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 …

Ancient and modern environmental DNA

MW Pedersen… - … of the Royal …, 2015 - royalsocietypublishing.org
DNA obtained from environmental samples such as sediments, ice or water (environmental
DNA, eDNA), represents an important source of information on past and present biodiversity …

AdapterRemoval v2: rapid adapter trimming, identification, and read merging

M Schubert, S Lindgreen, L Orlando - BMC research notes, 2016 - Springer
Background As high-throughput sequencing platforms produce longer and longer reads,
sequences generated from short inserts, such as those obtained from fossil and degraded …

Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France

L Slimak, C Zanolli, T Higham, M Frouin… - Science …, 2022 - science.org
Determining the extent of overlap between modern humans and other hominins in Eurasia,
such as Neanderthals and Denisovans, is fundamental to understanding the nature of their …

Genomic and archaeological evidence suggest a dual origin of domestic dogs

LAF Frantz, VE Mullin, M Pionnier-Capitan… - Science, 2016 - science.org
The geographic and temporal origins of dogs remain controversial. We generated genetic
sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog …

Widespread horse-based mobility arose around 2200 bce in Eurasia

P Librado, G Tressières, L Chauvey, A Fages, N Khan… - Nature, 2024 - nature.com
Horses revolutionized human history with fast mobility. However, the timeline between their
domestication and their widespread integration as a means of transport remains …

The prehistoric peopling of Southeast Asia

H McColl, F Racimo, L Vinner, F Demeter, T Gakuhari… - Science, 2018 - science.org
The human occupation history of Southeast Asia (SEA) remains heavily debated. Current
evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until~ 4000 …

EAGER: efficient ancient genome reconstruction

A Peltzer, G Jäger, A Herbig, A Seitz, C Kniep, J Krause… - Genome biology, 2016 - Springer
Background The automated reconstruction of genome sequences in ancient genome
analysis is a multifaceted process. Results Here we introduce EAGER, a time-efficient …

Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

M Sikora, A Seguin-Orlando, VC Sousa, A Albrechtsen… - Science, 2017 - science.org
Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a
population structure characterized by limited levels of within-band relatedness and …

Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability

A de Mendoza, TV Nguyen, E Ford, D Poppe… - Genome Biology, 2022 - Springer
Background Cytosine DNA methylation is widely described as a transcriptional repressive
mark with the capacity to silence promoters. Epigenome engineering techniques enable …