The selection landscape and genetic legacy of ancient Eurasians

The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer’s disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans

The first horse herders and the impact of early Bronze Age steppe expansions into Asia.

The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia

Population genomics of the Viking world.

The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent

The origins and spread of domestic horses from the Western Eurasian steppes

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: All collapsed and paired-end sequence data for samples sequenced in this study are available in compressed fastq format through the European Nucleotide Archive under accession number PRJEB44430, together with rescaled and trimmed bam sequence alignments against both the nuclear and mitochondrial horse reference genomes. Previously published ancient data used in this study are available under accession numbers PRJEB7537, PRJEB10098, PRJEB10854, PRJEB22390 and PRJEB31613, and detailed in Supplementary Table 1. The genomes of ten modern horses, publicly available, were also accessed as indicated in their corresponding original publications57,61,85-87.NOTE: see the published version available via the DOI in this record for the full list of authorsDomestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 BC. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture

The Beaker phenomenon and the genomic transformation of northwest Europe

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries

Dating of Prehistoric Burial Mounds by 14C Analysis of Soil Organic Matter Fractions

Dating of prehistoric anthropogenic earthworks requires either excavation for archaeological artifacts or macroscopic organic matter suitable for 14C analysis. Yet, the former, in many cases, is undesirable and the latter is difficult to obtain. Here we present a soil science procedure, which has the potential to overcome these problems. It includes careful sampling of buried former soil surfaces, acid-alkali-acid fractionation of soil organic matter (SOM), and subsequent 14C AMS dating. To test the procedure, soil from one of the largest known burial mounds in Scandinavia, Hohoj, and 9 other Danish burial mounds were sampled. The 14C dates from extracted SOM fractions were compared to reference ages obtained by other methods. We show that humic acid fractions in 7 of the 10 mounds had the same age as the reference, or were, at maximum, 280 yr older than the reference ages. The best age estimates were derived from an organic-rich layer from the upper cm of buried soil or sod. Differences among SOM fraction ages probably indicate the reliability of the dating. Hohoj dated to approximately 1400 BC and, thus, was up to 500 yr older than other dated Scandinavian mounds of comparable size. The remaining investigated burial mounds were dated to between 1700 and 1250 BC. We conclude that combined sampling of buried soil surfaces, SOM fractionation, and 14C analysis allows for dating of archaeological earthworks when minimal disturbance is required, or if no macroscopic organic remains are found.The Radiocarbon archives are made available by Radiocarbon and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform February 202

Genesis of spodic material underneath peat bogs in a Danish wetland

9 pages, 5 figures, 3 tables, 41 references.The chemistry of wet Spodosols (Aquods) differs from well-drained Spodosols. Two different hypotheses have been suggested to explain the contrasting genesis of wet spodic horizons. This study attempted to determine whether Aquods at a Danish peat-bog wetland site are a result of (i) in situ illuviation under a fluctuating water table, or (ii) degradation of a former Fe-rich, well-drained spodic horizon. Methods included soil surveys, wet chemical analyses, micromorphology, pollen analysis, and radiocarbon dating of soil organic matter (OM) fractions. Aquods, and soil material with spodic features, were exclusively found in sandy material at the margins of or underneath sphagnum peat bogs, whereas Inceptisols were found on well-drained sandy deposits only. Aluminum content was very high and Fe low in spodic materials with ortstein properties. Solid-state 13C nuclear magnetic resonance (NMR) spectra of wet sandy 2Bs horizons were dominated by alkyl C (70%) from water-insoluble OM and were clearly distinct from NMR spectra of overlying 2Bhsm material. Pollen analysis revealed that an open forest with a thick mor layer dominated until shortly after 5000 yr BP, when sphagnum was first recorded. Radiocarbon ages of bulk soil C in the spodic horizons had mean residence times of 4500 to 4400 yr. Accordingly, the spodic B horizon was probably formed by strong in situ illuviation of Al-OM complexes before the sphagnum peat bog formation. This suggests that spodic material formation and thus strong C accumulation underneath this Danish peat bog took place for a limited period, only in susceptible parent material, and at the margins of the expanding peat bogThe financial support from The Danish Veterinary and Agricultural Research Council is acknowledged.Peer Reviewe