Abstract
Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.
Highlights
Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation
It is timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates
The development of ancient DNA as a scientific tool can be divided into three phases
Summary
The development of ancient DNA (aDNA) as a scientific tool can be divided into three phases. First came the realization that DNA could be recovered from ancient remains and offer a temporal dimension to genetic analyses that modern data alone cannot provide [1] This was followed by a period when most studies were focused on recovering DNA from different taxa and placing them into a phylogenetic context. These studies revealed a general pattern of dynamic history during the Late Quaternary, often characterized by population replacements and losses of genetic diversity During this phase, it was demonstrated that short barcode sequences recovered from ancient sediments or faeces could be used to examine the composition of prehistoric plant and animal communities or the diet of ancient taxa [9,10]. The recent analyses of large-scale palaeogenomic datasets have been highly successful in investigating species-specific population histories
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