Reconstructing the genetic history of late Neanderthals

A high-coverage Neandertal genome from Vindija Cave in Croatia

(2017) Kay Prüfer et al.   SCIENCE

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

(2017) Cosimo Posth et al.   Nature Communications

The Divergence of Neandertal and Modern Human Y Chromosomes

(2016) Fernando L. Mendez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins

(2016) Matthias Meyer et al.   NATURE

Ancient gene flow from early modern humans into Eastern Neanderthals

(2016) Martin Kuhlwilm et al.   NATURE

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

The genetic history of Ice Age Europe

(2016) Qiaomei Fu et al.   NATURE

A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years

(2016) Priya Moorjani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

(2016) Frido Welker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis

(2016) Samantha Brown et al.   Scientific Reports

Neandertal cannibalism and Neandertal bones used as tools in Northern Europe

(2016) Hélène Rougier et al.   Scientific Reports

Reducing microbial and human contamination in DNA extractions from ancient bones and teeth

(2015) Petra Korlević et al.   BIOTECHNIQUES

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

(2015) Monika Karmin et al.   GENOME RESEARCH

Massive migration from the steppe was a source for Indo-European languages in Europe

(2015) Wolfgang Haak et al.   NATURE

An early modern human from Romania with a recent Neanderthal ancestor

(2015) Qiaomei Fu et al.   NATURE

Subcortical barrelette-like and barreloid-like structures in the prosimian galago (Otolemur garnetti)

(2015) Eva Kille Sawyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The modern human colonization of western Eurasia: when and where?

(2015) Jean-Jacques Hublin   QUATERNARY SCIENCE REVIEWS

Selective enrichment of damaged DNA molecules for ancient genome sequencing

(2014) Marie-Theres Gansauge et al.   GENOME RESEARCH

Ancient human genomes suggest three ancestral populations for present-day Europeans

(2014) Iosif Lazaridis et al.   NATURE

The timing and spatiotemporal patterning of Neanderthal disappearance

(2014) Tom Higham et al.   NATURE

Genome sequence of a 45,000-year-old modern human from western Siberia

(2014) Qiaomei Fu et al.   NATURE

leeHom: adaptor trimming and merging for Illumina sequencing reads

(2014) Gabriel Renaud et al.   NUCLEIC ACIDS RESEARCH

Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

(2014) Pontus Skoglund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers

(2013) Gabriel Renaud et al.   BIOINFORMATICS

A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

(2013) Qiaomei Fu et al.   CURRENT BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

A mitochondrial genome sequence of a hominin from Sima de los Huesos

(2013) Matthias Meyer et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

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

(2013) Marie-Theres Gansauge et al.   Nature Protocols

DNA analysis of an early modern human from Tianyuan Cave, China

(2013) Q. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) J. Dabney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries

(2012) Jesse Dabney et al.   BIOTECHNIQUES

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Partial Genetic Turnover in Neandertals: Continuity in the East and Population Replacement in the West

(2012) L. Dalen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Revised age of late Neanderthal occupation and the end of the Middle Paleolithic in the northern Caucasus

(2011) R. Pinhasi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Demographic history and rare allele sharing among human populations

(2011) S. Gravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia

(2010) Johannes Krause et al.   CURRENT BIOLOGY

The complete mitochondrial DNA genome of an unknown hominin from southern Siberia

(2010) Johannes Krause et al.   NATURE

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

The role of climate in the spread of modern humans into Europe

(2010) Ulrich C. Müller et al.   QUATERNARY SCIENCE REVIEWS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ebb and flow or regional extinctions? On the character of Neandertal occupation of northern environments

(2009) Jean-Jacques Hublin et al.   COMPTES RENDUS PALEVOL

Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

(2009) A. W. Briggs et al.   SCIENCE

New data on the late Neandertals: Direct dating of the Belgian Spy fossils

(2008) Patrick Semal et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

(2008) Richard E. Green et al.   CELL

Complete Mitochondrial Genome Sequence of the Tyrolean Iceman

(2008) Luca Ermini et al.   CURRENT BIOLOGY

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland

(2008) M. T. P. Gilbert et al.   SCIENCE