TY  - GEN
A1  - Westbury, Michael V.
A1  - Baleka, Sina Isabelle
A1  - Barlow, Axel
A1  - Hartmann, Stefanie
A1  - Paijmans, Johanna L. A.
A1  - Kramarz, Alejandro
A1  - Forasiepi, Analía M.
A1  - Bond, Mariano
A1  - Gelfo, Javier N.
A1  - Reguero, Marcelo A.
A1  - López-Mendoza, Patricio
A1  - Taglioretti, Matias
A1  - Scaglia, Fernando
A1  - Rinderknecht, Andrés
A1  - Jones, Washington
A1  - Mena, Francisco
A1  - Billet, Guillaume
A1  - de Muizon, Christian
A1  - Aguilar, José Luis
A1  - MacPhee, Ross D.E.
A1  - Hofreiter, Michael
T1  - A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica
T2  - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 793 
KW  - ancient DNA
KW  - evolutionary history
KW  - genome sequence
KW  - reveals
KW  - contamination
KW  - alignment
KW  - reads
KW  - bones
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-440801
SN  - 1866-8372
IS  - 793
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  -