References
Andrades Valtueña, Aida, Alissa Mittnik, Felix M Key, Wolfgang Haak,
Raili Allmäe, Andrej Belinskij, Mantas Daubaras, et al. 2017. “The
Stone Age Plague and Its Persistence in Eurasia.” Current
Biology: CB 27 (23): 3683–3691.e8. https://doi.org/10.1016/j.cub.2017.10.025.
Andrades Valtueña, Aida, Gunnar U Neumann, Maria A Spyrou, Lyazzat
Musralina, Franziska Aron, Arman Beisenov, Andrey B Belinskiy, et al.
2022. “Stone Age Yersinia Pestis Genomes Shed Light on the Early
Evolution, Diversity, and Ecology of Plague.” Proceedings of
the National Academy of Sciences of the United States of America
119 (17): e2116722119. https://doi.org/10.1073/pnas.2116722119.
Borry, Maxime, Alexander Hübner, Adam B Rohrlach, and Christina
Warinner. 2021. “PyDamage: Automated Ancient Damage
Identification and Estimation for Contigs in Ancient DNA de
Novo Assembly.” PeerJ 9 (July): e11845. https://doi.org/10.7717/peerj.11845.
Brealey, Jaelle C, Henrique G Leitão, Tom van der Valk, Wenbo Xu, Katia
Bougiouri, Love Dalén, and Katerina Guschanski. 2020. “Dental
Calculus as a Tool to Study the Evolution of the Mammalian Oral
Microbiome.” Molecular Biology and Evolution 37 (10):
3003–22. https://doi.org/10.1093/molbev/msaa135.
Briggs, Adrian W, Udo Stenzel, Philip L F Johnson, Richard E Green,
Janet Kelso, Kay Prüfer, Matthias Meyer, et al. 2007. “Patterns of
Damage in Genomic DNA Sequences from a Neandertal.”
Proceedings of the National Academy of Sciences of the United States
of America 104 (37): 14616–21. https://doi.org/10.1073/pnas.0704665104.
Cai, Dawei, Siqi Zhu, Mian Gong, Naifan Zhang, Jia Wen, Qiyao Liang,
Weilu Sun, et al. 2022. “Radiocarbon and Genomic Evidence for the
Survival of Equus Sussemionus Until the Late Holocene.”
eLife 11 (May). https://doi.org/10.7554/eLife.73346.
Fellows Yates, James A, Dorothée G Drucker, Ella Reiter, Simon Heumos,
Frido Welker, Susanne C Münzel, Piotr Wojtal, et al. 2017.
“Central European Woolly Mammoth Population Dynamics: Insights
from Late Pleistocene Mitochondrial Genomes.” Scientific
Reports 7 (1): 17714. https://doi.org/10.1038/s41598-017-17723-1.
Gansauge, Marie-Theres, Tobias Gerber, Isabelle Glocke, Petra Korlevic,
Laurin Lippik, Sarah Nagel, Lara Maria Riehl, Anna Schmidt, and Matthias
Meyer. 2017. “Single-Stranded DNA Library Preparation
from Highly Degraded DNA Using T4
DNA Ligase.” Nucleic Acids Research 45
(10): e79. https://doi.org/10.1093/nar/gkx033.
Hübler, Ron, Felix M Key, Christina Warinner, Kirsten I Bos, Johannes
Krause, and Alexander Herbig. 2019. “HOPS: Automated
Detection and Authentication of Pathogen DNA in
Archaeological Remains.” Genome Biology 20 (1): 280. https://doi.org/10.1186/s13059-019-1903-0.
Jónsson, Hákon, Aurélien Ginolhac, Mikkel Schubert, Philip L F Johnson,
and Ludovic Orlando. 2013. “mapDamage2.0: Fast Approximate Bayesian Estimates
of Ancient DNA Damage Parameters.”
Bioinformatics 29 (13): 1682–84. https://doi.org/10.1093/bioinformatics/btt193.
Meyer, Matthias, and Martin Kircher. 2010. “Illumina Sequencing
Library Preparation for Highly Multiplexed Target Capture and
Sequencing.” Cold Spring Harbor Protocols 2010 (6):
db.prot5448. https://doi.org/10.1101/pdb.prot5448.
Michelsen, Christian, Mikkel Winther Pedersen, Antonio Fernandez-Guerra,
Lei Zhao, Troels C Petersen, and Thorfinn Sand Korneliussen. 2022.
“MetaDMG – a Fast and Accurate Ancient
DNA Damage Toolkit for Metagenomic Data.”
bioRxiv. https://doi.org/10.1101/2022.12.06.519264.
Neukamm, Judith, Alexander Peltzer, and Kay Nieselt. 2021.
“DamageProfiler: Fast Damage Pattern Calculation for
Ancient DNA.” Bioinformatics 37 (20):
3652–53. https://doi.org/10.1093/bioinformatics/btab190.
Rohland, Nadin, Eadaoin Harney, Swapan Mallick, Susanne Nordenfelt, and
David Reich. 2015. “Partial Uracil-DNA-Glycosylase
Treatment for Screening of Ancient DNA.”
Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences 370 (1660): 20130624. https://doi.org/10.1098/rstb.2013.0624.
Shendure, Jay, and Hanlee Ji. 2008. “Next-Generation
DNA Sequencing.” Nature Biotechnology 26
(10): 1135–45. https://doi.org/10.1038/nbt1486.
Skoglund, Pontus, Bernd H Northoff, Michael V Shunkov, Anatoli P
Derevianko, Svante Pääbo, Johannes Krause, and Mattias Jakobsson. 2014.
“Separating Endogenous Ancient DNA from Modern Day
Contamination in a Siberian Neandertal.” Proceedings of the
National Academy of Sciences of the United States of America 111
(6): 2229–34. https://doi.org/10.1073/pnas.1318934111.
Star, Bastiaan, Sanne Boessenkool, Agata T Gondek, Elena A Nikulina,
Anne Karin Hufthammer, Christophe Pampoulie, Halvor Knutsen, et al.
2017. “Ancient DNA Reveals the Arctic Origin of
Viking Age Cod from Haithabu, Germany.” Proceedings of the
National Academy of Sciences of the United States of America 114
(34): 9152–57. https://doi.org/10.1073/pnas.1710186114.
Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy
McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome
to the Tidyverse.” Journal of Open Source Software 4
(43): 1686. https://doi.org/10.21105/joss.01686.