TY  - JOUR
A1  - Alberti, Federica
A1  - Gonzalez, Javier
A1  - Paijmans, Johanna L. A.
A1  - Basler, Nikolas
A1  - Preick, Michaela
A1  - Henneberger, Kirstin
A1  - Trinks, Alexandra
A1  - Rabeder, Gernot
A1  - Conard, Nicholas J.
A1  - Muenzel, Susanne C.
A1  - Joger, Ulrich
A1  - Fritsch, Guido
A1  - Hildebrandt, Thomas
A1  - Hofreiter, Michael
A1  - Barlow, Axel
T1  - Optimized DNA sampling of ancient bones using Computed Tomography scans
JF  - Molecular ecology resources
N2  - The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.
KW  - ancient DNA
KW  - computer tomography
KW  - palaeogenomics
KW  - paleogenetics
KW  - petrous bone
Y1  - 2018
U6  - https://doi.org/10.1111/1755-0998.12911
SN  - 1755-098X
SN  - 1755-0998
VL  - 18
IS  - 6
SP  - 1196
EP  - 1208
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Wutke, Saskia
A1  - Sandoval-Castellanos, Edson
A1  - Benecke, Norbert
A1  - Döhle, Hans-Jürgen
A1  - Friederich, Susanne
A1  - Gonzalez, Javier
A1  - Hofreiter, Michael
A1  - Lougas, Lembi
A1  - Magnell, Ola
A1  - Malaspinas, Anna-Sapfo
A1  - Morales-Muniz, Arturo
A1  - Orlando, Ludovic
A1  - Reissmann, Monika
A1  - Trinks, Alexandra
A1  - Ludwig, Arne
T1  - Decline of genetic diversity in ancient domestic stallions in Europe
JF  - Science Advances
N2  - Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.
Y1  - 2018
U6  - https://doi.org/10.1126/sciadv.aap9691
SN  - 2375-2548
VL  - 4
IS  - 4
PB  - American Assoc. for the Advancement of Science
CY  - Washington
ER  -