%0 Journal Article %1 racimo2016joint %A Racimo, Fernando %A Renaud, Gabriel %A Slatkin, Montgomery %D 2016 %I Public Library of Science %J PLOS Genetics %K MCMC ancient_DNA methods sequencing_error %N 4 %P 1-27 %R 10.1371/journal.pgen.1005972 %T Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans %U https://doi.org/10.1371/journal.pgen.1005972 %V 12 %X Author Summary When extracting and sequencing ancient DNA from human remains, a recurrent problem is the presence of DNA from the paleontologists, archaeologists or geneticists that may have handled the fossil. If a DNA library is highly contaminated, this will introduce biases in downstream analyses, so it is important to determine the amount of extraneous DNA. Different methods exist for this purpose, but few are applicable to the nuclear genome, and none of them can extract reliable genomic information from highly contaminated samples. Thus, samples with high rates of contamination are usually discarded. Here, we present a method to jointly estimate contamination and error rates, along with demographic parameters, like drift times and admixture rates. Our method can serve to uncover important details about the evolutionary history of archaic and early modern humans from ancient DNA samples, even if those samples are highly contaminated.

@article{racimo2016joint, abstract = {Author Summary When extracting and sequencing ancient DNA from human remains, a recurrent problem is the presence of DNA from the paleontologists, archaeologists or geneticists that may have handled the fossil. If a DNA library is highly contaminated, this will introduce biases in downstream analyses, so it is important to determine the amount of extraneous DNA. Different methods exist for this purpose, but few are applicable to the nuclear genome, and none of them can extract reliable genomic information from highly contaminated samples. Thus, samples with high rates of contamination are usually discarded. Here, we present a method to jointly estimate contamination and error rates, along with demographic parameters, like drift times and admixture rates. Our method can serve to uncover important details about the evolutionary history of archaic and early modern humans from ancient DNA samples, even if those samples are highly contaminated.}, added-at = {2018-01-04T19:36:20.000+0100}, author = {Racimo, Fernando and Renaud, Gabriel and Slatkin, Montgomery}, biburl = {https://www.bibsonomy.org/bibtex/2b4a2745193c32de3c5d71673d494c3e4/peter.ralph}, doi = {10.1371/journal.pgen.1005972}, interhash = {63b1182f97ce2cd9ac0c32bc4d04d4de}, intrahash = {b4a2745193c32de3c5d71673d494c3e4}, journal = {PLOS Genetics}, keywords = {MCMC ancient_DNA methods sequencing_error}, month = {04}, number = 4, pages = {1-27}, publisher = {Public Library of Science}, timestamp = {2018-01-04T19:36:20.000+0100}, title = {Joint Estimation of Contamination, Error and Demography for Nuclear {DNA} from Ancient Humans}, url = {https://doi.org/10.1371/journal.pgen.1005972}, volume = 12, year = 2016 }