The Genomic History of Southeastern Europe Supplementary Information Contents: Supplementary Note 1: Archaeological and osteological context of newly reported individuals (pages 1-48) Supplementary Note 2: Phenotypically informative markers in hunter-gatherer populations (pages 49-51) Supplementary Note 3: Admixture graph modeling of the relationship among Neolithic populations (pages 52-57) Supplementary Note 1: Archaeological and osteological context of newly reported individuals. This supplement provides archaeological details for individuals that have genome-wide ancient DNA data reported for the first time in this study. They are organized first by present- day country of origin, and then by site. We also provide a brief note describing the Danube Gorges region and approximate chronologies for the Balkan Peninsula and Ukraine. Austria ................................................................................................................... 3 Kleinhadersdorf Flur Marchleiten (2 individuals) .............................................................................. 3 Schletz (4 individuals) ..................................................................................................................................... 3 Bulgaria ................................................................................................................. 4 Beli Breyag (2 individuals) ............................................................................................................................ 4 Dzhulyunitsa (8 individuals) ........................................................................................................................ 4 Ivanovo (1 individual) ..................................................................................................................................... 5 Malak Preslavets (10 individuals) .............................................................................................................. 6 Merichleri – Kairyaka Necropolis (2 individuals) ............................................................................... 8 Mednikarovo (1 individual) .......................................................................................................................... 8 Ohoden (1 individual) ...................................................................................................................................... 9 Sabrano (1 individual) ..................................................................................................................................... 9 Samovodene (1 individual) ........................................................................................................................... 9 Smyadovo (6 individuals) .............................................................................................................................. 9 Sushina (3 individuals) .................................................................................................................................. 10 Varna I (5 individuals) ................................................................................................................................... 11 Yabalkovo (2 individuals) ............................................................................................................................ 13 Yunatsite (2 individuals) .............................................................................................................................. 14 Croatia ................................................................................................................. 15 Beli Manastir-Popova Zemlja (4 individuals) ...................................................................................... 15 Jazinka Cave (1 individual) .......................................................................................................................... 16 Radovanci (1 individual) .............................................................................................................................. 16 Vela Spila (1 individual) ................................................................................................................................ 16 Veliki Vanik (2 individuals) ......................................................................................................................... 17 Vučedol Tell (2 individuals) ........................................................................................................................ 17 Zemunica Cave (3 individuals) .................................................................................................................. 18 France .................................................................................................................. 18 Aven des Iboussières à Malataverne (2 individuals) ....................................................................... 18 Greece ................................................................................................................. 19 Diros, Alepotrypa Cave (3 individuals) .................................................................................................. 19 Franchthi Cave (1 sample) ........................................................................................................................... 19 Italy ..................................................................................................................... 20 Grotta d’Oriente (1 individual) .................................................................................................................. 20 Latvia ................................................................................................................... 21 Zvejnieki (17 individuals) ............................................................................................................................ 21 Macedonia ........................................................................................................... 22 Govrlevo (Cerje), Skopje (1 individual) .................................................................................................. 22 1 Poland ................................................................................................................. 23 Kierzkowo (8 individuals) ........................................................................................................................... 23 Romania .............................................................................................................. 24 Carcea (1 individual) ...................................................................................................................................... 24 Cotatcu (1 individual) .................................................................................................................................... 25 Ostrovul Corbului (2 individuals) ............................................................................................................. 25 Schela Cladovei (2 individuals) .................................................................................................................. 26 Măgura Buduiasca (Teleor 3) (1 individual) ....................................................................................... 27 Urziceni (2 individuals) ................................................................................................................................. 27 Serbia .................................................................................................................. 28 Gomolava (3 individuals) ............................................................................................................................. 28 Hajdučka Vodenica (4 individuals) .......................................................................................................... 29 Lepenski Vir (2 individuals) ........................................................................................................................ 30 Padina (12 individuals) ................................................................................................................................. 31 Saraorci-Jezava (1 individual) .................................................................................................................... 33 Vlasac (17 individuals) .................................................................................................................................. 33 Ukraine ................................................................................................................ 36 Dereivka I (20 individuals) .......................................................................................................................... 36 Ilyatka (3 indviduals) ..................................................................................................................................... 36 Ozera (1 individual) ........................................................................................................................................ 37 Shevchenko (2 individuals) ......................................................................................................................... 37 Vasil’evka (5 individuals) ............................................................................................................................. 38 Verteba Cave (5 individuals) .....................................................................................................................