A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica

Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoiseChelonoidis alburyorum

(2017) Christian Kehlmaier et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancient DNA from the extinct South American giant glyptodontDoedicurussp. (Xenarthra: Glyptodontidae) reveals that glyptodonts evolved from Eocene armadillos

(2016) Kieren J. Mitchell et al.   MOLECULAR ECOLOGY

First complete mitochondrial genome data from ancient South American camelids - The mystery of the chilihueques from Isla Mocha (Chile)

(2016) Michael Westbury et al.   Scientific Reports

Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates

(2015) Frido Welker et al.   NATURE

Ancient collagen reveals evolutionary history of the endemic South American 'ungulates'

(2015) M. Buckley   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Improving access to endogenous DNA in ancient bones and teeth

(2015) Peter B. Damgaard et al.   Scientific Reports

The future of ancient DNA: Technical advances and conceptual shifts

(2014) Michael Hofreiter et al.   BIOESSAYS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA

(2014) B. Shapiro et al.   SCIENCE

Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

(2014) K. J. Mitchell et al.   SCIENCE

Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

(2013) Meredith L. Carpenter et al.   AMERICAN JOURNAL OF HUMAN GENETICS

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

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

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

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

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

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

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

Ancient DNA Damage

(2013) J. Dabney et al.   Cold Spring Harbor Perspectives in Biology

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Evolution of the Earliest Horses Driven by Climate Change in the Paleocene-Eocene Thermal Maximum

(2012) R. Secord et al.   SCIENCE

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Middle Miocene Uruguaytheriinae (Mammalia, Astrapotheria) from Peruvian Amazonia and a review of the astrapotheriid fossil record in northern South America

(2011) Cyrielle Goillot et al.   GEODIVERSITAS

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Computational challenges in the analysis of ancient DNA

(2010) Kay Prüfer et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The conditioned reconstructed process

(2008) Tanja Gernhard   JOURNAL OF THEORETICAL BIOLOGY