Ancient DNA reveals diverse community organizations in the 5th millennium BCE Carpathian Basin

Introduction

The geographical position of the Carpathian Basin makes it a crossroads between South-East and Central Europe. The fertile river valleys of the Danube and its tributaries offered optimal conditions for settlement and facilitated the development of efficient transport and communication networks for early farming communities. Since the advent of the field of aDNA research, the prehistoric populations of the Carpathian Basin have been the subject of intensive study, primarily due to the critical role they played in the Neolithisation of Central Europe^1,2. The population genetic history of the Neolithic (6000–4500 calibrated BCE) of the Carpathian Basin is well-established^{3, 4, 5–6}. However, the subsequent Copper Age (4500–2800 cal BCE) is underrepresented in the available genetic data^{4,7, 8, 9–10}.

The Copper Age is characterized by the spread of significant technological innovations, including metallurgy^11,12 and the wheel and wagon^13,14, which profoundly impacted the later history of Europe. This period is thought to coincide with the emergence of salient social ranking and craft specialization^15,16.

During the Late Neolithic (4900–4500 cal BCE), tells and large horizontal settlements were established in the Carpathian Basin¹⁷, with some covering an area of up to 60-80 hectares (ha). These sites were distinguished by a concentration of population^{18, 19–20}. The number of inhabitants of the Late Neolithic settlements has been estimated to be several thousand based on the number of excavated buildings and burials^19,21. The use of these extensive settlements terminated by the end of this period, between 4500 and 4450 cal BCE²². Profound transformations were observed on the Great Hungarian Plain (GHP), affecting all segments of life. At the beginning of the Copper Age, in contrast to the large horizontal Late Neolithic settlements, a dense network of small, farm-like settlements emerged across the GHP^23,24. During the Late Neolithic, the deceased were buried within the settlement boundaries or through rites that left no archaeologically visible traces²⁵. However, in the Early Copper Age, from 4400−4350 cal BCE, formal cemeteries – the first in the Carpathian Basin – that were spatially separated from the settlements – appeared²². Meanwhile, the practice of settlement burials persisted^26,27, with even Late Neolithic tells being repurposed for burial...