100 ancient genomes show repeated population turnovers in Neolithic Denmark

Ancient DNA HLA typing reveals significant shifts in frequency in Europe since the Neolithic

Computational HLA typing has surged as a cost-effective strategy to uncover questions regarding the evolution of the HLA system, enabling immunogenic characterization from ancient DNA (aDNA) data. Nevertheless, it remains to be seen whether these methods are suitable for analyzing aDNA generated without target-enrichment. To investigate this, we evaluated the performance of five HLA typing tools using present-day data with simulated profiles typical of aDNA, as well as from high-coverage aDNA genomes downsampled at different read depths. We found that characterization of Class I genes at the first field resolution is feasible at read depths as low as 2x, where it retains an accuracy of ≈ 80%. Next, we used this insight to characterize HLA evolution in Europe from 154 ancient genomes by detecting allele frequency changes throughout distinct prehistoric European populations. We observed important shifts in alleles associated with infectious and autoimmune diseases, most of which are found by contrasting the HLA landscape of Neolithic Farmers to that of present-day. Interestingly, several of these observations are in line with findings that have been previously reported by target-enrichment-based studies. Our results highlight the feasibility of applying HLA typing on shotgun aDNA data to examine the evolution of this loci during important transitions.

Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana

Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift, environmental change (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections of Arabidopsis thaliana and combined these with published genomes. We sought a broader view of genomic diversity across the species, and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterized diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.

Estimating effective population size trajectories from time-series identity-by-descent segments

Long, identical haplotypes shared between pairs of individuals, known as identity-by-descent (IBD) segments, result from recently shared co-ancestry. Various methods have been developed to utilize IBD sharing for demographic inference in contemporary DNA data. Recent methodological advances have extended the screening for IBD segments to ancient DNA (aDNA) data, making demographic inference based on IBD also possible for aDNA. However, aDNA data typically have varying sampling times, but most demographic inference methods for modern data assume that sampling is contemporaneous. Here, we present Ttne (Time-Transect Ne), which models time-transect sampling to infer recent effective population size trajectories. Using simulations, we show that utilizing IBD sharing in time series increased resolution to infer recent fluctuations in effective population sizes compared with methods that only use contemporaneous samples. To account for IBD detection errors common in empirical analyses, we implemented an approach to estimate and model IBD detection errors. Finally, we applied Ttne to two aDNA time transects: individuals associated with the Copper Age Corded Ware Culture and Medieval England. In both cases, we found evidence of a growing population, a signal consistent with archaeological records.

Subsistence and population development from the Middle Neolithic B (2800-2350 BCE) to the Late Neolithic (2350-1700 BCE) in Southern Scandinavia

The present study aims to explore the hypothesis of a link between a population increase derived from intensified food production and the development from the widespread cultural diversity of the Middle Neolithic B (MNB) to the cultural unity towards the end of the Late Neolithic (LN) in Southern Scandinavia. We explore this through quantitative modelling of radiocarbon dates, aoristic time series of material culture and palynological data. On this basis, we propose three main results that may explain the transformation: (1) A supra-regional population increase, culminating in the middle of the LN (c. 2100 BCE). (2) A depopulation in Western Jutland at the transition from the MNB to the LN (c. 2400-2300 BCE) counterbalanced by a population increase in North and East Denmark. (3) A population boom in Southern Sweden around 2250-2000 BCE, possibly leading to migrations towards west. Furthermore, we propose an overall decline in population in the final LN (c. 1850 BCE).

Interbreeding between farmers and hunter-gatherers along the inland and Mediterranean routes of Neolithic spread in Europe

The Neolithic (i.e., farming and stockbreeding) spread from the Near East across Europe since about 9000 years before the common era (BCE) until about 4000 yr BCE. It followed two main routes, namely a sea route along the northern Mediterranean coast and an inland one across the Balkans and central Europe. It is known that the dispersive behavior of farmers depended on geography, with longer movements along the Mediterranean coast than along the inland route. In sharp contrast, here we show that for both routes the percentage of farmers who interbred with hunter-gatherers and/or acculturated one of them was strikingly the same (about 3.6%). Therefore, whereas the dispersive behavior depended on the proximity to the Mediterranean sea, the interaction behavior (incorporation of hunter-gatherers) did not depend on geographical constraints but only on the transition in the subsistence economy (from hunting and gathering to farming) and its associated way of life. These conclusions are reached by analyzing the clines of haplogroup K, which was virtually absent in hunter-gatherers and the most frequent mitochondrial haplogroup in early farmers. Similarly, the most frequent Y-chromosome Neolithic haplogroup (G2a) displays an inland cline that agrees with the percentage of interbreeding reported above.

Deep antiquity of seagrasses supporting European eel fisheries in the western Baltic

Protecting ocean habitats is critical for international efforts to mitigate climate impacts and ensure food security, but the ecological data upon which policy makers base conservation and restoration targets often reflect ecosystems that have already been deeply impacted by anthropogenic change. The archaeological record is a biomolecular archive offering a temporal scope that cannot be gathered from historical records or contemporary fieldwork. Insights from biogeochemical and osteometric analyses of fish bones, combined with context from contemporary field studies, show how prehistoric fisheries in the western Baltic relied on seagrass meadows. European eels (Anguilla anguilla) harvested by Mesolithic and Neolithic peoples over millennia showed a strong fidelity for eelgrass foraging habitats, an ecological relationship that remains largely overlooked today, demonstrating the value of protecting these habitats. These data open new windows onto ecosystem- and species-level behaviours, highlighting the need for wider incorporation of archaeological data in strategies for protecting our oceans.

The Role of Selection and Migration in the Evolution of (Auto)Immunity Genes

The genetic architecture of multiple sclerosis is complicated. Additionally, the disease incidence varies per population or per geographical region. A recent study gives convincing explanations about the north-south incidence gradient of multiple sclerosis in Europe, by analyzing ancient and modern human genomes. Interestingly, the evidence shows that multiple sclerosis associated immunogenetic variants underwent positive selection in Asian and European populations. Lifestyle and pathogen infections probably shaped the overall multiple sclerosis risk. These results complete the findings of previous studies that showed that a high percentage of the autoimmunity associated genetic variants are under selection pressure.

Late Neolithic collective burial reveals admixture dynamics during the third millennium BCE and the shaping of the European genome

The third millennium BCE was a pivotal period of profound cultural and genomic transformations in Europe associated with migrations from the Pontic-Caspian steppe, which shaped the ancestry patterns in the present-day European genome. We performed a high-resolution whole-genome analysis including haplotype phasing of seven individuals of a collective burial from ~2500 cal BCE and of a Bell Beaker individual from ~2300 cal BCE in the Paris Basin in France. The collective burial revealed the arrival in real time of steppe ancestry in France. We reconstructed the genome of an unsampled individual through its relatives' genomes, enabling us to shed light on the early-stage admixture patterns, dynamics, and propagation of steppe ancestry in Late Neolithic Europe. We identified two major Neolithic/steppe-related ancestry admixture pulses around 3000/2900 BCE and 2600 BCE. These pulses suggest different population expansion dynamics with striking links to the Corded Ware and Bell Beaker cultural complexes.

Population genomics of post-glacial western Eurasia

Western Eurasia witnessed several large-scale human migrations during the Holocene1-5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.