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A likelihood method for estimating present-day human contamination in ancient DNA samples using low-depth haploid chromosome data [article]

J. Víctor Moreno-Mayar, Thorfinn Sand Korneliussen, Anders Albrechtsen, Jyoti Dalal, Gabriel Renaud, Rasmus Nielsen, Anna-Sapfo Malaspinas
2019 bioRxiv   pre-print
method for estimating present-day human contamination in low-depth sequencing data.  ...  In contrast, our method provides accurate estimates for a depth of coverage as low as 0.5× on the X-chromosome when contamination is below 25%.  ...  It can accurately estimate present-100 day human contamination for male samples that are likely to be candidates for further evolutionary 101 analysis (i.e. when contamination is <25%) when the X-chromosome  ... 
doi:10.1101/594481 fatcat:l7lll3g3rjcz5dfvq56mp37pty

ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

Nathan Nakatsuka, Éadaoin Harney, Swapan Mallick, Matthew Mah, Nick Patterson, David Reich
2020 Genome Biology  
We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant  ...  Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors: for example, less than 1.5% standard error in cases with less than 10% contamination and 500,000  ...  Acknowledgements We thank Iosif Lazaridis and Mark Lipson for helpful discussions. Review history The review history is available as Additional file 6.  ... 
doi:10.1186/s13059-020-02111-2 pmid:32778142 fatcat:tzcufbbax5dqxkhp3f7s4y2qxq

AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination

Stéphane Peyrégne, Benjamin M. Peter
2020 Genome Biology  
We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries.  ...  Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses  ...  Acknowledgements We thank Johann Visagie for valuable input in the implementation of AuthentiCT, Alba Bossom Mesa, Cesare de Filippo, Mateja Hajdinjak, Janet Kelso, Matthias Meyer and Elena Zavala for  ... 
doi:10.1186/s13059-020-02123-y pmid:32933569 fatcat:akv7epdgyvb4ba2idm4mip5x7a

ContamLD: Estimation of Ancient Nuclear DNA Contamination Using Breakdown of Linkage Disequilibrium [article]

Nathan Joel Nakatsuka, Eadaoin Harney, Swapan Mallick, Matthew Mah, Nick Patterson, David E. Reich
2020 bioRxiv   pre-print
Here we report a method called ContamLD for estimating autosomal aDNA contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant  ...  Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors (e.g. less than 1.5% standard error in cases with <10% contamination and data from at least  ...  We used 257 data from male individuals selected due to very low X chromosome contamination estimates 258 (less than 1%) based on ANGSD [16] (developed first in Rasmussen et al. [9] ; we used method 259  ... 
doi:10.1101/2020.02.06.938126 fatcat:rwwvueh2cjgatnr4tnm4stpa2q

AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination [article]

Stėphane Peyrėgne, Benjamin M. Peter
2020 bioRxiv   pre-print
We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries.  ...  Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses  ...  For instance, 57 apparent heterozygous sites on the X chromosome of a male individual or sequences mapping to the Y 58 chromosome for a female individual represent evidence of DNA contamination.  ... 
doi:10.1101/2020.03.13.991240 fatcat:snvecd3evffpxhznlmtfldfqa4

The efficacy of whole human genome capture on ancient dental calculus and dentin

Kirsten A. Ziesemer, Jazmín Ramos-Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno Hoogland, Courtney A. Hofman, Domingo C. Salazar-García, Bruno Frohlich, George R. Milner, Anne C. Stone (+5 others)
2018 American Journal of Physical Anthropology  
Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques.  ...  Dental calculus is among the richest known sources of ancient DNA in the archaeological record.  ...  Given the low depth of human genome coverage in the ancient samples(Supporting Information Tables S2 and S3), we did not rely on called genotypes, but rather used a genotype likelihood-based approach to  ... 
doi:10.1002/ajpa.23763 pmid:30586168 pmcid:PMC6519167 fatcat:efdsen2zebbb7hlazo5ws5h6ne

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Maanasa Raghavan, Pontus Skoglund, Kelly E. Graf, Mait Metspalu, Anders Albrechtsen, Ida Moltke, Simon Rasmussen, Thomas W. Stafford Jr, Ludovic Orlando, Ene Metspalu, Monika Karmin, Kristiina Tambets (+19 others)
2013 Nature  
SI 5.1.3 Results Results are shown in .1 Description of the method Contamination estimates were obtained using data from the X chromosome of MA-1 and AG-2.  ...  Analysis of AG-2 using nucleotide misincorporation patterns Both mitochondrial and X-chromosomal data suggest that the sequence data from AG-2 is affected by substantial present-day DNA contamination (  ...  Note that mixtures where only a minor fraction is from one source such as the Dai and the French should likely be interpreted as false positives for mixture. AdmixedPop  ... 
doi:10.1038/nature12736 pmid:24256729 pmcid:PMC4105016 fatcat:aq5osbpupvd7vdjhwqly5sr4sm

Genomic insights into the peopling of the Southwest Pacific

Pontus Skoglund, Cosimo Posth, Kendra Sirak, Matthew Spriggs, Frederique Valentin, Stuart Bedford, Geoffrey R. Clark, Christian Reepmeyer, Fiona Petchey, Daniel Fernandes, Qiaomei Fu, Eadaoin Harney (+19 others)
2016 Nature  
We thank Murray Brilliant, Heather Norton, and Laura Scheinfeldt, for help in the preparation of the Bismarck samples and establishment of a repository for them at the Marshfield Foundation.  ...  Acknowledgments We thank the 356 volunteers who donated samples for genome-wide analysis. We thank Mark Stoneking for cofunding genotyping of the Bismarck samples.  ...  Since all four individuals were female, we could not estimate contamination using X-chromosome data.  ... 
doi:10.1038/nature19844 pmid:27698418 pmcid:PMC5515717 fatcat:irfupuararfdlffutk7cf655sm

Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia

Constanza de la Fuente, María C. Ávila-Arcos, Jacqueline Galimany, Meredith L. Carpenter, Julian R. Homburger, Alejandro Blanco, Paloma Contreras, Diana Cruz Dávalos, Omar Reyes, Manuel San Roman, Andrés Moreno-Estrada, Paula F. Campos (+9 others)
2018 Proceedings of the National Academy of Sciences of the United States of America  
We thank Consuelo Quinto for helpful comments on earlier versions of this manuscript. This work was supported by Comisión Nacional de Investigación Científica y Tecnológica  ...  depth mtDNA 151.8 148.9 164.1 164.7 Morphological sex estimation Female No data No data Male Molecular sex estimation Female Male Male Male Contamination percentage mtDNA 1.6 0.6 0.3  ...  The Y chromosome haplogroups were identified as Q1a2a1a1-M3 for the three male individuals (Samples and Methods).  ... 
doi:10.1073/pnas.1715688115 pmid:29632188 fatcat:wvpryuzjtnczfinutxpyreruq4

Salmonella enterica from a soldier from the 1652-siege of Barcelona (Spain) supports historical transatlantic epidemic contacts

Toni de-Dios, Pablo Carrión, Iñigo Olalde, Laia Llovera Nadal, Esther Lizano, Dídac Pàmies, Tomas Marques-Bonet, François Balloux, Lucy van Dorp, Carles Lalueza-Fox
2021 iScience  
We retrieved genome-wide data from two Spanish soldiers who were besieging the city of Barcelona in 1652, during the Reapers' War.  ...  Despite the proposed plague epidemic, we could not find solid evidence for the presence of the causative plague agent in these individuals.  ...  ACKNOWLEDGMENTS We are grateful to the Museum of the History of Barcelona (MUHBA) for allowing access to these samples.  ... 
doi:10.1016/j.isci.2021.103021 pmid:34527890 pmcid:PMC8430385 fatcat:c6vkoeurvrcmldvehroktulexm

Genetic origins of the Minoans and Mycenaeans

Iosif Lazaridis, Alissa Mittnik, Nick Patterson, Swapan Mallick, Nadin Rohland, Saskia Pfrengle, Anja Furtwängler, Alexander Peltzer, Cosimo Posth, Andonis Vasilakis, P. J. P. McGeorge, Eleni Konsolaki-Yannopoulou (+22 others)
2017 Nature  
All maps were plotted in R using the worldHiRes map of the 'mapdata' package (using public domain data from the CIA World Data Bank II).  ...  (Trifylia) museums for facilitating sample collection.  ...  X-chromosome (Methods).  ... 
doi:10.1038/nature23310 pmid:28783727 pmcid:PMC5565772 fatcat:3qtyfmcbgrhmbl7ww3wgiyseia

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

Hannes Schroeder, María C. Ávila-Arcos, Anna-Sapfo Malaspinas, G. David Poznik, Marcela Sandoval-Velasco, Meredith L. Carpenter, José Víctor Moreno-Mayar, Martin Sikora, Philip L. F. Johnson, Morten Erik Allentoft, José Alfredo Samaniego, Jay B. Haviser (+7 others)
2015 Proceedings of the National Academy of Sciences of the United States of America  
Contamination estimates Probabilistic-based method for estimating contamination using mtDNA reads To estimate contamination, we used a previously described method (54) that generates a momentbased estimate  ...  Because of low depth, we randomly sampled a single allele from both ancient and modern individuals, as done in ref. 13 .  ...  Late 17th-century artifacts found in the same layer as three Zoutsteeg burials. Reproduced with permission from ref. 11.  ... 
doi:10.1073/pnas.1421784112 pmid:25755263 pmcid:PMC4378422 fatcat:m354kxrnx5ba3iqmhp2nuvovtq

The genetic origins of Saint Helena's liberated Africans [article]

Marcela Sandoval-Velasco, Anuradha Jagadeesan, María C. Ávila-Arcos, Shyam Gopalakrishnan, Jazmín Ramos-Madrigal, J. Víctor Moreno-Mayar, Gabriel Renaud, Diana I. Cruz-Dávalos, Erna Johannesdóttir, Judy Watson, Kate Robson-Brown, Andrew Pearson (+3 others)
2019 bioRxiv   pre-print
The genetic data shows they came from West Central Africa, possibly the area of present-day Gabon and Angola.  ...  To investigate their origins, we generated genome-wide ancient DNA data for 20 individuals recovered from St Helena.  ...  Jónsson for assistance during data analysis, and I. Dull for thoughtful and valuable input into the manuscript. The research was supported by the EUROTAST project, a Marie  ... 
doi:10.1101/787515 fatcat:bod4uuqphnbaxmh5gjcxnbuv7y

Ancient human genomes suggest three ancestral populations for present-day Europeans [article]

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Karola Kirsanow, Peter H. Sudmant, Joshua G. Schraiber, Sergi Castellano, Mark Lipson, Bonnie Berger, Christos Economou (+108 others)
2013 bioRxiv   pre-print
We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations  ...  We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 year old hunter-gatherer from Luxembourg, and seven ~8,000 year old hunter-gatherers from southern Sweden.  ...  to show that DNA sequences retrieved from ancient samples are authentic and not due to present-day human contamination.  ... 
doi:10.1101/001552 fatcat:2sdclidul5fvjamoxktdqwbe44

Genome-wide patterns of selection in 230 ancient Eurasians

Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Nick Patterson, Songül Alpaslan Roodenberg, Eadaoin Harney, Kristin Stewardson, Daniel Fernandes, Mario Novak, Kendra Sirak, Cristina Gamba (+26 others)
2015 Nature  
'HO' consists of 592,169 SNPs, taking the intersection of the SNP targets and the Human Origins SNP array 4 ; we used this data set for co-analysis of present-day and ancient samples.  ...  chromosome X despite being male 45 , or an atypical ratio of X to Y sequences.  ... 
doi:10.1038/nature16152 pmid:26595274 pmcid:PMC4918750 fatcat:qg3loh5q4bddppfjr7xubg5yuy
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