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Post by Admin on Jul 15, 2021 22:50:35 GMT
Human population genetics The final 661,765 filtered human reads were used for the following downstream analyses. We used sequenceTools (Schiffels et al., 2016) to call pseudo-haplotype genotypes of the 1240K dataset (Lazaridis et al., 2016). A total of 11,116 pseudo-haploid positions were recovered. These genotypes were combined with data from 78 ancient genomes (Fu et al., 2014, 2015, 2016; Gamba et al., 2014; Jones et al., 2015; Lazaridis et al., 2016, 2018; van de Loosdrecht et al., 2018; Mathieson et al., 2015; Narasimhan et al., 2019; Olalde et al., 2014; Raghavan et al., 2014; Sikora et al., 2017; Yang et al., 2017a; Yu et al., 2020) (Table S2) and 2,335 present-day individuals from 149 different populations (Jeong et al., 2019; Lazaridis et al., 2014) (Table S2) that were projected on a PCA using eigensoft 7.2.1 (Patterson et al., 2006), using the 597,573 SNPs of the Human Origins (HO) dataset (Lazaridis et al., 2014). We used the option lsqproject in order to minimize the effect of the missing data on the distortion in the PCA location. Admixture analysis was run using ADMIXTURE 1.3.0 (Alexander et al., 2009) with all individuals from the Human Origins (HO) array and all the available sequences from the David Reich lab database (https://reich.hms.harvard.edu/). The HO dataset SNPs were pruned with option --indep-pairwise of PLINK 1.9 (Purcell et al., 2007) with parameters 250 50 0.4. The total number of remaining SNPs was 436,097. Figure 1C shows the 78 ancient individuals and SAT29 samples with PONG 1.4.9 (Behr et al., 2016). To explore the genetic affinities and the amount of shared derived SNPs we have used f3-outgroup statistics using admixtools 5.1 (Patterson et al., 2012) in the form f3 (SAT29,X;Mbuti). X represents both the 78 ancient genomes (Table S2) and the 149 modern populations (Table S2). For the ancient individual comparisons we restricted the analysis to 2,000 shared SNPs and reduced the modern comparisons to 4,000 shared SNPs. We further explored the possible clusterization of SAT29 and Dzuzuana2 individuals with f4 statistics in the form f4 (Dzuzuana2,X;SAT29,Mbuti), with X representing the ancient tested populations (Table S6). All these comparisons yielded no concluding results due to the lacking statistical significance due to the low coverage. In addition, we used qpWave from admixtools 5.1 to test the possible single genetic pool for SAT29 and Dzuduana2. We assigned these two populations as left populations and used Chimp, Altai Neanderthal, Ju_hoan_North, Khomani_San and Vindija as the right populations, from the HO dataset. This yielded to non-significant results (tail probability of. of 0.38).
Sex determination of SAT29 human reads For sex determination we used ry_compute (Skoglund et al., 2013). The results show that the SAT29 soil sample is compatible with a female: R_y value of 0.0089 and a CI of: 0.0078-0.0099.
Neanderthal ancestry in SAT29 We used F4 Ratio (Patterson et al., 2012) to explore the Neanderthal ancestry of the SAT29 sample. We used the genotype data from the 1240k dataset available in (https://reich.hms.harvard.edu/downloadable-genotypes-present-day-and-ancient-dna -data-compiled-published-papers) with the combination: (Chimp AltaiNeandertal : X Mbuti :: Chimp Altai_Neandertal : VindijaNeandertal Mbuti) .
Human mitochondrial analysis Following the human mtDNA target enrichment step we sequenced 25,483,930 captured reads. After clipping and discarding reads with a base quality score below 30, we had a total of 24,448,710 reads. 2,183,282 reads mapped to the mtDNA human genome. To assure no non-human reads were left after mapping, we used MEGAN 6.19.9 (Huson et al., 2007) and BLAST+ n 2.10 (Altschul et al., 1990) to remove non-human reads aligning all the reads against the whole nt database and selecting only the reads that MEGAN locates in the genus Homo. After removing duplicates, our final dataset contained 4,953 reads unique to H. sapiens, which represents 15.31-fold mtDNA genome coverage. The deamination rate of the mtDNA was 0.4 G>A at the 3’ end and 0.41 C>T at the 5’ end.
mtDNA contamination estimate The mtDNA coverage for SAT29 is too low to run a standard contamination check with Schmutzi (Renaud et al., 2015). Therefore, we binned our reads using libbam (Renaud, 2018) into three bins using the first and last 10 base pairs to check for deamination: deaminated reads, non-deaminated reads and all reads . We then ran the endocaller script from Schmutzi (Renaud et al., 2015) to compare the reads of the deaminated and non-deaminated bins to look for differences. In the case of contamination levels significant enough to affect consensus calling, we expect to see a difference in the deaminated (ancient reads) and non-deaminated (ancient and potential modern contaminant reads) bins. We only found four positions where the two bins differed and had low consensus conformity. All four positions are a mixture of C and Ts or G and As, indicating that these positions are possibly variable due to deamination, as even the non-deaminated bin of reads could have residual deamination farther into the reads (Table S7). While this method cannot estimate contamination levels directly, the level of contamination is low enough to not influence our consensus calling.
Presence of multiple individuals We applied two different methods to ascertain the presence of multiple human individuals in the SAT29 mtDNA. First we used a similar strategy described in Slon et al (Slon et al., 2017). We filtered the reads that showed the presence of deaminated bases in the last five positions on both ends with libbam (Renaud, 2018), and then we filtered for all the positions covered by at least 10 reads. After that we clipped the reads with trimbam from bamutil 1.0.14 (Jun et al., 2015) to minimize the effect of damage. A total of 2,961 positions of the mtDNA positions passed the filters, after which we examined the positions looking for differential base presence. Only 11 positions exhibited the presence of more than two bases different from the majority genotype, but all these positions could be explained by damage that was still present after clipping. Therefore we have not identified positions that could be explained by the presence of multiple individuals. No transversions or substitutions that were not compatible with damage were found. We then assessed the presence of multiple ancient sequences in the sample using Schmutzi, which indicated the possible presence of another ancient sequence with a percentage of 0.38% (0.355- 0.405%). However, a close analysis of the variants revealed that both sequences predicted by Schmutzi, both endogenous and the potential second ancient sequence, only differed in two positions: 310C and 16189C. Both positions are private mutations and supported by less than ⅔ of positions, while the assessment of the mtDNA haplogroup was the same. Therefore we conclude that the results suggest the presence of a single individual or several with the same mitochondrial haplogroup, but these results are inconclusive due to the low coverage.
Human mitochondrial tip dating We used six subsets of data for tip dating of the human SAT29 mtDNA: A) A full set of samples (238 samples as shown in Table S4), B) All ancient samples and 14 modern samples that fall close to SAT29 in the maximum parsimony tree as well as the RCRS ancestor (84 samples, Table S4), C) Only ancient samples as well as the RCRS ancestor (70 samples, Table S4), and D) For each of the above sets, a second set was included without the two samples BK-BB7_240 N and BK-CC7-335 N giving a total of six sets. The full dataset was aligned using Muscle 3.8.31 (Edgar, 2004) and uploaded to MEGA-X where a modeltest was run. The model TN93+G+I had the lowest Bayesian information criterion (Table S8). Each set was then selected and exported as a nexus file. The nexus file was uploaded to BEAUti version 1.10.4. Tip dates were set to the years before the present using the dates shown in Table S4. SAT29 and, if present, the samples BK-BB7_240 N and BK-CC7-335 N were put into their own taxon set and were sampled with individual priors. Each set was run four times with either a strict or an uncorrelated relaxed clock and a coalescent: constant size or coalescent: Bayesian skyline tree prior. SAT29 was given a prior age of 30,000 years BP with a normal distribution, while both BK samples were given a normal distribution prior of 46,000 years BP. BEAST 2.6.0 (Suchard et al., 2018) was run with a 100,000,000 MCMC chain length. The resulting log files were viewed with Tracer v1.7.1 and were checked for ESS above 200. The tree files were annotated with TreeAnnotator v1.10.4 and the resulting annotated trees were viewed with Figtree v1.4.4).
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Post by Admin on Nov 19, 2021 21:41:44 GMT
Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Iberia
Abstract The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA. INTRODUCTION During the last centuries of the third millennium BCE, the societies of Europe, the Near East, and Egypt experienced large-scale social and political upheavals. Settlement abandonment, depopulation, the disappearance of communication networks, and major political disruptions at the end of the Akkadian empire and the Old Kingdom in Egypt have often been interpreted in the light of a climatic crisis, known as the 4.2k event (1–3). Recently, the possibility of substantial population movements, causing social instability during the third millennium BCE, has been proposed as a further explanation for the changes observed at the end of the Copper Age (CA) in central and western Europe (4–7). Signs of social and economic turnover are particularly marked in the southern half of the Iberian Peninsula (8), where the CA is associated with exceptional demographic growth, a diversity of monumental settlements and funerary structures, widespread copper metallurgy, and a sophisticated, large-scale manufacture and exchange of symbolic goods, among others [e.g., (9, 10)]. Moreover, this period is characterized by a diversity of settlement types, including fortified sites, ditched enclosures, and so-called megasites, some of which exceeded 100 ha in size (e.g., Valencina de la Concepción and Marroquíes Bajos) and all of which were formed at around 3300 to 2800 BCE, therefore predating the Bell Beaker horizon. This period is also associated with a major increase in interconnectedness and mobility. On the basis of available radiogenic (Sr) isotope studies, the percentage of southern Iberian individuals who were buried in locations other than where they grew up ranges between 8 and 74% (11, 12). Ivory from Africa and the Near East (13–15), amber from Sicily (16), and ostrich eggshells from Africa (17) are indicative of transregional connections. However, evidence of a strong political centralization and economic inequality remains elusive or inconclusive (18–21). Archaeogenetics has suggested that the remarkable development during the (south) Iberian CA was coupled with a strong population continuity attested since the Neolithic [e.g., (4, 6, 7, 22–27)]. However, the Late CA anthropological and archaeological records from the north and central Iberia show the first individuals carrying “steppe-related ancestry” by ~2400 calibrated (cal) BCE, which are often but not exclusively linked to Bell Beaker–associated artifacts (6, 7). In parallel, African ancestry was also reported in one individual, which suggests discrete movement/mobility of people (7). The beginning of the Bronze Age [Early Bronze Age (EBA)] in Iberia (2200 to 1550 cal BCE) marks a clear population turnover, suggested by both the omnipresence of steppe-related ancestry in all individuals directly postdating 2200 BCE. An even more notable shift can be observed in the frequency of Y-chromosome haplogroups in males, which are almost exclusively of the R1b-P312 type that was completely absent in Iberia before 2400 BCE (6, 7, 25, 26). The turn from Late CA to the EBA at the end of the third millennium BCE saw the demise of fortified settlements such as Los Millares and ditched megasites such as Valencina and Perdigões in southern Iberia, while in the southeast it is concomitant with the rise of new hilltop occupations of smaller sizes (<0.5 ha) (8, 28, 29). Substantial and densely built hilltop settlements, distinguished by a specific intramural burial rite and characteristic ceramic and metal types, appear around 2200 BCE in the fertile tertiary basins framed by mountain ranges, running parallel to the coast of southeastern Iberia (8). This area of circa (c.) 3500 km2 is considered to be the core of the El Argar “culture,” which is one of the most outstanding examples of an early complex society in European prehistory with evidence for social stratification (8, 30, 31). The origins of El Argar are still unclear, as there are no hybrid contexts where El Argar elements appear in Late CA settlements or vice versa. Although the early El Argar material record shares some traits with the Bell Beaker complex (30), such as V-perforated buttons, Palmela-type points, or perforated stone plaques so-called “archers’ wristguards,” the characteristic Bell Beaker pottery is absent. Upon the discovery of the monumental fortification in the 5-ha hilltop settlement of La Bastida, dated to around 2200 BCE, a possible eastern Mediterranean contribution was reconsidered (32). The intramural burials in large storage vessels (pithoi), the circulation of silver rings and bracelets, and the characteristic footed Argar cup have also been interpreted as signs of Aegean or Near Eastern contacts (33), although all these features emerged during later phases of El Argar. The genealogy of different characteristic material traits of early El Argar, such as apsidal buildings, intramural burial, metal casting technology, and the halberds as distinguished weapons, is reminiscent of several social developments in southeastern, central, and western Europe, with possible links of still uncertain origin (31). Between 2000 and 1800/1750 BCE, El Argar expanded across a wider region of southeastern Iberia and entered the central Spanish Meseta. Characteristic El Argar items, such as halberds, are also present beyond this territory. The leading figures within El Argar society seem to have been a class of warriors armed with halberds and daggers. These weapons, occasionally associated with golden arm rings, also became the insignia of political domination in the male elite burials of central Europe around 2000 to 1800 BCE, a time when this specialized weapon had already gone out of use in the rest of Europe (34). At the same time, a growing part of the population, particularly children, was buried in cists, artificial caves, pottery vessels, or pits inside the distinctive settlements of El Argar. During its final phase (1800/1750 to 1550 BCE), El Argar reached an outstanding level of economic and social development. A vast amount of grinding tools, large workshops, and storage facilities found in the larger hilltop settlements (1 to 6 ha) imply that certain groups managed to control the flow of resources and the workforce of wider regions (35). The establishment of a dominant and hereditary class, as well as increasing social asymmetries, become recognizable in the intramural burials, monumental architecture (31, 36), and the spatial relation between both (31, 36, 37). Lull and colleagues (30, 38) have argued that social conflict and environmental degradation resulting from deforestation and extensive dry farming could have led to the abandonment or destruction of all El Argar settlements around 1550 BCE. However, the rise of a similar economic organization, architecture, and funerary record in inner Alicante, as highlighted by Cabezo Redondo, suggests that during the peak of El Argar at least some groups managed to establish themselves in a territory that was influenced by the Valencian BA, a neighboring “cultural group” located in southeastern Iberia. In this study, we aimed to understand the importance of population dynamics in the collapse of the highly dynamic Iberian CA world, the rise and development of El Argar, as well as its relations between neighboring BA groups in western Europe and the Balearic Late BA (LBA). We also explore the genetic makeup of the BA groups in Iberia and the Balearic Islands in relation to the other western and central Mediterranean islands, such as Sardinia and Sicily. In total, we characterize the genomic profiles of 96 BA individuals associated with El Argar and contemporaneous societies, as well as 34 CA and 6 LBA individuals.
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Post by Admin on Nov 20, 2021 4:14:04 GMT
RESULTS Here, we report genome-wide data in the form of 1.24 million ancestry-informative single-nucleotide polymorphisms (SNPs) for 136 southern Iberian individuals, covering a time span of 2000 years from the Late Neolithic (LN)/CA (3300 cal BCE) to the LBA (1200/1000 cal BCE) (Fig. 1, table S1.1, and text S1). Five of these individuals were also shotgun-sequenced to 1.5× to 5.2× coverage to reconstruct the complete genomes to add to the growing record of ancient western Eurasian genomes for future studies. Our new dataset includes various groups and types of sites such as sepulchral caves from the LN/CA (Cova d’en Pardo, n = 7; Cueva de las Lechuzas, n = 10), simple pit burials of pre–Bell Beaker CA megasites [Valencina (PP4-Montelirio), n = 11], a collective hypogeum with Late CA burials (Camino del Molino, n = 6), and EBA pit graves (Molinos de Papel, n = 3) to provide a diverse comparative dataset for the Argaric societies, which are at the center of our study. For the latter, we include the almost complete and archaeologically well-defined sites of La Almoloya (n = 67) and La Bastida (n = 10), alongside Cerro del Morrón (n = 3) and Lorca town [Madres Mercedarias Church (n = 1), Los Tintes (n = 1), and Zapatería (n = 1) sectors]. We also analyzed individuals of the so-called Valencian BA, including Cabezo Redondo (n = 1), Peñón de la Zorra (n = 1), Puntal de los Carniceros (n = 4), and La Horna (n = 3), individuals of the BA from Catalonia (Miquel Vives, n = 1), as well as LBA individuals from the Balearic Islands of Menorca (Es Forat de ses Aritges, n = 6) (Fig. 1, table S1.1, and text S1). Fig. 1. Geographic locations as well as cultural and chronological information of the studied sites.Map of Iberia with sites mentioned in the main text (table S1.1). The area shaded in teal highlights the maximum extent of EBA El Argar. Chronological time scale for published and new individuals analyzed in this study (bottom panel). Directly radiocarbon-dated individuals are plotted according to their mean calibrated date (2-sigma range), and jitter option within their specific time range was applied for individuals that were dated by archaeological context (table S2.1). Random jitter was applied to the Y axis to prevent overplotting. We initially screened 244 individuals for DNA preservation by shotgun sequencing ~5 million Illumina single end reads per partial uracil-DNA glycosylase (UDG)–treated DNA library (39), followed by assessment of % endogenous human DNA (>0.1%), average read length between 40 and 75 base pairs (bp), and characteristic ancient DNA (aDNA) damage patterns >3% (tables S1.1 and S1.2). Libraries fulfilling these criteria were retained for hybridization capture of 1.24 million informative sites (1240k SNP panel) in the human genome (22). Libraries were independently captured for mitochondrial genomes (tables S1.3 and S1.4 and text S2) [(40) modified following (41)] and mappable regions of the Y chromosome (table S1.1 and text S3) (42). Following standard aDNA processing pipelines (43), we quantified contamination rates at the autosomal (in males) (44) and mitochondrial levels (both genetic sexes) (45), showing low contamination estimates for the individuals in this study (<3% for nuclear and <1% for mitochondrial DNA; see Materials and Methods). By determining the genetic sex (46), we observed two cases of sex chromosome aneuploidies, one XXY (Klinefelter) individual and one XXX (trisomy X) individual (table S1.1, text S4, and fig. S1). We obtained endogenous human aDNA contents ranging from 1.3 to 29.5% on the targeted 1240k SNPs, which correspond to 2004 to 831,086 SNP positions covered (tables S1.1 and S1.2). For population genetic analyses, we only retained individuals with more than 40,000 SNPs on the 1240k panel, excluding 18 low-coverage individuals in downstream analyses. We performed kinship analysis (47–49) for all newly typed individuals (fig. S2; tables S1.5, S1.6, and S1.7; and text S5), the result of which will be featured in a separate study. From each pair of first-degree relatives, we then excluded the individual with lower SNP coverage. In summary, for in-depth population genetic analysis, we merged genome-wide data from 122 newly typed individuals with a comparative set of previously published ancient and modern-day individuals, which are reported by the Reich Lab (https://reich.hms.harvard.edu/datasets; please see the Supplementary Materials for a detailed list of references), as well as genotypes from recently published studies (table S2.1) (50–53). Genetic substructure in the Iberian CA We first explored the genetic affinities of the newly typed CA individuals by performing a principal components analysis (PCA) with relevant ancient individuals projected onto PCs calculated from a set of modern-day West Eurasian populations genotyped with the Human Origins (HO) SNP panel (Fig. 2A) (54). The new CA individuals from southern Iberia fall onto a position that partially overlaps with previous Middle Neolithic (MN), Middle/Late Neolithic (MLN), and CA (non-steppe) groups from Iberia but are slightly positively shifted in their coordinates for PC1 toward previously published Early Neolithic (EN) groups from Iberia and later groups such as Sardinia Chalcolithic, suggesting an equally small hunter-gatherer (HG) ancestry contribution in the CA individuals of southern Iberia. These results run counter to previous suggestions of steppe-related ancestry diffusion into southern Iberia in the early CA based on supposed formal similarities in one element of the Valencina material culture (55). To formally test the differential contribution of the main HG source in European Neolithic farmers, called Western HG (WHG), which represents the predominant form of ancestry in prefarming western Europe (4, 56), we calculated f4-statistics of the form f4(SE/SW_Iberia_CA, N/NE/C_Iberia_CA; WHG, Mbuti) and obtained a significantly negative value for N_Iberia_CA and C_Iberia_CA (Fig. 2B and table S2.2), indicative of higher WHG ancestry in these regions, a signal that is also present in the preceding MLN period, as shown by f4-statistics of the form f4(SE/SW_Iberia_MLN, N_Iberia_MLN; WHG, Mbuti) (table S2.2).
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Post by Admin on Nov 20, 2021 20:13:44 GMT
Fig. 2. Key population genetic analyses of CA groups.(A) PCA of published and newly genotyped CA groups projected onto 2018 modern-day West Eurasians (gray dots). Ancient individuals projected and their correspondent labels are listed in table S2.1. (B) f4-statistics showing significant differences in terms of WHG ancestry in northern and southern CA groups (error bars indicate 3 standard errors) (table S2.2 also includes the results for MLN groups). (C) f4-statistics highlighting the higher affinity of southern CA Iberian groups to GoyetQ2 (error bars indicate 3 standard errors) (table S2.3). (D) Modeling Iberian MLN and CA without steppe-related ancestry with a three-way qpAdm admixture model using distal sources Anatolia_N, WHG, and GoyetQ2. Southern MLN and CA Iberian groups show an extra minor ancestry component represented by GoyetQ2 (error bars indicate 1 standard error; numbers in brackets are P values for qpAdm model) (table S2.4). Leveraging insights from previous studies about the differential HG legacy in western Europe (7, 57–59), we explored the HG ancestry of geographically diverse CA Iberians in different ways. We first calculated f4-statistics of the form f4(GoyetQ2, WHG; test, Mbuti), where test represents all MLN and CA groups (Fig. 2C and table S2.3). Despite the resulting f4-values being significantly negative for all test groups (indicating WHG admixture), we observed a geographically related gradient with southern groups (MLN and CA) showing lower negative values, indicating a differential relationship with GoyetQ2, who acts as a proxy for Magdalenian-related ancestry (Fig. 2C). We confirmed this subtle signal using qpAdm outgroup-based ancestry modeling with Anatolia_Neolithic, WHG (Loschbour and KO1), EHG [Eastern European HGs; the predominant form of ancestry in pre-agropastoralist eastern Europe; (4)], and GoyetQ2 as distal sources (table S2.4). Here, we found that the CA groups from southern Iberia differ with respect to the overall quantity of HG ancestry, but the latter is also qualitatively different. Estimates of Magdalenian-associated HG ancestry in southern Iberian CA individuals vary from 6.1 ± 1.3% to 7.2 ± 1.3%, which reflects the geographic structure of local HG groups (7, 57) and suggests a certain amount of genetic continuity since the Neolithic (Fig. 2D and table S2.4). In the case of SE_Iberia_CA, adding GoyetQ2 as a third source improves the model fit slightly from P = 2.53 × 10−6 to P = 0.008. Adding Iran_N or Jordan_PPNB as a fourth source (Anatolia, WHG, GoyetQ2, and Iran_N/Jordan_PPNB) further improves the model fit for SE_Iberia_CA by an order of magnitude, i.e., from P = 0.008 to P = 0.014 (with Iran_N) or P = 0.027 (with Jordan_PPNB) (table S2.4, text S7, and fig. S3). In turn, adding other populations as a fourth source does not improve the model fit (text S7). The unknown source contributing to SE_Iberia_CA groups is likely to have carried an excess of Levantine and/or Iran_N-like ancestries compared to the distal source Anatolia_Neolithic, as these together have been found admixed in Anatolian and Levantine CA groups (~6000 to 5000 BCE) (53). This finding suggests a subtle contribution that was spread early along the Mediterranean or, alternatively, different sources of early farmer ancestry during the Neolithic transition with varying proportions of Levantine and/or Iran_N-like components when compared to Anatolia_N used here. Removing Anatolian HG (AHG) from the outgroups also improves the model fit (P = 0.045; table S2.4), indicating that the Neolithic ancestry is not well represented by using Anatolia_N as a distal proxy and might come from another farmer group more similar to AHG than Anatolia_N (text S7). More individuals from the Neolithic and CA across the Mediterranean will be needed to track this contribution more confidently. The Magdalenian-related ancestry was not detectable in other contemporaneous Mediterranean populations (e.g., Sardinia_Neolithic, Sardinia_Chalcolithic, Sardinia_EBA, Sicily_EBA, and Italy_CA), which renders gene flow in the direction from southern Iberia to the central Mediterranean less plausible. However, applying the same qpAdm model (text S7, fig. S3, and table S2.5), we detect a previously unreported amount of Iran_N-like ancestry in central Mediterranean groups from Sardinia, ranging from 2.8 ± 1.2% in Sardinia_Chalcolithic to 5.8 ± 1% in Sardinia_Nuragic_BA. Adding Iran_N as a source to model Sicily_EBA improves the model fit but without reaching P values ≥0.05, making gene flow from the Italian Peninsula to Sardinia more likely (Italy_CA also shows Iran_N-like ancestry) than from Sicily (Sicily_EBA) (text S7, fig. S3, and table S2.5). Notably, when modeling Sicily_EBA, we obtain P values ≥0.05 by removing AHG from the outgroups in a three-source model (Anatolia_Neolithic, WHG, and Yamnaya_Samara) or by removing Morocco_Iberomaurusian in a four-source model (Anatolia_Neolithic, WHG, Yamnaya_Samara, and Iran_N), which points to genetic substructure in the Mediterranean before the arrival of steppe-related ancestry. However, this finding does not rule out limited genetic input from other Mediterranean populations to southeastern CA Iberians (text S7).
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Post by Admin on Nov 21, 2021 2:18:18 GMT
Fig. 3. Evidence for steppe-related ancestry in EBA individuals from southeastern Iberia.(A) West Eurasian PCA calculated with modern populations (gray dots) (23) on which relevant ancient CA, Bell Beaker and BA groups discussed in the text were projected (correspondent labels are listed in table S2.1).(B) f4-statistics showing the increased affinity to Yamnaya_Samara (absent in CA individuals), which implies the presence of steppe-related ancestry in EBA Iberians. This plot also shows the almost-complete turnover in Y-chromosome lineages in male individuals (color-filled squares) during the southeastern Iberian EBA (error bars indicate 3 standard errors) (table S2.6). This observation suggests a substantial amount of steppe-related ancestry in El Argar BA individuals, which we tested formally and directly with f4-statistics of the form f4(Argar_Iberia_BA/SE_Iberia_BA, SE_Iberia_CA; Yamnaya_Samara, Mbuti) (fig. S5A and table S2.7). Significantly positive f4-values confirmed the presence of steppe-related ancestry in all BA individuals. We then tested for differences in affinity to steppe-related ancestry by contrasting northern versus southern BA individuals using f4(N/NE/C_Iberia_BA, Argar_Iberia_BA/SE_Iberia_BA; Yamnaya_Samara, Mbuti) (fig. S5B and table S2.8). The resulting f4-values confirmed a smaller amount of steppe-related ancestry in individuals from the Argaric sites La Almoloya and La Bastida compared to the rest of Iberia_BA groups, especially when compared to those from northern Iberia (fig. S5B and table S2.8), despite the complete turnover to lineage R1b-P312 (except for one subadult male in La Bastida) visible in the Y-chromosome record (Fig. 3B, table S2.6, and text S8). However, at the intrasite level, we observe no significant differences with respect to the amount of steppe-related ancestry between the early and late phase of La Almoloya and La Bastida based on PCA and formal f4-statistics (Fig. 3A and fig. S5), which suggests that the contribution is homogenized across the population. The newly analyzed LBA individuals from the Balearic Islands (Aritges_LBA) showed less steppe-related ancestry than the published Late CA individual from Mallorca (previously named Mallorca_EBA), confirming a decrease of steppe-related ancestry over time in agreement with (51). The amount of steppe-related ancestry in Mallorca_CA_Stp is similar to the first CA groups in Iberia (C_Iberia_CA_Stp and NW_Iberia_CA_Stp) (fig. S5A) and could have arrived at the same time, as there is no clear evidence of human occupation in the archipelago before their arrival (61, 62). Olalde and colleagues (7) had proposed for the Iberian Peninsula that the first contribution of steppe-related ancestry was diluted during the BA by admixture with descendants of local CA groups, but increased again during the LBA–Iron Age during a second pulse. We do not detect this second pulse in the Balearic Islands, in agreement with the findings of (51), albeit based on one LBA individual from Menorca (fig. S5, A and B). The situation observed in southern Iberia offers a specific example of the demographic changes occurring during the transition from CA to EBA societies around 2200 BCE. The absence of steppe-related ancestry in our newly typed individuals from the Early CA at Valencina (c. 2900 to 2800 BCE) and the Late CA collective burial cave Camino del Molino, which is contemporaneous with the Beaker Horizon (albeit without Beaker pottery) and the first appearance of steppe-related ancestry in a double tomb with Bell Beaker–associated artifacts at Molinos de Papel, a site only 400 m away from the latter, provides the temporal framework for the arrival of steppe-related ancestry in southern Iberia. Taking the youngest date from Camino del Molino [Beta-261524, 3830 ± 40 years before present (BP)] and the oldest from Molinos de Papel (MAMS-11826, 3780 ± 30 BP) as reference points, we can show that both C14 dates overlap at the 95% level and date the arrival of steppe-related ancestry in southeastern Iberia to ~2200 cal BCE. At a cross-regional scale, none of the south Iberian CA individuals analyzed so far show evidence of any steppe-related ancestry, whereas the oldest individuals from the El Argar sites of La Bastida (BAS024 and BAS025) and La Almoloya (ALM019), directly dated to the 21st century BCE based on the radiocarbon evidence, show clear evidence of such ancestry. Consequently, the population mixture must have occurred in the preceding 150 years at the latest. Estimating the time of admixture of the putative sources using the program DATES (Distribution of Ancestry Tracts of Evolutionary Signals; github.com/priyamoorjani/DATES) produced compatible admixture dates in all new BA groups, ranging from ~2550 BCE ± 189 years to ~1642 BCE ± 133 years (table S2.9 and text S8). This could have occurred after the collapse of the CA social system in some aggregation megasites such as Valencina at around 2350 BCE (63) and more or less contemporary in others, such as Los Millares at around 2300/2200 BCE (64). The demise of CA cultures ~2350 to 2200 cal BCE has been linked to the so-called 4.2–thousand year cal BP climatic event, as there is a temporal overlap between this event and the collapse of large megasites (63, 65–68), although direct, conclusive, paleoclimatic evidence for Iberia remains sparse (8, 69). The social and economic changes that lead into the BA, as well as the arrival of the new genetic ancestry, appear to have spread from North to South Iberia (7, 70) and thus might be linked. However, it remains unclear whether this expansion was opportunistic (i.e., followed the consequences of a potential climatic deterioration) or causal to the actual shifts observed in archaeology. Notably, the arrival of new genetic ancestry is not paralleled by the same social changes in all regions of Iberia. In the coastal regions of southeastern Iberia, the shift to single or double burial practices inside settlements occurred ~2200 BCE, coinciding with the beginning of El Argar. However, in inner Iberia, the associated grave goods and settlement pottery are more related to late Bell Beaker CA (leaf-shaped tanged point, V-perforated button, and incised Beaker pottery) than to the material culture of the early El Argar “core” territory (8). In La Mancha, the southern part of the central Spanish plateau, the first individual with a confirmed steppe-ancestry component (7), a male from tomb 4 of Castillejo del Bonete dated to ~2100 BCE, coincides with the foundation of monumental settlements, such as Las Motillas fortifications. This shows that while the genetic contribution of steppe-related ancestry to Iberia was a long-term process starting around 2400 cal BCE in the northern and central regions (7), from where it spread southward over ~300 years. At a local scale, this change might have occurred faster. A similar situation might have existed in central Portugal, where we still find individuals with no steppe-related ancestry in collective CA burials (Galería da Cisterna and Cova da Moura) around 2300 to 2200 cal BCE. However, after 2100 cal BCE, all individuals from all sites carry steppe-related ancestry, in line with R1b-P312 becoming the predominant Y-chromosomal lineage present not only in El Argar but also in the rest of BA Iberia.
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