A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia

Abstract

The recovery of DNA sequences from early modern humans (EMHs) could shed light on their interactions with archaic groups such as Neandertals and their relationships to current human populations. However, such experiments are highly problematic because present-day human DNA frequently contaminates bones [1, 2]. For example, in a recent study of mitochondrial (mt) DNA from Neolithic European skeletons, sequence variants were only taken as authentic if they were absent or rare in the present population, whereas others had to be discounted as possible contamination [3, 4]. This limits analysis to EMH individuals carrying rare sequences and thus yields a biased view of the ancient gene pool. Other approaches of identifying contaminating DNA, such as genotyping all individuals who have come into contact with a sample, restrict analyses to specimens where this is possible [5, 6] and do not exclude all possible sources of contamination. By studying mtDNA in Neandertal remains, where contamination and endogenous DNA can be distinguished by sequence, we show that fragmentation patterns and nucleotide misincorporations can be used to gauge authenticity of ancient DNA sequences. We use these features to determine a complete mtDNA sequence from a approximately 30,000-year-old EMH from the Kostenki 14 site in Russia.

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid ofYersinia pestisfrom victims of the Black Death

“…The majority of these DNA fragments were found to be consistent (all unique fragments overlapping the position showed the same substitution), suggesting that the majority of mtDNA fragments from each sample is derived from a single biological source (Fig. S4) (15,23). Individual mtDNA fragments were compared against the corresponding consensus sequence, and nucleotide substitutions were recorded for each position along the DNA fragment.…”

“…PCR-based approaches are ill-suited for large-scale genetic investigations of ancient DNA owing to their preferential amplification of less damaged templates that derive from exogenous contaminants and the highly fragmented nature of endogenous molecules (14,15). In contrast, targeted enrichment strategies (16) in combination with high-throughput DNA sequencing allow for long stretches of ancient DNA to be reconstructed from a complex metagenomic background, and it is clearly the way forward for ancient pathogen research.…”

“…In contrast, targeted enrichment strategies (16) in combination with high-throughput DNA sequencing allow for long stretches of ancient DNA to be reconstructed from a complex metagenomic background, and it is clearly the way forward for ancient pathogen research. The authenticity of endogenous ancient sequences can then be determined by looking for patterns of nucleotide damage typical of ancient DNA (15,17). To show the suitability of these methods for analyses of ancient pathogens, we have identified virulence-associated Y.…”

Complete mitochondrial DNA genome sequences from the first New Zealanders

“…These patterns are caused by deamination damage to the DNA after the death of an individual and can be used to distinguish aDNA from modern contamination (21,40,41). To confirm the authenticity of our sequence data, we therefore used the perl script mapdamage 0.3.5 (http://geogenetics.ku.dk/publications/mapdamage/) (42) to identify these characteristic aDNA damage patterns in all mapped sequencing reads.…”

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

“…The only damage pattern characteristic of ancient DNA sequence data was a slight increase of depurination (G only) immediately before the reads start ( Supplementary Fig. 3) [78][79][80][81] . Since we did not observe an increase in 5′ C-to-T substitutions and 3′ G-to-A substitutions (Supplementary Fig.…”