What's in a Sequencing Strategy?

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I recently presented a poster exploring the impacts of mixing and co-analyzing datasets that have been sequenced and generated using whole genome sequencing versus 1240K capture sequencing. I revisited some results about individuals from the site of Grotta Continenze in Italy that we published as part of a project looking at the population of Central Italy through time. https://www.science.org/doi/10.1126/science.aay6826



At the time, most of the geographically and chronologically relevant data was generated using 1240K capture technology. We used whole genome sequencing for the ancient genomes we generated and used the captured data to contextualize the individuals we were studying. Now, that there are many more published ancient genomes (https://www.nature.com/articles/d41586-023-01403-4), I wanted to revisit our models using only data generated with the same strategy, and we do actually see some differences. This has also been mentioned in a few papers:

Margaryan, Ashot, Daniel J. Lawson, Martin Sikora, Fernando Racimo, Simon Rasmussen, Ida Moltke, Lara M. Cassidy et al. "Population genomics of the Viking world." Nature 585, no. 7825 (2020): 390-396. https://www.nature.com/articles/s41586-020-2688-8

Davidson, Roberta, Matthew P. Williams, Xavier Roca‐Rada, Kalina Kassadjikova, Raymond Tobler, Lars Fehren‐Schmitz, and Bastien Llamas. "Allelic bias when performing in‐solution enrichment of ancient human DNA." Molecular Ecology Resources 23, no. 8 (2023): 1823-1840. https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13869 

Flegontov, Pavel, Ulaş Işıldak, Robert Maier, Eren Yüncü, Piya Changmai, and David Reich. "Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes." PloS Genetics 19, no. 9 (2023): e1010931. https://doi.org/10.1371/journal.pgen.1010931 

And the citation for the original 2019 paper on the population history of the Italian Penninsula. Antonio, M. L., Gao, Z., Moots, H. M., Lucci, M., Candilio, F., Sawyer, S., ... & Pritchard, J. K. (2019). Ancient Rome: A genetic crossroads of Europe and the Mediterranean. Science, 366(6466), 708-714. https://www.science.org/doi/10.1126/science.aay6826





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