Ancient Rome: A genetic crossroads of Europe and the Mediterranean

Antonio, Margaret L.; Gao, Ziyue; Moots, Hannah M.; Lucci, Michaela; Candilio, Francesca; Sawyer, Susanna; Oberreiter, Victoria; Calderon, Diego; Devitofranceschi, Katharina; Aikens, Rachael C.; Aneli, Serena; Bartoli, Fulvio; Bernardi, Alessandro; Cheronet, Olivia; Cotter, Daniel J.; Fernandes, Daniel; Gasperetti, Gabriella; Grifoni, Renata; Guidi, Alessandro; Pastina, Francesco La; Loreti, Ersilia; Manacorda, Daniele; Matullo, Giuseppe; Morretta, Simona; Nava, Alessia; Nicolai, Vincenzo Fiocchi; Nomi, Federico; Pavolini, Carlo; Pentiricci, Massimo; Pergola, Philippe; Piranomonte, Marina; Schmidt, Ryan; Spinola, Giandomenico; Sperduti, Alessandra; Rubini, Mauro; Bondioli, Luca; Coppa, Alfredo; Pinhasi, Ron; Pritchard, Jonathan K.

doi:10.1126/science.aay6826

Cited by 174 publications

(288 citation statements)

References 101 publications

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“…In addition, we found present-day Sardinian individuals sit within the broad range of ancestry observed in our ancient samples. A similar pattern is seen in Iberia 14 and central Italy 54 , where variation in individual ancestry increased markedly in the Iron Age, and later decreased until present-day. In terms of the fine-scale structure within Sardinia, we note the median position of modern individuals from the central regions of Ogliastra and Nuoro on the main PCA ( Fig.…”

Section: S S Se Se S S a A A A A A A A E Se E E E E E E E E E Se S A Asupporting

confidence: 68%

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia

et al. 2020

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The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.

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Section: S S Se Se S S a A A A A A A A E Se E E E E E E E E E Se S A Asupporting

confidence: 68%

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia

et al. 2020

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“…Previous aDNA studies have used Beagle 4.0 to impute ancient genomes 10 – 13 , which accepts genotype likelihood input to estimate genotypes at all sites in the reference panel in a single step. Another imputation tool recently developed for low-coverage sequencing data, GLIMPSE, functions in a similar way 9 .…”

Section: Resultsmentioning

confidence: 99%

“…In conclusion, we recommend using imputed genomes for downstream analyses incorporating genome-wide markers segregating at relatively high frequencies. They have been used in population genetics studies for detecting runs of homozygosity and identical-by-descent segments, and local ancestry deconvolution 10 – 13 , 25 . It has also been shown that low-coverage sequencing combined with imputation is more cost-effective in GWAS and generating polygenic risk scores 26 – 28 .…”

Section: Discussionmentioning

confidence: 99%

Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes

Hui

D’Atanasio

Cassidy

et al. 2020

Sci Rep

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Although ancient DNA data have become increasingly more important in studies about past populations, it is often not feasible or practical to obtain high coverage genomes from poorly preserved samples. While methods of accurate genotype imputation from > 1 × coverage data have recently become a routine, a large proportion of ancient samples remain unusable for downstream analyses due to their low coverage. Here, we evaluate a two-step pipeline for the imputation of common variants in ancient genomes at 0.05–1 × coverage. We use the genotype likelihood input mode in Beagle and filter for confident genotypes as the input to impute missing genotypes. This procedure, when tested on ancient genomes, outperforms a single-step imputation from genotype likelihoods, suggesting that current genotype callers do not fully account for errors in ancient sequences and additional quality controls can be beneficial. We compared the effect of various genotype likelihood calling methods, post-calling, pre-imputation and post-imputation filters, different reference panels, as well as different imputation tools. In a Neolithic Hungarian genome, we obtain ~ 90% imputation accuracy for heterozygous common variants at coverage 0.05 × and > 97% accuracy at coverage 0.5 ×. We show that imputation can mitigate, though not eliminate reference bias in ultra-low coverage ancient genomes.

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“…3). The only archaeological cluster (defined in annotations from the source dataset, modified for readability) with more than two individuals is 'Iron Age Republican Rome', where 3 of 11 samples reported in Antonio et al (2019) fall above the long ROH threshold. In the Pontic-Caspian Steppe region, 3 of 54 individuals who lived between 2,600-1,500 BP (5.6%, CI: 1.2-15.4%) exceed the threshold (Fig.…”

Section: Low Abundance Of Long Rohmentioning

confidence: 99%

Human Parental Relatedness through Time - Detecting Runs of Homozygosity in Ancient DNA

Ringbauer

Novembre

Steinrücken

2020

Preprint

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We present a novel method to detect runs of homozygosity (ROH) from low-coverage genotype data typical for ancient human DNA. ROH are the genetic signature of matings between related parents, and as such, the frequency and length distribution of these blocks can give insight into recent population history and mating patterns. Existing methods identify ROH by scanning for regions that lack heterozygote genotypes, but this strategy frequently fails for ancient individuals: The vast majority of ancient DNA data has low read depth (ă3ˆ), which makes reliable diploid genotype calling infeasible. To overcome this limitation, we make use of linkage disequilibrium information from a panel of modern reference haplotypes using a Hidden Markov Model. Our method scans for long stretches where the read data are consistent with only a single haplotype. When tested on simulated and down-sampled pseudo-haploid data from a targeted set of 1.24 million single nucleotide polymorphisms ("1240k SNPs") widely used in ancient DNA, our implementation robustly works for coverage down to 0.5ˆand can tolerate error rates up to 3%, with high power and low false positive rate for blocks longer than 4 centiMorgans. Therefore, the method can screen a substantial fraction of human genome-wide ancient DNA data for parental relatedness, which will yield new evidence for questions regarding past demography and social organization.

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Ancient Rome: A genetic crossroads of Europe and the Mediterranean

Cited by 174 publications

References 101 publications

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia

Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes

Human Parental Relatedness through Time - Detecting Runs of Homozygosity in Ancient DNA

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