Patterns of genetic connectedness between modern and medieval Estonian genomes reveal the origins of a major ancestry component of the Finnish population

Kivisild, Toomas; Saag, Lehti; Hui, Ruoyun; Biagini, Simone Andrea; Pankratov, Vasili; D’Atanasio, Eugenia; Pagani, Luca; Rootsi, Siiri; Mägi, Reedik; Metspalu, Ene; Valk, Heiki; Malve, Martin; Irdt, Kadri; Reisberg, Tuuli; Solnik, Anu; Scheib, Christiana L.; Seidman, Daniel; Williams, Amy L.; Tambets, Kristiina; Metspalu, Mait

doi:10.1016/j.ajhg.2021.07.012

Cited by 19 publications

(15 citation statements)

References 76 publications

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“…Finally, the major change we observed between medieval and modern periods in connectedness with modern Welsh and Scottish genomes is likely to reflect recent and ongoing migrations and mobility. In contrast to the highly region-specific LSAI sharing between modern and medieval genomes in Estonia (Kivisild et al, 2021), later medieval Cambridge genomes do not show increased affinity to modern East Anglia compared to other regions. These recent changes in genetic ancestry suggest that modern Biobank sources may not be ideal references for the study of population histories, highlighting the need for ancient DNA sampling of historic populations from different time points.…”

Section: Discussioncontrasting

confidence: 62%

“…On the other hand, three individuals from Cherry Hinton, seven from All Saints, two from the Hospital, one from the Friary, and a post-medieval Midsummer Common burial clustered closely with modern French samples from the UK Biobank in the PCA result (Figure 1B,. To study the genetic affinity changes across time at finer geographic resolution we defined inter-individual connections by identifying long (> 5cM) shared allele intervals (LSAI-s) with IBIS (Seidman et al, 2020) and explored the modularity of individual connectedness, PiC (Kivisild et al, 2021), among the historical and modern genomes. Similarly to PCA results, we find that the majority of historical genomes from Cambridgeshire cluster by their connectedness with modern UK Biobank genomes from East England (Figure 1D, Table S2) whereas a small fraction of later medieval and Roman period genomes, which display low connectivity (Figure 1E), cluster with the UK Biobank donors born in France who display low connectivity among themselves.…”

Section: Genetic Ancestrymentioning

confidence: 99%

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Medieval social landscape through the genetic history of Cambridgeshire before and after the Black Death

Hui

Scheib

D’Atanasio

et al. 2023

Preprint

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The extent of the devastation of the Black Death pandemic (1346-53) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at local scale in the context of the social stratification of medieval communities. Here we study 275 newly reported ancient genomes from later medieval and post-medieval Cambridgeshire, from individuals buried before, during, and after the Black Death. The majority of individuals examined had local genetic ancestries. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. Accounting for the genetic component for height accentuates the disparities between social groups in stature estimated from long bones, as a proxy for health and the quality of life. While we detect long-term shifts in local genetic ancestry in Cambridgeshire that either pre- or postdate the Black Death, we find no evidence of major changes in genetic ancestry nor, in contrast to recent claims, higher differentiation of immune loci between cohorts living before and after the Black Death.

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Section: Discussioncontrasting

confidence: 62%

Section: Genetic Ancestrymentioning

confidence: 99%

Medieval social landscape through the genetic history of Cambridgeshire before and after the Black Death

Hui

Scheib

D’Atanasio

et al. 2023

Preprint

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“…Several recent publications have applied methods designed to detect IBD in high-quality present-day data on imputed aDNA data (e.g. using GLIMPSE) [Kivisild et al, 2021, Allentoft et al, 2022]. To compare the performance of ancIBD to such methods, we used the downsampled empirical ancient aDNA data described above.…”

Section: Resultsmentioning

confidence: 99%

“…Sikora et al, 2017, Ferrando-Bernal et al, 2020]. First efforts to identify IBD based on imputed data have been fruitful [Kivisild et al, 2021, Allentoft et al, 2022, Ariano et al, 2022, Severson et al, 2022a], but those earlier works require higher coverage not routinely available for aDNA. Importantly, they do not include a systematic evaluation of the IBD calling pipelines but performance when screening for IBD is expected to decay for short segments and low-coverage data.…”

Section: Introductionmentioning

confidence: 99%

ancIBD - Screening for identity by descent segments in human ancient DNA

Ringbauer

Huang

Akbari

et al. 2023

Preprint

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Long DNA sequences shared between two individuals, known as Identical by descent (IBD) segments, are a powerful signal for identifying close and distant biological relatives because they only arise when the pair shares a recent common ancestor. Existing methods to call IBD segments between present-day genomes cannot be straightforwardly applied to ancient DNA data (aDNA) due to typically low coverage and high genotyping error rates. We present ancIBD, a method to identify IBD segments for human aDNA data implemented as a Python package. Our approach is based on a Hidden Markov Model, using as input genotype probabilities imputed based on a modern reference panel of genomic variation. Through simulation and downsampling experiments, we demonstrate that ancIBD robustly identifies IBD segments longer than 8 centimorgan for aDNA data with at least either 0.25x average whole-genome sequencing (WGS) coverage depth or at least 1x average depth for in-solution enrichment experiments targeting a widely used aDNA SNP set (‘1240k’). This application range allows us to screen a substantial fraction of the aDNA record for IBD segments and we showcase two downstream applications. First, leveraging the fact that biological relatives up to the sixth degree are expected to share multiple long IBD segments, we identify relatives between 10,156 ancient Eurasian individuals and document evidence of long-distance migration, for example by identifying a pair of two approximately fifth-degree relatives who were buried 1410km apart in Central Asia 5000 years ago. Second, by applying ancIBD, we reveal new details regarding the spread of ancestry related to Steppe pastoralists into Europe starting 5000 years ago. We find that the first individuals in Central and Northern Europe carrying high amounts of Steppe-ancestry, associated with the Corded Ware culture, share high rates of long IBD (12-25 cM) with Yamnaya herders of the Pontic-Caspian steppe, signaling a strong bottleneck and a recent biological connection on the order of only few hundred years, providing evidence that the Yamnaya themselves are a main source of Steppe ancestry in Corded Ware people. We also detect elevated sharing of long IBD segments between Corded Ware individuals and people associated with the Globular Amphora culture (GAC) from Poland and Ukraine, who were Copper Age farmers not yet carrying Steppe-like ancestry. These IBD links appear for all Corded Ware groups in our analysis, indicating that individuals related to GAC contexts must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups across Europe. These results show that detecting IBD segments in aDNA can generate new insights both on a small scale, relevant to understanding the life stories of people, and on the macroscale, relevant to large-scale cultural-historical events.

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“…The high-resolution of whole-genome sequencing (WGS) data facilitates the integration with ancient DNA data that are heterogenous in sequencing depth and quality to illustrate complex dynamics ( Ioannidis et al 2020 ; Almarri et al 2021 ; Kivisild et al 2021 ). In this study, we conducted high-depth WGS for a total of 131 individuals ( table 1 ) from two representative ethnic groups in Central Asia: Kyrgyz (Turkic language speakers) and Tajik (Indo-European language speakers; fig.…”

Section: Introductionmentioning

confidence: 99%

The Genetic Echo of the Tarim Mummies in Modern Central Asians

Dai

Sulaiman

Isakova³

et al. 2022

Molecular Biology and Evolution

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The diversity of Central Asians has been shaped by multiple migrations and cultural diffusion. Although ancient DNA studies have revealed the demographic changes of the Central Asian since the Bronze Age, the contribution of the ancient populations to the modern Central Asian remains opaque. Herein, we performed high-coverage sequencing of 131 whole genomes of Indo-European-speaking Tajik and Turkic-speaking Kyrgyz populations to explore their genomic diversity and admixture history. By integrating the ancient DNA data, we revealed more details of the origins and admixture history of Central Asians. We found that the major ancestry of present-day Tajik populations can be traced back to the admixture of the Bronze Age Bactria–Margiana Archaeological Complex and Andronovo related populations. Highland Tajik populations further received additional gene flow from the Tarim mummies, an isolated ancient North Eurasian related population. The West Eurasian ancestry of Kyrgyz is mainly derived from Historical Era populations in Xinjiang of China. Furthermore, the recent admixture signals detected in both Tajik and Kyrgyz are ascribed to the expansions of Eastern Steppe nomadic pastoralists during the Historical Era.

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Patterns of genetic connectedness between modern and medieval Estonian genomes reveal the origins of a major ancestry component of the Finnish population

Cited by 19 publications

References 76 publications

Medieval social landscape through the genetic history of Cambridgeshire before and after the Black Death

Medieval social landscape through the genetic history of Cambridgeshire before and after the Black Death

ancIBD - Screening for identity by descent segments in human ancient DNA

The Genetic Echo of the Tarim Mummies in Modern Central Asians

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