references.bib

@article{Briggs2007-ao,
  title    = {Patterns of damage in genomic {DNA} sequences from a Neandertal},
  author   = {Briggs, Adrian W and Stenzel, Udo and Johnson, Philip L F and
              Green, Richard E and Kelso, Janet and Prüfer, Kay and Meyer,
              Matthias and Krause, Johannes and Ronan, Michael T and Lachmann,
              Michael and Pääbo, Svante},
  journal  = {Proceedings of the National Academy of Sciences of the United
              States of America},
  volume   = 104,
  number   = 37,
  pages    = {14616--14621},
  abstract = {High-throughput direct sequencing techniques have recently opened
              the possibility to sequence genomes from Pleistocene organisms.
              Here we analyze DNA sequences determined from a Neandertal, a
              mammoth, and a cave bear. We show that purines are overrepresented
              at positions adjacent to the breaks in the ancient DNA, suggesting
              that depurination has contributed to its degradation. We
              furthermore show that substitutions resulting from miscoding
              cytosine residues are vastly overrepresented in the DNA sequences
              and drastically clustered in the ends of the molecules, whereas
              other substitutions are rare. We present a model where the
              observed substitution patterns are used to estimate the rate of
              deamination of cytosine residues in single- and double-stranded
              portions of the DNA, the length of single-stranded ends, and the
              frequency of nicks. The results suggest that reliable genome
              sequences can be obtained from Pleistocene organisms.},
  month    = sep,
  year     = 2007,
  url      = {http://dx.doi.org/10.1073/pnas.0704665104},
  doi      = {10.1073/pnas.0704665104},
  pmc      = {PMC1976210},
  pmid     = 17715061,
  issn     = {0027-8424}
}

@article{Jonsson2013-zb,
  title    = {{mapDamage2}.0: fast approximate Bayesian estimates of ancient
              {DNA} damage parameters},
  author   = {Jónsson, Hákon and Ginolhac, Aurélien and Schubert, Mikkel and
              Johnson, Philip L F and Orlando, Ludovic},
  journal  = {Bioinformatics},
  volume   = 29,
  number   = 13,
  pages    = {1682--1684},
  abstract = {Motivation: Ancient DNA (aDNA) molecules in fossilized bones and
              teeth, coprolites, sediments, mummified specimens and museum
              collections represent fantastic sources of information for
              evolutionary biologists, revealing the agents of past epidemics
              and the dynamics of past populations. However, the analysis of
              aDNA generally faces two major issues. Firstly, sequences consist
              of a mixture of endogenous and various exogenous backgrounds,
              mostly microbial. Secondly, high nucleotide misincorporation rates
              can be observed as a result of severe post-mortem DNA damage. Such
              misincorporation patterns are instrumental to authenticate ancient
              sequences versus modern contaminants. We recently developed the
              user-friendly mapDamage package that identifies such patterns from
              next-generation sequencing (NGS) sequence datasets. The absence of
              formal statistical modeling of the DNA damage process, however,
              precluded rigorous quantitative comparisons across
              samples.Results: Here, we describe mapDamage 2.0 that extends the
              original features of mapDamage by incorporating a statistical
              model of DNA damage. Assuming that damage events depend only on
              sequencing position and post-mortem deamination, our Bayesian
              statistical framework provides estimates of four key features of
              aDNA molecules: the average length of overhangs (λ), nick
              frequency (ν) and cytosine deamination rates in both
              double-stranded regions () and overhangs (). Our model enables
              rescaling base quality scores according to their probability of
              being damaged. mapDamage 2.0 handles NGS datasets with ease and is
              compatible with a wide range of DNA library
              protocols.Availability: mapDamage 2.0 is available at
              ginolhac.github.io/mapDamage/ as a Python package and
              documentation is maintained at the Centre for GeoGenetics Web site
              (geogenetics.ku.dk/publications/mapdamage2.0/).Contact:
              jonsson.hakon@gmail.comSupplementary information: Supplementary
              data are available at Bioinformatics online.},
  month    = jul,
  year     = 2013,
  url      = {http://bioinformatics.oxfordjournals.org/content/29/13/1682.abstract},
  doi      = {10.1093/bioinformatics/btt193},
  issn     = {1367-4803}
}

@article{Neukamm2021-ul,
  title     = {{DamageProfiler}: Fast damage pattern calculation for ancient
               {DNA}},
  author    = {Neukamm, Judith and Peltzer, Alexander and Nieselt, Kay},
  journal   = {Bioinformatics},
  publisher = {Oxford University Press},
  volume    = 37,
  number    = 20,
  pages     = {3652–3653},
  abstract  = {MOTIVATION: In ancient DNA research, the authentication of
               ancient samples based on specific features remains a crucial step
               in data analysis. Because of this central importance, researchers
               lacking deeper programming knowledge should be able to run a
               basic damage authentication analysis. Such software should be
               user-friendly and easy to integrate into an analysis pipeline.
               RESULTS: DamageProfiler is a Java based, stand-alone software to
               determine damage patterns in ancient DNA. The results are
               provided in various file formats and plots for further
               processing. DamageProfiler has an intuitive graphical as well as
               command line interface that allows the tool to be easily embedded
               into an analysis pipeline. AVAILABILITY: All of the source code
               is freely available on GitHub
               (https://github.com/Integrative-Transcriptomics/DamageProfiler).
               SUPPLEMENTARY INFORMATION: Supplementary data are available at
               Bioinformatics online.},
  month     = apr,
  year      = 2021,
  url       = {http://dx.doi.org/10.1093/bioinformatics/btab190},
  doi       = {10.1093/bioinformatics/btab190},
  pmid      = 33890614,
  issn      = {1367-4803,1367-4811},
  language  = {en}
}

@article{Hubler2019-qw,
  title    = {{HOPS}: automated detection and authentication of pathogen {DNA}
              in archaeological remains},
  author   = {Hübler, Ron and Key, Felix M and Warinner, Christina and Bos,
              Kirsten I and Krause, Johannes and Herbig, Alexander},
  journal  = {Genome Biology},
  volume   = 20,
  number   = 1,
  pages    = 280,
  abstract = {High-throughput DNA sequencing enables large-scale metagenomic
              analyses of complex biological systems. Such analyses are not
              restricted to present-day samples and can also be applied to
              molecular data from archaeological remains. Investigations of
              ancient microbes can provide valuable information on past
              bacterial commensals and pathogens, but their molecular detection
              remains a challenge. Here, we present HOPS (Heuristic Operations
              for Pathogen Screening), an automated bacterial screening pipeline
              for ancient DNA sequences that provides detailed information on
              species identification and authenticity. HOPS is a versatile tool
              for high-throughput screening of DNA from archaeological material
              to identify candidates for genome-level analyses.},
  month    = dec,
  year     = 2019,
  url      = {https://doi.org/10.1186/s13059-019-1903-0},
  doi      = {10.1186/s13059-019-1903-0},
  issn     = {1474-760X}
}

@article{Star2017-cj,
  title    = {Ancient {DNA} reveals the Arctic origin of Viking Age cod from
              Haithabu, Germany},
  author   = {Star, Bastiaan and Boessenkool, Sanne and Gondek, Agata T and
              Nikulina, Elena A and Hufthammer, Anne Karin and Pampoulie,
              Christophe and Knutsen, Halvor and André, Carl and Nistelberger,
              Heidi M and Dierking, Jan and Petereit, Christoph and Heinrich,
              Dirk and Jakobsen, Kjetill S and Stenseth, Nils Chr and Jentoft,
              Sissel and Barrett, James H},
  journal  = {Proceedings of the National Academy of Sciences of the United
              States of America},
  volume   = 114,
  number   = 34,
  pages    = {9152--9157},
  abstract = {Knowledge of the range and chronology of historic trade and
              long-distance transport of natural resources is essential for
              determining the impacts of past human activities on marine
              environments. However, the specific biological sources of imported
              fauna are often difficult to identify, in particular if species
              have a wide spatial distribution and lack clear osteological or
              isotopic differentiation between populations. Here, we report that
              ancient fish-bone remains, despite being porous, brittle, and
              light, provide an excellent source of endogenous DNA (15-46\%) of
              sufficient quality for whole-genome reconstruction. By comparing
              ancient sequence data to that of modern specimens, we determine
              the biological origin of 15 Viking Age (800-1066 CE) and
              subsequent medieval (1066-1280 CE) Atlantic cod (Gadus morhua)
              specimens from excavation sites in Germany, Norway, and the United
              Kingdom. Archaeological context indicates that one of these sites
              was a fishing settlement for the procurement of local catches,
              whereas the other localities were centers of trade. Fish from the
              trade sites show a mixed ancestry and are statistically
              differentiated from local fish populations. Moreover, Viking Age
              samples from Haithabu, Germany, are traced back to the North East
              Arctic Atlantic cod population that has supported the Lofoten
              fisheries of Norway for centuries. Our results resolve a
              long-standing controversial hypothesis and indicate that the
              marine resources of the North Atlantic Ocean were used to sustain
              an international demand for protein as far back as the Viking Age.},
  month    = aug,
  year     = 2017,
  url      = {http://dx.doi.org/10.1073/pnas.1710186114},
  keywords = {chromosomal inversion; fish bone; genomics; high-throughput
              sequencing; trade},
  doi      = {10.1073/pnas.1710186114},
  pmc      = {PMC5576834},
  pmid     = 28784790,
  issn     = {0027-8424,1091-6490},
  language = {en}
}

@article{Wickham2019-ot,
  title    = {Welcome to the Tidyverse},
  author   = {Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang,
              Winston and McGowan, Lucy and François, Romain and Grolemund,
              Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and
              Kuhn, Max and Pedersen, Thomas and Miller, Evan and Bache, Stephan
              and Müller, Kirill and Ooms, Jeroen and Robinson, David and
              Seidel, Dana and Spinu, Vitalie and Takahashi, Kohske and Vaughan,
              Davis and Wilke, Claus and Woo, Kara and Yutani, Hiroaki},
  journal  = {Journal of Open Source Software},
  volume   = 4,
  number   = 43,
  pages    = 1686,
  abstract = {Software archive},
  month    = nov,
  year     = 2019,
  url      = {https://joss.theoj.org/papers/10.21105/joss.01686},
  doi      = {10.21105/joss.01686},
  issn     = {2475-9066}
}

@article{Shendure2008-fh,
  title    = {Next-generation {DNA} sequencing},
  author   = {Shendure, Jay and Ji, Hanlee},
  journal  = {Nature biotechnology},
  volume   = 26,
  number   = 10,
  pages    = {1135--1145},
  abstract = {DNA sequence represents a single format onto which a broad range
              of biological phenomena can be projected for high-throughput data
              collection. Over the past three years, massively parallel DNA
              sequencing platforms have become widely available, reducing the
              cost of DNA sequencing by over two orders of magnitude, and
              democratizing the field by putting the sequencing capacity of a
              major genome center in the hands of individual investigators.
              These new technologies are rapidly evolving, and near-term
              challenges include the development of robust protocols for
              generating sequencing libraries, building effective new approaches
              to data-analysis, and often a rethinking of experimental design.
              Next-generation DNA sequencing has the potential to dramatically
              accelerate biological and biomedical research, by enabling the
              comprehensive analysis of genomes, transcriptomes and interactomes
              to become inexpensive, routine and widespread, rather than
              requiring significant production-scale efforts.},
  month    = oct,
  year     = 2008,
  url      = {http://dx.doi.org/10.1038/nbt1486},
  doi      = {10.1038/nbt1486},
  pmid     = 18846087,
  issn     = {1087-0156,1546-1696},
  language = {en}
}
@unpublished{Michelsen2022-nx,
  title    = {{MetaDMG} – A fast and accurate ancient {DNA} damage toolkit for
              metagenomic data},
  author   = {Michelsen, Christian and Pedersen, Mikkel Winther and
              Fernandez-Guerra, Antonio and Zhao, Lei and Petersen, Troels C and
              Korneliussen, Thorfinn Sand},
  journal  = {bioRxiv},
  pages    = {2022.12.06.519264},
  abstract = {AbstractMotivationUnder favourable conditions DNA molecules can
              persist for hundreds of thousands of years. Such genetic remains
              make up invaluable resources to study past assemblages,
              populations, and even the evolution of species. However, DNA is
              subject to degradation, and hence over time decrease to ultra low
              concentrations which makes it highly prone to contamination by
              modern sources. Strict precautions are therefore necessary to
              ensure that DNA from modern sources does not appear in the final
              data is authenticated as ancient. The most generally accepted and
              widely applied authenticity for ancient DNA studies is to test for
              elevated deaminated cytosine residues towards the termini of the
              molecules: DNA damage. To date, this has primarily been used for
              single organisms and recently for read assemblies, however, these
              methods are not applicable for estimating DNA damage for ancient
              metagenomes with tens and even hundreds of thousands of
              species.MethodsWe presentmetaDMG, a novel framework and toolkit
              that allows for the estimation, quantification and visualization
              of postmortem damage for single reads, single genomes and even
              metagenomic environmental DNA by utilizing the taxonomic branching
              structure. It bypasses any need for initial classification,
              splitting reads by individual organisms, and realignment. We have
              implemented a Bayesian approach that combines a modified geometric
              damage profile with a beta-binomial model to fit the entire model
              to the individual misincorporations at all taxonomic
              levels.ResultsWe evaluated the performance using both simulated
              and published environmental DNA datasets and compared to existing
              methods when relevant. We findmetaDMGto be an order of magnitude
              faster than previous methods and more accurate – even for complex
              metagenomes. Our simulations show thatmetaDMGcan estimate DNA
              damage at taxonomic levels down to 100 reads, that the estimated
              uncertainties decrease with increased number of reads and that the
              estimates are more significant with increased number of C to T
              misincorporations.ConclusionmetaDMGis a state-of-the-art program
              for aDNA damage estimation and allows for the computation of
              nucleotide misincorporation, GC-content, and DNA fragmentation for
              both simple and complex ancient genomic datasets, making it a
              complete package for ancient DNA damage authentication.},
  month    = dec,
  year     = 2022,
  url      = {https://www.biorxiv.org/content/10.1101/2022.12.06.519264v1.abstract},
  doi      = {10.1101/2022.12.06.519264},
  language = {en}
}
@article{Borry2021-lt,
  title     = {{PyDamage}: automated ancient damage identification and
               estimation for contigs in ancient {DNA} de novo assembly},
  author    = {Borry, Maxime and Hübner, Alexander and Rohrlach, Adam B and
               Warinner, Christina},
  journal   = {PeerJ},
  publisher = {PeerJ Inc.},
  volume    = 9,
  pages     = {e11845},
  abstract  = {DNA de novo assembly can be used to reconstruct longer stretches
               of DNA (contigs), including genes and even genomes, from short
               DNA sequencing reads. Applying this technique to metagenomic data
               derived from archaeological remains, such as paleofeces and
               dental calculus, we can investigate past microbiome functional
               diversity that may be absent or underrepresented in the modern
               microbiome gene catalogue. However, compared to modern samples,
               ancient samples are often burdened with environmental
               contamination, resulting in metagenomic datasets that represent
               mixtures of ancient and modern DNA. The ability to rapidly and
               reliably establish the authenticity and integrity of ancient
               samples is essential for ancient DNA studies, and the ability to
               distinguish between ancient and modern sequences is particularly
               important for ancient microbiome studies. Characteristic patterns
               of ancient DNA damage, namely DNA fragmentation and cytosine
               deamination (observed as C-to-T transitions) are typically used
               to authenticate ancient samples and sequences, but existing tools
               for inspecting and filtering aDNA damage either compute it at the
               read level, which leads to high data loss and lower quality when
               used in combination with de novo assembly, or require manual
               inspection, which is impractical for ancient assemblies that
               typically contain tens to hundreds of thousands of contigs. To
               address these challenges, we designed PyDamage, a robust,
               automated approach for aDNA damage estimation and authentication
               of de novo assembled aDNA. PyDamage uses a likelihood ratio based
               approach to discriminate between truly ancient contigs and
               contigs originating from modern contamination. We test PyDamage
               on both on simulated aDNA data and archaeological paleofeces, and
               we demonstrate its ability to reliably and automatically identify
               contigs bearing DNA damage characteristic of aDNA. Coupled with
               aDNA de novo assembly, Pydamage opens up new doors to explore
               functional diversity in ancient metagenomic datasets.},
  month     = jul,
  year      = 2021,
  url       = {https://peerj.com/articles/11845/},
  keywords  = {metagenomics; aDNA; ancient DNA; assembly; damage; de novo;
               automated},
  doi       = {10.7717/peerj.11845},
  issn      = {2167-8359},
  language  = {en}
}
@article{Skoglund2014-hj,
  title    = {Separating endogenous ancient {DNA} from modern day contamination
              in a Siberian Neandertal},
  author   = {Skoglund, Pontus and Northoff, Bernd H and Shunkov, Michael V and
              Derevianko, Anatoli P and Pääbo, Svante and Krause, Johannes and
              Jakobsson, Mattias},
  journal  = {Proceedings of the National Academy of Sciences of the United
              States of America},
  volume   = 111,
  number   = 6,
  pages    = {2229--2234},
  abstract = {One of the main impediments for obtaining DNA sequences from
              ancient human skeletons is the presence of contaminating modern
              human DNA molecules in many fossil samples and laboratory
              reagents. However, DNA fragments isolated from ancient specimens
              show a characteristic DNA damage pattern caused by miscoding
              lesions that differs from present day DNA sequences. Here, we
              develop a framework for evaluating the likelihood of a sequence
              originating from a model with postmortem degradation-summarized in
              a postmortem degradation score-which allows the identification of
              DNA fragments that are unlikely to originate from present day
              sources. We apply this approach to a contaminated Neandertal
              specimen from Okladnikov Cave in Siberia to isolate its endogenous
              DNA from modern human contaminants and show that the reconstructed
              mitochondrial genome sequence is more closely related to the
              variation of Western Neandertals than what was discernible from
              previous analyses. Our method opens up the potential for genomic
              analysis of contaminated fossil material.},
  month    = feb,
  year     = 2014,
  url      = {http://dx.doi.org/10.1073/pnas.1318934111},
  keywords = {human evolution; paleogenomics},
  doi      = {10.1073/pnas.1318934111},
  pmc      = {PMC3926038},
  pmid     = 24469802,
  issn     = {0027-8424,1091-6490},
  language = {en}
}

@article{Meyer2010-qc,
  title    = {Illumina sequencing library preparation for highly multiplexed
              target capture and sequencing},
  author   = {Meyer, Matthias and Kircher, Martin},
  journal  = {Cold Spring Harbor protocols},
  volume   = 2010,
  number   = 6,
  pages    = {db.prot5448},
  abstract = {The large amount of DNA sequence data generated by high-throughput
              sequencing technologies often allows multiple samples to be
              sequenced in parallel on a single sequencing run. This is
              particularly true if subsets of the genome are studied rather than
              complete genomes. In recent years, target capture from sequencing
              libraries has largely replaced polymerase chain reaction (PCR) as
              the preferred method of target enrichment. Parallelizing target
              capture and sequencing for multiple samples requires the
              incorporation of sample-specific barcodes into sequencing
              libraries, which is necessary to trace back the sample source of
              each sequence. This protocol describes a fast and reliable method
              for the preparation of barcoded (``indexed'') sequencing libraries
              for Illumina's Genome Analyzer platform. The protocol avoids
              expensive commercial library preparation kits and can be performed
              in a 96-well plate setup using multi-channel pipettes, requiring
              not more than two or three days of lab work. Libraries can be
              prepared from any type of double-stranded DNA, even if present in
              subnanogram quantity.},
  month    = jun,
  year     = 2010,
  url      = {http://dx.doi.org/10.1101/pdb.prot5448},
  doi      = {10.1101/pdb.prot5448},
  pmid     = 20516186,
  issn     = {1940-3402,1559-6095}
}

@article{Andrades_Valtuena2022-tq,
  title     = {Stone Age Yersinia pestis genomes shed light on the early
               evolution, diversity, and ecology of plague},
  author    = {Andrades Valtueña, Aida and Neumann, Gunnar U and Spyrou, Maria A
               and Musralina, Lyazzat and Aron, Franziska and Beisenov, Arman
               and Belinskiy, Andrey B and Bos, Kirsten I and Buzhilova,
               Alexandra and Conrad, Matthias and Djansugurova, Leyla B and
               Dobeš, Miroslav and Ernée, Michal and Fernández-Eraso, Javier and
               Frohlich, Bruno and Furmanek, Mirosław and Hałuszko, Agata and
               Hansen, Svend and Harney, Éadaoin and Hiss, Alina N and Hübner,
               Alexander and Key, Felix M and Khussainova, Elmira and Kitov,
               Egor and Kitova, Alexandra O and Knipper, Corina and Kühnert,
               Denise and Lalueza-Fox, Carles and Littleton, Judith and Massy,
               Ken and Mittnik, Alissa and Mujika-Alustiza, José Antonio and
               Olalde, Iñigo and Papac, Luka and Penske, Sandra and Peška,
               Jaroslav and Pinhasi, Ron and Reich, David and Reinhold, Sabine
               and Stahl, Raphaela and Stäuble, Harald and Tukhbatova, Rezeda I
               and Vasilyev, Sergey and Veselovskaya, Elizaveta and Warinner,
               Christina and Stockhammer, Philipp W and Haak, Wolfgang and
               Krause, Johannes and Herbig, Alexander},
  journal   = {Proceedings of the National Academy of Sciences of the United
               States of America},
  publisher = {Proceedings of the National Academy of Sciences},
  volume    = 119,
  number    = 17,
  pages     = {e2116722119},
  abstract  = {The bacterial pathogen Yersinia pestis gave rise to devastating
               outbreaks throughout human history, and ancient DNA evidence has
               shown it afflicted human populations as far back as the
               Neolithic. Y. pestis genomes recovered from the Eurasian Late
               Neolithic/Early Bronze Age (LNBA) period have uncovered key
               evolutionary steps that led to its emergence from a Yersinia
               pseudotuberculosis-like progenitor; however, the number of
               reconstructed LNBA genomes are too few to explore its diversity
               during this critical period of development. Here, we present 17
               Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide
               geographic expanse across Eurasia. This increased dataset enabled
               us to explore correlations between temporal, geographical, and
               genetic distance. Our results suggest a nonflea-adapted and
               potentially extinct single lineage that persisted over millennia
               without significant parallel diversification, accompanied by
               rapid dispersal across continents throughout this period, a trend
               not observed in other pathogens for which ancient genomes are
               available. A stepwise pattern of gene loss provides further clues
               on its early evolution and potential adaptation. We also discover
               the presence of the flea-adapted form of Y. pestis in Bronze Age
               Iberia, previously only identified in in the Caucasus and the
               Volga regions, suggesting a much wider geographic spread of this
               form of Y. pestis. Together, these data reveal the dynamic nature
               of plague’s formative years in terms of its early evolution and
               ecology.},
  month     = apr,
  year      = 2022,
  url       = {https://www.pnas.org/doi/abs/10.1073/pnas.2116722119},
  keywords  = {Yersinia pestis; ancient DNA; plague},
  doi       = {10.1073/pnas.2116722119},
  pmc       = {PMC9169917},
  pmid      = 35412864,
  issn      = {0027-8424,1091-6490},
  language  = {en}
}

@article{Gansauge2017-ge,
  title    = {Single-stranded {DNA} library preparation from highly degraded
              {DNA} using {T4} {DNA} ligase},
  author   = {Gansauge, Marie-Theres and Gerber, Tobias and Glocke, Isabelle and
              Korlevic, Petra and Lippik, Laurin and Nagel, Sarah and Riehl,
              Lara Maria and Schmidt, Anna and Meyer, Matthias},
  journal  = {Nucleic acids research},
  volume   = 45,
  number   = 10,
  pages    = {e79},
  abstract = {DNA library preparation for high-throughput sequencing of genomic
              DNA usually involves ligation of adapters to double-stranded DNA
              fragments. However, for highly degraded DNA, especially ancient
              DNA, library preparation has been found to be more efficient if
              each of the two DNA strands are converted into library molecules
              separately. We present a new method for single-stranded library
              preparation, ssDNA2.0, which is based on single-stranded DNA
              ligation with T4 DNA ligase utilizing a splinter oligonucleotide
              with a stretch of random bases hybridized to a 3΄ biotinylated
              donor oligonucleotide. A thorough evaluation of this ligation
              scheme shows that single-stranded DNA can be ligated to adapter
              oligonucleotides in higher concentration than with CircLigase (an
              RNA ligase that was previously chosen for end-to-end ligation in
              single-stranded library preparation) and that biases in ligation
              can be minimized when choosing splinters with 7 or 8 random
              nucleotides. We show that ssDNA2.0 tolerates higher quantities of
              input DNA than CircLigase-based library preparation, is less
              costly and better compatible with automation. We also provide an
              in-depth comparison of library preparation methods on degraded DNA
              from various sources. Most strikingly, we find that
              single-stranded library preparation increases library yields from
              tissues stored in formalin for many years by several orders of
              magnitude.},
  month    = jun,
  year     = 2017,
  url      = {http://dx.doi.org/10.1093/nar/gkx033},
  doi      = {10.1093/nar/gkx033},
  pmc      = {PMC5449542},
  pmid     = 28119419,
  issn     = {0305-1048,1362-4962},
  language = {en}
}

@article{Andrades_Valtuena2017-qr,
  title    = {The Stone Age Plague and Its Persistence in Eurasia},
  author   = {Andrades Valtueña, Aida and Mittnik, Alissa and Key, Felix M and
              Haak, Wolfgang and Allmäe, Raili and Belinskij, Andrej and
              Daubaras, Mantas and Feldman, Michal and Jankauskas, Rimantas and
              Janković, Ivor and Massy, Ken and Novak, Mario and Pfrengle,
              Saskia and Reinhold, Sabine and Šlaus, Mario and Spyrou, Maria A
              and Szécsényi-Nagy, Anna and Tõrv, Mari and Hansen, Svend and Bos,
              Kirsten I and Stockhammer, Philipp W and Herbig, Alexander and
              Krause, Johannes},
  journal  = {Current biology: CB},
  volume   = 27,
  number   = 23,
  pages    = {3683--3691.e8},
  abstract = {Yersinia pestis, the etiologic agent of plague, is a bacterium
              associated with wild rodents and their fleas. Historically it was
              responsible for three pandemics: the Plague of Justinian in the
              6th century AD, which persisted until the 8th century [1]; the
              renowned Black Death of the 14th century [2, 3], with recurrent
              outbreaks until the 18th century [4]; and the most recent 19th
              century pandemic, in which Y. pestis spread worldwide [5] and
              became endemic in several regions [6]. The discovery of molecular
              signatures of Y. pestis in prehistoric Eurasian individuals and
              two genomes from Southern Siberia suggest that Y. pestis caused
              some form of disease in humans prior to the first historically
              documented pandemic [7]. Here, we present six new European Y.
              pestis genomes spanning the Late Neolithic to the Bronze Age
              (LNBA; 4,800 to 3,700 calibrated years before present). This time
              period is characterized by major transformative cultural and
              social changes that led to cross-European networks of contact and
              exchange [8, 9]. We show that all known LNBA strains form a single
              putatively extinct clade in the Y. pestis phylogeny. Interpreting
              our data within the context of recent ancient human genomic
              evidence that suggests an increase in human mobility during the
              LNBA, we propose a possible scenario for the early spread of Y.
              pestis: the pathogen may have entered Europe from Central Eurasia
              following an expansion of people from the steppe, persisted within
              Europe until the mid-Bronze Age, and moved back toward Central
              Eurasia in parallel with human populations.},
  month    = dec,
  year     = 2017,
  url      = {http://dx.doi.org/10.1016/j.cub.2017.10.025},
  keywords = {Bronze Age; Late Neolithic; Yersinia pestis; ancient DNA;
              archaeogenetics; comparative genomics; plague},
  doi      = {10.1016/j.cub.2017.10.025},
  pmid     = 29174893,
  issn     = {0960-9822,1879-0445},
  language = {en}
}

@manual{glossary,
  title  = {glossary: Glossaries for Markdown and Quarto Documents},
  author = {Lisa DeBruine},
  year   = {2023},
  note   = {https://github.com/debruine/glossary,
            https://debruine.github.io/glossary/}
}

@article{Andrades_Valtuena2022-tq,
  title     = {Stone Age Yersinia pestis genomes shed light on the early
               evolution, diversity, and ecology of plague},
  author    = {Andrades Valtueña, Aida and Neumann, Gunnar U and Spyrou, Maria A
               and Musralina, Lyazzat and Aron, Franziska and Beisenov, Arman
               and Belinskiy, Andrey B and Bos, Kirsten I and Buzhilova,
               Alexandra and Conrad, Matthias and Djansugurova, Leyla B and
               Dobeš, Miroslav and Ernée, Michal and Fernández-Eraso, Javier and
               Frohlich, Bruno and Furmanek, Mirosław and Hałuszko, Agata and
               Hansen, Svend and Harney, Éadaoin and Hiss, Alina N and Hübner,
               Alexander and Key, Felix M and Khussainova, Elmira and Kitov,
               Egor and Kitova, Alexandra O and Knipper, Corina and Kühnert,
               Denise and Lalueza-Fox, Carles and Littleton, Judith and Massy,
               Ken and Mittnik, Alissa and Mujika-Alustiza, José Antonio and
               Olalde, Iñigo and Papac, Luka and Penske, Sandra and Peška,
               Jaroslav and Pinhasi, Ron and Reich, David and Reinhold, Sabine
               and Stahl, Raphaela and Stäuble, Harald and Tukhbatova, Rezeda I
               and Vasilyev, Sergey and Veselovskaya, Elizaveta and Warinner,
               Christina and Stockhammer, Philipp W and Haak, Wolfgang and
               Krause, Johannes and Herbig, Alexander},
  journal   = {Proceedings of the National Academy of Sciences of the United
               States of America},
  publisher = {Proceedings of the National Academy of Sciences},
  volume    = 119,
  number    = 17,
  pages     = {e2116722119},
  abstract  = {The bacterial pathogen Yersinia pestis gave rise to devastating
               outbreaks throughout human history, and ancient DNA evidence has
               shown it afflicted human populations as far back as the
               Neolithic. Y. pestis genomes recovered from the Eurasian Late
               Neolithic/Early Bronze Age (LNBA) period have uncovered key
               evolutionary steps that led to its emergence from a Yersinia
               pseudotuberculosis-like progenitor; however, the number of
               reconstructed LNBA genomes are too few to explore its diversity
               during this critical period of development. Here, we present 17
               Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide
               geographic expanse across Eurasia. This increased dataset enabled
               us to explore correlations between temporal, geographical, and
               genetic distance. Our results suggest a nonflea-adapted and
               potentially extinct single lineage that persisted over millennia
               without significant parallel diversification, accompanied by
               rapid dispersal across continents throughout this period, a trend
               not observed in other pathogens for which ancient genomes are
               available. A stepwise pattern of gene loss provides further clues
               on its early evolution and potential adaptation. We also discover
               the presence of the flea-adapted form of Y. pestis in Bronze Age
               Iberia, previously only identified in in the Caucasus and the
               Volga regions, suggesting a much wider geographic spread of this
               form of Y. pestis. Together, these data reveal the dynamic nature
               of plague’s formative years in terms of its early evolution and
               ecology.},
  month     = apr,
  year      = 2022,
  url       = {https://www.pnas.org/doi/abs/10.1073/pnas.2116722119},
  keywords  = {Yersinia pestis; ancient DNA; plague},
  doi       = {10.1073/pnas.2116722119},
  pmc       = {PMC9169917},
  pmid      = 35412864,
  issn      = {0027-8424,1091-6490},
  language  = {en}
}
@article{Fellows_Yates2017-rp,
  title    = {Central European Woolly Mammoth Population Dynamics: Insights from
              Late Pleistocene Mitochondrial Genomes},
  author   = {Fellows Yates, James A and Drucker, Dorothée G and Reiter, Ella
              and Heumos, Simon and Welker, Frido and Münzel, Susanne C and
              Wojtal, Piotr and Lázničková-Galetová, Martina and Conard,
              Nicholas J and Herbig, Alexander and Bocherens, Hervé and Krause,
              Johannes},
  journal  = {Scientific reports},
  volume   = 7,
  number   = 1,
  pages    = 17714,
  abstract = {The population dynamics of the Pleistocene woolly mammoth
              (Mammuthus primigenius) has been the subject of intensive
              palaeogenetic research. Although a large number of mitochondrial
              genomes across Eurasia have been reconstructed, the available data
              remains geographically sparse and mostly focused on eastern
              Eurasia. Thus, population dynamics in other regions have not been
              extensively investigated. Here, we use a multi-method approach
              utilising proteomic, stable isotope and genetic techniques to
              identify and generate twenty woolly mammoth mitochondrial genomes,
              and associated dietary stable isotopic data, from highly
              fragmentary Late Pleistocene material from central Europe. We
              begin to address region-specific questions regarding central
              European woolly mammoth populations, highlighting parallels with a
              previous replacement event in eastern Eurasia ten thousand years
              earlier. A high number of shared derived mutations between woolly
              mammoth mitochondrial clades are identified, questioning previous
              phylogenetic analysis and thus emphasizing the need for nuclear
              DNA studies to explicate the increasingly complex genetic history
              of the woolly mammoth.},
  month    = dec,
  year     = 2017,
  url      = {https://doi.org/10.1038/s41598-017-17723-1},
  doi      = {10.1038/s41598-017-17723-1},
  issn     = {2045-2322}
}

@article{Cai2022-rp,
  title     = {Radiocarbon and genomic evidence for the survival of Equus
               Sussemionus until the late Holocene},
  author    = {Cai, Dawei and Zhu, Siqi and Gong, Mian and Zhang, Naifan and
               Wen, Jia and Liang, Qiyao and Sun, Weilu and Shao, Xinyue and
               Guo, Yaqi and Cai, Yudong and Zheng, Zhuqing and Zhang, Wei and
               Hu, Songmei and Wang, Xiaoyang and Tian, He and Li, Youqian and
               Liu, Wei and Yang, Miaomiao and Yang, Jian and Wu, Duo and
               Orlando, Ludovic and Jiang, Yu},
  journal   = {eLife},
  publisher = {eLife Sciences Publications, Ltd},
  volume    = 11,
  abstract  = {The exceptionally rich fossil record available for the equid
               family has provided textbook examples of macroevolutionary
               changes. Horses, asses, and zebras represent three extant
               subgenera of Equus lineage, while the Sussemionus subgenus is
               another remarkable Equus lineage ranging from North America to
               Ethiopia in the Pleistocene. We sequenced 26 archaeological
               specimens from Northern China in the Holocene that could be
               assigned morphologically and genetically to Equus ovodovi, a
               species representative of Sussemionus. We present the first
               high-quality complete genome of the Sussemionus lineage, which
               was sequenced to 13.4× depth of coverage. Radiocarbon dating
               demonstrates that this lineage survived until ~3500 years ago,
               despite continued demographic collapse during the Last Glacial
               Maximum and the great human expansion in East Asia. We also
               confirmed the Equus phylogenetic tree and found that Sussemionus
               diverged from the ancestor of non-caballine equids ~2.3-2.7
               million years ago and possibly remained affected by secondary
               gene flow post-divergence. We found that the small genetic
               diversity, rather than enhanced inbreeding, limited the species'
               chances of survival. Our work adds to the growing literature
               illustrating how ancient DNA can inform on extinction dynamics
               and the long-term resilience of species surviving in cryptic
               population pockets.},
  month     = may,
  year      = 2022,
  url       = {https://elifesciences.org/articles/73346},
  keywords  = {ancient DNA; equids; equus ovodovi; evolutionary biology;
               evolutionary genomics; extinction; genetics; genomics},
  doi       = {10.7554/eLife.73346},
  pmc       = {PMC9142152},
  pmid      = 35543411,
  issn      = {2050-084X},
  language  = {en}
}

@article{Brealey2020-mu,
  title    = {Dental Calculus as a Tool to Study the Evolution of the Mammalian
              Oral Microbiome},
  author   = {Brealey, Jaelle C and Leitão, Henrique G and van der Valk, Tom and
              Xu, Wenbo and Bougiouri, Katia and Dalén, Love and Guschanski,
              Katerina},
  journal  = {Molecular biology and evolution},
  volume   = 37,
  number   = 10,
  pages    = {3003--3022},
  abstract = {Dental calculus, the calcified form of the mammalian oral
              microbial plaque biofilm, is a rich source of oral microbiome,
              host, and dietary biomolecules and is well preserved in museum and
              archaeological specimens. Despite its wide presence in mammals, to
              date, dental calculus has primarily been used to study primate
              microbiome evolution. We establish dental calculus as a valuable
              tool for the study of nonhuman host microbiome evolution, by using
              shotgun metagenomics to characterize the taxonomic and functional
              composition of the oral microbiome in species as diverse as
              gorillas, bears, and reindeer. We detect oral pathogens in
              individuals with evidence of oral disease, assemble near-complete
              bacterial genomes from historical specimens, characterize
              antibiotic resistance genes, reconstruct components of the host
              diet, and recover host genetic profiles. Our work demonstrates
              that metagenomic analyses of dental calculus can be performed on a
              diverse range of mammalian species, which will allow the study of
              oral microbiome and pathogen evolution from a comparative
              perspective. As dental calculus is readily preserved through time,
              it can also facilitate the quantification of the impact of
              anthropogenic changes on wildlife and the environment.},
  month    = oct,
  year     = 2020,
  url      = {http://dx.doi.org/10.1093/molbev/msaa135},
  keywords = {ancient DNA; antimicrobial resistance; metagenome-assembled
              genomes; metagenomics; oral pathogens},
  doi      = {10.1093/molbev/msaa135},
  pmc      = {PMC7530607},
  pmid     = 32467975,
  issn     = {0737-4038,1537-1719},
  language = {en}
}

@article{Rohland2015-xn,
  title    = {Partial uracil-{DNA}-glycosylase treatment for screening of
              ancient {DNA}},
  author   = {Rohland, Nadin and Harney, Eadaoin and Mallick, Swapan and
              Nordenfelt, Susanne and Reich, David},
  journal  = {Philosophical transactions of the Royal Society of London. Series
              B, Biological sciences},
  volume   = 370,
  number   = 1660,
  pages    = 20130624,
  abstract = {The challenge of sequencing ancient DNA has led to the development
              of specialized laboratory protocols that have focused on reducing
              contamination and maximizing the number of molecules that are
              extracted from ancient remains. Despite the fact that success in
              ancient DNA studies is typically obtained by screening many
              samples to identify a promising subset, ancient DNA protocols have
              not, in general, focused on reducing the time required to screen
              samples. We present an adaptation of a popular ancient library
              preparation method that makes screening more efficient. First, the
              DNA extract is treated using a protocol that causes characteristic
              ancient DNA damage to be restricted to the terminal nucleotides,
              while nearly eliminating it in the interior of the DNA molecules,
              allowing a single library to be used both to test for ancient DNA
              authenticity and to carry out population genetic analysis. Second,
              the DNA molecules are ligated to a unique pair of barcodes, which
              eliminates undetected cross-contamination from this step onwards.
              Third, the barcoded library molecules include incomplete adapters
              of short length that can increase the specificity of
              hybridization-based genomic target enrichment. The adapters are
              completed just before sequencing, so the same DNA library can be
              used in multiple experiments, and the sequences distinguished. We
              demonstrate this protocol on 60 ancient human samples.},
  month    = jan,
  year     = 2015,
  url      = {http://dx.doi.org/10.1098/rstb.2013.0624},
  keywords = {ancient DNA; authenticity; barcodes; flexibility; library
              preparation; target capture},
  doi      = {10.1098/rstb.2013.0624},
  pmc      = {PMC4275898},
  pmid     = 25487342,
  issn     = {0962-8436,1471-2970},
  language = {en}
}

@article{Chen2018-vg,
  title     = {fastp: an ultra-fast all-in-one {FASTQ} preprocessor},
  author    = {Chen, Shifu and Zhou, Yanqing and Chen, Yaru and Gu, Jia},
  journal   = {Bioinformatics},
  publisher = {Oxford University Press},
  volume    = 34,
  number    = 17,
  pages     = {i884--i890},
  abstract  = {Quality control and preprocessing of FASTQ files are essential to
               providing clean data for downstream analysis. Traditionally, a
               different tool is used for each operation, such as quality
               control, adapter trimming and quality filtering. These tools are
               often insufficiently fast as most are developed using high-level
               programming languages (e.g. Python and Java) and provide limited
               multi-threading support. Reading and loading data multiple times
               also renders preprocessing slow and I/O inefficient.We developed
               fastp as an ultra-fast FASTQ preprocessor with useful quality
               control and data-filtering features. It can perform quality
               control, adapter trimming, quality filtering, per-read quality
               pruning and many other operations with a single scan of the FASTQ
               data. This tool is developed in C++ and has multi-threading
               support. Based on our evaluation, fastp is 2–5 times faster than
               other FASTQ preprocessing tools such as Trimmomatic or Cutadapt
               despite performing far more operations than similar tools.The
               open-source code and corresponding instructions are available at
               https://github.com/OpenGene/fastp.},
  month     = sep,
  year      = 2018,
  url       = {https://academic.oup.com/bioinformatics/article/34/17/i884/5093234},
  doi       = {10.1093/bioinformatics/bty560},
  issn      = {1367-4803}
}


@article{Martin2011-ae,
  title     = {Cutadapt removes adapter sequences from high-throughput
               sequencing reads},
  author    = {Martin, Marcel},
  journal   = {EMBnet.journal},
  publisher = {EMBnet Stichting},
  volume    = 17,
  number    = 1,
  pages     = 10,
  abstract  = {When small RNA is sequenced on current sequencing machines, the
               resulting reads are usually longer than the RNA and therefore
               contain parts of the 3' adapter. That adapter must be found and
               removed error-tolerantly from each read before read mapping.
               Previous solutions are either hard to use or do not offer
               required features, in particular support for color space data. As
               an easy to use alternative, we developed the command-line tool
               cutadapt, which supports 454, Illumina and SOLiD (color space)
               data, offers two adapter trimming algorithms, and has other
               useful features. Cutadapt, including its MIT-licensed source
               code, is available for download at
               http://code.google.com/p/cutadapt/},
  month     = may,
  year      = 2011,
  url       = {https://journal.embnet.org/index.php/embnetjournal/article/view/200},
  keywords  = {next generation sequencing; small RNA; microRNA; adapter removal},
  doi       = {10.14806/ej.17.1.200},
  issn      = {2226-6089,2226-6089},
  language  = {en}
}
@article{Magoc2011-xl,
  title     = {{FLASH}: fast length adjustment of short reads to improve genome
               assemblies},
  author    = {Magoč, Tanja and Salzberg, Steven L},
  journal   = {Bioinformatics (Oxford, England)},
  publisher = {Oxford University Press (OUP)},
  volume    = 27,
  number    = 21,
  pages     = {2957--2963},
  abstract  = {MOTIVATION: Next-generation sequencing technologies generate very
               large numbers of short reads. Even with very deep genome
               coverage, short read lengths cause problems in de novo
               assemblies. The use of paired-end libraries with a fragment size
               shorter than twice the read length provides an opportunity to
               generate much longer reads by overlapping and merging read pairs
               before assembling a genome. RESULTS: We present FLASH, a fast
               computational tool to extend the length of short reads by
               overlapping paired-end reads from fragment libraries that are
               sufficiently short. We tested the correctness of the tool on one
               million simulated read pairs, and we then applied it as a
               pre-processor for genome assemblies of Illumina reads from the
               bacterium Staphylococcus aureus and human chromosome 14. FLASH
               correctly extended and merged reads >99\% of the time on
               simulated reads with an error rate of <1\%. With adequately set
               parameters, FLASH correctly merged reads over 90\% of the time
               even when the reads contained up to 5\% errors. When FLASH was
               used to extend reads prior to assembly, the resulting assemblies
               had substantially greater N50 lengths for both contigs and
               scaffolds. AVAILABILITY AND IMPLEMENTATION: The FLASH system is
               implemented in C and is freely available as open-source code at
               http://www.cbcb.umd.edu/software/flash. CONTACT:
               t.magoc@gmail.com.},
  month     = nov,
  year      = 2011,
  url       = {https://academic.oup.com/bioinformatics/article-pdf/27/21/2957/48863763/bioinformatics_27_21_2957.pdf},
  doi       = {10.1093/bioinformatics/btr507},
  pmc       = {PMC3198573},
  pmid      = 21903629,
  issn      = {1367-4803,1367-4811},
  language  = {en}
}

@article{Wegner2023-ca,
  title     = {A glimpse of the paleome in endolithic microbial communities},
  author    = {Wegner, Carl-Eric and Stahl, Raphaela and Velsko, Irina and
               Hübner, Alex and Fagernäs, Zandra and Warinner, Christina and
               Lehmann, Robert and Ritschel, Thomas and Totsche, Kai U and
               Küsel, Kirsten},
  journal   = {Microbiome},
  publisher = {Springer Science and Business Media LLC},
  volume    = 11,
  number    = 1,
  pages     = 210,
  abstract  = {BACKGROUND: The terrestrial subsurface is home to a significant
               proportion of the Earth's microbial biomass. Our understanding
               about terrestrial subsurface microbiomes is almost exclusively
               derived from groundwater and porous sediments mainly by using 16S
               rRNA gene surveys. To obtain more insights about biomass of
               consolidated rocks and the metabolic status of endolithic
               microbiomes, we investigated interbedded limestone and mudstone
               from the vadose zone, fractured aquifers, and deep aquitards.
               RESULTS: By adapting methods from microbial archaeology and
               paleogenomics, we could recover sufficient DNA for downstream
               metagenomic analysis from seven rock specimens independent of
               porosity, lithology, and depth. Based on the extracted DNA, we
               estimated between 2.81 and 4.25 × 105 cells × g-1 rock. Analyzing
               DNA damage patterns revealed paleome signatures (genetic records
               of past microbial communities) for three rock specimens, all
               obtained from the vadose zone. DNA obtained from deep aquitards
               isolated from surface input was not affected by DNA decay
               indicating that water saturation and not flow is controlling
               subsurface microbial survival. Decoding the taxonomy and
               functional potential of paleome communities revealed increased
               abundances for sequences affiliated with chemolithoautotrophs and
               taxa such as Cand. Rokubacteria. We also found a broader
               metabolic potential in terms of aromatic hydrocarbon breakdown,
               suggesting a preferred utilization of sedimentary organic matter
               in the past. CONCLUSIONS: Our study suggests that limestones
               function as archives for genetic records of past microbial
               communities including those sensitive to environmental stress at
               modern times, due to their specific conditions facilitating
               long-term DNA preservation. Video Abstract.},
  month     = sep,
  year      = 2023,
  url       = {https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01647-2},
  keywords  = {Chemolithotrophy; DNA damage; Endolithic; Metagenomics;
               Subsurface},
  doi       = {10.1186/s40168-023-01647-2},
  pmc       = {PMC10518947},
  pmid      = 37749660,
  issn      = {2049-2618,2049-2618},
  language  = {en}
}