) and 3' end (G to A) between the samples from Roman York, Iron Age and Anglo-Saxon. pmd_NO3423 ● pmd_6DRIF−3 ● pmd_6DRIF−23 ● pmd_6DRIF−22 ● pmd_6DRIF−21 ● pmd_6DRIF−18 ● pmd_3DRIF−26 ● pmd_3DRIF−16 ● pmd_M1489 ● NO3423 ● Sample 6DRIF−3 ● 6DRIF−23 ● 6DRIF−22 ● 6DRIF−21 ● 6DRIF−18 ● 3DRIF−26 ● 3DRIF−16 ● M1489 ● 0.000 0.025 0.050 0.075 0.100 Ry Supplementary Figure 7 - Sex identification based on shotgun sequencing data and comparison of results using reads with evidence of deamination (PMD score 3, squares) and unfiltered reads (lozenges). Ry - Ratio of the number of reads aligned to the Y-chromosome divided by the sum of the number reads aligned to the Y- and X-chromosomes. Gray shaded areas represent threshold for acceptance of assignment, calibrated with modern and ancient genomes. Error bars correspond to 95% confidence intervals. ● ● ● ●●● ● ●●●● ●●●Le●●●●●●● Ge ●●● ● ●● Ad●●● ●● ● ●●● ● ●●● ● ● ● ●●● ●● ● ● Ar●● ● ●●● ● ● ● ● ● ● ● ●● ● ●●●Tk ● ●● ● ●● ● ●●●●● ●● ●●● ● ● ● ●● ● Ira ● ●Dr ● ●● ● ●●● ● ●● ● ● ●● ● ●● ● ●● ●●● ●● ●●Cy●●● ●●●● ● ● ●●●●●●● ●● ● ● ●●Bu●Ro●●●● ●●●●●●Gr●● ● ● ● ● ● ● ● ● ● ●●●●BePo●●●●●●●● Ch●●●●●●● ● ●●●● ● ●●● ●● ● ●● ●●Li●●●●●Ru●●●●●●●●●●●●Hu● ● ●●●●●● ● ●Tu●● ●●●● ● ● ● ●● ●●● ●●●● Nor●●Or●We●●●GA●●● ● ●● ● ● ● ●● So●●● ● ● ● ● ● Fi●●●●●●●●●●ScEn●●●●●●●●●● ●NIt●●●● ●● ● ●● ●● Sy● ● ●● ● ● ● ●●●●Ir●●● ● ●●Fr●●●● ●WS●Ea●●●● ●●● ●●●●●●● ● ● ●●●● ●●● ● ●● ●●●●●● ●● ● ● ● ● ●● ●●●●●●●UAE ● ●● ● ●●●●●●●● ●●●● ● ● ● ●●●●●●●●●●● ● ●Sau ●● ● ●Ba●●●●●● ● ● ● ●●●Jo●●●●●● ●● ● ●● ● ●●●●● ●●●● ● ●●●● ● ●●●●●Pa● ●●● ● ● ● ●● Sp●● ●●●●● ● ●● ● ● ● ●●●●● ●●●●●Sa●●● ● ● ●● ● Bed ●●● ●● ●● ●●●● ●● ● ● ● ● ● ● ●●● ● ● ● ● ●● ● Ye ●● ● ● ●●● ● ● ● ● ● ● ● ● Eg●● ● ●●● ● ● ● ● ● ●● PC2 ● ● ● ● ● ● Tun ● ● ● ●● ● Mo ● ● ● ● N.W.Europe 0.05 0.00 0.05 ● ● ● − ● ● S.Europe ● ● ● ● E.Europe ● 0.10 ● ● − ● ● W.Asia ● ● ● Middle East ● 0.15 ● − North Africa Moz●● ● ● ●● ●● M1489 ●●●● ● NO3423 ● ● Roman −0.05 0.00 0.05 PC1 Supplementary Figure 8 - Principal Component Analysis of ancient individuals merged with genotypes from 780 European, West Asian, North African and Middle Eastern individuals using reads with evidence of deamination (PMD score 3). Population key: Ad - Adygei; Ar - Armenian; Ba - Basque; Bed - Bedouin; Be - Belorussian; Bu - Bulgarian; Ch - Chuvash; Cy - Cypriot; Dr - Druze; Ea - EastSicilian; Eg - Egyptian; En - English; Fi - Finnish; Fr - French; Ge - Georgian; GA - GermanyAustria; Gr - Greek; Hu - Hungarian; Ira - Iranian; Ir - Ireland; Jo - Jordanian; Le - Lezgin; Li - Lithuanian; Mo - Moroccan; Moz - Mozabite; NIt - NorthItalian; Nor - Norwegian; Or - Orcadian; Pa - Palestinian; Po - Polish; Ro - Romanian; Ru - Russian; Sa - Sardinian; Sau -
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