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Search: WFRF:(Guimaraes A) > Humanities

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  • Peripato, Vinicius, et al. (author)
  • More than 10,000 pre-Columbian earthworks are still hidden throughout Amazonia
  • 2023
  • In: Science (New York, N.Y.). - 1095-9203. ; 382:6666, s. 103-109
  • Journal article (peer-reviewed)abstract
    • Indigenous societies are known to have occupied the Amazon basin for more than 12,000 years, but the scale of their influence on Amazonian forests remains uncertain. We report the discovery, using LIDAR (light detection and ranging) information from across the basin, of 24 previously undetected pre-Columbian earthworks beneath the forest canopy. Modeled distribution and abundance of large-scale archaeological sites across Amazonia suggest that between 10,272 and 23,648 sites remain to be discovered and that most will be found in the southwest. We also identified 53 domesticated tree species significantly associated with earthwork occurrence probability, likely suggesting past management practices. Closed-canopy forests across Amazonia are likely to contain thousands of undiscovered archaeological sites around which pre-Columbian societies actively modified forests, a discovery that opens opportunities for better understanding the magnitude of ancient human influence on Amazonia and its current state.
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2.
  • Sarmento, Cindy, et al. (author)
  • A Study on Burrows-Wheeler Aligner’s Performance Optimization for Ancient DNA Mapping
  • 2022
  • In: Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021). - Cham : Springer. - 9783030862572 - 9783030862589 ; , s. 105-114
  • Book chapter (peer-reviewed)abstract
    • The high levels of degradation characteristic of ancient DNA molecules severely hinder the recovery of endogenous DNA fragments and the discovery of genetic variation, limiting downstream population analyses. Optimization of read mapping strategies for ancient DNA is therefore essential to maximize the information we are able to recover from archaeological specimens. In this paper we assess Burrows-Wheeler Aligner (BWA) effectiveness for mapping of ancient DNA sequence data, comparing different sets of parameters and their effect on the number of endogenous sequences mapped and variants called. We also consider different filtering options for SNP calling, which include minimum values for depth of coverage and base quality in addition to mapping quality. Considering our results, as well as those of previous studies, we conclude that BWA-MEM is a good alternative to the current standard BWA-backtrack strategy for ancient DNA studies, especially when the computational resources are limited and time is a constraint. 
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book chapter (1)
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Phillips, Oliver L. (1)
Kılınç, Gülşah Merve (1)
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ter Steege, Hans (1)
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