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Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments [article]

Logan Kistler, Oliver Smith, Roselyn Ware, Garry Momber, Richard Bates, Paul Garwood, Simon Fitch, Mark Pallen, Vincent Gaffney, Robin Allaby
2015 bioRxiv   pre-print
The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns.  ...  Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level.  ...  The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns.  ... 
doi:10.1101/032060 fatcat:nxjn555ojvclnkyhfjjdrf55de

Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA

Marianne Dehasque, Patrícia Pečnerová, Vendela Kempe Lagerholm, Erik Ersmark, Gleb K. Danilov, Peter Mortensen, Sergey Vartanyan, Love Dalén
2022 Genes  
Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.  ...  Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator  ...  The authors acknowledge support from the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory and also thank Illumina, inc. for partially co-funding the DNA sequencing, as  ... 
doi:10.3390/genes13040687 pmid:35456493 pmcid:PMC9032354 fatcat:ud2265r5jfgf3jojsjwolfwfg4

Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing [article]

Endre Neparaczki, Klaudia Kocsy, Gabor Endre Toth, Zoltan Maroti, Tibor Kalmar, Peter Bihari, Istvan Nagy, Gyorgy Palfi, Erika Molnar, Istvan Rasko, Tibor Torok
2016 bioRxiv   pre-print
The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly  ...  As part of the effort to create a high resolution representative sequence database of the medieval Hungarian conquerors we have resequenced the entire mtDNA genome of 24 published ancient samples with  ...  Ancient DNA damage patterns were assessed using MapDamage 2.0 (Jónsson et al., 2013) , and read quality scores were modified with the rescale option to account for post-mortem damage.  ... 
doi:10.1101/092239 fatcat:4xrxss6xjzcg7oxtbwb7xuv7m4

Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago

Veronika Siska, Eppie Ruth Jones, Sungwon Jeon, Youngjune Bhak, Hak-Min Kim, Yun Sung Cho, Hyunho Kim, Kyusang Lee, Elizaveta Veselovskaya, Tatiana Balueva, Marcos Gallego-Llorente, Michael Hofreiter (+5 others)
2017 Science Advances  
contrasts with that reported for Europe.  ...  Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia.  ...  Raw reads in FASTA format and aligned reads as bamfiles for all five ancient samples from Devil's Gate are available from the European Nucleotide Archive accession code PRJEB14817.  ... 
doi:10.1126/sciadv.1601877 pmid:28164156 pmcid:PMC5287702 fatcat:k46xip4m7zbpxhg4c2gcrv743e

Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing

Endre Neparáczki, Klaudia Kocsy, Gábor Endre Tóth, Zoltán Maróti, Tibor Kalmár, Péter Bihari, István Nagy, György Pálfi, Erika Molnár, István Raskó, Tibor Török, David Caramelli
2017 PLoS ONE  
The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly  ...  DNA extraction Ancient DNA work was performed in the specialized ancient DNA (aDNA) facilities of the Department of Genetics, University of Szeged, Hungary with strict clean-room conditions. 100 mg bone  ...  Ancient DNA damage patterns were assessed using MapDamage 2.0 [23] , and read quality scores were modified with the rescale option to account for post-mortem damage.  ... 
doi:10.1371/journal.pone.0174886 pmid:28422985 pmcid:PMC5396865 fatcat:bkguytyu5jajbglm4dr7eu52my

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens

Clemens L. Weiß, Verena J. Schuenemann, Jane Devos, Gautam Shirsekar, Ella Reiter, Billie A. Gould, John R. Stinchcombe, Johannes Krause, Hernán A. Burbano
2016 Royal Society Open Science  
Consequently, herbarium samples are ideal to study the temporal patterns of damage and decay kinetics of DNA.  ...  Additionally, we use the power of multiple DNA sequencing libraries to calculate DNA decay rate in plant desiccated tissue.  ...  for ancient bones.  ... 
doi:10.1098/rsos.160239 pmid:27429780 pmcid:PMC4929915 fatcat:7iqhocft6nf4riziiolbph6yca

The Potential of Sedimentary Ancient DNA to Reconstruct Past Ocean Ecosystems

Linda Armbrecht, The University of Adelaide
2020 Oceanography  
However, the field of marine sedaDNA research is still in its infancy; community reconstructions are complicated by the minuscule amounts of ancient DNA preserved in the sediments.  ...  Sedimentary ancient DNA (sedaDNA) offers a novel approach to investigating past marine ecosystems-from the smallest bacteria to phytoplankton and their predatorsover geological timescales.  ...  ACKNOWLEDGMENTS Detailed information on eukaryote, bacterial, and archaeal communities not shown in this paper is available on request.  ... 
doi:10.5670/oceanog.2020.211 fatcat:ert2f6jdyvexdpvxboy2nrrhf4

A new model for ancient DNA decay based on paleogenomic meta-analysis [article]

Logan Kistler, Roselyn Ware, Oliver Smith, Matthew Collins, Robin G Allaby
2017 bioRxiv   pre-print
We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows.  ...  The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly  ...  Briggs AW et al. (2007) Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci USA 104:14616-14621. 20.  ... 
doi:10.1101/109140 fatcat:7xegc4mb5jcgtb37aasli7kcwu

A new model for ancient DNA decay based on paleogenomic meta-analysis

Logan Kistler, Roselyn Ware, Oliver Smith, Matthew Collins, Robin G. Allaby
2017 Nucleic Acids Research  
We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows.  ...  The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation  ...  ACKNOWLEDGEMENTS We thank Ludovic Orlando, Beth Shapiro and Kes Schroer for comments on an early version of the manuscript.  ... 
doi:10.1093/nar/gkx361 pmid:28486705 pmcid:PMC5499742 fatcat:k2xq3byskvehpeig4wnhcywbhq

Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf

Giada Ferrari, Heidi Lischer, Judith Neukamm, Enrique Rayo, Nicole Borel, Andreas Pospischil, Frank Rühli, Abigail Bouwman, Michael Campana
2018 Genes  
However, as for all ancient DNA (aDNA) studies, environmental and laboratory contamination need to be specifically addressed.  ...  The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies.  ...  We are grateful to Sirisha Aluri, Jelena Kühn-Georgijevic, Catharine Aquino and Lennart Opitz at the Functional Genomics Center Zurich for assistance with sequencing.  ... 
doi:10.3390/genes9090436 pmid:30200350 pmcid:PMC6162753 fatcat:6xhrphi4brc3pc4zahtzlbuaci

Natural mummification of the human gut preserves bacteriophage DNA

Tasha M. Santiago-Rodriguez, Gino Fornaciari, Stefania Luciani, Scot E. Dowd, Gary A. Toranzos, Isolina Marota, Raul J. Cano, Andrew Millard
2015 FEMS Microbiology Letters  
The present study suggests that the natural mummification of the human gut results in the preservation of bacteriophage DNA, representing an opportunity to elucidate the ancient phageome and to hypothesize  ...  the preservation of bacteriophage DNA.  ...  We also performed the mapDamage analyses to assess patterns of DNA damage that could be consistent with ancient DNA (Der Sarkissian et al. 2014 ), but did not note these patterns with the phageomes tested  ... 
doi:10.1093/femsle/fnv219 pmid:26564967 pmcid:PMC5812488 fatcat:apx3ildyhnavvgdw6l723m5ilu

On Controls in Ancient Microbiome Studies, and Microbial Resilience in Ancient Samples

Tasha Santiago-Rodriguez, Gary Toranzos
2018 Genes  
In the following comment, we reply to Eisenhofer and Weyrich's letter "Proper authentication of ancient DNA is still essential" responding to the article "Gut Microbiome and Putative Resistome of Inca  ...  We also discuss controls in ancient microbiome studies, and aspects of microbial resilience in ancient samples.  ...  When DNA damage occurs, again, mostly upon cell death, tools such as mapDamage can aid to assess misincorporations within a particular sequence [28] .  ... 
doi:10.3390/genes9100471 fatcat:mipxbps6dfezdgtvmvbh3m3myi

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

Oliver Smith, Glenn Dunshea, Mikkel-Holger S. Sinding, Sergey Fedorov, Mietje Germonpre, Hervé Bocherens, M. T. P. Gilbert, Chris Tyler-Smith
2019 PLoS Biology  
While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments  ...  has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology.  ...  Roselyn Ware for facilitating laboratory resources and arranging consumables prior to work taking place, and Matthew Poulter/BGI Copenhagen for generating the sequencing data.  ... 
doi:10.1371/journal.pbio.3000166 pmid:31361744 pmcid:PMC6667121 fatcat:v5djwrbsonc3xnjgqcy2tyrvui

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival [article]

Oliver Smith, Glenn Dunshea, Mikkel-Holger S Sinding, Sergey Fedorov, Mietje Germonpre, Hervé Bocherens, M.T.P. Gilbert
2019 biorxiv/medrxiv   pre-print
While sequencing ancient DNA from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such  ...  for tissue identification, and possibly further uses such as in vivo genome activity and adaptation, when sequenced using this technology.  ...  Roselyn Ware for facilitating laboratory resources and arranging consumables prior to work taking place, and Matthew Poulter/BGI Copenhagen for generating the sequencing data.  ... 
doi:10.1101/546820 fatcat:eoenfg5xwbgy5ppzxjauzcpqaa

Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes [article]

Linda Armbrecht, Gustaaf Hallegraeff, Christopher Bolch, Craig Woodward, Alan Cooper
2020 bioRxiv   pre-print
Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and  ...  DNA damage profiles of a key phytoplankton, the ubiquitous coccolithophore Emiliania huxleyi.  ...  Acknowledgements We are grateful to Brian Brunelle from Arbor Biosciences, USA, for his expert assistance with designing Phytobaits1 and HABbaits1.  ... 
doi:10.1101/2020.09.25.310920 fatcat:2lltcjl6srdfxpnpkopjs7aefi
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