Ancient DNA analysis

L Orlando, R Allaby, P Skoglund… - Nature reviews …, 2021 - nature.com
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 …

Mammalian transposable elements and their impacts on genome evolution

RN Platt, MW Vandewege, DA Ray - Chromosome Research, 2018 - Springer
Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate
themselves in a genome. Mammalian genomes are dominated by TEs, which can reach …

Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Y Wang, MW Pedersen, IG Alsos, B De Sanctis… - Nature, 2021 - nature.com
During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic
changes, yet the nature, extent and rate of their responses are not fully understood …

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

J Dabney, M Knapp, I Glocke, MT Gansauge… - Proceedings of the …, 2013 - pnas.org
Although an inverse relationship is expected in ancient DNA samples between the number
of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly …

A draft sequence of the Neandertal genome

RE Green, J Krause, AW Briggs, T Maricic, U Stenzel… - science, 2010 - science.org
Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of
Europe and western Asia before disappearing 30,000 years ago. We present a draft …

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

M Schubert, L Ermini, CD Sarkissian, H Jónsson… - Nature protocols, 2014 - nature.com
Next-generation sequencing technologies have revolutionized the field of paleogenomics,
allowing the reconstruction of complete ancient genomes and their comparison with modern …

A field guide to whole‐genome sequencing, assembly and annotation

R Ekblom, JBW Wolf - Evolutionary applications, 2014 - Wiley Online Library
Genome sequencing projects were long confined to biomedical model organisms and
required the concerted effort of large consortia. Rapid progress in high‐throughput …

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

MT Gansauge, M Meyer - Nature protocols, 2013 - nature.com
This protocol describes a method for converting short single-stranded and double-stranded
DNA into libraries compatible with high-throughput sequencing using Illumina technology …

Applications of next generation sequencing in molecular ecology of non-model organisms

R Ekblom, J Galindo - Heredity, 2011 - nature.com
As most biologists are probably aware, technological advances in molecular biology during
the last few years have opened up possibilities to rapidly generate large-scale sequencing …

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

K Yoshida, VJ Schuenemann, LM Cano, M Pais… - elife, 2013 - elifesciences.org
Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the
Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its …