Phylogenetic analyses of ancient DNA data can provide a timeline for evolutionary change even in the absence of fossils. The power to infer the evolutionary rate is, however, highly dependent on the number and age of samples, the information content of the sequence data and the demographic history of the sampled population. In this issue of Molecular Ecology, Sheng et al. (2014) analysed mitoch...

Studies of ancient DNA specimens started 25 years ago. At that time short mitochondrial DNA (mtDNA) fragments were the main targets in ancient DNA studies. The last three years were especially productive in the development of new methods of DNA purification and analysis. Complete mtDNA molecules and relatively large fragments of nuclear DNA are the targets of ancient DNA studies today. Ancient ...

PCR analyses of ancient and degraded DNA suffer from their extreme sensitivity to contamination by modern DNA originating, in particular, from carryover contamination with previously amplified or cloned material. Any strategy for limiting carryover contamination would also have to be compatible with the particular requirements of ancient DNA analyses. These include the need (i) to amplify short...

Ancient DNA is a field of molecular evolutionary biology that usesDNA sequence data recovered frompoorly preserved organisms, usually deceased for hundreds to hundreds of thousands of years. Ancient DNA data can provide unique snapshots in time to better understand how populations and species evolve. The field was born in the early 1980s,when thefirst ancientDNAsequences were recovered from pre...

Although the first ancient DNA molecules were extracted more than three decades ago, nuclear genomes could only be characterized after high-throughput sequencing was invented. Genome-scale data have now been gathered from thousands of archaeological specimens, and number biological tissues amenable to genome is growing steadily. Ancient fragments are typically ultrashort carry extensive amounts...

1 Reconstructing Paleogenomes 245 1.1 Ancient DNA 245 1.1.1 The Nature of Ancient DNA 245 1.1.2 The Common Effects of DNA Damage 246 1.2 The Recovery and Sequencing of Ancient DNA 246 1.2.1 Ancient DNA Extraction 246 1.2.2 DNA Library Preparation 247 1.2.3 Capture-Based Target Enrichment 248 1.2.4 Quantification of aDNA and Sequencing 249 1.3 Assembly and Analysis of a Paleogenome 250 1.3.1 Ini...