The population genomics of archaeological transition in west Iberia: investigation of ancient substructure using imputation and haplotype-based methods

We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200–3500 BC) to the Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cult...本研究分析了来自葡萄牙14具古代个体的基因组数据（genomic data），测序深度为0.05–2.95×，年代跨度从中新石器时代（Middle Neolithic，公元前4200–3500年）至中青铜时代（Middle Bronze Age，公元前1740–1430年）；并结合已发表的古代欧亚人群基因组数据，对这批样本与已发表样本共同开展全基因组二倍体基因型（genomewide diploid genotypes）推断。尽管该区域向农业转型过程中存在明显的遗传不连续性，但基于单倍型的高灵敏度分析显示，当地狩猎采集者对后期伊比利亚新石器时代人群存在显著的遗传贡献。青铜时代还存在更为隐蔽的遗传流入事件，可通过多项分析得以检测：包括与古代及现代基因组的单倍型共享（haplotype sharing）、D统计量（D-statistics）分析以及Y染色体谱系（Y-chromosome lineages）分析。不过，这种基因渐渗（introgression）的规模有限，与公元前第三个千年北欧地区大规模的草原移民所导致的人群更替形成鲜明对比，却与伊比利亚地区非印欧语系语言（non-Indo-European language）的存续情况相呼应。欧洲人群个体身高的基因组预测值变化，也与这些重大文化……相关。