Accurate detection of identity-by-descent segments in human ancient DNA

[Tautalus]

Abstract
Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.

https://www.nature.com/articles/s41588-023-01582-w

Inferred IBD segments between various Eneolithic and Bronze Age West Eurasian Groups

 

[Tautalus]

Some excerpts from the article :

"We found that several nomadic Steppe groups associated with the Yamnaya culture that date to around 3,000 bce share comparably large amounts of IBD with each other (Fig. 4). This late Eneolithic to Early Bronze Age culture of pastoral nomads, who inhabited the Western Eurasian Pontic-Caspian Steppe often buried their death in tumuli (Kurgans) and were among the first people to use wagons, are suggested to have had a key role in the early spread of Indo-European languages. Notably, the Yamnaya IBD cluster includes also individuals associated with the contemporaneous Afanasievo culture thousands of kilometres east, an Eneolithic archaeological culture near the Central Asian Altai mountains. This signal of IBD sharing confirms the previous archaeological hypothesis that Afanasievo and Yamnaya are closely linked despite the vast geographic distance from Eastern Europe to Central Asia. A genetic link has already been evident from genomic similarity and Y haplogroups; however, the time depth of this connection remained unclear. We now identify IBD signals across all length scales, including several shared IBD segments even longer than 20 cM (Extended Data Fig. 3). Such long IBD links must be recent as recombination ends an IBD segment ~20 cM long on average every five meiosis. This long IBD sharing signal, at the same level as between various Yamnaya groups (Fig. 4), therefore clearly indicates that ancient individuals from Afanasievo contexts descend from people who migrated at most a few generations earlier across vast distances of the Eurasian Steppe."

"Moreover, there are several intriguing observations regarding individuals associated with the Corded Ware culture, an important archaeological culture that appears across a vast area of Eastern, Central and Northern Europe between 3,000 and 2,400 bce. Previous aDNA research showed Corded Ware groups to be the first people of these regions to carry high amounts of a distinct ancestry found in Eurasian Steppe pastoralists such as the Yamnaya, admixed with previous Final Neolithic farmer cultures. Using IBD, we find that individuals from diverse Corded Ware cultural groups, including from Sweden (associated with the Battle Axe culture), Russia (Fatyanovo) and East/Central Europe share high amounts of long IBD with each other and also have IBD sharing up to 20 cM with various Yamnaya groups (Fig. 4 and Extended Data Fig. 3a,b,c). We find a distinctive IBD signal with the so-called Globular Amphora culture, in particular from Poland and Ukraine, who were Copper Age (Eneolithic) farmers around 3,000 bce not yet carrying Steppe-like ancestry. This IBD link to Globular Amphora appears for all Corded Ware groups in our analysis, including from as far away as Scandinavia and Russia (Fig. 4), which indicates that individuals related to Globular Amphora contexts from Eastern Europe must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups."

"To showcase this potential, we have used ancIBD to generate evidence for the origins of the people culturally associated with the Corded Ware culture. Corded Ware groups of Eastern, Central and Northern Europe were identified to be among the first cultures affected by large-scale gene flows starting 3,000 bce which spread a distinct ancestry found in pastoralists of the Pontic-Caspian Steppes across Europe. Our analysis of long IBD segments reveals that the quarter of Corded Ware Complex ancestry associated with earlier European farmers can be pinpointed to people associated with the Globular Amphora culture of Eastern Europe, who carry no Steppe-like ancestry yet, while the remaining three-quarters must share recent co-ancestry with Yamnaya Steppe pastoralists in the late third millennium bce. This direct evidence that most Corded Ware ancestry must have genealogical links to people associated with Yamnaya culture spanning on the order of at most a few hundred years is inconsistent with the hypothesis that the Steppe-like ancestry in the Corded Ware primarily reflects an origin in as-of-now unsampled cultures genetically similar to the Yamnaya but related to them only a millennium earlier."

 

[Jovialis]

Finally will help to put an end to bad G25 models.

 

[Kirgonix Pereira]

"To showcase this potential, we have used ancIBD to generate evidence for the origins of the people culturally associated with the Corded Ware culture. Corded Ware groups of Eastern, Central and Northern Europe were identified to be among the first cultures affected by large-scale gene flows starting 3,000 bce which spread a distinct ancestry found in pastoralists of the Pontic-Caspian Steppes across Europe. Our analysis of long IBD segments reveals that the quarter of Corded Ware Complex ancestry associated with earlier European farmers can be pinpointed to people associated with the Globular Amphora culture of Eastern Europe, who carry no Steppe-like ancestry yet, while the remaining three-quarters must share recent co-ancestry with Yamnaya Steppe pastoralists in the late third millennium bce. This direct evidence that most Corded Ware ancestry must have genealogical links to people associated with Yamnaya culture spanning on the order of at most a few hundred years is inconsistent with the hypothesis that the Steppe-like ancestry in the Corded Ware primarily reflects an origin in as-of-now unsampled cultures genetically similar to the Yamnaya but related to them only a millennium earlier."

Watch this youtube video.

 

[Tautalus]

There will still be a lot of discussion about the ethnogenesis of Corded Ware, but what this study indicates is that Corded Ware must share recent co-ancestry with Yamnaya Steppe pastoralists, in the late third millennium BCE, that accounts for three-quarters of his own ancestry. And that these genealogical connections are on the order of at most a few hundred years.

 

[Omino]

Watch this youtube video.

Wtf is this?