V.1 Ikuspuntu linguistikoa
V.1.4 HAULen ezaugarriak
4.1 New strategy in authenticating genomic DNA from ancient female individuals
1. Furtwängler, A., Reiter E., Neumann G.U., Siebke I., Steuri N., Hafner A., Lösch S., Anthes N., Schuenemann V.J., Krause J. "Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis." Scientific reports 8.1 (2018):
14075.
Synopsis
Paper I presents a statistical analysis of the differences in the ratio of mitochondrial to nuclear DNA in diverse tissues typically used for ancient DNA retrieval. Furthermore, the impact of these differences on the contamination estimates is investigated. The aim of this statistical comparison was to find a strategy for evaluating the validity of the extrapolation from mitochondrial contamination estimates to the nuclear genome in female individuals where the estimation of X chromosomal contamination is not possible.
To achieve this, the ratio between mtDNA and nDNA was analysed in 317 samples. To obtain a dataset of this size, new data was generated and combined with data from previous publications. The results were that the ratio of mitochondrial to nuclear DNA was the smallest in petrous bones, meaning that these contain large amounts of nuclear DNA relative to their mtDNA content. The ratio was significantly larger in teeth and other bony skeletal parts than in the petrous bones.
A comparison of the mitochondrial DNA contamination estimates and the contamination estimates derived from X chromosomes in the samples from male individuals showed that the values of the estimates were the most similar in cases where the ratio was small. Therefore, large amounts of nDNA relative to mtDNA make the extrapolation from mtDNA contamination estimates to nDNA more reliable. The main conclusion of the paper, therefore, was that in order to use the
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mtDNA contamination estimates from female individuals as the sole authentication criterion besides damage patterns, the mtDNA to nDNA ratio should be taken into consideration.4.2 Identification of the best method for target enrichment in ancient DNA
2. Furtwängler A., Neukamm J., Böhme L., Reiter E., Vollstedt M., Arora N., SinghP, Cole S.T., KnaufS., Calvignac-Spencer S., Krause-Kyora B., Krause J., Schuenemann V.J., Herbig A. “Comparison of target enrichment strategies for ancient pathogen DNA”
Manuscript
Synopsis
Paper II presents a detailed statistical analysis of three different methods for the specific target enrichment of ancient pathogen DNA. A comparison was made of array capture, enrichment with DNA probes cleaved from arrays, and the myBaits®
kit utilising RNA probes from Arbor Biosciences. For this purpose, existing libraries of published studies on ancient and modern DNA from Mycobacterium leprae and Treponema pallidum were captured with these three different enrichment protocols in three independent replicates. The resulting dataset enabled statistical analysis regarding DNA yield, specificity and reproducibility.
The DNA yield – the efficiency of the enrichment – was assessed by comparing features such as mean coverage, enrichment factor and the percentage of the genome covered at least fivefold. The commercial myBaits® kit with two repetitions of the hybridisation shows good performance in these features for ancient and modern samples of both M. leprae and T. pallidum. In most cases, the myBaits®
kit with two repetitions also shows the highest percentage of M. leprae and T. pallidum reads when compared to general mycobacterial and treponemal reads and therefore the highest specificity. Values of the percentage of specific reads were in average 1.5 times higher than in the other methods. For the reproducibility of the capture performance, a high throughput approach with robot assistance and little manual
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handling seems to be advantageous as performed for the in-solution capture with DNA probes derived from arrays resulting in the least differences between independent replicates.Overall, the myBaits® kit with two rounds of hybridisation can be recommended due to the high DNA yield and high specificity for the work with ancient pathogen DNA. Besides its good performance, its major disadvantages are higher costs especially in case of large numbers of samples that need to be enriched.
In these cases, the in-solution capture with DNA baits can be recommended.
4.3 Population genetics analysis of Late and Final Neolithic individuals from what is now Switzerland
3. Furtwängler A., Rohrlach A.B., Lamnidis T.C., Papac L., Neumann G.U., Siebke I., Reiter E., Steuri N., Hald J., Denaire A., Schnitzler B., Wahl J., Ramstein M., Schuenemann V.J., Stockhammer P.W., Hafner A., Lösch S., Haak W., Schiffels S., Krause J. “Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland.” Nature Communications (2020)
Synopsis
Paper III is about a detailed population genetic analysis of Neolithic and Early Bronze Age individuals from what is now Switzerland. The focus of these analyses is the genetic turnover in the Central European population around 4,700 BP. To supplement the picture, samples from the Hegau region in Southern Germany and the Alsace region in France were also included.
This genetic turnover can be observed throughout Europe at relatively similar times. It is marked by the arrival of an additional ancestry component from the Pontic steppe, which can be found in almost all present-day Europeans in addition to components of the Western Hunter-Gatherer and Early Farmers from Western Anatolia. Large population genetics studies have investigated this turnover in areas
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like the Iberian Peninsula or the British Isles, while initial studies provided data for regions such as the Middle Elbe-Saale region in Eastern Germany. In this dissertation, we therefore present data for a region connecting these different points to complete the picture.Furthermore, through a very dense sampling over the entire time span of this turnover, further insights into the detailed processes of this population change were gathered, and it was revealed that this period of genetic change lasted over several generations. We were also able to identify female individuals with zero steppe ancestry dating to approximately one thousand years after the arrival of this component in Central Europe. Furthermore, hints of a non-local origin of these women suggest that female exogamy involving women with zero or little steppe ancestry results in the detected decrease in the relative amount of steppe ancestry seen in the centuries after its arrival.