@misc{KnappLaluezaFoxHofreiter2015,
  author    = {Knapp, Michael and Lalueza-Fox, Carles and Hofreiter, Michael},
  title     = {Re-inventing ancient human DNA},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {853},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43177},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431775},
  pages     = {14},
  year      = {2015},
  abstract  = {For a long time, the analysis of ancient human DNA represented one of the most controversial disciplines in an already controversial field of research. Scepticism in this field was only matched by the long-lasting controversy over the authenticity of ancient pathogen DNA. This ambiguous view on ancient human DNA had a dichotomous root. On the one hand, the interest in ancient human DNA is great because such studies touch on the history and evolution of our own species. On the other hand, because these studies are dealing with samples from our own species, results are easily compromised by contamination of the experiments with modern human DNA, which is ubiquitous in the environment. Consequently, some of the most disputed studies published - apart maybe from early reports on million year old dinosaur or amber DNA - reported DNA analyses from human subfossil remains. However, the development of so-called next- or second-generation sequencing (SGS) in 2005 and the technological advances associated with it have generated new confidence in the genetic study of ancient human remains. The ability to sequence shorter DNA fragments than with PCR amplification coupled to traditional Sanger sequencing, along with very high sequencing throughput have both reduced the risk of sequencing modern contamination and provided tools to evaluate the authenticity of DNA sequence data. The field is now rapidly developing, providing unprecedented insights into the evolution of our own species and past human population dynamics as well as the evolution and history of human pathogens and epidemics. Here, we review how recent technological improvements have rapidly transformed ancient human DNA research from a highly controversial subject to a central component of modern anthropological research. We also discuss potential future directions of ancient human DNA research.},
  language  = {en}
}
@misc{AlterMeyerPostetal.2015,
  author    = {Alter, S. Elizabeth and Meyer, Matthias and Post, Klaas and Czechowski, Paul and Gravlund, Peter and Gaines, Cork and Rosenbaum, Howard C. and Kaschner, Kristin and Turvey, Samuel T. and van der Plicht, Johannes and Shapiro, Beth and Hofreiter, Michael},
  title     = {Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {965},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43892},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438920},
  pages     = {1510 -- 1522},
  year      = {2015},
  abstract  = {Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.},
  language  = {en}
}
@misc{HofreiterPaijmansGoodchildetal.2015,
  author    = {Hofreiter, Michael and Paijmans, Johanna L. A. and Goodchild, Helen and Speller, Camilla F. and Barlow, Axel and Gonzalez-Fortes, Gloria M. and Thomas, Jessica A. and Ludwig, Arne and Collins, Matthew J.},
  title     = {The future of ancient DNA},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {908},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43881},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438816},
  pages     = {284 -- 295},
  year      = {2015},
  abstract  = {Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.},
  language  = {en}
}
@misc{JonesGonzalezFortesConnelletal.2015,
  author    = {Jones, Eppie R. and Gonz{\´a}lez-Fortes, Gloria M. and Connell, Sarah and Siska, Veronika and Eriksson, Anders and Martiniano, Rui and McLaughlin, Russell L. and Llorente, Marcos Gallego and Cassidy, Lara M. and Gamba, Cristina and Meshveliani, Tengiz and Bar-Yosef, Ofer and M{\"u}ller, Werner and Belfer-Cohen, Anna and Matskevich, Zinovi and Jakeli, Nino and Higham, Thomas F. G. and Currat, Mathias and Lordkipanidze, David and Hofreiter, Michael and Manica, Andrea and Pinhasi, Ron and Bradley, Daniel G.},
  title     = {Upper Palaeolithic genomes reveal deep roots of modern Eurasians},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1334},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43931},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439317},
  pages     = {8},
  year      = {2015},
  abstract  = {We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.},
  language  = {en}
}
@misc{PinhasiFernandesSiraketal.2015,
  author    = {Pinhasi, Ron and Fernandes, Daniel and Sirak, Kendra and Novak, Mario and Connell, Sarah and Alpaslan-Roodenberg, Song{\"u}l and Gerritsen, Fokke and Moiseyev, Vyacheslav and Gromov, Andrey and Raczky, P{\´a}l and Anders, Alexandra and Pietrusewsky, Michael and Rollefson, Gary and Jovanovic, Marija and Trinhhoang, Hiep and Bar-Oz, Guy and Oxenham, Marc and Matsumura, Hirofumi and Hofreiter, Michael},
  title     = {Optimal ancient DNA yields from the inner ear part of the human petrous bone},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschafliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschafliche Reihe},
  number    = {515},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-40955},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-409557},
  pages     = {13},
  year      = {2015},
  abstract  = {The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (similar to 1\% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,0001,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1\% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.},
  language  = {en}
}
@misc{ElsnerSchiblerHofreiteretal.2015,
  author    = {Elsner, Julia and Schibler, J{\"o}rg and Hofreiter, Michael and Schlumbaum, Angela},
  title     = {Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {727},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42976},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429763},
  pages     = {505 -- 515},
  year      = {2015},
  abstract  = {Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the—inevitable—heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions.},
  language  = {en}
}