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Comparison to other methods
We assessed the reliability of DATES in real data by comparing our results with published methods: Globetrotter, ALDER, and ROLLOFF. These methods are designed for the analysis of present-day samples that typically have high-quality data with limited missing variants. In addition, Globetrotter uses phased data which is challenging for ancient DNA samples. Thus, instead of rerunning other methods, we took advantage of the published results for contemporary samples presented in Hellenthal et al., 2014. Following Hellenthal et al., 2014, we created a merged dataset including individuals from HGDP (Li et al., 2008, Behar et al., 2010, and Henn et al., 2012) (Materials and methods). We applied DATES and ALDER to 29 target groups using the reference populations reported in Table S12 in Hellenthal et al., 2014, excluding one group where the population label was unclear. Interestingly, the majority of these groups (25/29) failed ALDER’s formal test of admixture; either because the results of the single reference and two reference analyses yielded inconsistent estimates or because the target had long-range shared LD with one of the reference populations (Appendix 1—table 5). Using DATES, we inferred significant dates of admixture in 20 groups, and 14 of those were consistent with estimates based on Globetrotter. In the case of the six populations that disagreed across the two methods, most of the populations appear to have a history of multiple pulses of gene flow either involving more than two populations (e.g., Brahui Pagani et al., 2017) or multiple instances of contact between the same two reference groups (e.g., Mandenka Price et al., 2009) or the model of admixture differed (e.g., recent ancient DNA studies suggest present-day Bulgarians have ancestry from western hunter-gatherers [HGs], Near Eastern farmers, and Steppe pastoralists from Eurasia [Haak et al., 2015] but were modeled as a mixture of Polish and Cypriots in Globetrotter). In case of complex admixture scenarios, the inconsistencies across the two methods are hard to interpret as Globetrotter and DATES could be capturing different events or the weighting of both events could differ. Finally, the estimated admixture timing based on DATES, ROLLOFF, and ALDER (assuming two-way admixture regardless of the formal test results) were found to be highly concordant (Appendix 1—table 5).
Fine-scale patterns of population mixtures in ancient Europe
Recent ancient DNA studies have shown that present-day Europeans derive ancestry from three distinct sources: (a) HG-related ancestry that is closely related to Mesolithic HGs from Europe; (b) Anatolian farmer-related ancestry related to Neolithic farmers from the Near East and associated to the spread of farming to Europe; and (c) Steppe pastoralist-related ancestry that is related to the Yamnaya pastoralists from Russia and Ukraine (Allentoft et al., 2015; Haak et al., 2015; Skoglund et al., 2012). Many open questions remain about the timing and dynamics of these population interactions, in particular related to the formation of the ancestral groups (which were themselves admixed) and their expansion across Europe. To characterize the spatial and temporal patterns of mixtures in Europe in the past 10,000 years, we used 1096 ancient European samples from 152 groups from the publicly available Allen Ancient DNA Resource (AADR) spanning a time range of ~8000–350 BCE (Materials and methods, Supplementary file 1A). Using DATES, we characterized the timing of the various gene flow events, and below, we describe the key events in chronological order focusing on three main periods.
Holocene to Mesolithic
Pre-Neolithic Europe was inhabited by HGs until the arrival of the first farmers from the Near East (Haak et al., 2010; Hofmanová et al., 2016). There was large diversity among HGs with four main groups – western hunter-gatherers (WHGs) that were related to the Villabruna cluster in central Europe, eastern hunter-gatherers (EHGs) from Russia and Ukraine related to the Upper Paleolithic group of Ancestral North Eurasians (ANEs), Caucasus hunter-gatherers (CHGs) from Georgia associated to the first farmers from Iran, and the GoyetQ2-cluster associated to the Magdalenian culture in Spain and Portugal (Fernandes et al., 2018; Fu et al., 2016; Jones et al., 2015; Rivollat et al., 2020; Skoglund et al., 2012). Most Mesolithic HGs fall on two main clines of relatedness: one cline that extends from Scandinavia to central Europe showing variable WHG-EHG ancestry, and the other in southern Europe with WHG-GoyetQ2 ancestry (Rivollat et al., 2020). The latter is already present in the 17,000 BCE El Mirón individual from Spain, suggesting that the GoyetQ2-related gene flow occurred well before the Holocene. However, the WHG-EHG cline was formed more recently during the Mesolithic period, though the precise timing remains less well understood.
To characterize the formation of the WHG-EHG cline, we used genomic data from 16 ancient HG groups (n=101) with estimated ages of ~7500–3600 BCE. We first verified the ancestry of each HG group using qpAdm that compares the allele frequency correlations between the target and a set of source populations to formally test the model of admixture and then infer the ancestry proportions for the best-fitted model (Haak et al., 2015). For each target population, we chose the most parsimonious model, that is, fitting the data with the minimum number of source populations. Consistent with previous studies, our qpAdm analysis showed that most HGs from Scandinavia, the Baltic Sea region, and central Europe could be modeled as a two-way mixture of WHG- and EHG-related ancestry (Supplementary file 2A). To confirm that the target populations do not harbor Anatolian farmer-related ancestry (that could lead to some confounding in estimated admixture dates), we applied D-statistics of the form D(Mbuti, target, WHG, Anatolian farmers) where target = Mesolithic HGs. We observed that none of the target groups had a stronger affinity to Anatolian farmers than WHG (Supplementary file 2B). Together, these results suggest that the mixtures we date below reflect pre-Neolithic contacts between the HGs.
To infer the timing of the mixtures in the history of Mesolithic European HGs, we applied DATES to HGs from Scandinavia, the Baltic regions, and central Europe using WHG- and EHG-related groups as reference populations. DATES infers the time of admixture in generations before the sample lived. Accounting for the average sampling age of the specimens and the mean human generation time of 28 years (Moorjani et al., 2016), we inferred the admixture time in years before present or in BCE (Materials and methods). We report the average dates (or median, where specified) in BCE in the main text and provide additional details in Figure 2 and Supplementary file 1B including the sample sizes, dates in generations, and BCE for each population. Among HGs, we inferred that the earliest admixture occurred in Scandinavian HGs from Norway and Sweden with a range of average dates of ~80–113 generations before the samples lived (Figure 2—figure supplement 1). This translates to admixture dates of ~10,200–8000 BCE, with the most recent dates inferred in Motala HGs from Sweden suggesting substantial substructure in HGs (Figure 2). In the Baltic region, we inferred the range of admixture dates of ~8700–6000 BCE in Latvia and Lithuania HGs, postdating the mixture in Scandinavia. In southeast Europe, the Iron Gates region of the Danube Basin shows widespread evidence of mixtures between HG groups and, in the case of some outliers, the mixture of HGs and Anatolian farmer-related ancestry as early as the Mesolithic period (Feldman et al., 2019). Further, these groups showed a strong affinity to the WHG-related ancestry in Anatolian populations, suggesting ancient interactions with Near Eastern populations (Feldman et al., 2019). We applied qpAdm to test the model of admixture in Iron Gates HG and found that the parsimonious model with WHG- and EHG-related ancestry provides a good fit to the data. Further, when we tested the model with Anatolian-related ancestry using Anatolian HG (AHG) as an additional source population, the AHG ancestry proportion was not significant (Supplementary file 2A). Applying DATES to Iron Gates HG with WHG and EHG as reference populations, we inferred this group was genetically formed in ~9200 BCE (95% confidence interval: 10,000–8400 BCE). Our samples of the Iron Gates HGs include a wide range of C14 dates between 8800 and 5700 BCE. We confirmed our dates were robust to the sampling age of the individuals as we obtained statistically consistent dates when all samples were combined as one group or when subsets of samples were grouped in bins of 500 years (Figure 2—figure supplement 2). The most recent dates of ~7500 BCE were inferred in eastern Europe in Ukraine HGs, highlighting how the WHG-EHG cline was formed over a period ~2000–3000 years (Figure 2, Supplementary file 1B).
We assessed the reliability of DATES in real data by comparing our results with published methods: Globetrotter, ALDER, and ROLLOFF. These methods are designed for the analysis of present-day samples that typically have high-quality data with limited missing variants. In addition, Globetrotter uses phased data which is challenging for ancient DNA samples. Thus, instead of rerunning other methods, we took advantage of the published results for contemporary samples presented in Hellenthal et al., 2014. Following Hellenthal et al., 2014, we created a merged dataset including individuals from HGDP (Li et al., 2008, Behar et al., 2010, and Henn et al., 2012) (Materials and methods). We applied DATES and ALDER to 29 target groups using the reference populations reported in Table S12 in Hellenthal et al., 2014, excluding one group where the population label was unclear. Interestingly, the majority of these groups (25/29) failed ALDER’s formal test of admixture; either because the results of the single reference and two reference analyses yielded inconsistent estimates or because the target had long-range shared LD with one of the reference populations (Appendix 1—table 5). Using DATES, we inferred significant dates of admixture in 20 groups, and 14 of those were consistent with estimates based on Globetrotter. In the case of the six populations that disagreed across the two methods, most of the populations appear to have a history of multiple pulses of gene flow either involving more than two populations (e.g., Brahui Pagani et al., 2017) or multiple instances of contact between the same two reference groups (e.g., Mandenka Price et al., 2009) or the model of admixture differed (e.g., recent ancient DNA studies suggest present-day Bulgarians have ancestry from western hunter-gatherers [HGs], Near Eastern farmers, and Steppe pastoralists from Eurasia [Haak et al., 2015] but were modeled as a mixture of Polish and Cypriots in Globetrotter). In case of complex admixture scenarios, the inconsistencies across the two methods are hard to interpret as Globetrotter and DATES could be capturing different events or the weighting of both events could differ. Finally, the estimated admixture timing based on DATES, ROLLOFF, and ALDER (assuming two-way admixture regardless of the formal test results) were found to be highly concordant (Appendix 1—table 5).
Fine-scale patterns of population mixtures in ancient Europe
Recent ancient DNA studies have shown that present-day Europeans derive ancestry from three distinct sources: (a) HG-related ancestry that is closely related to Mesolithic HGs from Europe; (b) Anatolian farmer-related ancestry related to Neolithic farmers from the Near East and associated to the spread of farming to Europe; and (c) Steppe pastoralist-related ancestry that is related to the Yamnaya pastoralists from Russia and Ukraine (Allentoft et al., 2015; Haak et al., 2015; Skoglund et al., 2012). Many open questions remain about the timing and dynamics of these population interactions, in particular related to the formation of the ancestral groups (which were themselves admixed) and their expansion across Europe. To characterize the spatial and temporal patterns of mixtures in Europe in the past 10,000 years, we used 1096 ancient European samples from 152 groups from the publicly available Allen Ancient DNA Resource (AADR) spanning a time range of ~8000–350 BCE (Materials and methods, Supplementary file 1A). Using DATES, we characterized the timing of the various gene flow events, and below, we describe the key events in chronological order focusing on three main periods.
Holocene to Mesolithic
Pre-Neolithic Europe was inhabited by HGs until the arrival of the first farmers from the Near East (Haak et al., 2010; Hofmanová et al., 2016). There was large diversity among HGs with four main groups – western hunter-gatherers (WHGs) that were related to the Villabruna cluster in central Europe, eastern hunter-gatherers (EHGs) from Russia and Ukraine related to the Upper Paleolithic group of Ancestral North Eurasians (ANEs), Caucasus hunter-gatherers (CHGs) from Georgia associated to the first farmers from Iran, and the GoyetQ2-cluster associated to the Magdalenian culture in Spain and Portugal (Fernandes et al., 2018; Fu et al., 2016; Jones et al., 2015; Rivollat et al., 2020; Skoglund et al., 2012). Most Mesolithic HGs fall on two main clines of relatedness: one cline that extends from Scandinavia to central Europe showing variable WHG-EHG ancestry, and the other in southern Europe with WHG-GoyetQ2 ancestry (Rivollat et al., 2020). The latter is already present in the 17,000 BCE El Mirón individual from Spain, suggesting that the GoyetQ2-related gene flow occurred well before the Holocene. However, the WHG-EHG cline was formed more recently during the Mesolithic period, though the precise timing remains less well understood.
To characterize the formation of the WHG-EHG cline, we used genomic data from 16 ancient HG groups (n=101) with estimated ages of ~7500–3600 BCE. We first verified the ancestry of each HG group using qpAdm that compares the allele frequency correlations between the target and a set of source populations to formally test the model of admixture and then infer the ancestry proportions for the best-fitted model (Haak et al., 2015). For each target population, we chose the most parsimonious model, that is, fitting the data with the minimum number of source populations. Consistent with previous studies, our qpAdm analysis showed that most HGs from Scandinavia, the Baltic Sea region, and central Europe could be modeled as a two-way mixture of WHG- and EHG-related ancestry (Supplementary file 2A). To confirm that the target populations do not harbor Anatolian farmer-related ancestry (that could lead to some confounding in estimated admixture dates), we applied D-statistics of the form D(Mbuti, target, WHG, Anatolian farmers) where target = Mesolithic HGs. We observed that none of the target groups had a stronger affinity to Anatolian farmers than WHG (Supplementary file 2B). Together, these results suggest that the mixtures we date below reflect pre-Neolithic contacts between the HGs.
To infer the timing of the mixtures in the history of Mesolithic European HGs, we applied DATES to HGs from Scandinavia, the Baltic regions, and central Europe using WHG- and EHG-related groups as reference populations. DATES infers the time of admixture in generations before the sample lived. Accounting for the average sampling age of the specimens and the mean human generation time of 28 years (Moorjani et al., 2016), we inferred the admixture time in years before present or in BCE (Materials and methods). We report the average dates (or median, where specified) in BCE in the main text and provide additional details in Figure 2 and Supplementary file 1B including the sample sizes, dates in generations, and BCE for each population. Among HGs, we inferred that the earliest admixture occurred in Scandinavian HGs from Norway and Sweden with a range of average dates of ~80–113 generations before the samples lived (Figure 2—figure supplement 1). This translates to admixture dates of ~10,200–8000 BCE, with the most recent dates inferred in Motala HGs from Sweden suggesting substantial substructure in HGs (Figure 2). In the Baltic region, we inferred the range of admixture dates of ~8700–6000 BCE in Latvia and Lithuania HGs, postdating the mixture in Scandinavia. In southeast Europe, the Iron Gates region of the Danube Basin shows widespread evidence of mixtures between HG groups and, in the case of some outliers, the mixture of HGs and Anatolian farmer-related ancestry as early as the Mesolithic period (Feldman et al., 2019). Further, these groups showed a strong affinity to the WHG-related ancestry in Anatolian populations, suggesting ancient interactions with Near Eastern populations (Feldman et al., 2019). We applied qpAdm to test the model of admixture in Iron Gates HG and found that the parsimonious model with WHG- and EHG-related ancestry provides a good fit to the data. Further, when we tested the model with Anatolian-related ancestry using Anatolian HG (AHG) as an additional source population, the AHG ancestry proportion was not significant (Supplementary file 2A). Applying DATES to Iron Gates HG with WHG and EHG as reference populations, we inferred this group was genetically formed in ~9200 BCE (95% confidence interval: 10,000–8400 BCE). Our samples of the Iron Gates HGs include a wide range of C14 dates between 8800 and 5700 BCE. We confirmed our dates were robust to the sampling age of the individuals as we obtained statistically consistent dates when all samples were combined as one group or when subsets of samples were grouped in bins of 500 years (Figure 2—figure supplement 2). The most recent dates of ~7500 BCE were inferred in eastern Europe in Ukraine HGs, highlighting how the WHG-EHG cline was formed over a period ~2000–3000 years (Figure 2, Supplementary file 1B).
