qpWave/qpAdm analysis

The qpWave/qpAdm (Haak et al., 2015; Lazaridis et al., 2017) framework was used to test for the number of migration waves of ancestry and to estimate the admixture proportion of a Test population based on Dataset I (Tables 3, S3, and S5; Document S1). Here a set of “Left” populations (Test population and potential source populations) together with a set of “Right” populations (diverse outgroups) allowed for the testing of the number of waves of ancestry from “Right” to “Left” populations, and for estimation of the admixture proportions of the Test population. Following Lazaridis et al., (2017), two sets of outgroups were used, one using early Neolithic sources and HG (16 populations, ultimate sources). Note that the African individual Mota was used as fixed outgroup.

All: Mota, AfontovaGora3, Anatolia_N, CHG, EHG, ElMiron, GoyetQ116-1, Iran_N, Kostenki14, Levant_N, MA1, Natufian, Ust_Ishim, Vestonice16, Villabruna, WHG.

Likewise, we also defined a second set (proximate sources) by adding younger populations down to the Bronze Age into the “All” set of populations. This may allow for the identification of simpler models underlying the likely complex admixed populations.

All+: All (see above) ∪ Anatolia_ChL, Armenia_ChL, Armenia_EBA, Armenia_MLBA, Europe_LNBA, Europe_MNChL, Iberia_BA, Iran_ChL, Levant_BA, Steppe_EMBA, Steppe_MLBA.

The Left set is chosen to include the Test population (for which the admixture proportions are being modeled) and N populations from the All (or All+) set. The Right set is then All \Left, testing against the maximal set of Right outgroups. To evaluate the relatedness of the BA Greek individuals, we also added our individual samples, as well as the Minoans and Mycenaeans from Lazaridis et al. (2017), and BA Balkan individual samples (Mathieson et al., 2018) as potential sources to the Left set. We further split the BA Balkan samples into EBA and LBA since the amount of reported Steppe admixture is increased in individuals from LBA (Mathieson et al., 2018). We infer the rank = N-1 using qpWave and estimate the admixture proportion for the test populations using qpAdm. We show only feasible admixture proportions (in the interval [0,1]) and use a significance threshold of α = 0.05 to reject models.

To make our results comparable to Lazaridis et al. (2017), we used the HO set of 591,642 SNPs for joined analyses of modern and ancient data and the HOIll set of 1,054,671 SNPs (1,054,637 SNPs retained after merging datasets) for analyses considering only ancient individuals (Dataset I).