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

Abstract

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.

Ancient DNA reveals the origins of the Albanians

“…3B) that persists for at least 1.500 years and transcends the linguistic boundaries identified by classical authors (7,9). Our findings are further reinforced by IBD-sharing between certain samples from Albania and North Macedonia (Table S20) (50).…”

“…To gain insight into the biological and linguistic origins of modern Albanians, we undertake a palaeogenomic transect of the Balkans from the Neolithic to the modern era (Fig. 1; Tables S1-S2), using more than 6000 previously published ancient genomes from western Eurasia, which we interrogate by means of state-of-the-art statistical analyses (Tables S3-S18), large-scale algorithms that quantify human mobility (Table S19), and a meta-analysis of ancient IBD-sharing data [Tables 20-21; (50)]. We also mine publicly available Y-chromosome haplogroup data from more than 2500 ancient and modern Balkan samples (Tables S22-S34), which reveal the proximate ancestors of modern Albanian men.…”

Bronze Age Northern Eurasian Genetics in the Context of Development of Metallurgy and Siberian Ancestry

“…BOO samples were imputed and phased using GLIMPSE 32 following the default parameters, and merged with already published data, in order to test for patterns of IBD sharing among the individuals using ancIBD 34 . IBD analyses were restricted to samples covering more than 600K SNPs with GP>=0.99 after genotype imputation.…”

Steppe Ancestry in western Eurasia and the spread of the Germanic Languages

“…Recent studies have shown that with dense ancient DNA sampling, at sufficient sequencing depth for imputation (∼0.1X for whole genomes), the detection of fine scale population structure in closely related ancient populations is possible 58–60 . To investigate the spread and diversification of Germanic-speaking populations, we sequenced 710 ancient genomes (Table, Supplementary Note S1A and S1B) from human populations across western Eurasia, with a focus on the northern European Iron Age and the bordering Celtic-speaking region of western Europe (Figure 1).…”

“…Migrations within Europe over the last 5,000 years would have represented interactions by much more closely related populations than the arrival of the Neolithic Farmers and Bronze Age Steppe Pastoralists, limiting the possibility of their detection in ancient DNA studies. Recent studies have shown that with dense ancient DNA sampling, at sufficient sequencing depth for imputation (~0.1X for whole genomes), the detection of fine scale population structure in closely related ancient populations is possible [58][59][60] . To investigate the spread and diversification of Germanic-speaking populations, we sequenced 710 ancient genomes (Table , Supplementary Note S1A and S1B) from human populations across western Eurasia, with a focus on the northern European Iron Age and the bordering Celtic-speaking region of western Europe (Figure 1).…”