% pubman genre = article @article{item_3348616, title = {{Ancient DNA analysis}}, author = {Orlando, Ludovic and Allaby, Robin and Skoglund, Pontus and Sarkissian, Clio Der and Stockhammer, Philipp W. and {\'A}vila-Arcos, Mar{\'\i}a C. and Fu, Qiaomei and Krause, Johannes and Willerslev, Eske and Stone, Anne C. and Warinner, Christina G.}, language = {eng}, issn = {2662-8449}, doi = {10.1038/s43586-020-00011-0}, publisher = {Nature Research}, address = {London}, year = {2021}, abstract = {{Although the first ancient DNA molecules were extracted more than three decades ago, the first ancient nuclear genomes could only be characterized after high-throughput sequencing was invented. Genome-scale data have now been gathered from thousands of ancient archaeological specimens, and the number of ancient biological tissues amenable to genome sequencing is growing steadily. Ancient DNA fragments are typically ultrashort molecules and carry extensive amounts of chemical damage accumulated after death. Their extraction, manipulation and authentication require specific experimental wet-laboratory and dry-laboratory procedures before patterns of genetic variation from past individuals, populations and species can be interpreted. Ancient DNA data help to address an entire array of questions in anthropology, evolutionary biology and the environmental and archaeological sciences. The data have revealed a considerably more dynamic past than previously appreciated and have revolutionized our understanding of many major prehistoric and historic events. This Primer provides an overview of concepts and state-of-the-art methods underlying ancient DNA analysis and illustrates the diversity of resulting applications. The article also addresses some of the ethical challenges associated with the destructive analysis of irreplaceable material, emphasizes the need to fully involve archaeologists and stakeholders as part of the research design and analytical process, and discusses future perspectives.}}, contents = {Experimentation - Material types - Ethical aDNA research - Writing archaeogenetic prehistory - aDNA facilities - DNA extraction - Post-mortem DNA damage removal - Mini-barcode PCR amplification - DNA library construction - DNA library amplification - Target enrichment - DNA sequencing - Information management systems Results - Read processing and alignment - Authentification - Error rates - Molecular sexing and kinship - Multivariate analyses - Population ancestry modelling - Genotype imputation - Microbiota profiling - DNA methylation Applications - Human genomics - Domestication - Pathogens and microbiomes - Extinction and climate change - Environmental DNA Reproducibility and data deposition - Possible confounding factors - Public repositories - Long-term legacy Limitations and optimization - Wet-laboratory methods - Dry-laboratory methods Outlook - Working together - Who conducts aDNA research? - Future directions}, journal = {{Nature reviews: Methods primers}}, volume = {1}, number = {14}, eid = {s43586-020-00011-0}, }