Post by Admin on Nov 21, 2021 21:24:34 GMT
Mediterranean and central European ancestries shaped the genetic profile of southeastern BA groups in Iberia
To explore the genetic turnover and the contribution of the local groups to the newly formed BA genetic profile in Iberia, we systematically tested a series of qpAdm models. We started by using the distal ancestry sources Anatolia_N, WHG, GoyetQ2, Yamnaya_Samara, and Iran_N to model the genetic ancestry components of Iberian BA groups (table S2.10 and fig. S6). We found that the local traces of GoyetQ2, a characteristic but variable component of southern Iberia CA individuals, were no longer detectable, suggesting a dissolution of geographic substructure in BA Iberia with respect to HG ancestry. We explain this by the spread of steppe-related ancestry from North to South (7) that also contributed northern and central Iberian ancestry to the South, diluting the subtle GoyetQ2 signal to a level beyond the limits of detection (text S8). By using the same qpAdm model, we also observed that Almoloya_Argar_Early, Almoloya_Argar_Late, SE_CabezoRedondo_BA, and Bastida_Argar cannot be modeled with Yamnaya_Samara as a single source but find better support with a combination of Iran_N and Yamnaya_Samara, however, without reaching P values ≥0.05 in Almoloya_Argar_Early and Late and SE_CabezoRedondo_BA (table S2.10 and fig. S6). These El Argar groups (Almoloya and Bastida) are also slightly shifted to the right on the PC1 axis, in the direction of Mediterranean BA groups with excess Iran_N-like ancestry, such as “Minoans,” who only carry Iran_N-like ancestry but not steppe-related ancestry, or “Mycenaeans,” who carry a mix of both (71), and that has also been shown for some BA individuals from Sicily_MBA (51) and for Sardinians here (Fig. 3A).
To explore the reasons for the model rejection observed in southeastern BA groups, we tested several qpAdm models (text S8). We used two- and three-way competitive qpAdm models to test whether a third source with Iran_N-like ancestry was needed. In the two-way model (table S2.11), Germany_Bell_Beaker (the largest number of individuals representing BB) was used as a fixed proximal ancestry source together with a local CA source (either N_Iberia_CA, C_Iberia_CA, or SE_Iberia_CA). For target groups in which these two sources were rejected, we iteratively tested central and eastern Mediterranean populations as a third source, as some of them are known to carry Iran_N-like ancestry (Fig. 4A and table S2.11). Using C_Iberia_CA as a local source of ancestry and Germany_Bell_Beaker as a proxy for steppe ancestry, only models with Almoloya_Argar_Early and Late as a target were rejected, suggesting that a third component was required for these Iberian BA groups. We found that adding any Mediterranean population as a third source improves the model fit, albeit without reaching P values >0.05. However, we obtained P values >0.05 when using Iran_Chalcolithic as a third source, which suggests that a higher proportion of Iran_N-like ancestry is needed (text S8 and table S2.11). Notably, when we exchanged C_Iberia_CA with the local SE_Iberia_CA, the model did not find support for a larger number of Iberian BA groups (N_Iberia_BA, SE_Iberia_BA, Almoloya_Argar_Early and Late, and C_Iberia_CA_Stp), and adding a third source in this constellation did not improve the model fit either (Fig. 4A and table S2.11).
Fig. 4. Modeling genetic ancestry in Iberian BA groups.(A) Modeling Iberian BA individuals with steppe-related ancestry as a two- and three-way qpAdm admixture model using proximal sources C_Iberia_CA/SE_Iberia_CA, Germany_Bell_Beaker, and Iran_C (table S2.11). (B) Modeling Iberian BA individuals with steppe-related ancestry as a two- and three-way qpAdm admixture model using proximal sources C_Iberia_CA_Stp, C_Iberia_CA/SE_Iberia_CA, and Iran_N (table S2.1). P values for each group are given inside each column. Faded colors indicate rejected models when applying a P value cutoff of ≤0.05.
To rule out that the rejection of models involving Germany_Bell_Beaker + C_Iberia_CA in La Almoloya (Early and Late) is due to specific north/central European LN admixture in Germany_Bell_Beaker that was not present in the source of steppe-related ancestry in Iberia, we fixed the source of direct steppe-related ancestry to Yamnaya_Samara, as we expect the same distal steppe source contributing to all Iberian groups, and iterated through the proximal local CA sources, which in these models contribute 100% of the Chalcolithic (i.e., Neolithic farmer) ancestry. We added distal Iran_N (instead of Iran_Chalcolithic, which could contribute other confounding CA ancestries) as a third source only when needed (table S2.12 and fig. S7). By using C_Iberia_CA and Yamnaya_Samara in a two-way model, we could successfully model all Iberian BA groups, but again to the exclusion of the southeastern Almoloya_Argar_Early and Late, and SE_CabezoRedondo_BA groups. Notably, Bastida_Argar also failed for the distal model 2 (table S2.10). However, these three groups returned values ≥0.05 in the proximal local CA substrate model when Iran_N was added as a third source (fig. S7 and table S2.12). In turn, when we exchanged C_Iberia_CA with a local SE_Iberian_CA source, most of the models were rejected, which confirms the genetic substructure in Iberia_CA groups. Using SE_Iberia_CA as substrate only improves the model fit for southeastern Iberian groups, suggesting that the first individuals who brought steppe-related ancestry to Iberia admixed locally with the different CA groups (table S2.12). Notably, SE_Iberia_CA is a sufficiently supported local proxy for Balearic CA_Stp, BA, and LBA groups. We interpret this signal with caution, as Mallorca_CA_Stp and Menorca_LBA are only represented by a single individual each; however, this signal is well supported in the newly typed Aritges_LBA group from Menorca, which consists of six individuals (fig. S7 and table S2.12).
We then tried to further specify the proximal sources without affecting the power of resolution to distinguish between them. We exchanged Yamnaya_Samara by C_Iberia_CA_Stp as the most proximal local source with steppe-related ancestry (6) and combined these with the different Iberian CA sources (table S2.13 and text S8) in two-way models, only adding Iran_N as a third source when needed. Using increasingly more possible proximal sources for steppe-related ancestry, we could replicate the results of the distal models. However, we can show that Almoloya_Argar_Early and Late, Bastida_Argar, SE_CabezoRedondo_BA, and Aritges_LBA still require Iran_N as a third source in all models with C_Iberia_CA and C_Iberia_CA_Stp. In contrast, Iran_N is not required when SE_Iberia_CA is used as a local substrate, although models for Almoloya_Argar_Early and Late are still rejected at P ≤ 0.05. This finding is best explained by either an unresolved distinctive ancestry of La Almoloya individuals or, alternatively, the ability to detect such subtle signals only in groups consisting of a larger number of individuals, as is the case for Almoloya_Argar_Early (n = 36) and Almoloya_Argar_Late (n = 22), which provide the statistical power to reject simpler models. When SE_Iberia_CA is used instead of C_Iberia_CA to model La Bastida, the model is no longer rejected, which suggests a direct contribution of local CA groups to those of the southeastern Iberian BA. Together, the results hint at an additional, albeit subtle, Iran_N-enriched ancestry that is present in SE_Iberia_CA groups and thus potentially predating the El Argar BA.
We also tested whether Almoloya_Argar_Early and Late can be modeled when Iran_N is exchanged by geographically more proximal Iran_N-rich sources involving central and eastern Mediterranean populations (table S2.14 and text S8) and by moving Iran_N to the outgroups. However, this did not result in any supported models (text S8). While we were not able to find a proximal Mediterranean source, we note that adding a central Mediterranean population to the outgroups (Sicily_EBA, Greece_EBA, or Greece_MBA) decreases the model support (P values) for Almoloya_Argar_Early and Almoloya_Argar_Late, indirectly attesting to the importance of central Mediterranean BA. However, we observed no changes in P values by adding other Mediterranean groups to the outgroups (text S8 and table S2.15).
The complete turnover on the Y chromosome to R1b-Z195 (a lineage derived from P312), observed in all males at La Almoloya (29 male individuals tested) and La Bastida (except for one E1b lineage dated around 2134 to 1947 cal BCE; 7 males tested), is another independent source of evidence of gene flow predominantly during the time of the CA-BA transition (table S1.1 and text S3). Notably, Y lineage R1b-Z195, the most common Y lineage in BA Iberia, ultimately derives from a common ancestor R1b-P312 in central Europe but already differs from other derived Bell Beaker R1b variants reported from central Europe and the British Isles. R1b-Z195 has been found in Sicily_CA_Stp (previously assigned to the EBA and thus considered outliers) and Sicily_EBA (51). However, the genealogical and geographic link to other R1b variants still remains unclear. The subtle presence of Iran_N-like ancestry in El Argar and Y haplogroup R1b-Z195 in Sicily opens the possibility of gene flow not only from Iberia to Sicily as previously suggested (51) but also in the opposite direction, implying reciprocal contact with the western and central Mediterranean during the BA, although direct contacts are hardly noticeable in the archaeological record.
Together, these results suggest a dual genetic contribution to the formation of the BA genetic profile of southeastern Iberians in addition to a local CA genetic substrate. The major additional ancestry source resembles central European Bell Beaker groups, which first contributed ancestry to northern Iberia, followed by a southward spread in the form of C_Iberia_CA_Stp. A second minor ancestry component is an Iran_N-rich/central Mediterranean source, which is restricted to individuals from BA El Argar contexts. The timing of the last contributing component remains unclear and points to either a Neolithic legacy that persisted throughout the local CA or a subtle trace of connections to insular central Mediterranean BA groups.
To explore the genetic turnover and the contribution of the local groups to the newly formed BA genetic profile in Iberia, we systematically tested a series of qpAdm models. We started by using the distal ancestry sources Anatolia_N, WHG, GoyetQ2, Yamnaya_Samara, and Iran_N to model the genetic ancestry components of Iberian BA groups (table S2.10 and fig. S6). We found that the local traces of GoyetQ2, a characteristic but variable component of southern Iberia CA individuals, were no longer detectable, suggesting a dissolution of geographic substructure in BA Iberia with respect to HG ancestry. We explain this by the spread of steppe-related ancestry from North to South (7) that also contributed northern and central Iberian ancestry to the South, diluting the subtle GoyetQ2 signal to a level beyond the limits of detection (text S8). By using the same qpAdm model, we also observed that Almoloya_Argar_Early, Almoloya_Argar_Late, SE_CabezoRedondo_BA, and Bastida_Argar cannot be modeled with Yamnaya_Samara as a single source but find better support with a combination of Iran_N and Yamnaya_Samara, however, without reaching P values ≥0.05 in Almoloya_Argar_Early and Late and SE_CabezoRedondo_BA (table S2.10 and fig. S6). These El Argar groups (Almoloya and Bastida) are also slightly shifted to the right on the PC1 axis, in the direction of Mediterranean BA groups with excess Iran_N-like ancestry, such as “Minoans,” who only carry Iran_N-like ancestry but not steppe-related ancestry, or “Mycenaeans,” who carry a mix of both (71), and that has also been shown for some BA individuals from Sicily_MBA (51) and for Sardinians here (Fig. 3A).
To explore the reasons for the model rejection observed in southeastern BA groups, we tested several qpAdm models (text S8). We used two- and three-way competitive qpAdm models to test whether a third source with Iran_N-like ancestry was needed. In the two-way model (table S2.11), Germany_Bell_Beaker (the largest number of individuals representing BB) was used as a fixed proximal ancestry source together with a local CA source (either N_Iberia_CA, C_Iberia_CA, or SE_Iberia_CA). For target groups in which these two sources were rejected, we iteratively tested central and eastern Mediterranean populations as a third source, as some of them are known to carry Iran_N-like ancestry (Fig. 4A and table S2.11). Using C_Iberia_CA as a local source of ancestry and Germany_Bell_Beaker as a proxy for steppe ancestry, only models with Almoloya_Argar_Early and Late as a target were rejected, suggesting that a third component was required for these Iberian BA groups. We found that adding any Mediterranean population as a third source improves the model fit, albeit without reaching P values >0.05. However, we obtained P values >0.05 when using Iran_Chalcolithic as a third source, which suggests that a higher proportion of Iran_N-like ancestry is needed (text S8 and table S2.11). Notably, when we exchanged C_Iberia_CA with the local SE_Iberia_CA, the model did not find support for a larger number of Iberian BA groups (N_Iberia_BA, SE_Iberia_BA, Almoloya_Argar_Early and Late, and C_Iberia_CA_Stp), and adding a third source in this constellation did not improve the model fit either (Fig. 4A and table S2.11).
Fig. 4. Modeling genetic ancestry in Iberian BA groups.(A) Modeling Iberian BA individuals with steppe-related ancestry as a two- and three-way qpAdm admixture model using proximal sources C_Iberia_CA/SE_Iberia_CA, Germany_Bell_Beaker, and Iran_C (table S2.11). (B) Modeling Iberian BA individuals with steppe-related ancestry as a two- and three-way qpAdm admixture model using proximal sources C_Iberia_CA_Stp, C_Iberia_CA/SE_Iberia_CA, and Iran_N (table S2.1). P values for each group are given inside each column. Faded colors indicate rejected models when applying a P value cutoff of ≤0.05.
To rule out that the rejection of models involving Germany_Bell_Beaker + C_Iberia_CA in La Almoloya (Early and Late) is due to specific north/central European LN admixture in Germany_Bell_Beaker that was not present in the source of steppe-related ancestry in Iberia, we fixed the source of direct steppe-related ancestry to Yamnaya_Samara, as we expect the same distal steppe source contributing to all Iberian groups, and iterated through the proximal local CA sources, which in these models contribute 100% of the Chalcolithic (i.e., Neolithic farmer) ancestry. We added distal Iran_N (instead of Iran_Chalcolithic, which could contribute other confounding CA ancestries) as a third source only when needed (table S2.12 and fig. S7). By using C_Iberia_CA and Yamnaya_Samara in a two-way model, we could successfully model all Iberian BA groups, but again to the exclusion of the southeastern Almoloya_Argar_Early and Late, and SE_CabezoRedondo_BA groups. Notably, Bastida_Argar also failed for the distal model 2 (table S2.10). However, these three groups returned values ≥0.05 in the proximal local CA substrate model when Iran_N was added as a third source (fig. S7 and table S2.12). In turn, when we exchanged C_Iberia_CA with a local SE_Iberian_CA source, most of the models were rejected, which confirms the genetic substructure in Iberia_CA groups. Using SE_Iberia_CA as substrate only improves the model fit for southeastern Iberian groups, suggesting that the first individuals who brought steppe-related ancestry to Iberia admixed locally with the different CA groups (table S2.12). Notably, SE_Iberia_CA is a sufficiently supported local proxy for Balearic CA_Stp, BA, and LBA groups. We interpret this signal with caution, as Mallorca_CA_Stp and Menorca_LBA are only represented by a single individual each; however, this signal is well supported in the newly typed Aritges_LBA group from Menorca, which consists of six individuals (fig. S7 and table S2.12).
We then tried to further specify the proximal sources without affecting the power of resolution to distinguish between them. We exchanged Yamnaya_Samara by C_Iberia_CA_Stp as the most proximal local source with steppe-related ancestry (6) and combined these with the different Iberian CA sources (table S2.13 and text S8) in two-way models, only adding Iran_N as a third source when needed. Using increasingly more possible proximal sources for steppe-related ancestry, we could replicate the results of the distal models. However, we can show that Almoloya_Argar_Early and Late, Bastida_Argar, SE_CabezoRedondo_BA, and Aritges_LBA still require Iran_N as a third source in all models with C_Iberia_CA and C_Iberia_CA_Stp. In contrast, Iran_N is not required when SE_Iberia_CA is used as a local substrate, although models for Almoloya_Argar_Early and Late are still rejected at P ≤ 0.05. This finding is best explained by either an unresolved distinctive ancestry of La Almoloya individuals or, alternatively, the ability to detect such subtle signals only in groups consisting of a larger number of individuals, as is the case for Almoloya_Argar_Early (n = 36) and Almoloya_Argar_Late (n = 22), which provide the statistical power to reject simpler models. When SE_Iberia_CA is used instead of C_Iberia_CA to model La Bastida, the model is no longer rejected, which suggests a direct contribution of local CA groups to those of the southeastern Iberian BA. Together, the results hint at an additional, albeit subtle, Iran_N-enriched ancestry that is present in SE_Iberia_CA groups and thus potentially predating the El Argar BA.
We also tested whether Almoloya_Argar_Early and Late can be modeled when Iran_N is exchanged by geographically more proximal Iran_N-rich sources involving central and eastern Mediterranean populations (table S2.14 and text S8) and by moving Iran_N to the outgroups. However, this did not result in any supported models (text S8). While we were not able to find a proximal Mediterranean source, we note that adding a central Mediterranean population to the outgroups (Sicily_EBA, Greece_EBA, or Greece_MBA) decreases the model support (P values) for Almoloya_Argar_Early and Almoloya_Argar_Late, indirectly attesting to the importance of central Mediterranean BA. However, we observed no changes in P values by adding other Mediterranean groups to the outgroups (text S8 and table S2.15).
The complete turnover on the Y chromosome to R1b-Z195 (a lineage derived from P312), observed in all males at La Almoloya (29 male individuals tested) and La Bastida (except for one E1b lineage dated around 2134 to 1947 cal BCE; 7 males tested), is another independent source of evidence of gene flow predominantly during the time of the CA-BA transition (table S1.1 and text S3). Notably, Y lineage R1b-Z195, the most common Y lineage in BA Iberia, ultimately derives from a common ancestor R1b-P312 in central Europe but already differs from other derived Bell Beaker R1b variants reported from central Europe and the British Isles. R1b-Z195 has been found in Sicily_CA_Stp (previously assigned to the EBA and thus considered outliers) and Sicily_EBA (51). However, the genealogical and geographic link to other R1b variants still remains unclear. The subtle presence of Iran_N-like ancestry in El Argar and Y haplogroup R1b-Z195 in Sicily opens the possibility of gene flow not only from Iberia to Sicily as previously suggested (51) but also in the opposite direction, implying reciprocal contact with the western and central Mediterranean during the BA, although direct contacts are hardly noticeable in the archaeological record.
Together, these results suggest a dual genetic contribution to the formation of the BA genetic profile of southeastern Iberians in addition to a local CA genetic substrate. The major additional ancestry source resembles central European Bell Beaker groups, which first contributed ancestry to northern Iberia, followed by a southward spread in the form of C_Iberia_CA_Stp. A second minor ancestry component is an Iran_N-rich/central Mediterranean source, which is restricted to individuals from BA El Argar contexts. The timing of the last contributing component remains unclear and points to either a Neolithic legacy that persisted throughout the local CA or a subtle trace of connections to insular central Mediterranean BA groups.