Ancient human genomes suggest three ancestral populations for present-day Europeans (1312.6639v2)

Abstract: We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.

• The paper identifies West European Hunter-Gatherers (WHG), Ancient North Eurasians (ANE), and Early European Farmers (EEF) as the three key ancestral groups for modern Europeans.
• It employs advanced genome sequencing alongside PCA, ADMIXTURE, and f-statistics to uncover migration and admixture events in prehistoric Europe.
• The findings highlight complex gene flow patterns, showing significant links between Neolithic farmers and Upper Paleolithic Siberians.

Analysis of Ancient Genomes Suggests Three Ancestral Populations in Present-Day Europeans

The paper 'Ancient human genomes suggest three ancestral populations for present-day Europeans' presents an insightful exploration into the genetic history of Europe through the analysis of ancient DNA. By examining genomes from ancient humans, this research identifies three principally differentiated ancestral populations contributing to the genetic makeup of contemporary Europeans: West European Hunter-Gatherers (WHG), Ancient North Eurasians (ANE), and Early European Farmers (EEF). The paper provides detailed evidence for migration events and population mixtures, offering nuanced insights into European prehistory.

Methodological Approach

The researchers utilized a comprehensive dataset, including newly sequenced genomes from nine ancient samples, supplemented by comparative analysis with previously reported ancient genomes and 2,345 present-day individuals genotyped at 594,924 autosomal SNPs. Notably, the ancient genomes included a ~7,000-year-old early farmer from Stuttgart, an ~8,000-year-old hunter-gatherer from Luxembourg, and seven ~8,000-year-old hunter-gatherers from southern Sweden. This dataset enabled the researchers to explore genetic discontinuities between ancient and contemporary populations, with advanced statistical models facilitating the inference of genetic admixture events.

Key Findings

1. Three Ancestral Populations: Ancestral genetic contributions to Europeans were derived from:
   • West European Hunter-Gatherers (WHG): Contributed to all Europeans but not Near Easterners.
   • Ancient North Eurasians (ANE): Notably associated with both Europeans and Near Easterners.
   • Early European Farmers (EEF): Predominantly of Near Eastern origin but also harboring WHG ancestry.
2. Migration and Genetic Admixture: The paper confirms the significant role of migration and admixture in shaping European genomes. The Stuttgart individual, representative of EEF, illustrates genetic connections with Neolithic people of Near Eastern origin, exhibiting a mix of WHG and "Basal Eurasian" lineages. The presence of ANE-related genetic components in Europe, distinct yet connected to populations such as the Upper Paleolithic Siberians, suggests prehistoric gene flow across vast geographical areas.
3. Mitochondrial and Y Chromosome Analysis: WHG individuals predominantly possessed mtDNA haplogroups U5 and U2, while EEFs were characterized by haplogroup T2. Most male samples carried Y-chromosome haplogroup I, widespread in pre-agricultural Europeans but less common today.
4. Ancestral Admixture and Population Structure: The researchers employed PCA, ADMIXTURE analyses, and f-statistics to interpret genetic relationships, identifying at least three source populations necessary to explain the genetic data from present-day Europeans. This underscores the complexity of population structures and suggests varying degrees of mixture beyond simple dichotomous models.

Implications for Understanding European Genetic History

The genetic diversity discovered in this paper elucidates the mosaic nature of present-day European ancestry. The research highlights the possibility of ancient population dynamics influencing genetic variance seen today, offering new avenues for studying how ancient migrations and adaptive processes shaped genetic landscapes.

Future Directions

The findings pave the way for future genetic studies to refine our understanding of human migrations and demographic patterns. Further sequencing of additional ancient genomes will likely enhance the clarity of genetic population history, allowing researchers to trace specific events contributing to the present genetic constitution of Europe.

Overall, this paper represents a significant contribution to the field of anthropological genetics, offering a detailed genetic narrative of European ancestry and prehistoric human adaptation.