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@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:
[email protected] 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}
}