TY  - GEN
A1  - Hofreiter, Michael
A1  - Paijmans, Johanna L. A.
A1  - Goodchild, Helen
A1  - Speller, Camilla F.
A1  - Barlow, Axel
A1  - Gonzalez-Fortes, Gloria M.
A1  - Thomas, Jessica A.
A1  - Ludwig, Arne
A1  - Collins, Matthew J.
T1  - The future of ancient DNA
BT  - technical advances and conceptual shifts
T2  - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 908 
KW  - ancient DNA
KW  - hybridisation capture
KW  - multi-locus data
KW  - next generation sequencing (NGS)
KW  - palaeogenomics
KW  - population genomics
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-438816
SN  - 1866-8372
IS  - 908
SP  - 284
EP  - 295
ER  - 
TY  - GEN
A1  - Basler, Nikolas
A1  - Xenikoudakis, Georgios
A1  - Westbury, Michael V.
A1  - Song, Lingfeng
A1  - Sheng, Guilian
A1  - Barlow, Axel
T1  - Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone
T2  - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
N2  - Objective:  A key challenge in ancient DNA research is massive microbial DNA contamination from the deposition site which accumulates post mortem in the study organism’s remains. Two simple and cost-effective methods to enrich the relative endogenous fraction of DNA in ancient samples involve treatment of sample powder with either bleach or Proteinase K pre-digestion prior to DNA extraction. Both approaches have yielded promising but vary-ing results in other studies. Here, we contribute data on the performance of these methods using a comprehensive and systematic series of experiments applied to a single ancient bone fragment from a giant panda (Ailuropoda melanoleuca).Results:  Bleach and pre-digestion treatments increased the endogenous DNA content up to ninefold. However, the absolute amount of DNA retrieved was dramatically reduced by all treatments. We also observed reduced DNA damage patterns in pre-treated libraries compared to untreated ones, resulting in longer mean fragment lengths and reduced thymine over-representation at fragment ends. Guanine–cytosine (GC) contents of both mapped and total reads are consistent between treatments and conform to general expectations, indicating no obvious biasing effect of the applied methods. Our results therefore confirm the value of bleach and pre-digestion as tools in palaeog-enomic studies, providing sufficient material is available.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 715 
KW  - ancient DNA (aDNA)
KW  - bleach
KW  - pre-digestion
KW  - endogenous content
KW  - palaeogenomics
KW  - paleogenomics
KW  - next generation sequencing (NGS)
KW  - giant panda
KW  - Ailuropoda melanoleuca
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-428151
SN  - 1866-8372
IS  - 715
ER  -