Multiple sequence alignments of newly reconstructed and published cervid and human mtDNA
Data files
Mar 20, 2023 version files 33.60 MB
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Aligned_cervid_mtDNA.fst
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Aligned_human_mtDNA_FINAL.fst
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probes_reich_n3_b8_CONTROL_BV09-BV09.txt.gz.bam_sorted.txt
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README.md
Abstract
Assigning prehistoric objects to specific individuals is usually impossible outside of burial contexts. Here we present a non-destructive method for gradually releasing DNA from ancient bone and tooth artifacts. Application of the method to an Upper Paleolithic deer tooth pendant from Denisova Cave (Russia) resulted in the recovery of DNA from both the deer and a female human individual. Genetic dates obtained from the deer and human mitochondrial genomes estimate the age of the pendant at approximately 20,000 to 24,000 years. Nuclear DNA from its presumed maker or wearer shows strong affinities to contemporaneous Ancient North Eurasian individuals previously found further east in Siberia. Our work opens up new possibilities for linking cultural and genetic records in prehistoric archaeology.
Methods
The non-destructive DNA extraction method described in the associated publication was used to recover DNA from a cervid tooth pendant found in the Upper Paleolithic layers of Denisova Cave. This DNA was converted into single-stranded libraries and enriched separately for human and cervid mitochondrial(mt) DNA via hybridization capture and sequenced. The human mtDNA capture resulted in 62-fold average coverage of the human mtDNA genome allowing for reconstruction of a near-complete mtDNA genome. This genome (DCP1 in Aligned_human_mtDNA.fst) was aligned to the revised Cambridge reference sequence with a selection of published ancient and present-day human mtDNA genomes. The cervid mtDNA capture resulted in 635-fold coverage, also allowing for reconstruction of a mtDNA genome. This genome (DCP1 in Aligned_cervid_mtDNA.fst) was alighed to a waipiti mtDNA genome with selection of ancient waipiti mtDNA genomes. Each of these multiple sequence alignments was used for tree building and molecular branch shortening. Finally, the list of SNPs enriched for in the hybridization capture of human nuclear DNA (probeset referred to as "AA204") is also included.
Usage notes
The two files are a multiple sequence alignment file and can be read in a text editor or any MSA viewing program (e.g. MEGA, Seaview, etc.). The SNP list is a tab-delimited file that can be read in a text editor.