@article{HofreiterHartmann2020,
  author    = {Hofreiter, Michael and Hartmann, Stefanie},
  title     = {Reconstructing protein-coding sequences from ancient DNA},
  series = {Odorant binding and chemosensory proteins},
  volume    = {642},
  journal   = {Odorant binding and chemosensory proteins},
  publisher = {Academic Press, an imprint of Elsevier},
  address   = {Cambridge, MA.},
  isbn      = {978-0-12-821157-1},
  issn      = {0076-6879},
  doi       = {10.1016/bs.mie.2020.05.008},
  pages     = {21 -- 33},
  year      = {2020},
  abstract  = {Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including mis-coding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.},
  language  = {en}
}
@misc{WestburyBalekaBarlowetal.2017,
  author    = {Westbury, Michael V. and Baleka, Sina Isabelle and Barlow, Axel and Hartmann, Stefanie and Paijmans, Johanna L. A. and Kramarz, Alejandro and Forasiepi, Anal{\´i}a M. and Bond, Mariano and Gelfo, Javier N. and Reguero, Marcelo A. and L{\´o}pez-Mendoza, Patricio and Taglioretti, Matias and Scaglia, Fernando and Rinderknecht, Andr{\´e}s and Jones, Washington and Mena, Francisco and Billet, Guillaume and de Muizon, Christian and Aguilar, Jos{\´e} Luis and MacPhee, Ross D.E. and Hofreiter, Michael},
  title     = {A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {793},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44080},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-440801},
  pages     = {8},
  year      = {2017},
  abstract  = {The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of B66Ma (95\% credibility interval, 56.64-77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives.},
  language  = {en}
}
@misc{BarlowHartmannGonzalezetal.2020,
  author    = {Barlow, Axel and Hartmann, Stefanie and Gonzalez, Javier and Hofreiter, Michael and Paijmans, Johanna L. A.},
  title     = {Consensify},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1033},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-47252},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-472521},
  pages     = {24},
  year      = {2020},
  abstract  = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.},
  language  = {en}
}
@article{BarlowHartmannGonzalezetal.2020,
  author    = {Barlow, Axel and Hartmann, Stefanie and Gonzalez, Javier and Hofreiter, Michael and Paijmans, Johanna L. A.},
  title     = {Consensify},
  series = {Genes / Molecular Diversity Preservation International},
  volume    = {11},
  journal   = {Genes / Molecular Diversity Preservation International},
  number    = {1},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4425},
  doi       = {10.3390/genes11010050},
  pages     = {22},
  year      = {2020},
  abstract  = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.},
  language  = {en}
}