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Abstract
Ancient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age transformed the social and genetic structure of European societies. Present-day Croatia lies at the heart of ancient migration routes through Europe, yet our knowledge about social and genetic processes here remains sparse. To shed light on these questions, we report new whole-genome data for 28 individuals dated to between ~ 4700 BCE–400 CE from two sites in present-day eastern Croatia. In the Middle Neolithic we evidence first cousin mating practices and strong genetic continuity from the Early Neolithic. In the Middle Bronze Age community that we studied, we find multiple closely related males suggesting a patrilocal social organisation. We also find in that community an unexpected genetic ancestry profile distinct from individuals found at contemporaneous sites in the region, due to the addition of hunter-gatherer-related ancestry. These findings support archaeological evidence for contacts with communities further north in the Carpathian Basin. Finally, an individual dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding an important data point to the substantial shift in ancestry that occurred in the region between the Bronze Age and today.
Genetic transformations from the Neolithic to Roman times
In order to understand the genetic affinities of the samples, we performed principal components analysis (PCA) (Methods) by projecting the new shotgun data and published ancient datasets onto the first two principal components constructed from 920 individuals selected from contemporary West Eurasian populations in the Human Origins (HO) dataset30 (Methods, Fig. 2). We also performed model-based clustering analysis in an unsupervised mode with ADMIXTURE (Methods) using 1311 present-day individuals taken from a panel of worldwide populations (Supplementary Fig. S2).
The newly-reported individuals fall along the European cline in PCA space, extending between Neolithic agriculturalist and Bronze Age pastoralist populations. Croatia_Pop_MN clusters tightly with other southeast and central European Neolithic and Copper Age individuals, including Copper Age Croatians from Radovanci and Vučedol, who were merged for further analysis into Croatia_North-East_CA, and share similar ADMIXTURE profiles that exhibit a major contribution from Anatolia-related ancestry (Anatolia_N) and a small contribution of Western European hunter-gatherer (WHG)-related ancestry (Supplementary Fig. S2). We also merged Croatia_Pop_MN and Croatia_Osijek_MN to form Croatia_North-East_MN for further analysis, before testing shared drift with other ancient and modern West Eurasian populations with outgroup f3-statistics of the form f3(Croatia_North-East_MN, Test; Mbuti.DG) (Supplementary Fig. S3a-b, Supplementary Table S3, Methods). This group shares most genetic drift with other Neolithic populations from the Balkans and Central Europe, and present-day Sardinians. We then quantified admixture proportions with qpAdm using distal sources of WHG and Anatolia_N to represent Mesolithic hunter-gatherer and Anatolian Neolithic farmer ancestries that are known to have contributed to European genomic diversity (Methods). We were able to model Croatia_North-East_MN as a mixture of 2.4 ± 1% WHG and 97.6 ± 1% Anatolia_N, and even a 100% Anatolia_N model fits the data (p = 0.11), which is congruent with previous studies that show very low WHG introgression in the Balkans and Hungarian Neolithic3,31 (Fig. 3a, Supplementary Fig. S4, Supplementary Table S4). Using Iron Gates hunter-gatherers (Iron_Gates_HG) instead of WHG produced very similar results (Supplementary Table S4). Using DATES (Methods), we estimated the timing of this admixture to between 19 and 42 generations before the contextual date of the samples (Supplementary Fig. S5, Supplementary Table S5, Methods), corresponding to the Early Neolithic. This further supports population continuity during the Middle Neolithic, in contrast to Middle Neolithic populations from central and Western Europe which show additional WHG gene flow during this time31.[/QUOTE]
We grouped the new Copper Age individual, POP39, with a previously published cladal individual, I3499 (Supplementary Table S2, Supplementary Table S6), who originates from the same site and time period (Croatia_Pop_CA). This group is shifted further up along PC2 and clusters with three previously reported Bronze Age samples from coastal Dalmatia (Croatia_Dal_BA), falling within the wide distribution of Bulgarian and Hungarian Bronze Age genomes and present-day southern Europeans in PCA space (Fig. 2) suggesting the presence of steppe-related ancestry. Indeed, distal admixture modelling with qpAdm estimates a contribution of 71 ± 8% from Anatolia_N and a further 29 ± 8% from Yamnaya_Samara, representing steppe-related ancestry absent in the Neolithic but found widely among Eurasian Copper and Bronze Age populations. (Fig. 3a, Supplementary Fig. S4, Supplementary Fig. S6, Supplementary Table S4). We obtained a feasible two-way admixture model with the more proximal, broadly contemporaneous pre-steppe group Croatia_North-East_CA (64 ± 8%) and Yamnaya_Samara (36 ± 8%) (Fig. 3b, Supplementary Table S4).
We considered the newly-reported Middle Bronze Age genomes from Jagodnjak (Croatia_Jag_MBA) a single group for further population genetic analysis based on common archaeological context and clustering on the PCA (Fig. 2). We observe a marked shift left along PC1 towards Western and Iron Gates hunter-gatherers, with which it shares the most drift in outgroup f3-statistics (Supplementary Fig. S3, Supplementary Table S3). Distal admixture modelling using sources WHG, Anatolia_N and Yamnaya_Samara confirms a large WHG component in Croatia_Jag_MBA (20 ± 2%), in contrast to Croatia_Pop_CA, and is more than double the fraction estimated for the broadly contemporaneous Dalmatian Bronze Age (Fig. 3a, Supplementary Fig. S4, Supplementary Table S4), also consistent with the significantly positive F4 tests of the form f4(Mbuti.DG, WHG; Croatia_Dal_BA, Croatia_Jag_MBA) (Z = 6.95) (Supplementary Table S7). The Jagodnjak group also harbours slightly greater steppe-related ancestry compared to the preceding Croatia_Pop_CA at 33 ± 5% (see also Supplementary Fig. S6), consistent with previous findings for the Balkan region2. Replacing WHG with Iron_Gates_HG harbours comparable results (Supplementary Table S4). This group falls at the left side of the wide distribution of Bronze Age populations from the Carpathian Basin in PCA space, as well as present-day NW European genomes such as French, suggesting an eastward expansion of the Western Bronze Age signature.
Genetic transformation following the Bronze Age
Neither the Jagodnjak nor the Dalmatian Bronze Age groups approximate present-day populations from the region in PCA space, indicating that further significant population changes have since occurred. Our single individual from Popova zemlja, Croatia_Pop_RomanP, provides rare genomic data for Croatia after the Bronze Age33. (Table 1, Fig. 4a, Supplementary Table S1). We find this individual clustering with present-day populations of Croatia, Bulgaria and Romania in PCA and UMAP space (Figs. 2, 3c).We investigated this clustering with f4-statistics and could confirm cladality of this individual with present-day Croatians compared to other ancient and present-day populations in Europe (Supplementary Table S7). We then tested population continuity with qpWave, and found Croatia_RomanP was consistent with forming a genetic clade with present-day Croatians, as well as Bulgarians or Hungarians (p = 0.78 respectively) (Supplementary Table S4). Although based on a single individual who may or may not be representative for the wider population in that time period, this data point indicates that a broadly present-day genetic signature had already formed by Roman times, and any further population turnovers were not as significant as previous ones.
https://www.nature.com/articles/s41598-021-94932-9