Local population structure in Cambridgeshire during the Roman occupation

Scheib, Christiana L.; Hui, Ruoyun; Rose, Allison; Solnik, Anu; D’Atanasio, Eugenia; Inskip, Sarah; Cessford, Craig; Griffith, Samuel J.; Wiseman, Rob; Neil, Benjamin; Biers, Trish; Harknett, Sarah-Jane; Sasso, Stefania; Biagini, Simone Andrea; Runfeldt, Göran; Duhig, Corinne; Evans, Christopher; O’Connell, Tamsin C.; Metspalu, Mait; Millett, Martin; Robb, John; Kivisild, Toomas

doi:10.1101/2023.07.31.551265

Cited by 3 publications

(1 citation statement)

References 57 publications

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“…Furthermore, the 1000 Genomes Project [40] dataset that was used for testing only included a very limited number of third-degree relatives. Nevertheless, other researchers have modified READv1 to classify up to third-degree relatives [25,41], suggesting that the READ approach might be able to perform such classifications in certain situations. For Figure 2, we also tested the ability of READv2 to classify third-degree relatives.…”

Section: Figurementioning

confidence: 99%

READv2: Advanced and user-friendly detection of biological relatedness in archaeogenomics

Alaçamlı,

Naidoo,

Aktürk

et al. 2024

Preprint

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The possibility to obtain genome-wide ancient DNA data from multiple individuals has facilitated an unprecedented perspective into prehistoric societies. Studying biological relatedness in these groups requires tailored approaches for analyzing ancient DNA due to its low coverage, post-mortem damage, and potential ascertainment bias. Here we present READv2 (Relatedness Estimation from Ancient DNA version 2), an improved Python 3 re-implementation of the most widely used tool for this purpose. While providing increased portability and making the software future-proof, we are also able to show that READv2 (a) is orders of magnitude faster than its predecessor; (b) has increased power to detect pairs of relatives using optimized default parameters; and, when the number of overlapping SNPs is sufficient, (c) can differentiate between full-siblings and parent-offspring, and (d) can classify pairs of third-degree relatedness. We further use READv2 to analyze a large empirical dataset that has previously needed two separate tools to reconstruct complex pedigrees. We show that READv2 yields results and precision similar to the combined approach but is faster and simpler to run. READv2 will become a valuable part of the archaeogenomic toolkit in providing an efficient and user-friendly classification of biological relatedness from pseudohaploid ancient DNA data.

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Section: Figurementioning

confidence: 99%

READv2: Advanced and user-friendly detection of biological relatedness in archaeogenomics

Alaçamlı,

Naidoo,

Aktürk

et al. 2024

Preprint

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Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders

Sasso,

Saag,

Spros

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

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The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother–daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.

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Bone adhered soil as a source of target and environmental DNA and proteins

de-Dios,

Bonucci,

Barbieri

et al. 2024

Preprint

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In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, locations with favourable conditions for ancient DNA (aDNA) preservation in sediments are scarce. In this study we analysed a set of samples obtained from soil adhered to different human skeletal elements, originating from Neolithic to Medieval sites in England, and performed metagenomics and metaproteomics analysis. From them, we were able to recover aDNA sequences matching the genomes of endogenous gut and oral microbiome bacteria. We also found the presence of genetic data corresponding to animals and plants. In particular we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medievalRattus rattus. Furthermore, we have also been able to reconstruct a partial human genome. The genetic profile of those human sequences matches the one recovered from the original skeletal element. Our results demonstrate that material usually discarded, as it is soil adhering to human remains, can be used to get a glimpse of the environmental conditions at the time of the death of an individual, even in contexts where due to harsh environmental conditions, the skeletal remains themselves are not preserved.

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Local population structure in Cambridgeshire during the Roman occupation

Cited by 3 publications

References 57 publications

READv2: Advanced and user-friendly detection of biological relatedness in archaeogenomics

READv2: Advanced and user-friendly detection of biological relatedness in archaeogenomics

Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders

Bone adhered soil as a source of target and environmental DNA and proteins

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