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Sökning: WFRF:(Dehasque Marianne) > (2020)

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1.
  • Dehasque, Marianne, et al. (författare)
  • Inference of natural selection from ancient DNA
  • 2020
  • Ingår i: Evolution Letters. - : JOHN WILEY & SONS LTD. - 2056-3744. ; 4:2, s. 94-108
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.
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2.
  • Feuerborn, Tatiana R., et al. (författare)
  • Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets
  • 2020
  • Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.Results: Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.Conclusions: We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.
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