Abstract
Applying high-throughput DNA sequencing technologies to the ancient DNA molecules preserved in subfossil material can provide genetic information from past individuals, populations and communities at the genomic scale. The combination of dedicated statistical techniques and specific molecular tools aimed at reducing the impact of post-mortem DNA damage can also help recover epigenetic data from ancient individuals. However, the capacity of different sequence aligners to identify ultrashort and deaminated ancient DNA templates, and their impact on the characterization of ancient methylomes, remain overlooked. In this study, we use both simulated and real ancient DNA sequence data to benchmark the performance of the read alignment tools most commonly used in ancient DNA research. We identify a read alignment strategy making use of the Bowtie2 aligner that substantially reduce computational times but shows increased sensitivity relative to previous recommendations based on the BWA aligner. This strategy significantly improves the genome coverage especially when DNA templates are shorter than 90bp, as is typically the case for ancient DNA. It also impacts on ancient DNA methylation estimates as it maximizes coverage improvement within CpG dinucleotide contexts, which hold the vast majority of DNA methylation marks in mammals. Our work contributes to improve the accuracy of DNA methylation maps and to maximize the amount of recoverable genetic information from archaeological and subfossil material. As the molecular complexity of ancient DNA libraries is generally limited, the mapping strategy recommended here is essential to both limit sequencing costs and sample destruction.
Highlights
The first genome from an ancient human individual was sequenced in 2010 (Rasmussen et al, 2010) and was immediately followed by the genome sequencing of a Neanderthal (Green et al, 2010) and Denisovan (Reich et al, 2010) individual, two extinct archaic hominins
Alignment performance was calculated by normalizing the genome coverage obtained in one mapping condition relative to that obtained when disabling seeding in BWA, after quality filtering and duplicate removal (Figure 1)
We report that Bowtie2 shows a higher performance than BWA when aligning ancient DNA data generated following USER treatment
Summary
The first genome from an ancient human individual was sequenced in 2010 (Rasmussen et al, 2010) and was immediately followed by the genome sequencing of a Neanderthal (Green et al, 2010) and Denisovan (Reich et al, 2010) individual, two extinct archaic hominins. The variation present in ancient DNA sequences does inform us about the genetic affinities of past individuals, populations, and species It can provide insights into ancient epigenetic landscapes, which play a crucial role in the regulation of gene expression (Lea et al, 2018) in response to infection (Smith et al, 2014; Pacis et al, 2015) as well as social (Laubach et al, 2019; Santos et al, 2019; Sanz et al, 2019; SnyderMackler et al, 2019) and environmental (Fagny et al, 2015) cues. Help predict individual phenotypes in the past (see Pedersen et al, 2014 and Hanghøj et al, 2016 for age predictions on ancient individuals, or Gokhman et al, 2019 for morphological predictions)
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