Abstract
A new method of next-generation sequencing analysis is presented which takes into account the biases characteristic of ancient, including Neandertal, DNA samples.
Highlights
Most of our understanding of how extinct species are related to living species has come from morphological analysis of fossil remains
Since the primary goal of many projects is to resolve the genetic relationship between extinct and extant species, we focus our analysis on the classification of endogenous fragments and the calculation of pairwise nucleotide differences and divergence
We investigated the accuracy of the observed number of pairwise nucleotide differences in each of these comparisons
Summary
Most of our understanding of how extinct species are related to living species has come from morphological analysis of fossil remains. Recovery and analysis of DNA extracted from fossil remains, so called 'ancient DNA', provide a complementary avenue for understanding evolution. With the enormous throughput of generation sequencers, it has become tractable to shotgun sequence DNA as it is recovered from fossil bones [9,10,11,12,13]. Despite the fact that most of the recovered DNA is from microbes that colonized the bone after death [4,14], the sheer volume of sequence generated means that the few percent that are typically from the species of interest still constitute a sequence dataset large enough for genomescale analysis. The mean ancient DNA fragment length has varied between 60 and 150 bp in most recent large-scale sequencing studies [911,13,16,17,18], but can vary greatly from sample to sample
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