Ancient Maltese genomes and the genetic geography of Neolithic Europe

Ariano, Bruno; Mattiangeli, Valeria; Breslin, Emily M.; Parkinson, Eóin W.; McLaughlin, Rowan; Thompson, Jess E.; Power, Ronika K.; Stock, Jay T.; Mercieca-Spiteri, Bernardette; Stoddart, Simon; Malone, Caroline; Gopalakrishnan, Shyam; Cassidy, Lara M.; Bradley, Daniel G.

doi:10.1016/j.cub.2022.04.069

Cited by 13 publications

(9 citation statements)

References 95 publications

(190 reference statements)

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“…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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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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“…In order to identify segments of the genome that are identical by descent, we exploited the program IBDseq-vr1206 [89] on the imputed dataset, following the procedure illustrated in Ariano et al [90]. In detail, with Plink-1.9 [74] we filtered out SNPs showing genotype missingness > 0.02 and a MAF < 0.05 (parameters --geno 0.02 and --maf 0.05 in Plink).…”

Section: Methodsmentioning

confidence: 99%

The Genomic portrait of the Picene culture: new insights into the Italic Iron Age and the legacy of the Roman expansion in Central Italy

Ravasini,

Niinemäe,

Solnik

et al. 2024

Preprint

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Background: The Italic Iron Age was characterized by the presence of various ethnic groups partially examined from a genomic perspective. To explore the evolution of Iron Age Italic populations and the genetic impact of Romanization, we focused on the Picenes, one of the most fascinating pre-Roman civilizations, who flourished on the Middle Adriatic side of Central Italy between the 9th and the 3rd century BCE, until the Roman colonization. Results: We analyzed more than 50 samples, spanning more than 1,000 years of history from the Iron Age to Late Antiquity. Despite cultural diversity, our analysis reveals no major differences between the Picenes and other coeval populations, suggesting a shared genetic history of the Central Italian Iron Age ethnic groups. Nevertheless, a slight genetic differentiation between populations along the Adriatic and Tyrrhenian coasts can be observed, possibly due to genetic contacts between populations residing on the Italian and Balkan shores of the Adriatic Sea. Additionally, we found several individuals with ancestries deviating from their general population. Lastly, In the Late Antiquity period, the genetic landscape of the Middle Adriatic region drastically changed, indicating a relevant influx from the Near East. Conclusions: Our findings, consistently with archeological hypotheses, suggest genetic interactions across the Adriatic Sea during the Bronze/Iron Age and a high level of individual mobility typical of cosmopolitan societies. Finally, we highlighted the role of the Roman Empire in shaping genetic and phenotypic changes that greatly impacted the Italian peninsula.

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“…Today, the islands house a population approaching half a million people, sustained by the economic and political power of the European Union. By contrast, for the study of prehistoric ritual, we have to envisage much more intimate population levels of low thousands of individuals and even smaller breeding networks of several hundred (Ariano et al 2022). These are the scales of interaction recorded in the rituals of the villages of modern Malta, albeit with many differences.…”

Section: The Structurellementioning

confidence: 99%

“…Other raw materials such as some cherts (Chatzimpaloglou 2020a(Chatzimpaloglou , 2020b, hard stones (Dixon et al 2009) and obsidian (Malone et al 2009, pp. 250-53) were similarly imported on a small scale and were probably accompanied by a continuing exchange of humans, both to provide the transport and what we currently assess to have been a limited exchange of genetic material (Ariano et al 2022). The exotic provenance of materials can be proved, but these materials are difficult to quantify or date.…”

Section: The Longue Duréementioning

confidence: 99%

“…The degree of movement of humans (measured by oxygen and strontium isotopes) is even more difficult to assess, because of the similarities of neighbouring geologies for strontium and the complex pathways for oxygen (Stoddart et al in press). What is, however, clear is that it was no small venture, compared with today, to cross the waters to Sicily or Africa and what evidence there is of the biology of the inhabitants suggests transmission was affected by biogeographical factors (Ariano et al 2022).…”

Section: The Longue Duréementioning

confidence: 99%

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Neolithic Ritual on the Island Archipelago of Malta

Stoddart

2022

Religions

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This paper addresses the ritual of Neolithic Malta in its island context drawing on recent research by the FRAGSUS project. Ritualised club houses placed in horticultural enclosures formed the focal point of the prehistoric Maltese landscape in the fourth and third millennia BC, providing a stable exploitation of the islands by the small populations of the period. This was a period when connectivity was more challenging than in the Bronze Age which followed, when Malta became part of the wider ritual patterns of the central Mediterranean and beyond. The paper provides discussion of the leading issues and arguments applied to this rich case study of island ritual.

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Ancient Maltese genomes and the genetic geography of Neolithic Europe

Cited by 13 publications

References 95 publications

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

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

The Genomic portrait of the Picene culture: new insights into the Italic Iron Age and the legacy of the Roman expansion in Central Italy

Neolithic Ritual on the Island Archipelago of Malta

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