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  - 
TY  - JOUR
A1  - Yuan, Junxia
A1  - Sheng, Guilian
A1  - Preick, Michaela
A1  - Sun, Boyang
A1  - Hou, Xindong
A1  - Chen, Shungang
A1  - Taron, Ulrike Helene
A1  - Barlow, Axel
A1  - Wang, Linying
A1  - Hu, Jiaming
A1  - Deng, Tao
A1  - Lai, Xulong
A1  - Hofreiter, Michael
T1  - Mitochondrial genomes of Late Pleistocene caballine horses from China belong to a separate clade
JF  - Quaternary science reviews : the international multidisciplinary research and review journal
N2  - There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage I, and the individuals in this study together with one Yakut specimen forming lineage II. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95% CI: 0.86-1.24 Ma), and the two Old World lineages (I & II) split at 0.88 Ma (95% CI: 0.69-1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95% CI: 0.15-0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species.
KW  - Equus dalianensis
KW  - Equus przewalskii
KW  - Pleistocene caballine horses
KW  - ancient DNA
KW  - phylogenetic relationship
KW  - divergence time
Y1  - 2020
U6  - https://doi.org/10.1016/j.quascirev.2020.106691
SN  - 0277-3791
VL  - 250
PB  - Elsevier
CY  - Amsterdam [u.a.]
ER  -